The Family Beggiatoaceae

Teske, Andreas; Salman, Verena

doi:10.1007/978-3-642-38922-1_290

Andreas Teske⁷ &
Verena Salman⁷

6133 Accesses
11 Citations

Abstract

The family Beggiatoaceae contains a wide range of morphologically conspicuous, aerobic, or nitrate-dependent sulfide-oxidizing bacteria that span the range from obligate sulfur-based chemolithoautotrophy to heterotrophic growth supplemented by sulfur oxidation. The Beggiatoaceae are the model organisms for the concept of chemolithotrophy, developed by Sergei Winogradsky during his postgraduate studies using natural populations of filamentous freshwater Beggiatoaceae collected in sulfur springs. Since the metabolism of the Beggiatoaceae requires access to reduced sulfur species and oxidants such as oxygen or nitrate, these bacteria thrive in microbial mats, surficial sediments, and sediment–water interfaces where these electron donors and acceptors coexist and can be intercepted for microbial energy generation before gradual abiotic sulfide oxidation sets in. All Beggiatoaceae have the ability to oxidize sulfide to elemental sulfur that is stored as intracellular sulfur globules, which make the cells highly refractory and conspicuous with the unaided eye and under the microscope. This characteristic, together with the absence of photosynthetic pigments, has led to their traditional designation as members of the “colorless sulfur bacteria,” in contrast to the photosynthetic purple and green sulfur bacteria or the cyanobacteria. The white, yellow, or occasionally orange color of the Beggiatoaceae, their frequently filamentous or chain-like morphology, their growth pattern in flocs and mats on sediment surfaces, and their large cell size and capacity for storing several different compounds intracellularly have made these organisms fascinating research targets. Extensive microscopic and morphological surveys have focused on these bacteria since the late nineteenth and early twentieth century. To a surprising extent, early microscopic and morphological observations on large, morphologically conspicuous sulfur bacteria can be reintegrated into the emerging molecular and phenotypic taxonomy of the Beggiatoaceae today.

Access provided by Autonomous University of Puebla. Download reference work entry PDF

Large Sulfur-Oxidizing Bacteria at Gulf of Mexico Hydrocarbon Seeps

Blue-Green Algae (Cyanobacteria) in Rivers

Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments

Article 28 February 2015

Keywords

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Taxonomy, Historical and Current

The family Beggiatoaceae represents one of the major mutually exclusive phylogenetic lineages of the morphologically conspicuous sulfur bacteria (Bavendamm 1924) within the Gammaproteobacteria. The Beggiatoaceae have undergone major expansions and revisions in the recent past: The genera Beggiatoa and Thioploca were recognized as phylogenetically intertwined (Teske et al. 1999) and in need of taxonomic revision that better reflects their natural evolutionary relationships in relation to each other and to Thiomargarita (Jørgensen et al. 2005; Teske and Nelson 2006). To accommodate the emerging natural diversity among these bacteria after substantive revision based on 16S rRNA and its sequences, cell morphology, and physiology, the family Beggiatoaceae retains the currently recognized genera Beggiatoa, Thioploca, and Thiomargarita in revised form and also includes the recently proposed genus-level Candidatus groups Maribeggiatoa, Marithioploca, Marithrix, Isobeggiatoa, Parabeggiatoa, Allobeggiatoa, Halobeggiatoa, and Thiopilula, the revived candidate genus Thiophysa, and some distinct phylogenetic lineages that for now remain unnamed (Salman et al. 2011; Hinck et al. 2011; Grünke et al. 2012). The Beggiatoaceae do not include the filamentous, heterotrophic freshwater bacterium Vitreoscilla, a betaproteobacterium that does not form intracellular sulfur globules (Strohl et al. 1986).

Recently, the combined family name Thiotrichaceae was introduced to include the genera Beggiatoa, Thioploca, Thiomargarita, Thiothrix, Leucothrix, Achromatium, Thiobacterium, and Thiospira (Garrity et al. 2005). However, this polyphyletic assemblage comprises physiologically and phylogenetically divergent bacteria, including the type genera (Beggiatoa, Leucothrix, and Achromatium) of the validly published families Beggiatoaceae, Leucotrichaceae, and Achromatiaceae. The genera Beggiatoa, Thioploca and Thiomargarita form a monophyletic lineage within the Gammaproteobacteria (Ahmad et al. 2006; Jørgensen et al. 2005); the genera Thiothrix and Leucothrix form the second (Howarth et al. 1999); the genus Achromatium constitutes the third of these lineages (Head et al. 1996); Thiobacterium is not yet phylogenetically assigned (Grünke et al. 2010). This phylogenetic framework based on 16S rRNA sequences is remarkably consistent with the validly published families Beggiatoaceae (Leadbetter 1974; Strohl 1989), Leucotrichaceae (Brock 1974), and Achromatiaceae (Van Niel 1948) that were based on distinct cell morphology and physiological characteristics and hold up well in the light of modern molecular taxonomy. Since each family is monophyletic, they provide a robust, natural phylogenetic framework that can accommodate future updates and novel taxa and should be retained.

This chapter provides an overview of the family Beggiatoaceae that synthesizes published taxonomic descriptions, physiology based on pure cultures and field samples, morphology and size of filaments, cell clusters and single cells, and 16S rRNA gene sequences obtained from pure cultures and single cells (Fig. 6.1 ).

Beggiatoaceae Migula 1894.

Beg.gia.to.a’ce.ae. N.L. fem.n. Beggiatoa type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Beggiatoaceae the Beggiatoa family.

Type genus: Beggiatoa (Trevisan 1842).

Beg.gia.to’a. M.L. fem.n. Beggiatoa named for F.S. Beggiatoa, a physician of Vicenza.

Molecular Analyses

Molecular analyses have uncovered wide phylogenetic diversity within the family Beggiatoaceae and delineated the Beggiatoaceae from other families of morphologically conspicuous sulfur bacteria. Early on, Beggiatoa alba and Thiothrix nivea were recognized as distinct lineages of the Gammaproteobacteria, initially by reverse transcription sequencing of extracted 5S rRNA (Stahl et al. 1987) and 16S rRNA (Lane et al. 1992) and later by sequencing of PCR-amplified and cloned 16S rRNA genes (Teske et al. 1995). Since then, 16S rRNA gene sequencing of individual filaments or single cells has played a crucial role in defining mutually exclusive monophyletic phylogenetic lineages that form the basis for several proposed candidate genera and species. Since these taxa are mostly uncultured and therefore incompletely described, no type strains can be given; listed instead are the currently known 16S rRNA gene sequences, morphological and physiological characteristics, and the environmental origin of natural samples and specimens.

A fundamental caveat for the study of natural Beggiatoaceae samples has to be kept in mind: Some key physiological characteristics (for example, intracellular nitrate accumulation) cannot be identified from the same filament or cell that is used for sequence identification; instead, morphologically indistinguishable filaments or cells from the same sampling site are used for parallel phylogenetic identification, as well as phenotypic and physiological characterization. Therefore, genotype/morphotype matches are to some extent inferred, especially for newly defined taxa with a small sample base. Repeated and consistent identification of natural populations in different settings and locations will solidify the evolving taxonomy of the Beggiatoaceae.

Genus Beggiatoa

In contrast to all other genera and candidate lineages of the Beggiatoaceae, the genus Beggiatoa has cultured representatives and a well-characterized type species, Beggiatoa alba strain B18LD, isolated from freshwater sediments near Baton Rouge, Louisiana, USA (Fig. 6.2c) (Mezzino et al. 1984). Beggiatoa alba is a deeply branching member of the Beggiatoaceae in 16S rRNA phylogenies (Ahmad et al. 2006); its phylogenetic position near the root of the Beggiatoaceae, among multiple lineages of freshwater and marine Beggiatoaceae, was recently confirmed in a comprehensive reanalysis of all known members of this group (Salman et al. 2011). Beggiatoa alba B18LD (AF110274; Strohl et al. 1981a) forms a monophyletic cluster with the closely related freshwater strains, Beggiatoa alba B15LD (L40944, Strohl and Larkin 1978a; Strohl et al. 1982), Beggiatoa sp. OH-75-2a (Fig. 6.2a) (AF110273; Nelson and Castenholz 1981a, b), and Beggiatoa sp. D-401 and D-402 (AY583995 and AY583996; Grabovich et al. 1998, 2001). The molecular mass of the Beggiatoa alba genome has been determined by CoT analysis as 2.02 × 10⁹, which corresponds to 3.03 × 10⁶ base pairs, similar to E. coli (Genthner et al. 1985). The G+C content for Beggiatoa alba strains B18LD, B15LB, and B25RD ranged from 40 to 42.7 mol%. The phenotypically similar strain L1401-15 had a different G+C content of 51.7 mol% and appeared to be genetically distinct (Mezzino et al. 1984). The three former Beggiatoa alba strains contained plasmids with molecular masses of 12.3 to 12.8 × 10⁶ or 18.9–19.7 kb with no described function (Minges et al. 1983). Independent analyses (Nelson, unpublished) determined the following mol G+C values: B18LD (37.1 %), B25RD (35.5 %), and OH-75-2a (38.5 %). Beggiatoa alba B18LD contains the genes for the linear C₁-oxidation pathway of alpha-, beta-, and gammaproteobacterial methylotrophic bacteria (Jewell et al. 2008). Beggiatoa alba B15LD (DSM 1416) also contains the soxB gene, shared with a wide range of sulfur-oxidizing Proteobacteria and Chlorobia (Genbank accession number EF618583) (Meyer et al. 2007), and the chaperonin-60 gene (Genbank accession number JF745935). Genome sequencing of type strain Beggiatoa alba B18LD has been completed at the Joint Genome Institute (JGI Project ID 16466). Pending additional analyses, only the Beggiatoa alba cluster may constitute the phylogenetically validated genus Beggiatoa in the strict sense.

Beggiatoa alba (Vaucher 1803) Trevisan 1842

Al’ba. L. adj. albus, white.

B. alba grows chemoorganotrophically and aerobically, with a preference for microaerobic conditions. When grown in the presence of reduced sulfur sources, sulfur is deposited in inclusions surrounded by the cytoplasmic membrane. Anaerobic cell maintenance with sulfur as electron acceptor is possible. Necridia and hormogonia can be formed. Colonies on agar may appear as circuitously curled filaments. The filaments of B. alba are about 1.5–4 μm in diameter and may vary with growth conditions. Cells are usually 3.0–9.0 μm long, with filament lengths averaging 60–120 μm.

The neotype strain, B18LD, was isolated from an enrichment obtained from a rice paddy in Lacassine, Louisiana, USA. This strain is described in detail by Mezzino et al. (1984). The well-characterized strains OH-75-2a and B15LD should be considered strains of B. alba.

Type strain: LSU B18LD, ATCC 33555.

Genbank accession numbers of 16S rRNA gene sequence: AF110274.

Other morphologically and physiologically similar isolates and enrichments of filamentous sulfur bacteria constitute sister lineages to Beggiatoa alba radiating near the base of the Beggiatoaceae; these form separate 16S rRNA branches and cannot be subsumed under the Beggiatoa alba lineage (Ahmad et al. 2006). These lineages were termed “cluster XII” (Fig. 6.1 ), understood as a temporary designation until more taxonomic work establishes several well-defined groups (Salman et al. 2011). Several of these “cluster XII” organisms appear in the literature under the genus name Beggiatoa, but they are overdue for updated formal description and taxonomic revision, as suggested previously based on 16S rRNA sequences (Salman et al. 2011) and also by heterogeneous G+C content of genomic DNA (Mezzino et al. 1984). This taxonomic revision has started with the recently proposed Candidatus genus-level group “Allobeggiatoa” (Hinck et al. 2011). Two additional groups of Beggiatoaceae within “cluster XII” require taxonomic revisions (Fig. 6.1 ):

1.
Filamentous Beggiatoa-like bacteria from freshwater habitats include not only the B. alba strains B15LD and B18LD (L40994 and AF11024, Strohl and Larkin 1978a; Strohl et al. 1981, 1982), but also the pure culture strains Beggiatoa sp. OH-75-2a (AF110273, Ahmad et al. 2006), Beggiatoa sp. AA5A (Genbank No. AF110275, Ahmad et al. 2006), Beggiatoa sp. D-401 and D-402 (AY583995 and AY583996, Grabovich et al. 1998, 2001), Beggiatoa sp. 1401–13 (L40997; Pringsheim 1964), Beggiatoa sp. LPN from a sewage outlet (EU015402, Kamp et al. 2006), and thin (5–7 μm diameter) Beggiatoa filaments naturally enriched in a cave stream for which a 16S rRNA FISH probe has been designed (DQ133935; Macalady et al. 2006, 2008). The older literature contains several studies of Beggiatoa strains that grew preferentially under heterotrophic conditions or with organic carbon amendments to chemoautotrophic media (Faust and Wolfe 1961; Scotten and Stokes 1962; Morita and Stave 1963; Burton et al. 1966; Kowallik and Pringsheim 1966; Pringsheim 1967); these strains might have their taxonomic home in “Group XII” as well. A 16S rRNA gene sequencing survey and further characterization of those strains that might have survived in culture collections (for example, Schlösser 1982) are overdue. A sequence-based study should also reexamine the taxonomic borders between heterotrophic Beggiatoa spp. and morphologically similar, filamentous Vitreoscilla spp. that share the same freshwater benthic habitat; the genus Vitreoscilla differs from Beggiatoa by not forming sulfur globules (Strohl et al. 1986).
2.
A second group consists of uncultured marine morphotypes from hypersaline lagoons (GU117706 and GU117707; de Albuquerque et al. 2010), several phylotypes from the Håkon Mosby mud volcano in the Arctic Ocean (FR847882 to FR847887; Grünke et al. 2012), the cultured autotrophic marine strain MS-81-6 (AF110277) from Sippewissett salt marsh near Woods Hole, MA (Nelson et al. 1982; no longer available in culture), brackish-water filaments enriched from sediments off southeast India (HM598303, JN588607, JN674459; Saravanakumar et al. 2012), and the cultured marine strain 35Flor (FR717278) originating from corals infected with black band disease. The members of this marine cluster have filament diameters of ca. 2–7 μm (compiled in Brock et al. 2012). Near the root of this cluster branches the autotrophic marine strain MS-81-1c, also isolated from Sippewissett salt marsh (AF110276; Nelson et al. 1982) but no longer available in culture (Fig. 6.2b). Currently, strain 35Flor is the only marine Beggiatoa strain that is available in culture (coculture with a Pseudovibrio sp.); it has been studied extensively for its polyphosphate inclusions (Fig. 6.2d) (Brock and Schulz-Vogt 2011; Brock et al. 2012) and anaerobic sulfur respiration (Schwedt et al. 2012).

Genus Thioploca. Lauterborn 1907

Thi.o.plo’ca Gr. neut. n. thein (latin transliteration thium) sulfur; Gr. fem.n. ploke a braid, a twist; M.L. fem. n. Thioploca sulfur braid. The genus Thioploca includes thin filaments occurring in sheathed bundles that inhabit freshwater and brackish-water surficial sediments and decaying plant material (Fig. 6.3g). The type species of the genus Thioploca, T. schmidlei from Lake Constance, Germany (Lauterborn 1907), has been observed recently in Lake Baikal, Russia (Zemskaya et al. 2009), but it is not represented by 16S rRNA gene sequences. The second described species T. ingrica is morphologically similar to T. schmidlei, but has a smaller filament diameter (Wislouch 1912; Maier 1984). T. ingrica is represented by a tight cluster of mutually similar 16S rRNA gene sequences (AF452892; AY115530; AB263619; FR690997; FR690998; EU718069-71; L40998; AB699673 to AB699684) that were obtained from filaments in temperate freshwater lakes of Japan and Germany (Kojima et al. 2003, 2006), from Lake Baikal (DQ338566; Zemskaya et al. 2009), from brackish fjords in Denmark (Høgslund et al. 2010; Salman et al. 2011), and from a shallow tropical lake in Cambodia (Nemoto et al. 2012). A specific 16S rRNA FISH probe for this cluster has validated the 16S rRNA sequencing results for environmental filaments (Kojima et al. 2003). The microbial epibionts inhabiting the sheaths produced by T. ingrica have been analyzed by 16S rRNA gene sequencing and FISH, yielding predominantly Chloroflexi phylotypes (Kojima et al. 2006; Nemoto et al. 2011). Intergenic spacer region and partial 23S rRNA gene sequences (AB699673 to AB699684) allow for a fine-scale resolution of the genus Thioploca; the tropical Thioploca phylotypes diverge from their temperate lake counterparts (Nemoto et al. 2012).

Thioploca schmidlei. Lauterborn 1907

schmid’le.i. M.L. gen.n., schmidlei of Schmidle.

Identified from sediments of freshwater and brackish-water localities in Europe and from Lake Baikal, Russia. Originally found in Lake Constance, southern Germany. Multicellular filaments, diameter 5–9 μm, constant width over the entire length of the filament, forming bundles, gliding motility.

Type strain: none isolated.

Thioploca ingrica. Maier 1984

In’gri.ca. M.L. adj. ingrica pertaining to Ingria, ancient district of St. Petersburg, Russia.

Identified from sediments of freshwater and brackish-water localities in central Europe, from Lake Erie, USA; from Lake Biwa, Japan; and Lake Tonle Sap, Cambodia. Multicellular filaments, constant width over the entire length of the filament, diameter 2–4.5 μm, forming bundles; gliding motility.

Type strain: none isolated.

Genbank accession number of 16S rRNA gene sequence: L40998.

Taxonomic note: The genus Thioploca is not represented by pure cultures; its type species T. schmidlei is only rarely found, and its sole described species, T. ingrica, remains uncultured and incompletely characterized. Such a combination is usually characteristic of a Candidatus group; at present, Thioploca retains its status as a validly described genus due to historical precedent.

“Candidatus Marithioploca”. Salman et al. 2011

This group of uncultured, filamentous, sheath-forming sulfide-oxidizing bacteria (Fig. 6.3a–f) was originally included in the genus Thioploca and contained the large marine Thioploca species T. araucae and T. chileae (Maier and Gallardo 1984b). Since it constitutes a monophyletic 16S rRNA gene lineage distinct from freshwater Thioploca (Teske et al. 1995, 1999) and also shows substantial physiological differences, the marine and freshwater Thioploca sp. were separated into two taxonomic groups. The smaller brackish and freshwater representatives are retained as the genus Thioploca sensu stricto, and the large marine strains constitute the Candidatus taxon “Marithioploca” (Salman et al. 2011). FISH hybridization experiments with group-specific 16S rRNA probes have validated the 16S rRNA sequences obtained from size-sorted and cleaned filaments (Teske et al. 1995, 1999). The “Marithioploca” group forms two separate, yet mutually closely related subclusters. One subcluster contains the original published partial sequence of Thioploca araucae (L41043; Teske et al. 1995), the near-complete sequence of a large, single, marine Beggiatoa-like filament from the Bay of Concepción (AF035956; Teske et al. 1999), and several sequences from bundled and single filaments collected offshore Concepción, Chile (FR690987 to FR690993; Salman et al. 2011). The filament diameter range within this group is largely congruent with the range given in the original description of T. araucae (30–43 μm; Maier and Gallardo 1984b). The second subcluster contains the original partial sequences for T. chileae (L40999; Teske et al. 1999) and three other sequences originating again from bundled and single filaments (FR690994 to FR690996; Salman et al. 2011) that are congruent with the published size range for T. chileae (12–20 μm; Maier and Gallardo 1984b). 16S rRNA gene sequence identities among the two clusters are as high as 98.3–99.5 %, which could argue against a taxonomic separation. On the other hand, the two species show not only nonoverlapping filament diameter distributions but also distinct environmental distributions and habitat preferences (Schulz et al. 1996, 2000). Based on mutually consistent ecophysiological, morphological, and molecular differences, the two species are retained.

“Marithioploca araucae”. Salman et al. 2011

Ma.ri.thi.o.plo’ca. L. gen. n. maris of the sea; N.L. fem. n. Thioploca a genus name; N.L. fem. n. Marithioploca the Thioploca of the sea, the truly marine Thioploca; T. araucae (Maier and Gallardo 1984b), Approved Lists 1980; a.rau’ca.e. N.L. fem. adj. araucae of Arauco in Central Chile.

Identified from oxygen-poor upwelling area offshore Concepción, Chile. Multicellular filaments either free-living filaments or bundled by a common mucous sheath; filament diameter 25–43 μm; constant width over the entire length of the filament; gliding motility; vacuolated; ability to store nitrate; sulfur inclusions, marine.

Genbank accession number of 16S rRNA gene sequence: L41043; FR690987 to FR690993.

“Marithioploca chileae”. This Publication

Ma.ri.thi.o.plo’ca. L. gen. n. maris of the sea; N.L. fem. n. Thioploca a genus name; N.L. fem. n. Marithioploca the Thioploca of the sea, the truly marine Thioploca; T. chileae (Maier and Gallardo 1984b), Approved Lists 1980; chi’le.ae. N.L. gen.n. chileae of Chile.

Identified from oxygen-poor upwelling area offshore Concepción, Chile. Multicellular filaments either free-living filaments or bundled by a common mucous sheath; filament diameter 12–20 μm; constant width over the entire length of the filament; gliding motility; vacuolated; ability to store nitrate; sulfur inclusions, marine.

Genbank accession number of 16S rRNA gene sequence: L40999, FR690994, FR690995, FR690996.

Taxonomic note: The near-identical 16S rRNA gene sequences of filaments growing as sheathed filament bundles and those thriving as single, free-living filaments affiliating with this taxon show that the morphological (sheath-based) distinction of the genera Beggiatoa and Thioploca was phylogenetically shallow (Teske et al. 1999; Salman et al. 2011).

Genus Thiomargarita. Schulz et al. 1999

The first discovery of nonfilamentous, very large, vacuolated, nitrate-accumulating, and spherical cells in highly reducing marine sediments offshore Namibia led to the description of the new genus Thiomargarita based on a distinct morphology (Fig. 6.4a) and 16S rRNA gene sequence (AF129012) (Schulz et al. 1999). Thiomargarita is among the largest known bacteria by volume; observed cell diameters diverge widely, and current observations indicate a range of 16–750 μm (Salman et al. 2011). Large Thiomargarita cells are discussed as an alternate explanation for late proterozoic microfossils that are commonly regarded as eukaryotic blastocytes (Bailey et al. 2007).

The chain-forming Thiomargarita specimens of the original description have been supplemented by 16S rRNA gene sequencing of numerous unicellular (Fig. 6.4b) or aggregate-forming (Fig. 6.4e) Thiomargarita cells from Namibia, Chile, and Costa Rica (FN811663; FR690879 to FR690921); these phylotypes cluster together and form the species Thiomargarita namibiensis (Salman et al. 2011). Two additional Thiomargarita species are proposed as species-level Candidate taxa. Candidatus “Thiomargarita joergensenii” forms a distinct clade of 16S rRNA gene sequences (FR690922 to FR690925) and shows a homogenous morphology: multiple spherical cells are inhabiting an intact centric diatom frustule that has no openings or passages for fully grown cells, suggesting an initial colonization of the frustule by substantially smaller daughter cells (Salman et al. 2011).

This morphology/lifestyle is also found in the candidatus taxon “Thiopilula.” Cells belonging to the candidate species “Thiomargarita nelsonii” occur in a wide range of morphologies (Fig. 6.4c, d), i.e., spherical unicells; cylindrical cells in chains; symmetrically arranged, fourfold-divided aggregates; aggregates of several tens of cells; attached budding cells (Fig. 6.4f); and nonattached, extremely large spherical cells with budding spherical caps. This species is also represented by a distinct 16S rRNA gene lineage (FR690926 to FR690967, FN811658, FN811659, FN811661, FN811662, HF954103, HF954105, HF954106, HF954108-110, HF954113) (Salman et al. 2011; Bailey et al. 2011; Salman et al. 2013). Specific PCR primers for the genus Thiomargarita were developed for specific amplification of 16S rRNA genes from contamination-prone single cells (Bailey et al. 2011; Salman et al. 2011).

Members of the genus Thiomargarita contain up to four self-splicing introns within their 16S rRNA genes; they enlarge the 16S rRNA genes considerably (up to app. 3.5 kb) and interfere with PCR amplification of 16S rRNA genes (Salman et al. 2012). One or two introns are also found within the 16S rRNA genes of the candidate genera “Marithioploca,” “Thiopilula,” and “Thiophysa.” The introns occur in specific, conserved positions within the 16S rRNA gene (E. coli positions 795, 1078, 1396, and 1495) and often encode genes for intron-encoded homing endonuclease proteins. Intron persistence within the large, vacuolated sulfide-oxidizing bacteria might be connected to their suggested degree of polyploidy (Salman et al. 2012); an unusually high amount of nucleoids is documented for cells of Thiomargarita namibiensis (Schulz 2006). A few intron-encoded endonucleases would be sufficient to jump-start endonuclease-catalyzed spread of intron sequences throughout the polyploid genome (Salman et al. 2012).

Thiomargarita namibiensis Schulz et al. 1999

Thi’o.mar.ga.ri’ta Gr. neut. n. theion (Latin transliteration thium), sulfur; L. n. margarita pearl; N.L. fem. n. Thiomargarita sulfur pearl; na.mi.bi.en’sis. M.L. gen. n. namibiensis of Namibia.

Spherical cells, occurring unicellular, in chains or in aggregates; single cells occasionally motile by slow jerky rolling; vacuolated; can store nitrate in vacuole (up to 800 mM); sulfur inclusions; in sediments off Namibia, Chile, and Costa Rica and at mud volcano off Egypt; marine.

Genbank accession numbers of 16S rRNA gene sequence: FR690879-FR690921, FN811663, HF954102, HF954104.

“Candidatus Thiomargarita joergensenii” Salman et al. 2011

Thi.o.mar.ga.ri’ta. Gr. neut. n. theion (Latin transliteration thium), sulfur; L. n. margarita pearl; N.L. fem. n. Thiomargarita sulfur pearl; joer.gen.se’ni.i. N.L. gen. n., joergensenii of Jørgensen, named in honor of Bo Barker Jørgensen, a Danish microbiologist.

Single, spherical cells; occurring in empty diatom frustules; sporadic slow jerky rolling movement; vacuolated; sulfur inclusions; in sediments off Namibia; marine.

Genbank accession numbers of 16S rRNA gene sequence: FR690922–FR690925, HF954107.

“Candidatus Thiomargarita nelsonii” Salman et al. 2011

Thi.o.mar.ga.ri’ta. Gr. neut. n. theion (Latin transliteration thium), sulfur; L. n. margarita pearl; N.L. fem. n. Thiomargarita sulfur pearl; nel.so’ni.i. N.L. gen. n. nelsonii of Nelson, named in honor of Douglas C. Nelson, an American microbiologist.

Cells of highly diverse morphology and life modes; ability to divide in multiple planes, to attach, or to form gonidia; single cells or those in envelopes sporadic slow jerky rolling movement; vacuolated; sulfur inclusions; in sediments off Namibia, Chile, and Costa Rica and around cold seeps at Hydrate Ridge and Costa Rica; marine.

Genbank accession numbers of 16S rRNA gene sequence: FR690926–FR690967, FN811658–FN811659, FN811661, FN811662, HF954103, HF954105, HF954106, HF954108-110, HF954113.

Taxonomic comment: The partial 16S rRNA sequence of the original publication (AF129012) of T. namibiensis matches the “T. nelsonii” phylotype and not T. namibiensis. Obviously, the chains of cylindrical cells of “T. nelsonii” can be mistaken for the large, spherical cells in T. namibiensis chains.

“Candidatus Maribeggiatoa” Salman et al. 2011

Beggiatoa-like, large, vacuolated, nitrate-accumulating filaments from reducing marine sediments form this monophyletic lineage based on 16S rRNA gene sequences from individual filaments (Salman et al. 2011). The group contains phylotypes from the central Californian coast, Monterey Canyon (AF064543, Ahmad et al. 1999), Carmel Canyon (AY580013, Kalanetra et al. 2004), and Monterey Bay (FJ814745, FJ814753). Large individual filament diameters are found in this group: 20–76 μm for Carmel Canyon and 65–85 μm for Monterey Canyon filaments (Fig. 6.5a–b). With the exception of clone FJ814753, the sequences cluster tightly together and constitute the species-level candidate taxon “Maribeggiatoa vulgaris” (Salman et al. 2011). Phylotypes related to “Maribeggiatoa” were also obtained by sequencing of reverse-transcribed 16S rRNA from microbial mats in the Gulf of Mexico (partial sequences with Genbank numbers AY324499, AY324511) (Mills et al. 2004). A FISH probe for “Maribeggatoa” has been developed to distinguish “Maribeggiatoa” from “Marithioploca” (Ahmad et al. 1999).

“Candidatus Maribeggiatoa vulgaris” Salman et al. 2011

Ma.ri.beg.gi.a.to’a. L. gen. n. maris of the sea; N.L. fem. n. Beggiatoa a genus name; N.L. fem. n. Maribeggiatoa the Beggiatoa of the sea, the truly marine Beggiatoa; vul.ga’ris. L. fem. adj. vulgaris usual, common.

Disc-shaped cells forming multicellular filaments; constant width over the entire length of the filament, rounded terminal cells; gliding motility; vacuolated; ability to store nitrate; sulfur inclusions; marine; at seep sites and hydrothermal vents.

Genbank accession numbers of 16S rRNA gene sequence: FJ814745, AY580013, AF064543.

Taxonomic note: Two clusters of large, vacuolated, nitrate-accumulating marine Beggiatoa-like filaments from Guaymas Basin hydrothermal sediments consist of orange filaments with ca. 25–35 μm diameter (JN793553, JN793555, JN793556) and of very large colorless filaments of ca. 120 μm diameter (JN793554, JN793557) and form a multilineage cluster with the Candidatus taxa “Maribeggiatoa” and “Marithioploca” (McKay et al. 2012). The near-complete genome of a single orange filament has been obtained and analyzed after whole genome amplification (MacGregor et al. 2013a, b, c). Although published as “Maribeggiatoa,” it became apparent that the orange Guaymas filaments share only weak bootstrap support (between 50 % and 60 %) with “Maribeggiatoa” (Salman et al. 2013). The white Guaymas filaments do not fit into currently described candidatus taxa (Salman et al. 2013). Therefore, the orange and the white Guaymas filaments are included here as separate lineages of Beggiatoaceae (Fig. 6.1 ).

“Candidatus Marithrix” Salman et al. 2011

Large, vacuolated filaments growing attached to hydrothermal vent chimneys and surrounding methane and mud seeps are exposed alternately to sulfidic and oxygenated seawater (Fig. 6.5e) and form this monophyletic lineage among the Beggiatoaceae (Kalanetra et al. 2004; Heijs et al. 2005; Kalanetra and Nelson 2010; Grünke et al. 2011, 2012). The 16S rRNA gene sequences of “Marithrix” filaments have been determined by multiple PCR amplifications with general and specifically developed group-specific primers and were validated by FISH hybridization of fresh filaments, using the rRNA equivalent of the group-specific PCR primer site as probe target (Kalanetra et al. 2004). The filament diameters of the target organism are variable: positive FISH hybridizations were obtained with filaments in the range of 10–38 μm, plus a few larger filaments (Kalanetra et al. 2004). Attached filaments from the Juan de Fuca vents ranged in diameter mostly from 9–30 μm; a minority of larger filaments reached up to 96 μm (Kalanetra and Nelson 2010). So far, filaments from two deep-sea hydrothermal areas (Juan de Fuca, Escanaba Trough) and a coastal hydrothermal vent (White Point, California) have identical 16S rRNA sequences (AY883933; AY883934; AY496953); very similar 16S rRNA transcripts were recently obtained from the Menez Gwen hydrothermal vent site (FR827864; Grünke et al. 2012) and Lucky Strike hydrothermal field (FR670384; Crépeau et al. 2011) on the Mid-Atlantic Ridge, from the Amon (FR666859, Grünke et al. 2011) and Milano (AY592917, Heijs et al. 2005) mud volcanoes in the Mediterranean Sea, and from a Storegga gas chimney off Norway (FR847874, Grünke et al. 2012). Overall, the members of this group share 16S rRNA gene sequence similarities of at least 98 %. The name of this candidate genus and species, Candidatus “Marithrix sessilis,” reflects their distinctive surface-attached and rosette-forming growth mode that is otherwise seen in the genus Thiothrix (Salman et al. 2011).

“Candidatus Marithrix sessilis”Salman et al. 2011

Ma’ri.thrix. L. gen. n. maris of the sea; Gr. n. thrix hair; N.L. fem. n. Marithrix hair of the sea; ses’si.lis. L. adj. sessilis sitting, adhering to a surface.

Attached, multicellular filaments, constant width over the entire length of the filament; diameter of most filaments in the range of 10–38 μm (outliers up to 112 μm have been observed), rounded ends, sometimes forming rosettes; ability to produce gonidia; nonmotile; sulfur inclusions; vacuolated or non-vacuolated; marine; at cold seeps and hydrothermal vents.

Genbank accession numbers of 16S rRNA gene sequences: AY883933–AY883934, AY496953, FR827864.

“Candidatus Isobeggiatoa” Salman et al. 2011

Beggiatoa-like, vacuolated, nitrate-accumulating filamentous bacteria from a wide range of marine sediments constitute the genus-level candidate taxon “Isobeggiatoa,” defined as a monophyletic lineage by 16S rRNA analysis (Salman et al. 2011). At present, this group contains representatives from Arctic fjords of Svalbard, Norway (FN561862; Jørgensen et al. 2010); Tokyo Bay, Japan (AB108786; Kojima and Fukui 2003); the Chilean coast (FJ875195; Aranda et al. 2010); and a cluster of similar sequences from Limfjorden in Denmark (AF532775) and Jadebusen in Germany (AF532769; Mussmann et al. 2003) that have been proposed as the candidate species-level taxon “Isobeggiatoa divolgata” (Salman et al. 2011). Filament diameters of geographically separated populations with distinct 16S rRNA sequences show a wide range from approximately 10–30 μm (Jørgensen et al. 2010; Aranda et al. 2010). A single filament from Eckernförde Bay in Germany (Filament PS; near 30 μm diameter) was used for whole genome amplification and subsequent pyrosequencing, yielding a partial genome of 6.769 contigs with 17x coverage and a total sequencing length of 7.6 Mb (Mussmann et al. 2007).

“Candidatus Isobeggiatoa divolgata” Salman et al. 2011

I.so.beg.gi.a.to’a. Gr. adj. isos equal, similar; N.L. fem. n. Beggiatoa a genus name; N.L. fem. n. Isobeggiatoa the bacterium similar to Beggiatoa; di.vol.ga’ta. L. fem. adj. divolgata widespread, common.

Disc-shaped cells forming multicellular filaments; constant width over the entire length of the filament, rounded terminal cells; gliding motility; vacuolated; ability to store nitrate; sulfur inclusions; brackish or marine, also arctic latitudes.

Genbank accession numbers of 16S rRNA gene sequence: AF532769, AF532775, FJ875195, AB108786, FN561862.

“Candidatus Parabeggiatoa” Salman et al. 2011

Morphologically similar to medium-sized, filamentous marine “Isobeggiatoa,” this monophyletic group of uncultured, sulfide-oxidizing large filamentous bacteria is defined by 16S rRNA gene sequencing of single filaments (Salman et al. 2011). These bacteria occur in two distinct phylogenetic clusters: one cluster represented by filaments from brackish sediments of Limfjorden in Denmark (AF532770; AF532772-774; Mussmann et al. 2003) contains the candidatus taxon “Parabeggiatoa communis” (Salman et al 2011). The 16S rRNA sequences of this cluster are validated by FISH with a group-specific 16S rRNA probe; the FISH-stained filaments of this cluster range in diameter from approximately 33–40 μm (Mussmann et al. 2003). The second cluster consists of filaments with diameters in the range of 20–30 μm that were collected from reducing marine sediment underneath the cages of a salmon farm in southern Chile (FJ875196 to FJ875199) (Aranda et al. 2010). A single filament from Eckernförde Bay in Germany (Filament SS, ca. 30 μm diameter) was used for whole genome amplification and subsequent Sanger sequencing, yielding a low-coverage (3x) partial genome assembly of 1,091 contigs with a total sequencing length of 1.3 Mb (Mussmann et al. 2007). Recently, “Parabeggiatoa” was also found in extensive sulfide-oxidizing mats on hydrothermal sediments of Guaymas Basin in the Gulf of California, Mexico (JN793555; McKay et al. 2012).

“Candidatus Parabeggiatoa communis” Salman et al. 2011

Pa.ra.beg.gi.a.to’a. Gr. prep. para beside, like; N.L. fem. n. Beggiatoa a genus name; N.L. fem. n. Parabeggiatoa resembling the genus Beggiatoa; com.mu’nis. L. fem. adj. communis common, widespread.

Disc-shaped cells forming multicellular filaments; diameter 33–40 μm, constant width over the entire length of the filament, rounded terminal cells; gliding motility; vacuolated; ability to store nitrate; sulfur inclusions; brackish or marine.

Genbank accession numbers of 16S rRNA gene sequence: AF532770, AF532772–AF532774, FJ875196–FJ875199.

“Candidatus Allobeggiatoa” Hinck et al. 2011

Strains of the genus-level Candidatus group “Allobeggiatoa” (Fig. 6.2e) were enriched from solar salterns in Spain and hypersaline cyanobacterial mats in Spain and Mexico (Hinck et al. 2007, 2011) and represent a monophyletic lineage in 16S rRNA phylogenies (EF428583 and EU919200; Hinck et al. 2007; FR687024 to FR687036; Hinck et al. 2011). The phylogenetically clustered filaments from Spain constitute the species-level candidate group “Allobeggiatoa salina” (Hinck et al. 2011). The 16S rRNA gene sequences have been validated by group-specific FISH probes and hybridization experiments (Hinck et al. 2011). The “Allobeggiatoa” group constitutes a sister lineage to Beggiatoa alba and related deeply branching Beggiatoa-like filamentous bacteria (Hinck et al. 2011). It differs not only by 16S rRNA phylogeny but also morphologically. The filaments of “Allobeggiatoa” are vacuolated (Fig. 6.2e) and have a diameter of predominantly 6–14 μm, which is distinct from the non-vacuolated, thinner (2–3 μm) filaments for Beggiatoa alba and its freshwater relatives (Hinck et al. 2011).

“Candidatus Allobeggiatoa salina”Hinck et al. 2011

Al.lo.beg.gi.a.to′a. L. gen. n. allos the other; Beggiatoa genus name; M.L. fem. n. Allobeggiatoa, the other Beggiatoa; sa.li′na. L. fem. adj. salina salted, saline.

Disc-shaped cells, forming filaments of 6–14 μm in diameter, constant width over the entire length of the filament, rounded terminal cells; gliding motility; intracellular storage of nitrate (up to 650 mM); each cell contains a large central vacuole; the vacuole accounts for about 80 % of cellular biovolume and is surrounded by a cytoplasmic layer; intracytoplasmic sulfur storage (up to 250 mM); facultative anaerobic and presumably performing reduction of intracellular nitrate; microaerophilic; chemolithoautotrophic sulfide oxidizer; halotolerant (tested range 3–15 % salinity); filaments do not form macroscopically visible mats, but are distributed within certain cyanobacterial mat layers that are exposed to sulfide gradients; habitat: sulfide-rich microbial mats at shallow permanently hypersaline lakes and ponds of solar saltern systems with salinities reaching up to 15 %.

Genbank accession numbers of 16S rRNA gene sequence: EF428583, EU919200, FR687024 to FR687033.

Taxonomic note: The detection of filamentous sulfur bacteria in hypersaline environments implied that the organisms were halophilic. Yet, culture studies showed identical growth at salinities ranging from 3–15 %, a characteristic that should be called halotolerant. In order to refer to the highly saline habitat where filaments were encountered, instead to an understudied physiological capability, the species name “halophila” was changed to “salina” before publication in Hinck et al. (2011). Care should be taken because the published phylogenetic tree (Hinck et al. 2011) contains the erroneous name “Allobeggiatoa halophila,” which has been corrected by the erratum in Environmental Microbiology Vol. 14, Issue 12, p. 3287.

“Candidatus Halobeggiatoa” Grünke et al. 2012

The genus-level Candidatus group “Halobeggiatoa” represents a monophyletic group (95.9–100 % 16S rRNA gene sequence identity) of nitrate-accumulating marine single filaments of up to 10 μm diameter (Fig. 6.5c). The sequences of this phylogenetic group were obtained from filaments collected from white mats at the Håkon Mosby mud volcano offshore northern Norway (FR847864 to FR847873; Grünke et al. 2012) and from nearshore sediments in Tokyo Bay (AB106784, AB106785; Kojima and Fukui 2003).

“Candidatus Halobeggiatoa borealis” Grünke et al. 2012

Ha.lo.beg.gi.a.to’a. Gr. n, hals salt; N.L. fem. n. Beggiatoa a genus name; N.L. fem. n. Halobeggiatoa the salt Beggiatoa; bo.re.al.is. L. fem. adj. borealis northern

This species-level candidate group is based on seven identical 16S rRNA gene sequences from filaments collected at the Håkon Mosby mud volcano (HMMV) offshore northern Norway (Lichtschlag et al. 2010; Grünke et al. 2012).

Disc-shaped cells, forming filaments of 8–10 μm in diameter, constant width over the entire length of the filament; intracellular nitrate accumulation; gliding motility; filaments occur in conspicuous white mats on HMMV methane seep sediments. Genbank numbers are FR847864 to FR847870.

Taxonomic note: Given the diversity of filamentous Beggiatoa-like organisms in the HMMV mats, the identification of “Candidatus Halobeggiatoa borealis” should be regarded as preliminary and requires future validation by FISH hybridization and filament-specific physiological characterization.

“Candidatus Thiopilula” Salman et al. 2011

The candidate genus-level group “Thiopilula” includes large, nonfilamentous, vacuolated cells that resemble Thiomargarita in spherical cell morphology but occur attached to surfaces (Bailey et al. 2011), in colony-like aggregates or within diatom frustules, and form a distinct 16S rRNA lineage (Salman et al. 2011). Specimens collected from benthic marine sediments off Namibia and attached in the vicinity of seeps off Costa Rica have been sequenced (FR690968 to FR690981; FN811660 and FN811664) and are proposed as members of the species-level candidate taxon “Thiopilula aggregata” (Salman et al. 2011).

“Candidatus Thiopilula aggregata”Salman et al. 2011

Thi.o.pi’lu.la. Gr. neut. n. theion (Latin transliteration thium), sulfur; L. fem. n. pilula little ball, little globule; N.L. fem. n. Thiopilula little sulfur ball; ag.gre.ga’ta. L. fem. adj. aggregata joined together.

Spherical cells aggregated in variable arrangements; recorded diameters 15–65 μm; ability to attach and form gonidia; sporadic slow jerky rolling movement; vacuolated; sulfur inclusions; marine.

Genbank accession numbers of 16S rRNA gene sequence: FR690968–FR690980, FN811660, FN811664.

“Candidatus Thiophysa” Salman et al. 2011

The candidate genus-level group “Thiophysa” includes large, nonfilamentous, motile single spherical cells with sulfur inclusions that by 16S rRNA gene sequence (FR690982 to FR690986) form a distinct monophyletic group (Salman et al. 2011). Comparable cells have been described originally as Thiophysa volutans (Hinze 1903) and were later reclassified as members of the genus Achromatium (A. volutans, Van Niel 1948). However, 16S rRNA gene analysis places these bacteria clearly into the Beggiatoaceae, not into the Achromatiaceae. Therefore, the genus name Thiophysa has been revived and the species-level candidatus taxon “Thiophysa hinzei” proposed (Salman et al. 2011).

“Candidatus Thiophysa hinzei”Salman et al. 2011

Thi.o.phy’sa. Gr. neut. n. theion (Latin transliteration thium), sulfur; Gr. fem. n. physa bubble, breath; N.L. fem n. Thiophysa sulfur bubble; hin’zei. N.L. gen. n. hinzei of Hinze; named in remembrance of G. Hinze, a German microbiologist, who first described marine, large, spherical sulfur bacteria.

Single, spherical cells; recorded diameters from 56 to 90 μm; vacuolated; sporadic slow jerky rolling movement; sulfur inclusions; marine.

Genbank accession numbers of 16S rRNA gene sequence: FR690982–FR690986.

Phenotypic Analyses

Phenotypic Characteristics of the Beggiatoaceae

One of the basic, defining features of the Beggiatoaceae is the formation of intracellular sulfur globules by oxidation of reduced sulfur sources (e.g., Figs. 6.2a and 6.4b). The physiological roles of sulfide oxidation and sulfur accumulation are complex and diverge between different physiological types of the Beggiatoaceae. Sulfide is a source of energy and electrons for autotrophic carbon fixation and growth (Dworkin 2012; Winogradsky 1887); it can be oxidized with oxygen or nitrate as terminal electron acceptors and can be supplemented or replaced by organic carbon compounds as energy source for heterotrophic growth; in the latter case, elemental sulfur from sulfide oxidation is stored as an alternate electron acceptor. For overview purposes, the diverse genera and candidatus groups within the Beggiatoaceae can be divided into several groups with shared phenotypic characteristics.

(A) The heterotrophic non-vacuolate freshwater strains with thin filament diameter are represented by several well-studied strains: the type strain of the genus Beggiatoa, B. alba B18LD (Fig. 6.2c, Mezzino et al. 1984); the B. alba strains B15LB (Strohl and Larkin 1978a, b; Strohl et al. 1982); OH-75-2a (Fig. 6.2a, Nelson and Castenholz 1981a, b); and the distantly related strain L1401-13 (Pringsheim 1964; Kowallik and Pringsheim 1966). (B) The autotrophic non-vacuolate marine strains with thin filament diameters are represented by the facultatively autotrophic strain MS-81-6, by the obligately autotrophic strains MS-81-1c (Fig. 6.2b, Nelson et al. 1982; Nelson and Jannasch 1983; Nelson et al. 1986b; Hagen and Nelson 1996, 1997), and by the marine strain 35Flor (Fig. 6.2d, Kamp et al. 2008; Brock et al. 2012; Schwedt et al. 2012). These strains exhibit strong chemotactic behavior and orient themselves as Beggiatoa “plates” in the steep oxygen/sulfide gradients which they maintain by fast sulfide oxidation under microoxic conditions (Fig. 6.6 ). (C) The small freshwater and brackish-water genus Thioploca is characterized by sheathed bundles of thin filaments embedded in surface sediment or decaying plant material (Fig. 6.3g, Høgslund et al. 2010). (D) The large, vacuolated, nitrate-accumulating autotrophic marine Candidatus groups “Maribeggiatoa,” “Isobeggiatoa,” “Parabeggiatoa,” (Fig. 6.5a, b, d) and related Beggiatoaceae remain uncultured so far. The cells of these large, marine Beggiatoaceae filaments are hollow, i.e., composed of a thin cylinder of cytoplasm surrounding a large central vacuole. This extensive vacuolation is usually linked to high intracellular nitrate concentration (Hinze 1901; Jannasch et al. 1989; Nelson et al. 1989; Larkin and Henk 1996; McHatton et al. 1996), with the possible exception of “Candidatus Marithrix,” in which nitrate could not yet be detected in the vacuoles (Kalanetra et al. 2004) (Fig. 6.5e). (E) Large size, vacuolation, and the ability to accumulate nitrate also apply to Thiomargarita and “Candidatus Marithioploca,” although these organisms are set apart by their conspicuous morphology and lifestyle: the filaments of “Marithioploca” occur predominantly in bundles within sheaths embedded in surface sediment and move within their sheaths to bridge spatially separated pools of the electron donor sulfide in the sediment and the electron acceptor nitrate in the overlying seawater (Hüttel et al. 1996) (Figs. 6.3a–f and 6.7 ). (F) In contrast, Thiomargarita, “Thiopilula,” and “Thiophysa” have very limited mobility or grow even attached to surfaces (Fig. 6.4 ); they rely primarily on their large cell size and high intracellular storage capacity to survive fluctuating redox regimes and temporary electron donor and acceptor shortages (Schulz and Jørgensen 2001).

Genus Beggiatoa

A physiological characterization of the genus Beggiatoa depends on how its taxonomic borders are drawn. If the genus is not reduced to its only recognized species, the heterotrophic freshwater filamentous bacterium Beggiatoa alba B15LD and B18LD (Strohl and Larkin 1978a; Strohl et al. 1981, 1982) and its close relative OH-75-2a (Nelson and Castenholz 1981a, b), it should also include a wide variety of freshwater and marine strains with small filament diameters and a metabolic spectrum that reaches from aerobic heterotrophy coupled with auxiliary sulfur metabolism (sulfur respiration under anoxia) in freshwater strains to microaerophilic, sulfur-based autotrophy in marine strains (Nelson et al. 1982; Nelson and Jannasch 1983). Beggiatoa strain 35Flor is the only marine strain currently available in culture; it is capable of autotrophic growth by aerobic sulfide oxidation, and it can survive anoxic episodes by changing to anaerobic sulfur respiration (Schwedt et al. 2012).

Beggiatoa alba

Beggiatoa alba requires organic carbon substrates for aerobic, heterotrophic growth and resembles in this regard numerous freshwater strains (Faust and Wolfe 1961; Burton et al. 1966; Pringsheim 1964; Kowallik and Pringsheim 1966; Scotten and Stokes 1962; Strohl and Larkin 1978a, b; Nelson and Castenholz 1981a, b). Most Beggiatoa strains examined can grow with acetate as a sole source of carbon and energy. All strains of the type species Beggiatoa alba (B18LD, B15LD, B25RD) grow well in the presence of sulfide and additions of 0.001–0.05 % acetate (Mezzino et al. 1984), very similar to previous results on other freshwater Beggiatoa strains that, when grown with H₂S as energy source, required acetate additions in the range of 0.01–0.0001 % (w/v) (Kowallik and Pringsheim 1966). Beggiatoa alba B18LD can use acetate as an energy source and oxidize both acetate C atoms to CO₂; it can also incorporate ¹⁴C-labeled acetate into a wide range of cellular and storage compounds, e.g., poly-β-hydroxyalkanoates (Fig. 6.2c). Also, acetate significantly increases the capability of this strain to assimilate CO₂, probably through anaplerotic reactions of the tricarboxylic acid (TCA) cycle (Strohl et al. 1981a). Recently, it was shown that Beggiatoa alba B18LD and its close relative OH-75-2a can grow on methanol as the sole carbon substrate, when cultured in sulfide gradient tubes (Jewell et al. 2008); the strains are therefore facultative methylotrophs. Other methylated substrates or methane did not support growth (Jewell et al. 2008).

A functional TCA cycle with a glyoxylate bypass has been demonstrated in detailed enzymological studies of Beggiatoa strain OH-75-2a (Nelson and Castenholz 1981b), a close relative of Beggiatoa alba B18DL and most likely a strain of the same species (Mezzino et al. 1984; Ahmad et al. 2006), and in the chemoheterotrophic Beggiatoa strain D-405 (Grabovich et al. 1993). Beggiatoa strain OH-75-2a can grow on acetate, ethanol, lactate, pyruvate with a small addition of yeast extract, and TCA cycle intermediates in combination with acetate.

The heterotrophic Beggiatoa strain OH-75-2a was quantitatively studied for autotrophic and mixotrophic growth by sulfide and thiosulfate oxidation (Nelson and Castenholz 1981a) to test whether these inorganic electron donors reduce the need for carbon oxidation, lead to increased carbon assimilation and biomass yield, and increase the ecophysiological flexibility of Beggiatoa in nature (Pringsheim 1967; Strohl and Schmidt 1984). Sulfide oxidation does not result in additional biomass yield for Beggiatoa strain OH-75-2a beyond that obtained from the oxidation of organic carbon sources; mixotrophic growth enhancement by sulfide oxidation was not found (Nelson and Castenholz 1981a). Other attempts to demonstrate mixotrophy for this strain showed experimental shortcomings and need to be revisited (Güde et al. 1981; Nelson and Jannasch 1983). Sulfur globules serve as an electron acceptor reserve that allows a rudimentary anaerobic respiration with sulfur. In Beggiatoa strain OH-75-2a, sulfur globules that had accumulated during aerobic thiosulfate oxidation subsequently sustained anaerobic metabolism and growth during several days of anoxia (Nelson and Castenholz 1981a). Reduction of sulfur globules to sulfide, coupled to de novo synthesis of cell material, was also found in Beggiatoa alba B18LD during anoxic incubation (Schmidt et al. 1987). This mechanism helps the filaments to survive periods of anoxia in their natural interface habitat (Schmidt et al. 1987).

These results for strain OH-75-2a indicate that Beggiatoa alba B18LD does not use sulfur as a chemolithoautotrophic or mixotrophic source of energy. There is circumstantial evidence that acetate and sulfide oxidation compete for oxygen; the addition of acetate and other carbon sources inhibited sulfide oxidation and accumulation of intracellular sulfur globules in Beggiatoa alba B18LD considerably (Schmidt et al. 1987). The obligately aerobic oxidation of reduced sulfur compounds in Beggiatoa alba B18LD, consistent with the presence of c-type cytochromes (Cannon et al. 1979), stops essentially at the stage of the elemental sulfur globules. Under a wide range of test conditions, Beggiatoa alba B18LD filaments harboring sulfur globules did not release significant amounts of soluble sulfur oxidation products into the surrounding medium (Schmidt et al. 1987). During anoxic incubation, Beggiatoa alba B18LD reduces sulfur globules to sulfide, coupled to de novo synthesis of cell material (Schmidt et al. 1987). Thus, a major physiological role for sulfide oxidation in Beggiatoa alba is the formation of internal sulfur globules as an alternate electron acceptor reservoir.

Beggiatoa alba strains can use nitrate, nitrite, ammonia, and casamino acids as sole nitrogen source (Mezzino et al. 1984), and the list also includes urea, aspartate, asparagine, alanine, and thiourea that tested positive for strain B18LD (Vargas and Strohl 1985a). Beggiatoa alba B18LD assimilates ammonia by the glutamine synthetase–glutamate synthase pathway (Vargas and Strohl 1985a). Nitrate cannot be used as electron acceptor for growth with sulfide oxidation; it allows a limited degree of acetate oxidation, but does not sustain growth as the sole electron acceptor. The enzyme activity is associated with the soluble fraction, not with the cell membranes, and generates ammonia as the waste product. Based on its cellular localization and biochemical properties, the nitrate reductase of Beggiatoa alba appears to be an assimilatory nitrate reductase (Vargas and Strohl 1985b). In contrast to Beggiatoa alba, other freshwater Beggiatoa strains can use nitrate as terminal electron acceptor (Sweerts et al. 1990; Kamp et al. 2006).

Beggiatoa alba tests positive for nitrogen fixation and thus contributes to total nitrogen fixation in its natural habitats. Nitrogenase activity in Beggiatoa alba is strongly regulated by nitrogen bioavailability: nitrate and nitrite additions to the growth medium prevent induction of nitrogenase; in vivo nitrogenase activity is inhibited by ammonia and urea (Polman and Larkin 1988). Similar nitrogenase repression was found in the heterotrophic freshwater strain OH-75-2a and several other strains isolated from a warm freshwater spring (Nelson and Castenholz 1981a, b). Tightly regulated nitrogenase activity is also shared with marine autotrophic strains MS-81-6 and MS-81-1c (Nelson et al. 1982).

Beggiatoa sp. MS-81-6 and MS-81-1c

These two marine strains, although phylogenetically distinct from Beggiatoa alba, remain the best-studied examples for autotrophic carbon fixation and chemolithotrophic sulfur oxidation among the Beggiatoaceae (Fig. 6.2b). Carbon assimilation processes and pathways of Beggiatoa came under investigation shortly after Winogradsky began to develop the concept of microbial chemolithoautotrophy based on his initial investigations with this organism (Winogradsky 1887). Almost a century later, the first clearly autotrophic Beggiatoa strains MS-81-6 and MS-81-1c were isolated in pure culture (Nelson et al. 1982; Nelson and Jannasch 1983). In autotrophic Beggiatoa strains, carbon fixation occurs via the Calvin cycle, as judged by the activity level and regulation of RuBPC/O (Ribulose-1,5-bisphosphate carboxylase/oxygenase). In the obligately autotrophic strain MS-81-1c, RuBPC/O cannot be repressed by acetate additions and is always active at similar levels. The facultatively autotrophic strain MS-81-6 tightly regulates autotrophic vs. heterotrophic growth and is almost certainly mixotrophic with regard to both carbon and energy metabolism (Hagen and Nelson 1996). Acetate additions reduce the activity of RuBPC/O to a small fraction of its activity in organic-free medium; increase the activity of 2-oxoglutarate dehydrogenase (Hagen and Nelson 1996), a key enzyme of the citric acid cycle; and open the way to respiratory oxidation of C₂ substrates. Under sulfide-induced autotrophic growth conditions, 2-oxoglutarate dehydrogenase is not expressed thus “interrupting” the citric acid cycle at the stage of 2-oxoketoglutarate. As a result, autotrophically fixed carbon is not oxidized, but used for synthesis of cellular compounds.

Even the obligately autotrophic Beggiatoa strain MS-81-1c increases its growth yield by ca. 20 % after addition of acetate, indicating that acetate can be used as an auxiliary carbon source for the synthesis of cell material in a manner analogous to other chemolithoautotrophic sulfide-oxidizing bacteria (Hagen and Nelson 1996).

Autotrophic growth of Beggiatoa strain MS-81-6 was achieved in sulfide gradient cultures, where Beggiatoa filaments grew as a defined band in a slush soft agar column at the sulfide–oxygen interface (Nelson and Jannasch 1983). The Beggiatoa filaments in the gradient culture migrated over time and kept themselves positioned at the sulfide–oxygen interface. Their growth depends on the availability of both compounds, oxygen and sulfide, in opposed overlapping gradients (Fig. 6.6 , Nelson and Jannasch 1983; Nelson et al. 1986b). Depending on growth stage, Beggiatoa strain MS-81-6 adjusts the oxidation pathways of sulfide. When sulfide is abundant, it is oxidized to the stage of elemental sulfur; when the supply of sulfide is limited and has to be used more effectively, sulfide oxidation proceeds to sulfate (Nelson et al. 1986b). Sulfide is biologically oxidized at a rate that is roughly three orders of magnitude faster than the competing chemical oxidation, with half-life times of a few seconds in the oxygen–sulfide transition zone (Nelson et al. 1986b). In comparison to other autotrophic sulfide-oxidizing bacteria, both marine autotrophic Beggiatoa strains tested have high molar growth yields (8 g/mol for Beggiatoa str. MS-81-6 and 16 g/mol for MS-81-1c) on sulfide in gradient cultures (Nelson et al. 1986b; Hagen and Nelson 1997).

Physiological differences between the obligately autotrophic strain MS-81-1c and the facultatively autotrophic strain MS-81-6 are apparent in different enzyme systems for sulfur oxidation (Hagen and Nelson 1997). Beggiatoa strain MS-81-1c uses APS reductase (adenosine 5’-phosphosulfate reductase, located in the cytosol) in the AMP-dependent oxidation of sulfite to APS. In a second step catalyzed by the enzyme ATP sulfurylase, the pyrophosphate-dependent substrate-level phosphorylation of APS produces ATP and sulfate:

1.
SO₃ ²⁻ + AMP + acceptor_oxidized → APS + acceptor_reduced
2.
APS + PP_i → SO₄ ²⁻ + ATP

Both enzymes are highly active regardless of the sulfur source (H₂S gradient, thiosulfate, or thiosulfate with acetate). Substrate-level phosphorylation during sulfur oxidation opens a new source of energy for this Beggiatoa strain, in contrast to other Beggiatoa strains that appear to lack this pathway and depend on respiratory sulfur oxidation instead. Beggiatoa strain MS-81-6 completely lacks APS reductase activity. The activity of the ATP sulfurylase is two orders of magnitudes lower than in strain MS-81-1c and in the typical range for assimilatory ATP sulfurylases. An assimilatory role for the ATP sulfurylase is supported by the ability of strain MS-81-6 to grow with acetate on sulfate as the only sulfur source (Nelson and Jannasch 1983).

An AMP-independent, apparently membrane-associated, sulfite:acceptor oxidoreductase systems represent a second sulfur oxidation pathway, which is found in Beggiatoa strains MS-81-1c, MS-81-6, and also in the heterotrophic strain OH-75-2a. Since these sulfite oxidases are localized in the cell membrane, they are most likely integrated with the respiratory chain and use cytochrome c as electron acceptor. In strain MS-81-1c, sulfite:acceptor oxidoreductase is upregulated in the presence of H₂S and is at least 3 times higher than in strain MS-81-6. The different rates of respiratory sulfur oxidation and additional substrate phosphorylation coupled to sulfite oxidation by the APS reductase system in strain MS-81-1c probably contribute to the differences in molar growth yield between strains MS-81-1c and MS-81-6 (Hagen and Nelson 1997).

DNA hybridizations were used to check the presence of dissimilatory ATP sulfurylase genes in different Beggiatoa strains. The gene probe was a fragment of the ATP sulfurylase gene of the autotrophic, sulfur-oxidizing endosymbiont of the hydrothermal vent tube worm Riftia pachyptila; the endosymbiont utilizes ATP sulfurylase and APS reductase in dissimilatory sulfur metabolism. DNA of the autotrophic strain MS-81-1c hybridized positively, whereas DNA of the facultatively heterotrophic strain MS-81-6 and of the heterotrophic strain OH-75-2a hybridized negatively, indicating that the latter two strains harbor assimilatory, not dissimilatory ATP sulfurylases (Laue and Nelson 1994).

Strain 35Flor

The marine Beggiatoa strain 35Flor was isolated in 2001 from a microbial community associated with scleractinian corals suffering from black band disease off the coast of Florida. This Beggiatoa strain grows under chemolithoautotrophic conditions in an agar-stabilized oxygen–sulfide gradient medium gaining energy from the aerobic oxidation of sulfide (Kamp et al. 2008; Brock and Schulz-Vogt 2011), and it grows in obligate coculture with a Pseudovibrio strain (Brock and Schulz-Vogt 2011; Schwedt et al. 2012). Currently, strain 35Flor is the only marine, autotrophic strain within the Beggiatoaceae that is continuously maintained in monospecific culture. Strain 35Flor is a member of the same monophyletic lineage as strain MS-81-6 and can be considered its closest cultured relative. This strain was the first marine isolate capable of sulfur respiration with concurrent PHA dissolution under anoxic conditions (Schwedt et al. 2012). Most likely, the stored carbohydrates are oxidized and excreted, while S globules are reduced to sulfide. In this way, strain 35Flor removes excess sulfur globules that accumulate intracellularly during microoxic sulfide oxidation (Schwedt et al. 2012).

Comparative Aspects

Interestingly, the heterotrophic freshwater Beggiatoa strain OH-75-2a showed a similar spectrum of sulfide- and sulfur-oxidizing enzymes as the facultative autotrophs. AMP-independent sulfite:acceptor oxidoreductase was present and active in a similar range as in strain MS-81-6, allowing in principle the energy-gaining oxidation of sulfur compounds. However, the activities of ATP sulfurylase were an order of magnitude lower than in strain MS-81-6 and three orders of magnitude lower than the ATP sulfurylase in strain MS-81-1c; thus, the ATP sulfurylase appears to be assimilatory rather than dissimilatory (Hagen and Nelson 1997).

The sulfur-oxidizing enzyme system of the facultatively autotrophic freshwater Beggiatoa strain D-402 shared important features with strains MS-81-6 and OH-75-2a. AMP-dependent APS reductase was absent; sulfur-oxidizing enzymes that are not involved in substrate-level phosphorylation (sulfite:cytochrome C oxidoreductase and thiosulfate:ferricyanide oxidoreductase) were active and were upregulated under autotrophic cultivation conditions with thiosulfate as sulfur source (Grabovich et al. 1998, 2001; Patritskaya et al. 2001). The unusually high activities of RubisCo and of sulfur-oxidizing enzymes in strain D-402 could be connected to its high growth yield (12.2 g/mol oxidized thiosulfate). Direct comparisons of Beggiatoa strains with identical culture conditions, sulfur sources, and enzyme assays are necessary to determine the physiological diversity and activity of sulfur-oxidizing enzymes in marine and freshwater Beggiatoa.

Photoresponses of Beggiatoa spp.

The migrations of Beggiatoa filaments in microbial mats and sediments are not only regulated by the combined effects of oxygen and sulfide, but are in parallel controlled by light. Experiments with Beggiatoa cultures from a warm freshwater spring (Hunter Spring) have shown a statistically significant photophobic response of individual Beggiatoa filaments that was still detectable at low ambient light levels as low as ca. 2 % of full summer sunlight intensity. Filaments were most sensitive in the blue to blue-green (400–500 nm) spectrum that in nature is blocked out by cyanobacterial carotenoids. Beggiatoa filaments in field material maintained in the laboratory enrichments retreated into the sediment after short periods of illumination and returned to the sediment surface after several hours of darkness (Nelson and Castenholz 1982). Such distinct responses to blue light invite closer examination. In the genome of an undescribed Beggiatoa sp., a DNA sequence encodes an adenylyl cyclase directly linked to a BLUF (blue light receptor using FAD) type light sensor domain, which led to the working hypothesis of a light-triggered cyclic AMP signaling mechanism (Stierl et al. 2011).

Genus Thioploca

The genus Thioploca is widespread in freshwater and brackish-water habitats (Fig. 6.3g), for example, in sediments of Lake Constance and other lakes in Germany (Lauterborn 1907; Koppe 1924; Maier and Preissner 1979), in the Neva river at St. Petersburg (Wislouch 1912), in the Rhine and in Baltic coastal lagoons (Kolkwitz 1912), in Lake Erie (Maier 1980), in Lake Ontario (Dermott and Legner 2002), in Lake Baikal in Siberia (Namsaraev et al. 1994; Zemskaya et al. 2001), and in Lake Biwa, Japan (Nishino et al. 1998; Kojima et al. 2003). Studies on field samples of freshwater and brackish-water Thioploca spp. (T. ingrica) from Japan (Kojima et al. 2007) and Denmark (Høgslund et al. 2010) have provided an initial outline of their physiology. Autoradiography experiments have shown that T. ingrica assimilates acetate and bicarbonate, although bicarbonate incorporation could not be detected in the specimens from Japan (Høgslund et al. 2010; Kojima et al. 2006). It is assumed that T. ingrica links inorganic carbon assimilation to sulfur oxidation; however, only indirect support for sulfur oxidation is available. A correlation of elevated sulfate concentrations and T. ingrica biomass was shown (Kojima et al. 2007), but enzymatic or genetic studies of carbon assimilation are currently lacking. Oxygen and nitrate are required for carbon assimilation (Høgslund et al. 2010). Nitrate is accumulated intracellularly at concentrations of 2–3 mM; given environmental nitrate concentrations of ca. 10–20 μM (Lake Biwa) to ca. 100 μM (Danish fjords), T. ingrica concentrates nitrate by one to two orders of magnitude (Høgslund et al. 2010; Kojima et al. 2007). The large, nitrate-accumulating vacuoles that are typical of many large members of the Beggiatoaceae (e.g., Fig. 6.4d) are not found in T. ingrica; therefore, nitrate must be accumulated and stored in some other way, such as within smaller cytoplasmatic vacuoles, in the cytoplasm itself, or in the periplasm that can feature cytoplasmic membrane invaginations extending into the cytoplasm (Maier and Murray 1965). However, elemental sulfur, and not nitrate, is the electron acceptor of choice during prolonged anoxia. Anoxic incubation experiments in closed bottles have shown that storage globules of elemental sulfur serve as the electron acceptor during prolonged oxygen and nitrate depletion; T. ingrica can survive as a sulfur-reducing heterotroph for over 2–3 months (Høgslund et al. 2010). Therefore, elemental sulfur has the same role in T. ingrica as in Beggiatoa alba and other thin marine and freshwater Beggiatoa that rely on their intracellular sulfur reservoir under anaerobic conditions.

Genus Thiomargarita

Cells of the genus Thiomargarita show spherical, barrel-like, or bulbous shapes and either are unicellular (Fig. 6.4b), are organized in chains surrounded by a mucous sheath (e.g., Fig. 6.4a and d), form clusters or aggregates (Fig. 6.4e), or grow attached to surfaces (Fig. 6.4f, Schulz et al. 1999; Kalanetra et al. 2005; Schulz 2006; Salman et al. 2011). They are among the contenders for the largest prokaryotic cells on earth; the initial discovery of Thiomargarita in organic-rich and sulfidic sediments on the continental shelf of Namibia reported individual cells of up to 750 μm in diameter, although sizes of 100–300 μm were more common (Schulz et al. 1999). Their nitrate-storing vacuoles fill the cell volume and restrict the cytoplasm to a thin layer sandwiched between cell membrane and vacuolar membrane; the cytoplasm presumably also contains the intracellular sulfur globules (Schulz 2006). Although some rolling motility is now reported for some morphotypes in this genus, Thiomargarita cannot move over long distances vertically within the surficial sediments, such as Marithioploca, to efficiently bridge spatially separated pools of oxidant and reductant. Instead, Thiomargarita relies on its extreme storage capacity for sulfur and nitrate, an essential capability in benthic habitats that experience long periods of sulfidic conditions and oxygen or nitrate depletion (Schulz et al. 1999). Thiomargarita is currently the only sulfur bacterium that combines four types of intracellular inclusions that ensure prolonged survival under energy limitation: nitrate-storing vacuoles and sulfur inclusions provide intracellular reserves of electron acceptor and donor, polyphosphate inclusions serve as an additional energy buffer, and glycogen (or another polyglucose) represents a carbon reserve (Schulz and Schulz 2005).

Based on analogies with previously characterized “Marithioploca” and “Maribeggiatoa” spp., Thiomargarita is most likely a facultative chemolithoautotrophic sulfur oxidizer. Thiomargarita namibiensis cells can take up and utilize acetate as a carbon source, although not as an electron donor (Schulz and de Beer 2002), and can store this organic carbon intracellularly as glycogen (Schulz and Schulz 2005). Sulfide oxidation and sulfide flux towards Thiomargarita cells are stimulated by the presence of oxygen; even highly oxygenated conditions (ca. 200 μM O₂ in solution) were tolerated, showing that Thiomargarita is not a microaerophile such as “Marithioploca” and “Maribeggiatoa” (Schulz and de Beer 2002). Oxygen additions to anoxic medium increased the sulfide flux into Thiomargarita cell chains by ca. 1/3 (from approximately 5–7.5 pmol sulfide per cm² s), indicating that while oxygen stimulated the sulfide flux, most of it was still sustained by intracellularly stored nitrate. This flexibility in usage of electron acceptor and tolerance to different electron donor and acceptor concentrations may explain the long survival of Thiomargarita cells in natural sediment samples in the lab.

The large cell size of Thiomargarita, and the spatial extent of its cytoplasm and membranes, requires a mechanism to overcome diffusional limitations to intracellular transport, signaling pathways, and coordinated gene expression across the cell volume. Assuming the absence of directional transportation via bacterial tubulins or other analogs to mitotic spindles, how does messenger RNA reach the portions of the cytoplasm that are separated by hundreds of micrometers from the location of the genome? Nucleic acid-stained condensed genomic equivalents or nucleoids are distributed throughout the cytoplasm (Schulz 2006) and suggest a polyploid genome (Angert 2012) similar to the large bacterial endosymbiont Epulopiscium fishelsoni (Robinow and Angert 1998; Mendell et al. 2008; Angert 2012).

“Candidatus Marithioploca”

Members of “Candidatus Marithioploca” are large, vacuolated, sulfide-oxidizing, and nitrate-reducing filamentous bacteria (Fig. 6.3 a–f) capable of assimilating inorganic carbon as well as organic substrates for biomass production (Jørgensen and Gallardo 1999). Multiple filaments are usually surrounded by a sheath that is embedded in surficial sediment. The unique combination of high storage capacity for electron donor (sulfur) and acceptor (nitrate) and vertical migration capability between bottom seawater and sediment enables “Marithioploca” to thrive at sediment–water interfaces where electron donor and acceptor undergo major fluctuations in concentration, availability, and spatial separation (Fig. 6.7 ).

All physiological studies on “Marithioploca” have been performed on freshly collected, sheathed filament bundles from the continental shelf of Chile (Maier and Gallardo 1984a, b; Fossing et al. 1995; Otte et al. 1999; Høgslund et al. 2009). The two dominant members of “Marithioploca” from the Chilean continental shelf, previously named Thioploca chileae and T. araucae and distinguished by filament diameter (12–20 μm and 30–43 μm) (Maier and Gallardo 1984b), were both able to incorporate radiolabeled bicarbonate as well as acetate and amino acids (Maier and Gallardo 1984a). In freshly collected “Marithioploca” samples, CO₂ fixation occurred at rates of 0.4–1.5 nmol carbon per minute and mg protein, similar to those of large hydrothermal vent Beggiatoaceae (Otte et al. 1999). Acetate was incorporated at a rate roughly equal to CO₂, with no apparent terminal oxidation, suggesting that “Marithioploca” spp. are mixotrophic with respect to carbon source (Otte et al. 1999). Mixotrophic potential was also supported by quantitative microautoradiography experiments that showed increased inorganic carbon fixation after the addition of acetate and propionate (Høgslund et al. 2009).

Oxidation of reduced sulfur compounds is linked to nitrate reduction. Incubation experiments of freshly collected “Marithioploca” with ¹⁵N-labeled nitrate have shown that nitrate is taken up and subsequently reduced to ammonia at rates of 5–6.5 and 1–4 nmol nitrate uptake and reduction per minute and mg protein, respectively (Høgslund et al. 2009). “Marithioploca” filaments respond with positive chemotaxis to nitrate additions (20–30 μm) and emerge, while remaining anchored in their sediment-embedded sheaths, up to several centimeters into nitrate-amended, flowing seawater (Hüttel et al. 1996). Subsequently, the filaments can retreat (at a speed of 3–5 mm h⁻¹) into the sediment and use their stored nitrate for sulfide oxidation (Hüttel et al. 1996). Nitrate can be stored within large vacuoles at concentrations between 10 and 500 mM (Otte et al. 1999; Fossing et al. 1995; Zopfi et al. 2001); however, nitrate can be reduced to ammonia directly without prior storage and dilution of the ¹⁵N-signal in the vacuole (Otte et al. 1999). Small amounts of dinitrogen are also produced (Otte et al. 1999), but these denitrification activities result from bacterial epibionts and contaminants on the “Marithioploca” sheaths (Høgslund et al. 2009). Due to nitrate ammonification, ammonia accumulates in “Marithioploca”-harboring sediment surface layers (Thamdrup and Canfield 1996; Hüttel et al. 1996) and can be microbially reassimilated; such a trend would counteract nitrogen loss through denitrification (Farias et al. 1996; Farias 1998). On the other hand, ammonia can also be reoxidized in situ by anammox bacteria (Candidatus Scalindua) that grow on “Marithioploca” sheaths; this microbial consortium then amplifies denitrification and enhances nitrogen efflux towards parity of ammonia and N₂ loss from the sediment (Prokopenko et al. 2006, 2013).

Oxygen can be consumed at rates comparable to nitrate, but aerobic respiration during sulfide oxidation can be sustained only at low external oxygen concentrations (ca. 30 μM, 10 % oxygen saturation) that leave the filaments within the “Marithioploca” bundles anoxic. Higher oxygen concentrations (ca. 100 μM, 30 % oxygen saturation) penetrated into the bundles and killed the filaments within 8 h of oxygen exposure (Høgslund et al. 2009). In closed-flume system experiments, dissolved oxygen concentrations of 100–150 μM in seawater triggered a retreat of seawater-exposed filaments into the sediment (Hüttel et al. 1996). Thus, “Marithioploca” can oxidize sulfur as a microaerophile, but does not survive at higher oxygen concentrations, and avoids them by retreating into the sediment.

Sulfide oxidation and ammonia production rates in “Marithioploca” samples showed a stoichiometric ratio of ca. 2, indicating that nitrate reduction to ammonia is accompanied by concomitant sulfide oxidation to elemental sulfur (stoichiometric ratio 1:4) and sulfate (ratio 1:1); no sulfur intermediates were detected. Apparently, sulfide is oxidized first to elemental sulfur, which acts as an intracellular electron donor reservoir, and then in a second step to sulfate. In the absence of sulfide, the ratio of ammonia production from nitrate (requiring 8 electrons per ammonia) and elemental sulfur oxidation to sulfate (yielding 6 electrons per sulfate) is close to the predicted stoichiometric ratio of 4/3 (Otte et al. 1999). Elemental sulfur is an essential electron donor that can be accumulated and stored until needed. The high intracellular concentrations of sulfur and nitrate are correlated to the position and activity of “Marithioploca” filaments in the gradient. Deeply located “Marithioploca” filaments tend to consume their nitrate content for sulfide oxidation and build up sulfur globules and replenish their nitrate stocks at the surface where sulfur is consumed (Zopfi et al. 2001). Given the fluctuations in sulfide supply, intracellular sulfur storage provides an essential electron donor reservoir. “Marithioploca” is capable of faster sulfide uptake than sulfide oxidation (0.5–15 compared to 2–3 nmol per minute and mg protein), indicating that sulfide can be just as limiting as nitrate and has to be taken up rapidly when available (Otte et al. 1999; Høgslund et al. 2009).

“Candidatus Maribeggiatoa”

Members of the genus-level candidate taxon “Maribeggiatoa” are large, vacuolated, nitrate-accumulating sulfide-oxidizing filamentous bacteria (Fig. 6.5 a, b) with autotrophic capabilities; they resemble “Candidatus Marithioploca” spp. in vacuolation and nitrate storage capacity (McHatton et al. 1996). Uncultured “Maribeggiatoa” from cold sulfide seeps in the Monterey Canyon (McHatton et al. 1996) and “Maribeggiatoa”-related filaments from the Guaymas Basin hydrothermal sediments (Nelson et al. 1989) showed high RuBisCO activity in the range of 7.5–15 and 5–6 nmol C fixed per minute and mg protein, respectively. Carbon assimilation by the Calvin cycle was consistent with the ¹³C-isotopic signature of large “Maribeggiatoa”-like filaments from cold seep sediments in the Gulf of Mexico (Larkin et al. 1994).

Filaments of “Candidatus Maribeggiatoa” accumulate nitrate intracellularly in vacuoles and—as suggested by analogy to “Candidatus Marithioploca”—use nitrate as a respiratory electron acceptor for sulfur oxidation. The “Maribeggiatoa” population at Monterey Canyon showed an intracellular nitrate concentration of ca. 160 mM (McHatton et al. 1996); the Guaymas Basin population of “Maribeggiatoa”-like mat-forming filaments accumulated intracellular nitrate in the range of 50–100 mM (McKay et al. 2012). These concentrations would not be possible with dissolved oxygen; its saturation concentration in fully aerated seawater at 1 atm pressure and 7 °C is limited to ca. 300 μM. In comparison to other Beggiatoaceae, the “Maribeggiatoa” population at Monterey Canyon showed the highest level of nitrate reductase activity. Nitrate reductase activity was predominantly found in the particulate fraction, indicating a membrane-bound location within the respiratory chain (McHatton et al. 1996). The Monterey Canyon “Maribeggiatoa” also consume oxygen at a rate considerably greater than the average rate of nitrate consumption (8–25 nmol O₂ compared ca. 1–4 nmol NO₃ ⁻ per minute and mg protein) (Kalanetra and Nelson 2010).

Nitrate transformations in mats of “Maribeggiatoa” and related Beggiatoaceae provide new avenues for biochemical research. The nearly complete genome sequence of a single orange filament (related to “Candidatus Maribeggiatoa,” pending more detailed classification) from a hydrothermal microbial mat in Guaymas Basin (Gulf of California, Mexico) harbored the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (MacGregor et al. 2013a). The predicted protein sequence grouped with octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. In the context of Beggiatoaceae physiology, nitrite reduction was inferred as the most likely in vivo role of the octaheme protein (MacGregor et al. 2013a). The surficial sediments associated with the Beggiatoaceae mats in Guaymas Basin showed high denitrification activities that were inhibited by sulfide accumulation; the working hypothesis can be inferred that sulfide removal by Beggiatoaceae may catalyze denitrification in the Guaymas Basin sediments (Bowles et al. 2012).

Detailed studies of sulfide and sulfur oxidation pathways and activities are currently lacking for “Maribeggiatoa.” However, their conspicuous content of sulfur globules, as in “Marithioploca,” suggests that sulfide serves as energy source and elemental sulfur as a storage compound and electron donor when sulfide is not available. In “Maribeggiatoa”-related large, orange-colored Beggiatoaceae from the Guaymas Basin (30 μm filament diameter, sample 1615), diverse c-type cytochromes were found, whose hemes have appropriate oxidation–reduction midpoint potentials for respiratory sulfide oxidation (Prince et al. 1988). The near-complete genome of an orange-colored filament in this size class from Guaymas Basin showed a wide repertoire of sulfur oxidation and assimilation pathways (MacGregor et al. 2013c).

“Candidatus Marithrix”

The physiology of “Candidatus Marithrix” presents a conundrum: the large filaments contain sulfur globules and large vacuoles, but so far nitrate could not be detected in the filaments (Kalanetra et al. 2004; Kalanetra and Nelson 2010). Given that “Marithrix” grows on surfaces that are alternately exposed to mixed sulfidic vent fluids and oxygenated seawater, oxygen is the most likely electron acceptor (Kalanetra et al. 2004). Since the vacuoles are not used for nitrate storage, they could serve either as oxygen reservoirs that provide storage capacity for a few minutes of oxic respiration (Kalanetra and Nelson 2010) or as structural element contributing to filament strength. “Marithrix” has autotrophic capability (average 2.5 nmol CO₂ fixed per min and mg protein), similar to “Maribeggiatoa” and “Marithioploca” (Kalanetra and Nelson 2010).

“Candidatus Isobeggiatoa”

Filaments of the genus-level candidate taxon “Isobeggiatoa” are vacuolated and accumulate nitrate as well as sulfur intracellularly (Mussmann et al. 2003; Jørgensen et al. 2010). Instead of forming conspicuous microbial mats on the sediment surface, “Candidatus Isobeggiatoa” strains occur within surficial sediment layers where oxygen and sulfide are excluded or occur only at low concentrations. Although these sediment layers often show high sulfate reduction rates, porewater sulfide is rapidly consumed by sulfide-oxidizing bacteria or by reoxidation with metals and does not build up. In this habitat, “Isobeggiatoa” filaments do not dominate in terms of sulfide-oxidizing activity or cell number, although they constitute a larger proportion of sedimentary biomass due to large cell size (Jørgensen et al. 2010). A partial genome for an “Isobeggiatoa” filament matches the sulfide-oxidizing, nitrate-reducing physiology that can be inferred from the habitat characteristics (Mussmann et al. 2007). The partial genome contains a sulfide quinone oxidoreductase and flavocytochrome c-sulfide dehydrogenase for sulfide oxidation, the reverse dissimilatory sulfate reductase pathway for sulfur oxidation, and a partial sox pathway for thiosulfate oxidation (Mussmann et al. 2007). Sulfur respiration is also supported by the presence of genes for the respiration of dimethyl sulfoxide and the reduction of thiosulfate (Mussmann et al. 2007). The genome has a partial nitrate reduction pathway, but the preferred end product of nitrate reduction (N₂ or NH₃) cannot be inferred. Two cytochrome c oxidases that most likely differ by oxygen affinity indicate the capability for aerobic respiration (Mussmann et al. 2007). The “Isobeggiatoa” genome combines a nearly complete tricarbonic acid cycle with some key genes of the Calvin cycle, including form I RubisCO. “Candidatus Isobeggiatoa” has genes for glycolate oxidation, for the synthesis of the storage compound poly-beta-hydroxybutyric acid, for glycogen synthesis, and for ATP synthesis through substrate-level phosphorylation by fermenting pyruvate to lactate (Mussmann et al. 2007). The genome indicates a major role for phosphate uptake and storage; it encodes a phytase for accessing inorganic phosphates, selective porins and ABC phosphate transporters for phosphate uptake, and a polyphosphate kinase for intracellular polyphosphate synthesis (Mussmann et al. 2007). Non-ribosomal peptide synthetases and polyketide synthetases indicate the potential for secondary metabolite synthesis. Numerous glycoproteins in “Candidatus Isobeggiatoa” are most likely involved in cell adhesion and aggregation. These two gene categories have often cyanobacterial affinities, suggesting horizontal gene transfer between Cyanobacteria and Beggiatoaceae in shared sedimentary and microbial mat habitats during long periods of coexistence in the earth’s past (Mussmann et al. 2007).

“Candidatus Parabeggiatoa”

Members of “Candidatus Parabeggiatoa” were originally found in surficial sediments of a brackish fjord, Limfjorden, in Denmark, and formed a monophyletic cluster of large (33–40 μm filament diameter), vacuolated, presumably nitrate-accumulating filaments (Mussmann et al. 2003). “Parabeggiatoa” and “Isobeggiatoa” were identified during a reexamination of previously discovered Beggiatoa-like filaments within surficial sediments of Limfjorden (Jørgensen 1977). These filaments did not occur in the narrow zone of overlapping oxygen and sulfide gradients at the sediment surface, but in the surficial sediment interval where oxygen was no longer available but sulfide did not visibly accumulate. In retrospect, this was the first indication of the nitrate-reducing and potentially sulfur-reducing mode of metabolism that sustains these bacteria in their anoxic habitat. The filaments of “Parabeggiatoa” were larger than those of their sister group “Isobeggiatoa” (33–40 μm vs. 9–17 μm filament diameter, respectively) and occurred preferentially deeper in the sediment in close proximity to the sulfidic zone (Mussmann et al. 2003), possibly due to a greater reservoir of intracellular electron acceptors, nitrate, and elemental sulfur. At present, nitrate and sulfur content of the Limfjorden “Parabeggiatoa” are incompletely reported; the smaller “Isobeggiatoa” filaments from Limfjorden contain 156 ± 71 mM nitrate, but the nitrate content of the larger “Parabeggiatoa” filaments is unspecified. The elemental internal sulfur concentration of all measured Limfjorden filaments was 369 ± 176 mM, indicating large sulfur storage capacity in a similar range as nitrate concentrations (Mussmann et al. 2003). A single filament from Eckernförde Bay in Germany (Filament SS) was used for whole genome amplification and subsequent Sanger sequencing, yielding a low-coverage (3x) partial genome assembly of 1,091 contigs with a total sequencing length of 1.3 Mb (Mussmann et al. 2007). The”Parabeggiatoa” partial genome is more incomplete and fragmented than the “Isobeggiatoa” partial genome that was reported in the same study. Both partial genomes contain genes for the reverse dissimilatory sulfate reductase pathway, for putative nitrate reductases, and for genes that channel acetate into general metabolism (acetate/cation symporters, acetate kinase, and acetyl-CoA (coenzyme A) synthase) (Mussmann et al. 2007).

“Candidatus Allobeggiatoa”

Thin, sulfur- and nitrate-accumulating vacuolated filaments with diameters of 6–14 μm from hypersaline cyanobacterial mats (Fig. 6.2e) constitute the candidate genus “Candidatus Allobeggiatoa.” So far, “Allobeggiatoa” has been observed and identified by 16S rRNA sequencing and FISH in hypersaline cyanobacterial mats in saline lagoons and salterns in Spain and Mexico (Hinck et al. 2007, 2011). Given the preference of this group for hypersaline conditions, previous observations of Beggiatoa-like filaments in the hypersaline cyanobacterial mat of Guerrero Negro, Mexico, most likely include populations of “Allobeggiatoa” (Garcia-Pichel et al. 1994; Jørgensen and DesMarais 1986). Within hypersaline cyanobacterial mats, “Allobeggiatoa” occur predominantly at the upper sulfide horizon where oxygen and sulfide meet during daytime photosynthetic activity; they remain almost stationary at night and do not follow the retreating oxygen gradients towards the mat surface (Hinck et al. 2007). Intracellular sulfur and nitrate concentrations are highly variable. In sulfide-gradient enrichment culture, where they could be sustained for several weeks, “Allobeggiatoa” grow at the sulfide–oxygen interface where they most likely respire with oxygen; under these conditions they accumulate nitrate to high concentrations (430–650 mM) and deplete their intracellular sulfur store (6–25 mM). In their cyanobacterial mat habitat, intracellular nitrate concentrations are depleted (4 mM), and elemental sulfur accumulates (250 mM); thus, “Allobeggiatoa” appears to be nitrate-limited in its natural habitat (Hinck et al. 2011).

“Candidatus Halobeggiatoa”

The preliminary phenotypic characterization of this filamentous group is based on a habitat study of “Halobeggiatoa” from white mat patches at the Håkon Mosby mud volcano at 1,260 m depth in the Barents Sea (Fig. 6.5c, Lichtschlag et al. 2010; Grünke et al. 2012). These filamentous sulfur oxidizers grow in an intermediate zone of the mud volcano where the sulfide supply is high enough to support growth, but not to exceed the available oxygen and nitrate supply. Sulfide is sequentially oxidized with elemental sulfur as intermediate. The filaments have a diameter of approx. 8–10 μm and accumulate nitrate intracellularly (average 110 mM, range 73–149 mM) in the same range as intracellular S° (average 120 mM, range 45–289 mM) (Lichtschlag et al. 2010). The cells of this population disintegrate at temperatures higher than 8 °C and therefore represent genuine psychrophiles that are adapted to the permanently cold (−0.7 °C) in situ temperature in their habitat (Grünke et al. 2012).

“Candidatus Thiopilula”

The candidate genus “Thiopilula” was described from free-living specimens in Namibian sediments and from specimens attached to solid substrates in sediments of the Costa Rica margin (Salman et al. 2011). These large, spherical cells (25–67 μm diameter) occur mostly in aggregates within a thick mucus envelope; smaller individual cells (11–24 μm diameter) of the same phylogenetic lineage reside in diatom frustules (Salman et al. 2011). Similar-sized cells in mucus-ensheathed clusters were also documented earlier from Namibian sediment samples (Schulz 2006). The cells contain sulfur inclusions. Most cells are vacuolated and could store nitrate, but intracellular nitrate concentrations have not been tested yet. The attached cells are most likely dividing by budding from mother cells attached to solid substrates (Bailey et al. 2011). Cells within aggregates and diatom frustules show binary division stages and occasional motility by jerking, rolling movement (Salman et al. 2011).

“Candidatus Thiophysa”

The candidate genus “Candidatus Thiophysa” is physiologically almost entirely uncharacterized. These large, single, spherical cells (56–90 μm diameter) from Namibian sediments contain sulfur inclusions and also vacuoles that could store nitrate, but intracellular nitrate concentrations remain to be tested (Salman et al. 2011). They are motile by slow, rolling, and jerking motions (Salman et al. 2011). The genus was originally described from sandy sediments of shallow marine sulfur springs in the Gulf of Naples, strongly smelling of hydrogen sulfide (Hinze 1903). These specimens lost their sulfur inclusions during 1 or 2 days of incubation in oxygenated seawater, consistent with a sulfur-oxidizing metabolism (Hinze 1903). The Namibian and Neapolitan specimens resemble each other in morphology; the original, beautifully detailed microscopic drawings (Hinze 1903) are close equivalents of the modern microphotographs (Salman et al. 2011). Yet, the cell diameter of the Neapolitan “Thiophysa” is given as 7–18 μm (Hinze 1903), approx. 1/5 to 1/8 of the Namibian specimens. This difference suggests unexplored morphotype and species diversity either within the candidate genus “Thiophysa” or other taxa of the family Beggiatoaceae.

Cell Structure

Vacuolation

The cells of many large members of the Beggiatoaceae appear hollow in microscopic examination; they are composed of a thin cylinder of cytoplasm surrounding a large central vacuole, or several large vacuoles, a characteristic that has been initially observed and described more than a century ago (Hinze 1901, Figs. 6.4d and 6.8a, b). This extensive vacuolation is characteristic for most large Beggiatoaceae (Jannasch et al. 1989; Nelson et al. 1989) above a size threshold of approx. 10 μm (Larkin and Henk 1996). Since vacuolation commonly coincides with high intracellular nitrate concentration (McHatton et al. 1996), the vacuoles are presumed to be the locations where nitrate is accumulated for respiration, either by denitrification or by dissimilatory reduction to ammonia. However, important caveats apply: the small, freshwater species Thioploca ingrica lacks the extensive vacuolation of large, marine Beggiatoaceae (Maier and Murray 1965), but is still capable of nitrate accumulation (Høgslund et al. 2009). Analyses of “Candidatus Marithrix” demonstrate that large vacuoles cannot be equated with nitrate accumulation (Kalanetra et al. 2004).

The large intracellular vacuoles have been studied in greater physiological detail in “Allobeggiatoa,” using a combination of vacuolar pH measurements (Beutler et al. 2009), immunostaining, and selective inhibition of membrane proteins (Beutler et al. 2012). Nitrate addition increased the vacuolar proton motive force and acidified the vacuole; the resulting proton gradient from vacuole interior to cytoplasm can be used for ATP and pyrophosphate generation in the cytoplasm. Nitrate addition also led to the production of nitric oxide (NO) from its precursor nitrite in the vacuole (Beutler et al. 2012); subsequently, NO could be reduced to the denitrification intermediate nitrous oxide (N₂O).

Cell Envelope

Ultrastructural analyses of cell envelope and cell inclusions have focused on freshwater Beggiatoa alba (Strohl et al. 1982; Strohl and Larkin 1978b), on Thioploca ingrica (Maier and Murray 1965), and on marine filamentous Beggiatoaceae (de Albuquerque et al. 2010; Larkin and Henk 1996). Thin sectioning and freeze-etching techniques have shown that filaments of the freshwater species Beggiatoa alba (strain B15LD) have a cell envelope consisting of five distinct layers that is continuous over the entire filament (Fig. 6.8c); the individual cells within each filament are separated only by their cytoplasmic membranes plus a septum that is contiguous with the inner layer of the envelope (Strohl et al. 1982). In other freshwater Beggiatoa strains, similar multilayer cell envelops and single-layer cell septa have been observed, in lower resolution due to technical limitations (Morita and Stave 1963; Drawert and Metzner-Küstner 1958). Recently, marine Beggiatoa filaments (non-vacuolated, average diameter 4.4 μm, related to the marine autotrophic strain MS-81-6) were shown to have a five-layer envelope and a single-layer cell septum (presumably murein) that is contiguous with the inner layer of the envelope (de Albuquerque et al. 2010). Large, vacuolated marine Beggiatoaceae (size not explicitly specified, but most likely 10–30 μm filament diameter) showed a similarly complex cell envelope composed of four distinct layers (de Albuquerque et al. 2010) (Fig. 6.8d, e).

Surrounding the cell envelope and embedding the thin marine filaments, a sheath-like outer layer of fibrillar or striated material was observed (de Albuquerque et al. 2010). Large marine filaments show small round pores, ca. 15 nm in diameter, arranged in rows on the outer surface of a filament; a possible role in mucus secretion was suggested (Larkin and Henk 1996). Linearly arranged longitudinal fibrils have been observed on the cell envelope surface layer of Beggiatoa alba; most likely, they expel mucus forming a trail of mucilage around the filaments, inside which they can glide (Strohl et al. 1982). In Beggiatoa alba, the mucilage trail is composed of neutral polysaccharides (mannose and glucose) (Larkin and Strohl 1983). Earlier electron microscopic observations of conspicuously striated sheath material in freshwater Beggiatoa spp. (Drawert and Metzner-Küstner 1958) could correspond to such an outer cell envelope layer of longitudinal fibrils, or to the mucilaginous coating itself. Mucilaginous coats surrounding individual Beggiatoa are significant for filament movement (Møller et al. 1985); they could be a direct homolog for the larger sheaths surrounding Thioploca and “Marithioploca” filament bundles. Consistent with such a derivation, these sheaths appear to have a striated texture that runs parallel to the filaments; epibiotic filamentous bacteria on and within the sheath matrix tend to be aligned parallel to the sheath striation and the “Marithioploca” filaments (Fukui et al. 1999; Muyzer and Ramsing 1995) (Fig. 6.3f).

A cell envelope similar to Beggiatoa spp. has been observed in an electron microscopic ultrastructure survey of Thioploca ingrica filaments (Maier and Murray 1965). The envelope surrounds the entire filament, including the filament tips, and consists of multiple distinct layers. Adjacent to the cytoplasmic membrane, an electron-dense inner layer is contiguous with the cell septa and then follows a complex, multilayered “quadruple profile” and on the outside two distinct outer envelope layers (Maier and Murray 1965). A similar cell envelope is found in the Chilean “Marithioploca” filaments (Maier et al. 1990). The inner layer, which is continuous with cell septa, is followed by interstitial material and the adjacent undulating “triple layer”; after a gap, two outer layers are completing the cell envelope. On the inside of the cell envelope, periplasmic spaces appear in some locations, followed by the cytoplasmic membrane. Incomplete cell septa branch off from the cell envelope inner layer and extend into the cytoplasm and the ventral vacuole. However, they do not close off a cell, but they remain surrounded by the cytoplasmic membrane and the vacuolar membrane (Maier et al. 1990). The incomplete septa seen in various lengths suggest a mode of cell division where growing septa bisect a cell and its central vacuole. Interestingly, the early study by Hinze (1901) records a similar mechanism of cell division in microscopic drawings of large Beggiatoaceae.

Cell Inclusions

Four types of inclusions have been reported for members of the Beggiatoaceae: polyhydroxyalkanoates (PHA) (Pringsheim 1964; Pringsheim and Wiessner 1963; Strohl and Larkin 1978a; Strohl et al. 1982; Schwedt et al. 2012), glycogen or a similar polyglucose (Schulz and Schulz 2005), polyphosphate (Maier and Murray 1965; Schulz and Schulz 2005; Brock et al. 2012), and sulfur (Strohl et al. 1981b, 1982; Winogradsky 1887).

PHA Inclusions

Production of PHA appears to be a universal feature of heterotrophic freshwater strains (Fig. 6.2c). Interestingly, in heterotrophic Beggiatoa spp. the deposition of the alkanoate polyhydroxybutyrate seems to correlate primarily with high aeration (Pringsheim 1964), and it can account for up to 50 % of total dry weight under aerated conditions in the absence of sulfide (Güde et al. 1981). Numerous cell inclusions that resemble PHA were also found by TEM in the freshwater and brackish-water species Thioploca ingrica (Kojima et al. 2003). In the marine Beggiatoaceae strain 35Flor, PHA is used up under prolonged anoxia, most likely by oxidation using intracellular sulfur as electron acceptor (Schwedt et al. 2012).

Sulfur Inclusions

The sulfur inclusions of Beggiatoa are periplasmic in location, being enclosed in invaginations of the cell membrane. The sulfur globules are surrounded by their own electron-dense monolayered envelope, followed by the cytoplasmic membrane (de Albuquerque 2010). In large, vacuolated filaments, the sulfur inclusions are located in the narrow cytoplasmic space between the cell membrane and the large central vacuole (Jannasch et al. 1989; Larkin and Henk 1996; de Albuquerque et al. 2010). Very similar observations were made for the Chilean “Marithioploca” species; a thin cytoplasmic layer containing membrane-enclosed sulfur globules surrounds the central vacuole (Maier et al. 1990). The vacuole is surrounded by its own vacuolar membrane in addition to the cytoplasmic membrane.

In Beggiatoa alba strain B15LD, the sulfur globules are enclosed within a multilayered sulfur inclusion envelope of 12–14 nm thickness (Strohl et al. 1982), while in other strains the S° globule envelope appears to be composed of a single protein layer 4–5 nm thick (Strohl et al. 1981b). The extraction of S° globules with solvents such as pyridine and their refractile appearance when intact cells are viewed with phase contrast microscopy have proven very useful in confirming their presence (Skerman et al. 1957). Beggiatoa cells grown in the absence of reduced sulfur compounds apparently contained small, “rudimentary” S° inclusion envelopes (Strohl et al. 1982). Dehydration solvents (e.g., ethanol) that are necessary for preparation of electron microscopy dissolve the S° and complicate the determination whether the rudimentary inclusions completely lack elemental sulfur. The sulfur globules consist of fine-grained, microcrystalline elemental sulfur in the common, stable S₈ ring configuration (Pasteris et al. 2001; Prange et al. 2002) without significant additions of other elements (Lawry et al. 1981); they are surrounded by extensions of the cytoplasmic membrane plus an inner sulfur inclusion envelope (Lawry et al. 1981; Strohl et al. 1981b). The cyclooctasulfur globules of Beggiatoa alba (strain DMSZ 1416) and of Thiomargarita namibiensis differ from sulfur globules produced by other sulfur oxidizers, such as polythionate sulfur globules of Acidithiobacillus thiooxidans and sulfur chain-dominated sulfur globules of anoxygenic phototrophs (Prange et al. 2002); the differences in sulfur speciation probably reflect different sulfur deposition pathways.

Polyphosphate Inclusions

Cells of Thiomargarita namibiensis accumulate phosphate intracellularly and store it as polyphosphate granules (Schulz and Schulz 2005). Polyphosphate accumulation and phosphate release by Thiomargarita lead to the precipitation and accumulation of phosphate-rich minerals (Schulz and Schulz 2005). These observations link microbially catalyzed precipitation of authigenic phosphate minerals in marine sediments to the in situ activities of sulfur-oxidizing bacteria and sulfate-reducing bacteria (Arning et al. 2009; Williams and Reimers 1983) and realize earlier suggestions made after the discovery of the Chilean Marithioploca mats (Gallardo 1977b). Although it is very likely that these granules provide an energy buffer for Thiomargarita cells, the environmental or biogeochemical triggers for polyphosphate accumulation and degradation in Thiomargarita remain to be identified.

In addition to Thiomargarita, polyphosphate inclusions have been documented for different filamentous Beggiatoaceae (Maier and Murray 1965; de Albuquerque et al. 2010; Brock and Schulz-Vogt 2011); they appear to be absent from “Marithioploca,” at least at the time of sampling (Holmkvist et al. 2010). Experiments with Beggiatoa strain 35Flor—a strain that accumulates phosphate intracellularly as large inclusions surrounded by lipids, most likely a membrane (Brock et al. 2012)—have shown that phosphate is released in response to increasing sulfide concentrations; acetate additions have a similar effect on Thiomargarita but most likely act by stimulation of sulfate reduction and concomitant sulfide production in the sediment (Brock and Schulz-Vogt 2011).

Isolation, Enrichment, and Maintenance Procedures

Enrichments from Natural Environments

Natural enrichments of Beggiatoaceae can be transplanted into the laboratory for observation and community succession studies; a highly reducing Beggiatoa-rich sediment can be maintained in an aquarium for continued observation. For example, the development of a Beggiatoa mat in the laboratory unfolded over 10 days and revealed a succession of different Beggiatoa size classes (Bernard and Fenchel 1995).

Similar aquarium setups can be used for selective enrichments (Nelson 1992). The bottom of a shallow pan or aquarium (approximately 30 × 30 × 12 cm) is covered with a few centimeters of sand; seaweed or shredded paper is added as a source of complex organic polymers, plus approx. 20 g of CaSO₄ and a few grams of K₂HPO₄, followed by several centimeters of sulfide-rich marine mud and sufficient seawater to overlay the entire enrichment by about 1–2 cm. Subsequent dark incubation minimizes competition with phototrophic bacteria. The enrichment is certain to contain the proper sulfide–oxygen interface somewhere in the vessel if air is introduced near the sediment surface using an airstone. Water lost by evaporation should be replaced by distilled water. Alternatively, a slow steady flow of freshly aerated seawater, with a drain maintaining a constant level, will provide the necessary O₂. A similar freshwater enrichment inoculated with mud from a sulfur spring and maintained on a light–dark cycle (10 h:14 h) provided viable tufts of Beggiatoa spp. for almost 1 year (Nelson and Castenholz 1982). Sewage treatment plants are also an excellent source of enrichment material (Burton and Lee 1978; Williams and Unz 1985).

Enrichment in extracted hay medium (Cataldi 1940) provides a useful strategy for enriching Beggiatoaceae, and several modifications of this method have been employed successfully for enriching freshwater Beggiatoa strains from decaying plant material and aquatic sediment (Faust and Wolfe 1961; Joshi and Hollis 1976; Saravanakumar et al. 2012). These materials provide good inocula even when conspicuous mats are absent; as filaments break at necridia or “sacrifical cells,” trichomes as short as 3–10 μm are produced and widely dispersed (Pringsheim 1964; Strohl and Larkin 1978b; Kamp et al. 2008). Enriched tufts of Beggiatoa filaments then provide start material for single filament isolation by excising individual filaments after transfer of tufts on agar plates (Faust and Wolfe 1961).

Liquid Media

Liquid media can be used for enrichment, MPN enumeration, and bulk cultivation of Beggiatoa. Early attempts to use liquid media for bulk cultivation (Kowallik and Pringsheim 1966) had already demonstrated the importance of small amounts of carbon substrates, either soil or hay extracts or small amounts of acetate, for successful cultivation of heterotrophic or mixotrophic freshwater Beggiatoa. The type species and strain, Beggiatoa alba B18LD, and related strains, are generally grown in liquid media that include a salt base, acetate as carbon source, and variable yeast extract and sulfide additions (Mezzino et al. 1984; Schmidt et al. 1986).

In an extensive study, Strohl and Larkin (1978a) have tested several liquid media formulations for isolation and MPN enumeration of heterotrophic Beggiatoa filaments from organic-rich freshwater ditches and lakes. A soil extract amended with 0.05 % (w/v) acetate, 15–35 U catalase per mL, and 1 % (w/v) hay extract yielded the best results. Following a recently published version of this protocol (Saravanakumar et al. 2012), hay is extracted by boiling in tap water for about 30 min and the water is decanted. Repeated boiling and decanting is carried out at least five times with cold tap water rinses between each boiling/decanting step. The extracted hay is left in water overnight and then decanted and dried at room temperature for 2 days. Approximately 1 g of dried hay is added to 100 mL of artificial seawater in a 250-mL Erlenmeyer flask and autoclaved. Filter-sterilized catalase is added to the medium at a final concentration of 35 U/mL. The medium is subsequently inoculated with 1–2 g of sediment sample. After 1–2 weeks incubation at 28 °C in the dark, the enrichments are checked for the presence of whitish threadlike mats and tufts, and these are examined microscopically for the presence of typical Beggiatoa filaments. The tufts from enrichment cultures are washed twice with sterile 0.01 % sodium azide solution (Strohl and Larkin 1978a) prepared in artificial seawater, followed by two washes and a 5-min soak in filtered artificial seawater containing catalase (35 U/mL). Washed filaments are then used for pure culture isolation procedures using heterotrophic media (Burton and Lee 1978; Strohl and Larkin 1978a) or sulfide gradient cultures (Nelson and Jannasch 1983).

Isolations on Agar Plates

Agar plate enrichments have commonly led to the isolation of heterotrophic Beggiatoa strains, but can be adjusted for autotrophic enrichments by minimizing or removing the organic carbon source in the agar medium. Tufts of Beggiatoa filaments are collected from the environment or an enrichment, washed in a sterile washing solution, and placed on an agar plate that contains dilute organic substrates, such as small amounts (1–0.25 ‰ w/v) of peptone or yeast extract or 0.5 mM acetate. Growing filaments that move away from the central inoculum are cut out on agar blocks and are used as inoculum for new agar plates (Pringsheim 1967); individual filaments can also be pulled away from the inoculum with a suitable micromanipulation needle or finely pointed watchmaker’s forceps (Nelson 1992). The surface of the agar plates should be dry and free of condensation water droplets.

To enrich and isolate heterotrophic freshwater Beggiatoa, the representative DTA medium (Nelson 1992) for agar plates is prepared as follows. The pH is adjusted to 7.0 prior to autoclaving.

ND stock solution	50 mL
(NH₄)₂SO₄	0.13 g
Sodium acetate	0.68 g (may be reduced)
K₂HPO₄	0.027 g
Na₂S₂O₃ × 5H₂O	0.50 g
CaCl₂	0.10 g
Distilled water	950 mL
Agar	12 g

ND stock solution (Castenholz 1988)
Distilled water	1000 mL
NTA (nitrilotriacetic acid)	2.0 g
Micronutrient solution	10 mL
FeCl₃ solution	(0.29 g/L) 20 mL
CaSO₄ × 2H₂O	1.2 g
MgSO₄ × 7H₂O	2.0 g
NaCl	0.16 g
Na₂HPO₄	1.4 g
KH₂PO₄	0.72 g

Micronutrient solution
Distilled water	1,000 mL
H₂SO₄ (concentrated)	0.5 mL
MnSO₄ × H₂O	2.28 g
ZnSO₄ × 7H₂O	0.50 g
H₃BO₃	0.50 g
CuSO₄ × 5H₂O	0.025 g
Na₂MoO₄ × 2H₂O	0.025 g
CoCl₂ × 6H₂O	0.045 g

By using defined mineral media and reducing the organic carbon content of the agar medium (Nelson and Castenholz 1981b), heterotrophic contaminants are selected against, and the enrichment and isolation of autotrophic Beggiatoa is favored. Agar plates made with filtered seawater, trace elements, and vitamin mix and supplemented with sodium sulfide, ammonium sulfate, sodium thiosulfate, and sodium acetate were used for the isolation of marine Beggiatoa strains that in subsequent tests showed autotrophic growth (Nelson et al. 1982). The marine basal medium (J3) without carbon substrate amendments can be used for agar plates selecting for autotrophic Beggiatoa spp. (Nelson 1992) and is prepared starting with three solutions that are separately autoclaved in Erlenmeyer flasks.

Solution 1:
Aged natural seawater (salinity 3.2–3.5 %), 500 mL
Prefiltered (Whatman #1 or Gelman GF/F) and filtered (0.45 μm)

Solution 2 (in larger flask):
Distilled water	200 mL
Agar	9.0 g

Solution 3:
NH₄NO₃	0.06 g
Trace element solution SL8	0.75 mL
Mineral stock	50 mL

The aged natural seawater can be replaced by artificial seawater, containing per liter NaCl, 27.5 g; MgCl₂ × 6H₂O; MgSO₄ × 7H₂O, 4.1 g; CaCl₂ × 2H₂O, 0.66 g; and KCl, 1.02 g (Kamp et al. 2008).

The trace element solution SL8 (Pfennig and Biebl 1981) contains per liter Na₂EDTA, 5.2 g; FeCl₂ × 4H₂O, 1.5 g; ZnCl₂, 0.070 g; MnCl₂ × 4H₂O, 0.100 g; H₃BO₃, 0.062 g; CoCl₂ × 6H₂O, 0.19 g; CuCl₂ × 2H₂0, 0.017 g; NiCl₂ × 6H₂O, 0.024 g; and Na₂MoO₄ × 2H₂O, 0.036 g.

The mineral stock contains per liter K₂HPO₄, 0.52 g; Na₂MoO₄, 0.05 g; FeCl₃ × 6H₂O, 0.29 g; Na₂S₂O₅ (sodium pyrosulfite), 0.75 g; and phenol red, 10 mL of a sterile 0.5 % solution (Gibco) (Nelson 1992).

After cooling to 50 °C, the autoclaved solutions are aseptically combined in the solution 2 flask (volume > 750 mL) and supplemented with 0.2 mL of Va vitamin solution, which contains (in mg per liter) B₁₂, 1; thiamine, 200; biotin, 1; folic acid, 1; para-aminobenzoic acid, 10; nicotinic acid, 100; inositol, 1; and calcium pantothenate, 100.

J3 basal medium is amended to produce an isolation medium (J-TS) by adding the following three sterile stocks, with final concentrations in parentheses (Nelson 1992): (1) 7.5 mL of 200 mM Na₂S₂O₃ (2 mM) and (2) 3.75 mL of freshly neutralized 200 mM Na₂S (1 mM). The Na₂S stock is autoclaved as a basic solution and then neutralized with an equimolar quantity of sterile HCl just prior to use. The Na₂S stock solution is kept for approx. a month during oxic storage, unless it is stored under N₂ gas. (3) 15 mL of 1 M NaHCO₃ (20 mM). To make this stock, autoclave 8.4 g of NaHCO₃ (dry), and add 100 mL sterile water when cool. The medium is buffered by the bicarbonate in conjunction with the atmospheric CO₂.

Immediately after solidification, plates are incubated in a bell jar for 24 h or more under anoxic conditions (99.5 % N₂, 0.5 % CO₂), with desiccant present to absorb water evaporating from the surface of the plates. After inoculation with a tuft of Beggiatoa spp., plates are placed in a microoxic atmosphere (0.5 % CO₂; 0.2 % O₂; balance N₂). The medium and the bacteria tolerate temporary air exposure during inoculation or single-filament isolation (Nelson 1992).

Methods for isolating marine Beggiatoa strains on agar under microoxic conditions should in principle work for freshwater Beggiatoa as well. While freshwater strains were typically isolated on a variety of media equilibrated with full air (Nelson and Castenholz 1981b; Strohl and Larkin 1978a; Williams and Unz 1985), microoxic conditions may be required on occasion: the cultivation of a freshwater Beggiatoa strain in liquid mineral medium on thiosulfate and HCO₃ ⁻ required dissolved oxygen concentrations in the range of 3–16 μM (0.1–0.5 mg O₂/L) (Patritskaya et al. 2001).

Isolations and Cultivation in Gradient Media

Motile Beggiatoa spp. display strong chemotactic movement and adjust their position in gradients of oxygen and sulfide; they form platelike aggregates near the microoxic surface of semisolid agar tubes or—in liquid culture—reticulate networks of filaments surrounding an FeS pellet as sulfide source (Faust and Wolfe 1961). These observations were extended into a cultivation approach based on gradient media, where two layers of agar (a sulfide-rich agar plug at the bottom overlaid with sulfide-free soft agar) containing opposed sulfide and oxygen gradients provide a suitable gradient habitat for maintaining and propagating marine, autotrophic, non-vacuolate Beggiatoa spp. (Fig. 6.6 ) (Nelson and Jannasch 1983).

Marine gradient medium JG8 (Nelson 1992) is constructed as follows: first a 4 mL quantity of J3 agar (pH 8.4; the NaHCO₃ concentration is lowered to 2.0 mM; thiosulfate may be omitted) supplemented with freshly neutralized Na₂S is solidified in the bottom of a screw-capped tube (Hungate tube, 16 × 150 mm or similar). The bottom agar plug contained initially a sulfide concentration of 8 mM (Nelson and Jannasch 1983), but 3–4 mM sulfide is sufficient (Kamp et al. 2008; Jewell et al. 2008); agar strength can be reduced from 1.5 % to 0.75 % (Kamp et al. 2008). This bottom agar is then overlaid with 8.0 mL of semisolid J3 agar (0.25 % agar; NaHCO₃ concentration lowered to 2.0 mM; no sulfide or thiosulfate, but may contain nitrate). The resulting two layers of agar contain opposed sulfide and oxygen gradients that allow the growth of a well-defined Beggiatoa layer at the sulfide–oxygen interface (Nelson et al. 1986a, b). The overlying air headspace reservoir in the tube constitutes an oxygen reservoir. Tubes are loosely capped to permit exchange of headspace gasses with the atmosphere.

Aging new gradient media for 2–3 days prior to inoculation establishes a sulfide–oxygen interface that is quite stable in both position and rates of nutrient fluxes; however, molecular diffusion and nonbiological reactions between sulfide and oxygen gradually alter the gradient (Nelson et al. 1986a, b). The sulfide–oxygen interface near the top of the agar column spreads out in the absence of a Beggiatoa inoculum and contracts after inoculation. For example, sulfide and oxygen overlapped for 6–7 mm in uninoculated medium during slow, nonbiological sulfide oxidation (Nelson et al. 1986b), in marked contrast to an overlap of 0.2 mm or less in active Beggiatoa cultures where sulfide oxidation proceeded quickly (Nelson 1992). Whether inoculated at the surface of this medium or stabbed throughout the upper few centimeters, the filaments rapidly proliferate at the sulfide–oxygen interface, forming a marked layer or “plate” of variable thickness. Gliding motility and negative chemotactic responses allow these bacteria to track this interface as it slowly descends due to the gradual depletion of the sulfide reservoir.

The gradient approach is not limited to marine Beggiatoa. For cultivation of estuarine strains, the soft agar medium is based on a 2/3-strength natural seawater medium that lacks reduced sulfur compounds but includes trace elements and vitamin mix and was supplemented with ammonium nitrate (J2 Medium) (Nelson and Jannasch 1983). For gradient culture of freshwater Beggiatoaceae (Kamp et al. 2006), the basal mineral medium is adjusted accordingly (per liter: EDTA, 0.010 g; CaSO₄ × 2 H₂O, 0.120 g; MgSO₄ × 7 H₂O, 0.200 g; NaCl, 0.016 g; Na₂HPO₄, 0.140 g; NaH₂PO₄, 0.138 g; CaCl₂ × 2 H₂O, 0.264 g; FeCl₃ solution [0.290 g/L]; 1 mL micronutrient solution). The micronutrient solution contains per liter 0.5 mL H₂SO₄ (>98 %); MnSO₄ × H₂O, 2.28 g; ZnSO₄ × 7 H₂O, 0.5 g; H₃BO₃, 0.5 g; CuSO₄ × 5 H₂O, 0.025 g; Na₂MoO₄ × 2 H₂O, 0.025 g; and CoCl₂ × 6 H₂O, 0.045 g (Kamp et al. 2006); the vitamin solution remains the same.

Coculture and Obligate Associations

Some Beggiatoaceae could only be cultured in association with nonfilamentous bacteria (Kamp et al. 2006). One of these cocultures, an obligate association of the marine Beggiatoa strain 35Flor with a single, specific Pseudovibrio strain has been studied in more detail (Kamp et al. 2008; Brock and Schulz-Vogt 2011; Schwedt et al. 2012). Strain 35Flor grows only in the presence of an accompanying Pseudovibrio sp. strain that can be cultured without the Beggiatoa sp., but not vice versa. Since members of the genus Pseudovibrio are commonly isolated from marine invertebrates, the 35Flor-associated strain may have originated from the coral from which Beggiatoa sp. 35Flor had been isolated (Bondarev et al. 2013). Genome sequencing revealed that the Pseudovibrio symbiont has the genomic potential to attach to host cells, to produce secondary metabolites, and to provide the host organism with enzymatic cofactors (Bondarev et al. 2013).

Cultivation of Thioploca

Currently, no pure cultures or enrichments of Thioploca species or strains exist. All biochemical, physiological, and molecular work has been performed on Thioploca filaments collected from their natural environment, marine or freshwater sediments. Natural Thioploca populations can be kept alive in the laboratory for months or even years. Maier (1989) described the following procedures for freshwater Thioploca. Filaments may be maintained in jars overlaid with tap water at 8–20 °C in the dark; at approximately yearly intervals, a few stems of extracted grass (Scotten and Stokes 1962) may be stuck into the sediment, and Thioploca often colonizes these stems. Alternatively, 0.2–0.3 g of pulverized extracted hay is autoclaved in 60 mL of tap water in 125 mL Erlenmeyer flasks and inoculated with 4–10 mL of sediment (Maier 1980). After a month of undisturbed incubation at room temperature to avoid periods of maximum H₂S development, Thioploca bundles are added, and incubation continues for many weeks with intermittent inspection.

Attempts to enrich marine “Marithioploca” spp. have met little success. They may be maintained for months in undisturbed cores sampled from the natural populations and kept near the in situ temperature of 13 °C in a basin of anoxic seawater with nitrate added (H. Schulz-Vogt, pers. comm.). Physiological studies with harvested “Marithioploca” filaments required careful handling of the filaments, and avoidance of oxygen and air exposure, in order to prevent significant losses in enzymatic activities (Otte et al. 1999). Future cultivation approaches have to take into account the sensitivity of “Marithioploca” to high sulfide concentrations and to oxygen exposure and should maintain the delicate balance of sulfide, nitrate, and oxygen concentrations that characterizes its natural habitat (Hüttel et al. 1996; Schulz et al. 2000).

Strain Maintenance

Freshwater and marine strains of Beggiatoa spp. can be maintained in sulfide–oxygen gradient media. The smooth oxygen and sulfide gradients coupled with the chemotactic motility of the bacteria, which directs them to the proper microenvironment, make this approach especially attractive for obligately microaerophilic strains (Nelson et al. 1986b). A low concentration of acetate must be provided for the strains that do not show autotrophic capacity. For the typical medium geometry employed (Nelson 1992), transfers to new tubes of gradient medium should be made every 2–3 weeks. Gradient medium should be stored no more than 4–6 weeks; transfers into aged gradient media will not survive as long as those into freshly prepared media (Nelson 1992). Sustained propagation of heterotrophic freshwater strains on agar plates in the presence of full air is straightforward. By contrast, propagation of marine strains on agar plates under microoxic regimes in bell jars is best reserved for initial isolation and any required repurification steps. Cryopreservation of strains has proved problematic (Nelson and Schulz, pers. comm..).

Ecology

The Beggiatoaceae are gradient bacteria that occupy an ecological niche at the interface where fluxes of sulfide as electron donor and oxygen or nitrate as electron acceptor meet; different genera have adapted to this niche in characteristic ways and prefer different types of interface habitats. These ecophysiological strategies of efficient sulfur oxidation are directly reflected in the structure of the mats and in the arrangement and the movements of the filaments and cells within the oxic/anoxic gradient. Thus, physicochemical habitat characteristics are directly linked to occurrence patterns, morphology, and physiology of Beggiatoaceae in nature.

Their ecophysiological flexibility allows the Beggiatoaceae to colonize a wide spectrum of freshwater and marine environments; Beggiatoaceae can be found in a wide range of habitats, including organic-rich, coastal marine sediments (Jørgensen 1977; Klas 1937; Mussmann et al. 2003; Rosenberg and Diaz 1993); benthic microbial mats (Teske and Stahl 2002) salt marshes (Nelson et al. 1982); eutrophic, oxygen-depleted bays (Graco et al. 2001; Vallius 2006); marine oxygen-minimum zones (Schmaljohann et al. 2001); oxygen-depleted marine basins (Williams and Reimers 1983); geothermally active submarine caves (Mattison et al. 1998); hydrothermal vents (Jannasch et al. 1989; Nelson et al. 1989); cold sulfide seeps (Sassen et al. 1994); and hydrocarbon seeps (Larkin et al. 1994). Freshwater habitats include sulfur springs (Uphof 1927; Caldwell et al. 1975; Nelson and Castenholz 1981b; Fukui et al. 1999); freshwater ditches, puddles, wetlands, and lake sediments (Koppe 1924; Pringsheim 1964; Scotten and Stokes 1962; Strohl and Larkin 1978a); terrestrial salt springs (Kolkwitz 1918); and sulfidic cave streams (Macalady et al. 2006, 2008). The cave stream study is of special interest for the ecology of the Beggiatoaceae since it outlines the environmental preferences of Beggiatoa-like filaments against single-celled sulfur-oxidizing epsilonproteobacteria and filamentous Thiothrix spp. that compete for different microhabitats within the same cave ecosystem. The Epsilonproteobacteria dominated extremely oxygen-depleted stagnant water with very little turbulent flow and oxygen in-mixing; the Thiothrix-like filaments preferred locations characterized by strong turbulent mixing, higher oxygen availability, and reduced sulfide concentrations, whereas the Beggiatoa-like filaments inhabited intermediate habitats over a wide range of oxygen and sulfide concentrations, as long as a sedimentary substrate allowing for mat formation was available (Macalady et al. 2008).

The Oxygen–Sulfide Interface at the Sediment Surface

The small freshwater and marine Beggiatoa spp. position themselves as a narrow layer at the oxygen–sulfide interface and separate the two compounds efficiently from each other. High sulfate reduction rates in surficial sediments maintain high fluxes of sulfide in the range of 10–100 mmol m⁻² day⁻¹ (see literature compilation in Schwedt et al. 2012); sulfide is then oxidized within Beggiatoa mats at the sediment–water interface. Oxygen from the overlying water is also consumed within Beggiatoa mats and does not penetrate the underlying sulfidic sediment (Jørgensen and Revsbech 1983; Møller et al. 1985; Nelson et al. 1986a; Fenchel and Bernard 1995). The microoxic growth zone of Beggiatoa is characterized by oxygen concentrations in the range of 1–2.5 μM (Nelson et al. 1986a). This microoxic niche of Beggiatoa is created by the highly dynamic sulfide-oxidizing metabolism of the Beggiatoa filaments themselves, but once established, it is remarkably stable (Fig. 6.6 ). Laboratory gradient cultures remain active for several weeks and died only when the sulfide in the bottom agar was exhausted (Nelson et al. 1986a). A phobic response to high oxygen concentrations seems to be a driving force in establishing well-defined Beggiatoa mats. Beggiatoa filaments on a sediment surface adjust their position to short-term fluctuations in the sulfide and oxygen supply; they avoid high oxygen concentrations by contracting into the diffusive boundary layer directly at the sediment surface and expand after the oxygen stress has passed (Møller et al. 1985). Oxidative damage to essential enzymes by peroxide formation is one of the presumed reasons for the general oxygen sensitivity of Beggiatoa spp.; for example, H₂O₂ exposure inhibited fumarate hydratase, an essential TCA cycle enzyme, in the heterotrophically growing Beggiatoa freshwater strain D-405 (Grabovich et al. 1993).

The Anoxic, Non-sulfidic Surficial Sediment

In coastal, organic-rich marine sediments, Beggiatoaceae are often found in the intermediate sediment layer where porewater oxygen and nitrate are already depleted, but sulfide does not yet accumulate—a conspicuous departure from growth in overlapping oxygen–sulfide gradients at the sediment–water interface (Jørgensen 1977; Mussmann et al. 2003; Preisler et al. 2007; Jørgensen et al. 2010). These sediment populations do not form visually conspicuous mats at the sediment surface; their abundance becomes clear only after microscopic counts of the sediment-embedded filaments. Especially “Isobeggiatoa” and “Parabeggiatoa” occur in this habitat; their intracellular storage capacity for nitrate and sulfur is crucial in bridging the gap between the sedimentary porewater pools of electron acceptor and donor (Mussmann et al. 2003; Preisler et al. 2007). Even when they are abundant, these Beggiatoa-like filaments contribute only to a minor extent to overall anaerobic sulfide oxidation; precipitation with Fe²⁺ and oxidation with Fe³⁺ dominated sedimentary sulfide oxidation (Preisler et al. 2007). Filaments position themselves in the anoxic, sulfide-free zone by responding chemotactically to porewater concentrations of oxygen and sulfide; filaments in the favored zone reversed course frequently and were gliding shorter distances in randomized directions between reversals, whereas filaments in oxic or sulfidic sediments took more time between reversals and therefore glided longer distances (Dunker et al. 2010).

Hypersaline Cyanobacterial Mats

Beggiatoaceae, including members of the halotolerant Candidatus genus “Allobeggiatoa,” occur in hypersaline benthic cyanobacterial mats (Hinck et al. 2007, 2011; Dillon et al. 2009). Cyanobacterial mats form a diurnally shifting gradient habitat (Jørgensen 1982). At daytime, the upper layers of cyanobacterial mats are photosynthetically active and become supersaturated with oxygen. At night, oxygen production ceases, and sulfide produced by sulfate reduction moves up towards the mat surface (Jørgensen et al. 1979; Jørgensen and Revsbech 1983). If this interface remains outside of the photic zone during the day, photosynthetic sulfide-oxidizing bacteria are excluded, and colorless sulfur bacteria grow along the oxic/anoxic interface (Jørgensen and DesMarais 1986). The response of motile filaments in the mat is modulated by their physiology. Migrating Beggiatoa-like filaments closely follow the diel up-and-down movement of the oxygen–sulfide interface, whereas a nonmigratory population in the same mat remains stationary at ca. 1 mm depth (Garcia-Pichel et al. 1994). Interestingly, nitrate-storing Beggiatoaceae do not migrate towards the mat surface to escape nighttime anoxia, but remain in the mat and stay several millimeters below the oxic surface layer (Hinck et al. 2007).

Close associations with cyanobacteria in microbial mat habitats may have left a genomic imprint in some Beggiatoaceae that is especially visible in genetic elements involved in cell differentiation (MacGregor et al. 2013b). The draft genome sequence of a single orange “Maribeggiatoa”-related filament from hydrothermal mats shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and Group I intron within the 23S rRNA gene; several Group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; and multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria) all have close non-Beggiatoaceae matches with cyanobacterial sequences (MacGregor et al. 2013b). Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria (MacGregor et al. 2013b). Thus, gene transfer and evolutionary linkages between Beggiatoaceae and other filamentous bacteria (Reichenbach and Dworkin 1981) might be more significant than expected.

Hydrothermal Vents

Large filamentous sulfide oxidizers (“Maribeggiatoa” spp. and “Marithrix” spp.) occupy a distinct ecological niche characterized by fluctuating sulfide and oxidant levels. Conspicuous examples of this habitat have been studied in the hydrothermal sediments of Guaymas Basin in the Gulf of California (Jannasch et al. 1989; Nelson et al. 1989). Here, massive “Maribeggiatoa”-like mats of several cm thickness growing on hydrothermally active sediments are exposed to irregularly fluctuating pulses of oxygenated seawater and sulfidic sediment fluids (Gundersen et al. 1992) (Fig. 6.9a, b). The gradients of sulfide, DIC, and (most likely) low molecular weight organic compounds become steeper towards the center of a hydrothermal hot spot and appear to select for different morphotypes and genotypes in the center and in the periphery of the hydrothermally active sediment region (McKay et al. 2012). Orange filaments with a diameter of ca. 25–40 μm (Fig. 6.9c) dominate the center of the mat (Fig. 6.6c), whereas larger white filaments (>120 μm diameter, Fig. 6.9c–e) form the periphery of the mat (McKay et al. 2012). High temperature is unlikely to select for these different populations; in situ temperatures at the sediment–water interface across the multicolored mats remained cool (near 10 °C when measured with the Alvin temperature probe) and suitable for psychrophilic bacteria (McKay et al. 2012).

Filamentous mats do not only grow on hydrothermal sediments, but essentially on all solid substrates with a suitable regime where oxygenated seawater and reduced hydrothermal fluids mix, including the exterior of gradually seeping chimneys (Fig. 6.9b) and gaps and cracks in rocky debris that channel the flow of reduced fluids (Fig. 6.9f). Convective mixing of reduced vent fluids and oxygenated seawater also characterizes the habitat of “Marithrix” filaments; substrate-attached growth as rosettes allows “Marithrix” filaments to persist on exposed surfaces, such as hydrothermal chimneys (Kalanetra et al. 2004; Heijs et al. 2005; Kalanetra and Nelson 2010; Grünke et al. 2012). Most likely, these filaments have a higher oxygen tolerance than those in the Guaymas Basin mats.

Hydrocarbon Seeps

At hydrocarbon seeps, sediment areas characterized by active seepage of methane- and sulfide-rich fluids host conspicuous mats of Beggiatoa-like filaments (Fig. 6.10 ). Currently, most observations of this habitat type come from the continental slope of the northern Gulf of Mexico, an area exceptionally rich in hydrocarbon seeps (Larkin et al. 1994; Nikolaus et al. 2003). A cross section from the center to the margin of a mat-covered sediment area in the Gulf of Mexico (MC118) showed that the mat area coincided with high sulfate reduction and anaerobic methane oxidation rates in the surficial sediments; the microbial community underneath the mat was dominated by deltaproteobacterial sulfate-reducing bacteria and by methane-oxidizing archaea (Lloyd et al. 2010). The rates declined in bare sediments adjacent to the mat, and the microbial communities in the surficial sediments diversified considerably (Lloyd et al. 2010). The sulfidic seep sediments underneath the mats select for a specialized sulfur- and methane-cycling microbial community of reduced diversity (Lloyd et al. 2010).

The large filamentous sulfur oxidizers from Gulf of Mexico hydrocarbon seeps (with filament diameters up to 200 μm; Larkin and Henk 1989, 1996) are taxonomically unidentified but resemble large “Maribeggiatoa” filaments (e.g., Fig. 6.10e). In several investigations of cold hydrocarbon seeps in the Gulf of Mexico, colorful Beggiatoaceae mats showed a Guaymas-like spatial distribution of orange mats with white peripheries (Wirsen et al. 1992; Sassen et al. 1994; Larkin and Henk 1996; Nikolaus et al. 2003). Hydrocarbon analysis of sediments under Beggiatoaceae mats revealed that, in comparison to white filaments, adjacent orange filaments reside over sediments with elevated concentrations of unresolved petroleum hydrocarbons, and 1–3 orders of magnitude higher methane and ethane concentrations (Sassen et al. 1994). A recent survey in the Gulf of Mexico identified colorless, vacuolated, large filaments with diameters near 90–120 μm and smaller, vacuolated, orange-colored filaments near 35 μm (Fig. 6.10a–e); these coloration and size classes resembled those of the Guaymas Basin Beggiatoaceae (Teske, unpublished results). Rates of hydrocarbon seepage could control the composition of Gulf of Mexico mats similarly as hydrothermal seepage in Guaymas Basin.

The physiological capacity of hydrocarbon seep-associated Beggiatoaceae is an open research field. White filaments from Gulf of Mexico seeps assimilate CO₂ autotrophically, whereas orange filaments show strongly reduced capacity for CO₂ uptake and appear to be heterotrophs (Wirsen et al. 1992; Nikolaus et al. 2003). When methane-derived DIC or low molecular weight organic compounds reach the sediment surface, Beggiatoaceae mats can take up ¹³C-depleted CO₂ derived from methane oxidation and acquire the isotopically light signature (δ¹³C in the range of −50 to −60‰) of partially methane-derived biomass (Paull et al. 1992; Orphan et al. 2002). In most cases, mixed Beggiatoaceae mat samples collected at cold seeps in the Gulf of Mexico have δ¹³C isotopic signatures near −26 to −29‰, indicating that carbon sources of planktonic, photosynthetic origin are assimilated (Zhang et al. 2005).

In contrast to the commonly studied filamentous mats at hydrocarbon seeps, Beggiatoaceae occurring at a methane seep off Costa Rica have an attached habitus (Fig. 6.4f). Nonfilamentous sulfur bacteria (certain Thiomargarita sp. and Thiopilula sp.) are attached to solid surfaces like rocks, shells, or the byssus of mussels, where they are exposed to turbulent mixing of alternating sulfidic and oxygenated water (Bailey et al. 2011).

Mud Volcanoes

When fluidized mud flows from the subsurface reach the seafloor, they form extensive mud volcanoes characterized by high gas flow and an unstable sediment–water interface. At the center of mud volcanoes, the highly dynamic sediment–water interface does not allow the formation of sulfide-oxidizing microbial mats; more quiescent regions towards the periphery of the mud volcano provide the stable sediment–water interface that is required for growth of filamentous sulfide-oxidizing bacteria (Niemann et al. 2006; de Beer et al. 2006; Grünke et al. 2011; Girnth et al. 2011) (Fig. 6.10h).

Mud volcanoes with periodic flows of subsurface-derived brines (for example, the Amon mud volcano on the Nile Deep Sea fan in the Eastern Mediterranean; Girnth et al. 2011) present a special habitat. The brine flows cover the sediment surface at irregular intervals with dense, highly sulfidic brine; under these conditions, stationary Thiomargarita spp. have an advantage against “Maribeggiatoa” and “Marithioploca.” The latter two would spend energy by chemotactic responses to the shallow brine flow, whereas the stationary Thiomargarita cells avoid this energy expenditure and await the end of the sulfidic brine flow episode (Girnth et al. 2011). This strategy resembles the stationary survival mode of Thiomargarita namibiensis, which relies on environmental perturbations for sulfide and nitrate exposure and uptake (Schulz 2006). Attached Beggiatoaceae (“Marithrix” spp.) have a similar ecological advantage under the highly fluctuating regimes of oxidized and reduced bottom waters and passing brine flows (Heijs et al. 2005; Grünke et al. 2011, 2012).

Nearshore Upwelling Areas: The Chilean Continental Shelf

Nearshore upwelling areas are characterized by oxygen-depleted or anoxic bottom water overlying organic-rich sediments; sulfate reduction in the sediments produces sulfide that is oxidized by microaerophilic and nitrate-reducing mats of large filamentous sulfide oxidizers (Fig. 6.3a–c). By geographical extent, these mats are probably the most widespread sulfide-oxidizing mat ecosystem on earth. Currently, the ecologically and oceanographically best documented mat systems are the complex sulfide-oxidizing bacterial mats on the Pacific continental shelf of Chile and Peru dominated by the large nitrate-accumulating filaments of “Candidatus Marithioploca” (Gallardo 1963, 1977a, b; Fossing et al. 1995; Gallardo and Espinoza 2007) (Fig. 6.3a–f).

The predominantly vertically oriented “Marithioploca” filaments can bridge and exploit the vertically separated pools of sediment sulfide and seawater nitrate (Hüttel et al. 1996; Schulz et al. 1996) and thus improve on the “holding your breath” strategy of nitrate accumulation and respiration of large, marine “Maribeggiatoa” spp. Large “Marithioploca” spp. from the Chilean continental shelf have turnover times of 8–10 days for their intracellular nitrate and sulfur reserves (Otte et al. 1999). For long-term survival, “Marithioploca” filaments require just the right balance of nitrate availability in oxygen-depleted bottom water and sulfide availability in the sediment. The annual fluctuations in mat abundance during a seasonal upwelling cycle (Schulz et al. 2000) can be exacerbated by prolonged summer anoxia, when the mats cannot cope with increased sulfate reduction and sulfide inundation; the result is mat die-off (Gallardo 1992) and high porewater sulfide concentrations in previously sulfide-free surficial sediments (Holmkvist et al. 2010). On the other hand, increased oxygen exposure and decreased water column productivity and organic matter input during El Niño years adversely affect the “Marithioploca” mats. During such events, bottom water oxygen concentrations increase from near detection limit (<2 μM) to ca. 20–40 μm; at the same time, “Marithioploca” biomass decreases considerably, from up to 160 g m⁻² (Schulz et al. 2000) to <1 to 5 g m⁻² (Schubert et al. 2000; Neira et al. 2001).

The spatial structure of the Chilean “Marithioploca” mats is conducive to the microbial lifestyle of bridging sulfide and nitrate pools. The densest mat matrix of randomly oriented filaments and bundles is found in the uppermost centimeter layer, while predominantly vertically oriented, less densely packed “Marithioploca” bundles reach down to a depth of generally 4–8 cm; they peter out at approx. 10–15 cm (Schulz et al. 1996) and are only rarely found in deeper sediment layers. The surface layer of the mat is generally well supplied with nitrate; it can penetrate several centimeters into the hydraulically conductive, porous, and soft “Marithioploca” mat sediments (Hüttel et al. 1996). The upper 1–5 cm of the sediment also shows the highest sulfate reduction rates, up to 1,500 nmol cm⁻³ d⁻¹, which are extremely high rates for marine sediments. Nevertheless, efficient in situ reoxidation of sulfide keeps the sulfide concentrations in the “Marithioploca” mat sediments low, mostly in the range of 5–50 μm, while sulfate concentrations were never depleted below bottom water concentrations (Ferdelman et al. 1997; Thamdrup and Canfield 1996). “Marithioploca” mats contribute significantly to in situ anaerobic oxidation of sulfide produced by sulfate reduction; their share can range from 6 to 91 %, but most measurements indicate a contribution between 20 % and 30 % (Fossing et al. 1995; Thamdrup and Canfield 1996; Ferdelman et al. 1997; Otte et al. 1999). The sulfide-oxidizing activity of “Marithioploca” is most significant in the upper 4 or 5 cm of sediment and quickly declines towards deeper sediment layers (Zopfi et al. 2008).

Sulfur recycling within the “Marithioploca” mats most likely benefits from the close spatial association between sulfate-reducing and sulfide-oxidizing bacteria in “Marithioploca” mats. Mat biomass and cultivable MPN numbers of sulfate-reducing bacteria both peak in the surface layer of the mat (Teske et al. 2009). Filamentous sulfate reducers of the genus Desulfonema grow on and within the “Marithioploca” sheaths and thus contribute to a cycle of sulfate reduction and reoxidation within a single “Marithioploca” bundle (Fukui et al. 1999; Teske et al. 2009).

Nearshore Upwelling Areas: The Benguela Upwelling System

The survival strategy of “Marithioploca” spp. contrasts with the ecophysiology of its relative Thiomargarita namibiensis. This immobile, giant sulfide oxidizer, the largest known prokaryote by volume, relies on its enormous storage capacity for sulfur and nitrate, to carry it through irregular natural fluctuations of sulfide and nitrate availability in its sedimentary habitat in the Benguela upwelling region offshore Namibia (Schulz et al. 1999). The high input of diatom-dominated phytoplankton debris fuels extremely high sulfate reduction rates that deplete sulfate within a few centimeters of the sediment surface and generate extremely sulfidic conditions (up to 20 mM) in the extremely soft diatomaceous ooze bottom sediments (Fig. 6.4a) (Brüchert et al. 2003). In this habitat, Thiomargarita cells reach a biomass density of up to 170 g m⁻² sediment, similar to the “Marithioploca” mats offshore Chile (Brüchert et al. 2003). Filamentous sulfur bacteria, free-living or bundled, are scarce in the sulfidic Namibian liquid sediments; although previous reports suggest the possibility, only a few specimens were found in recent surveys (Gallardo et al. 1998; Salman et al. 2013). In contrast to the oxygen-sensitive Chilean “Marithioploca” spp., Thiomargarita namibiensis tolerates prolonged oxygen exposure and, in addition to nitrate, appears to be able to use oxygen for sulfide oxidation if acetate is provided (Schulz and de Beer 2002). This respiratory flexibility in combination with its large intracellular storage capacity helps Thiomargarita namibiensis to tolerate fluctuations of sulfide, nitrate, and oxygen during irregular resuspension episodes due to massive sulfide and methane outgassing events in its natural habitat (Emeis et al. 2004; Weeks et al. 2002, 2004).

Ecosystem Roles of Beggiatoaceae

The Beggiatoaceae serve as indicator organisms of beginning or advanced oxygen depletion and sulfidic bottom conditions in aquatic habitats; these conditions go generally together with increased oxygen demand due to seasonal biomass degradation (Bernard and Fenchel 1995). Point sources of anthropogenic pollution (Elliott et al. 2006) and fish farm eutrophication (Bissett et al. 2007; Gallardo and Espinoza 2007; Aranda et al. 2010) favor the development of Beggiatoaceae mats; sea grass beds (Zostera marina) are replaced by sulfidic bottom mud with bacterial mats (Elliott et al. 2006).

As a result of their growth pattern at the sediment–water interface, Beggiatoaceae mats play a significant role for the benthic–pelagic exchange of sulfur in the marine environment. They act as a sulfide trap that prevents sulfide from entering the water column; during this process they enrich the sulfur content of surface sediments and allow resuspension and recycling of partially oxidized sulfur species in the water column (Grant and Bathmann 1987).

A significant ecosystem service of Beggiatoaceae mats, catalyzing phosphorous retention in benthic sediments, was recently proposed in a geochemical modelling study (Yekta and Rahm 2011). Sulfide oxidation by Beggiatoaceae contributes to shifting the redox balance of iron in surficial marine sediments from Fe-II to Fe-III and changes the balance of the resulting iron solid phases in surficial sediments from iron sulfide and pyrite to ferric oxyhydroxides; the latter absorb and immobilize phosphate in surficial sediments. This mechanism could provide a strategy for phosphorus retention in hypoxic marine sediments affected by eutrophication, a widespread problem in the Baltic Sea (Yekta and Rahm 2011). It remains a matter of debate whether the sulfur-oxidizing activities and biomass of Beggiatoaceae in situ are sufficient to turn around the redox state of the sedimentary iron pool (Preisler et al. 2007).

Local “hot spots” of decaying biomass that sustains mat-forming Beggiatoaceae can range from whale carcasses (Smith et al. 1989; Deming et al. 1997) to coral heads, where environmental stressors can induce the formation of mucus, which is then colonized by sulfate reducers and filamentous sulfur bacteria (Mitchell and Chet 1975). In black band coral disease, cyanobacterial mats and diverse heterotrophic bacteria are overgrowing and degrading coral tissue; colorless sulfur bacteria are a significant component of these mats growing on necrotic coral tissue (Carlton and Richardson 1995). Functional gene studies using the widely distributed sulfur oxidation key gene soxB show that uncultured Alphaproteobacteria are the dominant component of these mats; the Beggiatoaceae are morphologically conspicuous but appear as a minority in functional gene surveys (Bourne et al. 2013) or remain undetected in standard 16S clone library surveys (Sekar et al. 2006).

Many associations of Beggiatoaceae with other organisms benefit the partner organisms. The addition of cultured Beggiatoa filaments and tufts to different soils with rice plant seedlings reduced hydrogen sulfide levels in the flooded soil and increased oxygen production by the rice seedlings (Pitts et al. 1972; Joshi and Hollis 1977). Sulfide removal and detoxification has also been invoked to explain the conspicuous association of filamentous marine Beggiatoaceae with protists and nematodes in highly reducing marine sediments (Bernhard et al. 2003). Specific nematodes also inhabit Beggiatoaceae mats and the underlying sediment at the Håkon Mosby mud volcano and shape a meiofaunal community that is taxonomically distinct from and less diverse than its counterpart outside of the mat area (Van Gaever et al. 2010). On the Pacific continental shelf offshore Chile, benthic invertebrates (polychaetes, crustaceans, mollusks, anthozoa) occurred in greater abundance and diversity at sampling locations with well-developed “Marithioploca” mats than at sites where mats were sparse or absent (Carrasco et al. 1999). The Chilean “Marithioploca” mats also provide nursery habitat for marine invertebrates, such as squat lobster larvae (Roa et al. 1995; Gallardo et al. 1994). These effects are not only attributable to food source availability but also to sulfide sequestration.

Due to nitrate reduction and ammonification by “Candidatus Marithioploca,” ammonia accumulates at high rates in “Marithioploca”-harboring sediment surface layers (Thamdrup and Canfield 1996). The “Marithioploca” mats turn the sediments from a denitrifying nitrogen sink into an ammonia-producing nitrogen source; ammonia would constitute a readily utilized and recycled nitrogen source for the water column (Farias et al. 1996; Farias 1998). Similar findings have been reported for mats of large, vacuolated Beggiatoa-like filaments in Tokyo Bay (Sayama 2001) and in Aarhus Bay marine sediments (Sayama et al. 2005). Here, Beggiatoaceae separate the sulfide and nitrate porewater pools by pushing the nitrate-reducing sulfide oxidation horizon down into the sediment; in parallel, the predominant nitrate and nitrite reduction pathway in the Beggiatoa-inoculated sediment shifts from denitrification to N₂ towards dissimilatory nitrate reduction to ammonia (Sayama et al. 2005). The product of anaerobic sulfide oxidation, sulfur, is then transported to the sediment surface and oxidized aerobically to sulfate. This spatial separation of anaerobic and aerobic sulfur oxidation pathways, and parsimonious use of nitrate only for the initial oxidation step (of sulfide to sulfur), counteracts nitrate depletion during complete oxidation of sulfide to sulfate.

In a fascinating twist, microbial associations of “Marithioploca” filaments and sheath-associated anaerobic ammonia-oxidizing bacteria (“Candidatus Scalindua”) can recycle ammonia by anaerobic oxidation to dinitrogen via conproportionation with nitrite (Prokopenko et al. 2006, 2013). Freshly generated bioavailable reduced nitrogen in the sediments would be lost in a coupled nitrate ammonification/anammox process that, from the outside, looks like straightforward denitrification. In a detailed case study of the Soledad basin offshore Baja California, the “Marithioploca”-catalyzed nitrogen loss from the sediment was very similar to the measured efflux of ammonia; anammox rate measurements and geochemical modelling showed that the Marithioploca/Scalindua consortium contributed ca. 20–57 % of the total N₂ production. In this way, “Marithioploca” catalyzes nitrogen loss in organic-rich, highly reducing sediments where otherwise limited diffusion of the oxidants nitrate and nitrate into the sediment limits denitrification (Prokopenko et al. 2011, 2013). Thus, benthic mats of nitrate-accumulating, sulfur-oxidizing Beggiatoaceae represent simultaneously a source and a sink of bioavailable nitrogen, and the relative contributions of these processes will depend to a large extent on the redox state and organic carbon load of benthic sediments.

References

Ahmad A, Barry JP, Nelson DC (1999) Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Appl Environ Microbiol 65:270–277
PubMed CAS PubMed Central Google Scholar
Ahmad A, Kalanetra KM, Nelson DC (2006) Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria. Can J Microbiol 52:591–598
PubMed CAS Google Scholar
Angert ER (2012) DNA replication and genomic architecture of very large bacteria. Annu Rev Microbiol 66:197–212
PubMed CAS Google Scholar
Aranda C, Paredes J, Valenzuela C, Lam P, Guillou L (2010) 16S rRNA gene-based molecular analysis of mat-forming and accompanying bacteria covering organically-enriched marine sediments underlying a salmon farm in Southern Chile (Calbuco Island). Gayana 74:125–135
Google Scholar
Arning ET, Birgel D, Brunner B, Peckmann J (2009) Bacterial formation of phosphatic laminites off Peru. Geobiology 7:295–307
PubMed CAS Google Scholar
Bailey JV, Joye SB, Kalanetra KM, Flood BE, Corsetti FA (2007) Evidence of giant sulphur bacteria in Neoproterozoic phosphorites. Nature 445:198–201
PubMed CAS Google Scholar
Bailey JV, Salman V, Rouse GW, Schulz-Vogt HN, Levin LA, Orphan VJ (2011) Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria. ISME J 5:1926–1935
PubMed CAS PubMed Central Google Scholar
Bavendamm W (1924) Die farblosen und roten Schwefelbakterien des Süß- und Salzwassers. Pflanzenforsch 2:1–156
Google Scholar
Bernard C, Fenchel T (1995) Mats of colourless sulphur bacteria 2. Structure, composition of biota and successional patterns. Mar Ecol Prog Ser 128:171–179
Google Scholar
Bernhard JM, Visscher PT, Bowser SS (2003) Submillimeter life positions of bacteria, protists, and metazoans in laminated sediments of the Santa Barbara Basin. Limnol Oceanogr 48:813–828
Google Scholar
Beutler M, Hinck S, de Beer D (2009) A method for imaging of low pH in live cells based on excited state saturation. J Microbial Methods 77:98–101
CAS Google Scholar
Beutler M, Milucka J, Hinck S, Schreiber F, Brock J, Mussmann M, Schulz-Vogt HN, de Beer D (2012) Vacuolar respiration of nitrate coupled to energy conservation in filamentous Beggiatoaceae. Environ Microbiol 14:2911–2919
PubMed CAS Google Scholar
Bissett A, Burke C, Cook PLM, Bowman JP (2007) Bacterial community shifts in organically perturbed sediments. Environ Microbiol 9:46–60
PubMed CAS Google Scholar
Bondarev V, Richter M, Romero S, Piel J, Schwedt A, Schulz-Vogt HN (2013) The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol 15:2095–2113
PubMed CAS PubMed Central Google Scholar
Bourne DG, van der Zee MJJ, Botté ES, Sato Y (2013) Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions. Environ Microbiol Rep 5:518–524
PubMed CAS Google Scholar
Bowles MW, Nigro LM, Teske AP, Joye SB (2012) Denitrification and environmental factors influencing nitrate removal in Guaymas Basin hydrothermally-altered sediments. Front Microbiol 3:377. doi:10.3389/fmicb.2012.03377
PubMed CAS PubMed Central Google Scholar
Brock J, Rhiel E, Beutler M, Salman V, Schulz-Vogt HN (2012) Unusual polyphosphate inclusions observed in a marine Beggiatoa strain. Antonie Van Leeuwenhoek 101:347–357
PubMed CAS PubMed Central Google Scholar
Brock J, Schulz-Vogt HN (2011) Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain. ISME J 5:497–506
PubMed CAS PubMed Central Google Scholar
Brock TD (1974) Family IV. Leucotrichaceae Buchanan 1957. In: Buchanan RE, Gibbons NE (eds) Bergey's manual of determinative bacteriology, 8th edn. Williams & Wilkins, Baltimore, pp 118–119
Google Scholar
Brüchert V, Jørgensen BB, Neumann K, Riechmann D, Schlosser M, Schulz HN (2003) Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central Namibian coastal upwelling zone. Geochim Cosmochim Acta 67:4505–4518
Google Scholar
Burton SD, Morita RY, Miller W (1966) Utilization of acetate by Beggiatoa. J Bacteriol 91:1192–1200
PubMed CAS PubMed Central Google Scholar
Burton SD, Lee JD (1978) Improved enrichment and isolation procedures for obtaining pure cultures of Beggiatoa. Appl Environ Microbiol 45:614–617
Google Scholar
Caldwell DE, Caldwell SJ, Tiedje JM (1975) An ecological study on the sulfur bacteria from the littoral zone of a Michigan Lake and a sulfur spring in Florida. Plant Soil 43:101–114
Google Scholar
Castenholz RW (1988) The green sulfur and nonsulfur bacteria of hot springs. In: Olson JM, Ormerod JG, Amesz J, Stackebrandt E, Trüper HG (eds) Green photosynthetic bacteria. Plenum, New York, pp 243–255
Google Scholar
Cannon GC, Strohl WR, Larkin JM, Shively JM (1979) Cytochromes in Beggiatoa alba. Curr Microbiol 2:263–266
CAS Google Scholar
Carrasco FD, Gallardo VA, Baltazar M (1999) The structure of the benthic macrofauna collected across a transect at the central Chile shelf and relationships with giant sulfur bacteria Thioploca spp. mats. Cah Biol Mar 40:195–202
Google Scholar
Carlton RG, Richardson LL (1995) Oxygen and sulfide dynamics in a horizontally migrating cyanobacterial mat: black band disease of corals. FEMS Microbiol Ecol 18:155–162
CAS Google Scholar
Cataldi MS (1940) Aislamiento de Beggiatoa alba en cultivo puro. Rev Inst Bacteriol Dept Nacl Hig (Buenos Aires) 9:393–423
Google Scholar
Crépeau V, Cambon Bonavita MA, Lesongeur F, Randrianalivelo H, Sarradin P-M, Sarrazin J, Godfroy A (2011) Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field. FEMS Microbiol Ecol 76:524–540
PubMed Google Scholar
de Albuquerque JP, Keim CN, Lins U (2010) Comparative analysis of Beggiatoa from hypersaline and marine environments. Micron 41:507–517
PubMed Google Scholar
De Beer D, Sauter E, Niemann H, Kaul N, Foucher JP, Witte U et al (2006) In situ fluxes and zonation of microbial activity in surface sediments of the Håkon Mosby Mud volcano. Limnol Oceanogr 51:1315–1331
Google Scholar
Deming J, Reysenbach A-L, Macko S, Smith CR (1997) Evidence for the microbial basis of a chemoautotrophic invertebrate community at a whale fall on the deep seafloor: bone-colonizing bacteria and invertebrate endobionts. Microsc Res Tech 37:162–170
PubMed CAS Google Scholar
Dermott R, Legner M (2002) Dense mat-forming bacterium Thioploca ingrica (Beggiatoaceae) in eastern Lake Ontario: implications to the benthic food web. J Great Lakes Res 28:688–697
CAS Google Scholar
Dillon JG, Miller S, Bebout B, Hullar M, Pinel N, Stahl DA (2009) Spatial and temporal variability in a stratified hypersaline microbial mat community. FEMS Microbiol Ecol 68:46–58
PubMed CAS Google Scholar
Drawert H, Metzner-Küstner I (1958) Fluoreszenz- und elektronenmikroskopische Unitersuchungen an Beggiatoa alba und Thiothrix nivea. Arch Mikrobiol 31:422–434
Google Scholar
Dunker R, Røy H, Kamp A, Jørgensen BB (2010) Motility patterns of filamentous sulfur bacteria Beggiatoa spp. FEMS Microbiol Ecol 77:176–185
Google Scholar
Dworkin M (2012) Sergei Winogradsky: a founder of modern microbiology and the first microbial ecologist. FEMS Microbiol Rev 36:364–379
PubMed CAS Google Scholar
Elliott JK, Spear E, Wyllie-Echeverria S (2006) Mats of Beggiatoa bacteria reveal that organic pollution from lumber mills inhibits growth of Zostera marina. Marine Ecol 27:372–380
Google Scholar
Emeis KC, Brüchert V, Currie B, Endler R, Ferdelman T, Kiessling A, Leipe T, Noli-Peard K, Struck U, Vogt T (2004) Shallow gas in shelf sediments of the Namibian coastal upwelling ecosystem. Cont Shelf Res 24:627–642
Google Scholar
Farias L (1998) Potential role of bacterial mats in the nitrogen budget of marine sediments: the case of Thioploca spp. Marine Ecol Prog Ser 170:291–292
Google Scholar
Farias L, Chuecas LA, Salamanca MA (1996) Effect of coastal upwelling on nitrogen regeneration from sediments and ammonium supply to the water column in Concepcion Bay, Chile. Estuar Coast Shelf Sci 43:137–155
CAS Google Scholar
Faust L, Wolfe RS (1961) Enrichment and cultivation of Beggiatoa alba. J Bacteriol 81:99–106
PubMed CAS PubMed Central Google Scholar
Fenchel T, Bernard C (1995) Mats of colourless sulphur bacteria. I. Major microbial processes. Mar Ecol Prog Ser 128:161–170
Google Scholar
Ferdelman TG, Lee C, Pantoja S, Harder J, Bebout BM, Fossing H (1997) Sulfate reduction and methanogenesis in a Thioploca-dominated sediment off the coast of Chile. Geochim Cosmochim Acta 61:3065–3079
CAS Google Scholar
Fossing H, Gallardo VA, Jørgensen BB, Hüttel M, Nielsen LP, Schulz H, Canfield DE, Forster S, Glud RN, Gundersen JK, Küver J, Ramsing NB, Teske A, Thamdrup B, Ulloa O (1995) Concentration and transport of nitrate by the mat-forming sulfur bacterium Thioploca. Nature 374:713–715
CAS Google Scholar
Fukui M, Teske A, Assmus B, Muyzer G, Widdel F (1999) Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema). Arch Microbiol 172:193–203
PubMed CAS Google Scholar
Gallardo VA (1963) Notas sobre la densidad de la fauna bentonica en el sublitoral del norte de Chile. Guyana 10:3–15
Google Scholar
Gallardo VA (1977a) Large benthic microbial communities in sulfide biota under Peru-Chile subsurface countercurrent. Nature 268:331–332
Google Scholar
Gallardo VA (1977b) On the discovery of a large microbial community living in the soft bottoms of the continental shelf off Chile and Peru. In: Annales del Instituto de Investigaciones Marinas de Punta de Betin. Suplemento No. 1: Memorias del seminario internacional sobre problemas de la ecologia marina actual y el futuro del hombre, Colombia, Marzo, pp 23–30
Google Scholar
Gallardo VA, Cañete JI, Roa R, Enríquez-Briones S, Baltazar M (1994) Recruitment of the squat lobster Pleuroncodes monodon on the continental shelf off Central Chile. J Crustacean Biol 14:665–669
Google Scholar
Gallardo VA, Carrasco FD, Roa R, Canete JI (1995) Ecological patterns in the benthic macrobiota across the continental shelf off central Chile. Ophelia 40:167–188
Google Scholar
Gallardo VA (1992) On the presence of metal stained organic material in Thioploca shelf bottoms off Bay of Concepcion, Chile. Gayana Oceanol 1:27–33
Google Scholar
Gallardo VA, Klingelhoeffer E, Arntz W, Graco M (1998) First report of the bacterium Thioploca in the Benguela ecosystem off Namibia. J Mar Biol Assoc UK 78:1007–1010
Google Scholar
Gallardo VA, Espinoza C (2007) New communities of large filamentous sulfur bacteria in the eastern South Pacific. Int Microbiol 10:97–102
PubMed Google Scholar
Garcia-Pichel F, Mechling M, Castenholz RW (1994) Diel migration of microorganisms within a benthic, hypersaline mat community. Appl Environ Microbiol 60:1500–1511
PubMed CAS PubMed Central Google Scholar
Garrity GM, Bell JA, Lilburn T (2005) Family I. Thiotrichaceae fam. nov. In: Garrity BM, Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, p 131
Google Scholar
Genthner FJ, Hook LA, Strohl WR (1985) Determination of the molecular mass of bacterial genomic DNA and plasmid copy number by high-pressure liquid chromatography. Appl Environ Microbiol 50:1007–1013
PubMed CAS PubMed Central Google Scholar
Girnth A-C, Grünke S, Lichtschlag A, Felden J, Knittel K, Wenzhöfer F, de Beer D, Boetius A (2011) A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano. Environ Microbiol 13:495–505
PubMed CAS Google Scholar
Grabovich MY, Dubinina GA, Churikova VV, Korovina TI, Glushkov AF, Churikov SN (1993) Carbon metabolism of Beggiatoa leptomitiformis under conditions of chemo-organoheterotrophic growth. Microbiology 62:267–271 (Engl. translation of Mikrobiologiya)
Google Scholar
Grabovich MY, Dubinina GA, Lebedeva VY, Churikova VV (1998) Mixotrophic and lithoheterotrophic growth of the freshwater filamentous sulfur bacterium Beggiatoa leptomitiformis D-402. Microbiology 67:383–388
CAS Google Scholar
Grabovich MY, Patritskaya VY, Muntyan MS, Dubinina GA (2001) Lithoautotrophic growth of the freshwater strain Beggiatoa D-402 and energy conservation in a homogeneous culture under microoxic conditions. FEMS Microbiol Lett 204:341–345
PubMed CAS Google Scholar
Graco M, Farias L, Molina V, Gutierrez D, Nielsen LP (2001) Massive developments of microbial mats following phytoplankton blooms in a naturally eutrophic bay: implications for nitrogen cycling. Limnol Oceanogr 46:821–832
CAS Google Scholar
Grant J, Bathmann UV (1987) Swept away: resuspension of bacterial mats regulates benthic-pelagic exchange of sulfur. Science 236:1472–1474
PubMed CAS Google Scholar
Grünke S, Lichtschlag A, de Beer D, Kuypers M, Lösekann-Behrens T, Ramette A, Boetius A (2010) Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats. ISME J 4:1031–1043
PubMed Google Scholar
Grünke S, Felden J, Lichtschlag A, Girnth A-C, de Beer D, Wenzhöfer F, Boetius A (2011) Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea). Geobiology 9:330–348
PubMed Google Scholar
Grünke S, Lichtschlag A, de Beer D, Felden J, Salman V, Ramette A, Schulz-Vogt HN, Boetius A (2012) Mats of psychrophilic thiotrophic bacteria associated with cold seeps of the Barents Sea. Biogeosciences 9:2947–2960
Google Scholar
Güde H, Strohl WR, Larkin JM (1981) Mixotrophic and heterotrophic growth of Beggiatoa alba in continuous culture. Arch Microbiol 129:357–360
PubMed Google Scholar
Gundersen JK, Jørgensen BB, Larsen E, Jannasch HW (1992) Mats of giant sulphur bacteria on deep-sea sediments due to fluctuating hydrothermal flow. Nature 360:454–455
Google Scholar
Hagen KD, Nelson DC (1996) Organic carbon utilization by obligately and facultatively autotrophic Beggiatoa strains in homogeneous and gradient cultures. Appl Environ Microbiol 62:947–953
PubMed CAS PubMed Central Google Scholar
Hagen KD, Nelson DC (1997) Use of reduced sulfur compounds by Beggiatoa spp.: enzymology and physiology of marine freshwater strains in homogeneous and gradient cultures. Appl Environ Microbiol 63:3957–3964
PubMed CAS PubMed Central Google Scholar
Head IM, Gray ND, Clarke KJ, Pickup RW, Jones JG (1996) The phylogenetic position and ultrastructure of the uncultured bacterium Achromatium oxaliferum. Microbiology 142:2341–2354
PubMed CAS Google Scholar
Heijs SK, Damste JSS, Forney LJ (2005) Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea. FEMS Microbiol Ecol 54:47–56
PubMed CAS Google Scholar
Hinck S, Neu TR, Lavik G, Mussmann M, De Beer D, Jonkers HM (2007) Physiological adaptation of a nitrate-storing Beggiatoa sp. to diel cycling in a phototrophic hypersaline mat. Appl Environ Microbiol 73:7013–7022
PubMed CAS PubMed Central Google Scholar
Hinck S, Mussmann M, Salman V, Neu TR, Lenk S, de Beer D, Jonkers HM (2011) Vacuolated Beggiatoa-like filaments from different hypersaline environments form a novel genus. Environ Microbiol 13:3194–3205
PubMed Google Scholar
Hinze G (1901) Über den Bau der Zellen von Beggiatoa mirabilis Cohn. Ber Dtsch Bot Ges 19:369–374
Google Scholar
Hinze G (1903) Thiophysa volutans, ein neues Schwefelbakterium. Ber Dtsch Bot Ges 21:309–316
Google Scholar
Høgslund S, Revsbech NP, Kuenen JG, Jørgensen BB, Gallardo VA, van de Vossenberg J, Nielsen JL, Arning ET, Nielsen LP (2009) Physiology and behaviour of marine Thioploca. ISME J 3:647–657
PubMed Google Scholar
Høgslund S, Nielsen JL, Nielsen LP (2010) Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments. FEMS Microbiol Ecol 73:110–120
PubMed Google Scholar
Holmkvist L, Arning ET, Küster-Heins K, Vandieken V, Peckmann J, Zabel M, Jørgensen BB (2010) Phosphate geochemistry, mineralization processes, and Thioploca distribution in shelf sediments off central Chile. Mar Geol 41:19–28
Google Scholar
Howarth R, Unz RF, Seviour EM, Seviour RJ, Blackall LL, Pickup RW, Jones JG, Yaguchi J, Head IM (1999) Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov. Int J Syst Bacteriol 49:1817–1827
PubMed CAS Google Scholar
Hüttel M, Forster S, Klöser S, Fossing H (1996) Vertical migration in these sediment-dwelling sulfur bacteria Thioploca spp. in overcoming diffusion limitations. Appl Environ Microbiol 62:1863–1872
Google Scholar
Jannasch HW, Nelson DC, Wirsen CO (1989) Massive natural occurrence of unusually large bacteria (Beggiatoa spp.) at a hydrothermal deep-sea vent site. Nature 342:834–836
CAS Google Scholar
Jewell T, Huston SL, Nelson DC (2008) Methylotrophy of freshwater Beggiatoa alba strains. Appl Environ Microbiol 74:5575–5578
PubMed CAS PubMed Central Google Scholar
Jørgensen BB (1977) Distribution of colorless sulfur bacteria (Beggiatoa spp.) in a coastal marine sediment. Mar Biol 41:19–28
Google Scholar
Jørgensen BB (1982) Ecology of the bacteria of the sulphur cycle with special reference to anoxic-oxic interface environments. Phil Trans R Soc Lond B 298:543–561
Google Scholar
Jørgensen BB, Revsbech NP, Blackburn TH, Cohen Y (1979) Diurnal cycle of oxygen and sulfide microgradients and microbial photosynthesis in a cyanobacterial mat. Appl Environ Microbiol 38:46–58
PubMed PubMed Central Google Scholar
Jørgensen BB, Revsbech NP (1983) Colorless sulfur bacteria, Beggiatoa spp. and Thiovulum spp., in O₂ and H₂S microgradients. Appl Environ Microbiol 45:1261–1270
PubMed PubMed Central Google Scholar
Jørgensen BB, DesMarais DJ (1986) Competition for sulfide among colorless and purple sulfur bacteria in cyanobacterial mats. FEMS Microbiol Ecol 38:179–186
PubMed Google Scholar
Jørgensen BB, Gallardo VA (1999) Thioploca spp: filamentous sulfur bacteria with nitrate vacuoles. FEMS Microbiol Ecol 28:301–313
Google Scholar
Jørgensen BB, Teske A, Ahmad A (2005) Genus VII Thioploca Lauterborn. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of determinative bacteriology, vol 2, 2nd edn. Springer, New York, pp 171–178
Google Scholar
Jørgensen BB, Dunker R, Grünke S, Roy H (2010) Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 degrees N). FEMS Microbiol Ecol 73:500–513
PubMed Google Scholar
Joshi MM, Hollis JP (1976) Rapid enrichment of Beggiatoa from soil. J Appl Microbiol 40:223–224
CAS Google Scholar
Joshi MM, Hollis JP (1977) Interaction of Beggiatoa and rice plant: detoxification of hydrogen sulfide in the rice rhizosphere. Science 195:179–180
PubMed CAS Google Scholar
Kalanetra KM, Huston SL, Nelson DC (2004) Novel, attached, sulfur-oxidizing bacteria at shallow hydrothermal vents possess vacuoles not involved in respiratory nitrate accumulation. Appl Environ Microbiol 70:7487–7496
PubMed CAS PubMed Central Google Scholar
Kalanetra KM, Joye SB, Sunseri NR, Nelson DC (2005) Novel vacuolated sulfur bacteria from the Gulf of Mexico reproduce by reductive division in three dimensions. Environ Microbiol 7:1451–1460
PubMed CAS Google Scholar
Kalanetra KM, Nelson DC (2010) Vacuolate-attached filaments: highly productive Ridgeia piscesae epibionts at the Juan de Fuca hydrothermal vents. Mar Biol 157:791–800
PubMed PubMed Central Google Scholar
Kamp A, Stief S, Schulz-Vogt HN (2006) Anaerobic sulfide oxidation with nitrate by a freshwater Beggiatoa enrichment culture. Appl Environ Microbiol 72:4755–4760
PubMed CAS PubMed Central Google Scholar
Kamp A, Roy H, Schulz-Vogt HN (2008) Video-supported analysis of Beggiatoa filament growth, breakage, and movement. Microb Ecol 56:484–491
PubMed PubMed Central Google Scholar
Klas Z (1937) Über den Formenkreis von Beggiatoa mirabilis. Arch Mikrobiol 8:312–320
Google Scholar
Kojima H, Teske A, Fukui M (2003) Morphological and phylogenetic characterizations of freshwater Thioploca species from Lake Biwa, Japan, and Lake Constance, Germany. Appl Environ Microbiol 69:390–398
PubMed CAS PubMed Central Google Scholar
Kojima H, Fukui M (2003) Phylogenetic analysis of Beggiatoa spp. from organic rich sediment of Tokyo Bay, Japan. Water Res 37:3216–3223
PubMed CAS Google Scholar
Kojima H, Koizumi Y, Fukui M (2006) Community structure of bacteria associated with sheaths of freshwater and brackish Thioploca species. Microb Ecol 52:765–773
PubMed Google Scholar
Kojima H, Nakajima T, Fukui M (2007) Carbon source utilization and accumulation of respiration-related substances by freshwater Thioploca species. FEMS Microbiol Ecol 59:23–31
PubMed CAS Google Scholar
Kolkwitz R (1912) Über die Schwefelbakterie Thioploca ingrica Wislouch. Ber Deutsch Bot Ges 30:662–666
Google Scholar
Kolkwitz R (1918) Über die Schwefelbakterien-Flora des Solgrabens von Artern. Ber Deutsch Bot Ges 36:374–380
Google Scholar
Koppe F (1924) Die Schlammflora der ostholsteinischen Seen und des Bodensees. Arch Hydrobiol 14:619–672
Google Scholar
Kowallik U, Pringsheim EG (1966) The oxidation of hydrogen sulfide by Beggiatoa. Am J Bot 53:801–806
CAS Google Scholar
Lane DJ, Harrison AP, Stahl DA, Pace B, Giovannoni SJ, Olsen GJ, Pace NR (1992) Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J Bacteriol 174:269–278
PubMed CAS PubMed Central Google Scholar
Larkin JM, Henk MC, Aharon P (1994) Beggiatoa in microbial mats at hydrocarbon vents in the Gulf of Mexico and Warm Mineral Springs, Florida. Geo-Mar Lett 14:97–103
CAS Google Scholar
Larkin JM, Henk MC (1989) Is “hollowness” an adaptation of large prokaryotes to their largeness? Microbiol Lett 42:69–72
Google Scholar
Larkin JM, Henk MC (1996) Filamentous sulfide-oxidizing bacteria at hydrocarbon seeps of the Gulf of Mexico. Microsc Res Tech 33:23–31
PubMed CAS Google Scholar
Larkin LM, Strohl NR (1983) Beggiatoa, Thiothrix and Thioploca. Annu Rev Microbiol 37:341–367
PubMed CAS Google Scholar
Laue BE, Nelson DC (1994) Characterization of the gene encoding the autotrophic ATP sulfurylase from the bacterial endosymbiont of the hydrothermal vent tube worm Riftia pachyptila. J Bacteriol 176:3723–3729
PubMed CAS PubMed Central Google Scholar
Lauterborn R (1907) Eine neue Gattung der Schwefelbakterien (Thioploca schmidlei nov. gen. nov. spec.). Ber Dtsch Bot Ges 25:238–242
Google Scholar
Lawry NH, Jani V, Jensen TE (1981) Identification of the sulfur inclusion body in Beggiatoa alba B18LD by energy-dispersive X-ray microanalysis. Curr Microbiol 6:71–74
CAS Google Scholar
Leadbetter ER (1974) Family II. Beggiatoaceae. In: Buchanan RE, Gibbons NE (eds) Bergey’s manual of determinative bacteriology, 8th edn. Williams & Wilkins, Baltimore, pp 112–116
Google Scholar
Lichtschlag A, Felden J, Brüchert V, Boetius A, de Beer D (2010) Geochemical processes and chemosynthetic primary production in different thiotrophic mats of the Håkon Mosby mud volcano (Barents Sea). Limnol Oceanogr 55:931–949
CAS Google Scholar
Lloyd KG, Albert DB, Biddle JF, Chanton JP, Pizarro O, Teske A (2010) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One 5:e8738
PubMed PubMed Central Google Scholar
Macalady JL, Lyon EH, Koffman B, Albertson LK, Meyer K, Galdenzi S, Mariani S (2006) Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Appl Environ Microbiol 72:5596–5609
PubMed CAS PubMed Central Google Scholar
Macalady JL, Dattagupta S, Schaperdoth I, Jones DS, Druschel GK, Eastman D (2008) Niche differentiation among sulfur-oxidizing bacterial populations in cave waters. ISME J 2:590–601
PubMed CAS Google Scholar
MacGregor BJ, Biddle JF, Siebert JR, Staunton E, Hegg EL, Matthysse AG, Teske A (2013a) Why orange Guaymas Basin Beggiatoa (Maribeggiatoa) spp. are orange: single-filament genome-enabled identification of an abundant octaheme cytochrome with hydroxyl-amine oxidase, hydrazine oxidase, and nitrite reductase activities. Appl Environ Microbiol 79:1183–1190
PubMed CAS PubMed Central Google Scholar
MacGregor BJ, Biddle JF, Teske A (2013b) Mobile elements in a single-filament orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. draft genome: evidence for genetic exchange with cyanobacteria. Appl Environ Microbiol 79:3974–3985
PubMed CAS PubMed Central Google Scholar
MacGregor BJ, Biddle JF, Harbort C, Matthysse AG, Teske A (2013c) Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. filament. Mar Genomics 11:53–65
Google Scholar
Maier S, Murray RGE (1965) The fine structure of Thioploca ingrica and a comparison with Beggiatoa. Can J Microbiol 11:645–655
PubMed CAS Google Scholar
Maier S (1980) Growth of Thioploca ingrica in a mixed culture system. Ohio J Sci 80:30–32
Google Scholar
Maier S (1984) Description of Thioploca ingrica sp. nov., nom. rev. Int J Syst Bacteriol 34:344–345
Google Scholar
Maier S (1989) Genus III. Thioploca Lauterborn 1907. In: Bergey’s manual of systematic bacteriology. Williams and Wilkins, Baltimore, pp 2101–2105
Google Scholar
Maier S, Preissner WC (1979) Occurrence of Thioploca in lake constance and lower saxony, Germany. Microb Ecol 5:117–119
PubMed CAS Google Scholar
Maier S, Gallardo VA (1984a) Nutritional characteristics of two marine thioplocas determined by autoradiography. Arch Microbiol 139:218–220
CAS Google Scholar
Maier S, Gallardo VA (1984b) Thioploca araucae sp. nov., and Thioploca chileae sp. nov. Int J Syst Bacteriol 34:414–418
Google Scholar
Maier S, Völker H, Beese HM, Gallardo VA (1990) The fine structure of Thioploca araucae and Thioploca chileae. Can J Microbiol 36:438–448
Google Scholar
Mattison RG, Abbiati M, Dando PR, Fitzsimons MF, Pratt SM, Southward AJ, Southward EC (1998) Chemoautotrophic microbial mats in submarine caves with hydrothermal sulphidic springs at Cape Palinuro, Italy. Microb Ecol 35:58–71
PubMed CAS Google Scholar
McHatton SC, Barry JP, Jannasch HW, Nelson DC (1996) High nitrate concentrations in vacuolate, autotrophic marine Beggiatoa. Appl Environ Microbiol 62:954–958
PubMed CAS PubMed Central Google Scholar
McKay LJ, MacGregor BJ, Biddle JF, Mendlovitz HP, Hoer D, Lipp JS, Lloyd KG, Teske AP (2012) Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments. Deep-Sea Res I 67:21–31
CAS Google Scholar
Mendell JE, Clements KD, Choat JH, Angert ER (2008) Extreme polyploidy in a large bacterium. Proc Natl Acad Sci U S A 105:6730–6734
PubMed CAS PubMed Central Google Scholar
Meyer B, Imhoff JF, Küver J (2007) Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria—evolution of the Sox sulfur oxidation enzyme system. Environ Microbiol 9:2957–2977
PubMed CAS Google Scholar
Mezzino M, Strohl WR, Larkin JM (1984) Characterization of Beggiatoa alba. Arch Microbiol 137:139–144
CAS Google Scholar
Migula W (1894) Über ein neues System der Bakterien. Arbeit aus dem bakteriologischen Institut der technischen Hochschule zu Karlsruhe, vol 1, pp 235–238
Google Scholar
Minges CG, Titus JA, Strohl WR (1983) Plasmid DNA in colourless filamentous gliding bacteria. Arch Microbiol 134:38–44
PubMed CAS Google Scholar
Mills HJ, Martinez RJ, Story S, Sobecky PA (2004) Identification of members of the metabolically active microbial populations associated with Beggiatoa species mat communities from Gulf of Mexico cold-seep sediments. Appl Environ Microbiol 70(9):5447–5458
PubMed CAS PubMed Central Google Scholar
Mitchell R, Chet I (1975) Bacterial attack of corals in polluted seawater. Mar Biol 2:227–233
CAS Google Scholar
Møller MM, Nielsen LP, Jørgensen BB (1985) Oxygen responses and mat formation of Beggiatoa spp. Appl Environ Microbiol 50:373–382
PubMed PubMed Central Google Scholar
Morita RY, Stave PW (1963) Electron micrograph of an ultrathin section of Beggiatoa. J Bacteriol 85:940–942
PubMed CAS PubMed Central Google Scholar
Mussmann M, Schulz HN, Strotmann B, Kjaer T, Nielsen LP, Rosselló- Mora RA, Amann RI, Jørgensen BB (2003) Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments. Environ Microbiol 5:523–533
PubMed CAS Google Scholar
Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJH, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD (2007) Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 5:e230. doi:10.1371/journal.pbio.0050230
PubMed PubMed Central Google Scholar
Muyzer G, Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci Technol 32:1–9
CAS Google Scholar
Namsaraev BB, Dulov LE, Dubinina GA, Zemskaya TI, Granina LZ, Karabanov EV (1994) Bacterial synthesis and destruction of organic matter in microbial mats of Lake Baikal. Microbiology 63:193–197
Google Scholar
Neira C, Sellanes J, Soto A, Gutiérrez D, Gallardo VA (2001) Meiofauna and sedimentary organic matter off central Chile: response to changes caused by the 1997–1998 El Niño. Oceanol Acta 24:313–328
CAS Google Scholar
Nelson DC (1992) The genus Beggiatoa. In: Balows A, Trueper HG, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 3171–3180
Google Scholar
Nelson DC, Castenholz RW (1981a) Use of reduced sulfur compounds by Beggiatoa sp. J Bacteriol 147:140–154
PubMed CAS PubMed Central Google Scholar
Nelson DC, Castenholz RW (1981b) Organic nutrition of Beggiatoa sp. J Bacteriol 147:236–247
PubMed CAS PubMed Central Google Scholar
Nelson DC, Castenholz RW (1982) Light responses of Beggiatoa. Arch Microbiol 131:146–155
Google Scholar
Nelson DC, Waterbury JB, Jannasch HW (1982) Nitrogen-fixation and nitrate utilization by marine and freshwater Beggiatoa. Arch Microbiol 133:172–177
CAS Google Scholar
Nelson DC, Jannasch HW (1983) Chemoautotrophic growth of a marine Beggiatoa in sulfide-gradient cultures. Arch Microbiol 136:262–269
CAS Google Scholar
Nelson DC, Revsbech NP, Jørgensen BB (1986a) Microoxic-anoxic niche of Beggiatoa spp.: microelectrode survey of marine and freshwater strains. Appl Environ Microbiol 52:161–168
PubMed CAS PubMed Central Google Scholar
Nelson DC, Jørgensen BB, Revsbech NP (1986b) Growth pattern and yield of a chemoautotrophic Beggiatoa sp. in oxygen-sulfide microgradients. Appl Environ Microbiol 52:225–233
PubMed CAS PubMed Central Google Scholar
Nelson DC, Wirsen CO, Jannasch HW (1989) Characterization of large, autotrophic Beggiatoa spp. abundant at hydrothermal vents of the Guaymas Basin. Appl Environ Microbiol 55:2909–2917
PubMed CAS PubMed Central Google Scholar
Nemoto F, Kojima H, Fukui M (2011) Diversity of freshwater Thioploca species and their specific association with filamentous bacteria of the phylum Chloroflexi. Microb Ecol 62:753–764
PubMed Google Scholar
Nemoto F, Kojima H, Ohtaka A, Fukui M (2012) Filamentous sulfur-oxidizing bacteria of the genus Thioploca from Lake Tonle Sap in Cambodia. Aquat Microb Ecol 66:295–300
Google Scholar
Niemann H, Lösekann T, de Beer D, Elvert M, Nadalig T, Knittel K, Amann R, Sauter EJ, Schlüter M, Klages M, Foucher JP, Boetius A (2006) Novel microbial communities of the Håkon Mosby mud volcano and their role as a methane sink. Nature 443:854–858
PubMed CAS Google Scholar
Nikolaus R, Ammerman JW, MacDonald IR (2003) Distinct pigmentation and trophic modes in Beggiatoa from hydrocarbon seeps in the Gulf of Mexico. Aquat Microb Ecol 32:85–93
Google Scholar
Nishino M, Fukui M, Nakajima T (1998) Dense mats of Thioploca, gliding filamentous sulfur-oxidizing bacteria in Lake Biwa, central Japan. Water Res 32:953–957
CAS Google Scholar
Otte S, Kuenen GJ, Nielsen LP, Paerl HW, Zopfi J, Schulz HN, Teske A, Strotmann B, Gallardo VA, Jørgensen BB (1999) Nitrogen, carbon and sulfur metabolism in natural Thioploca samples. Appl Environ Microbiol 65:3148–3157
PubMed CAS PubMed Central Google Scholar
Orphan VJ, House CH, Hinrichs K-U, McKeegan KD, DeLong EF (2002) Multiple groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci U S A 99:7663–7668
PubMed CAS PubMed Central Google Scholar
Pasteris JD, Freeman JJ, Goffredi SK, Buck K (2001) Raman spectroscopic and laser scanning confocal microscopic analysis of sulfur in living sulfur-precipitating marine bacteria. Chem Geol 180:3–18
CAS Google Scholar
Patritskaya VY, MYu G, Muntyan MS, Dubinina GA (2001) Lithoautotrophic growth of the freshwater colorless sulfur bacterium Beggiatoa ‘leptomitiformis’ D-402. Microbiology 70:145–150 (Engl. translation of Mikrobiologiya)
CAS Google Scholar
Paull CK, Chanton JP, Neumann AC, Coston JA, Martens CS (1992) Indicators of methane-derived carbonates and chemosynthetic organic carbon deposits: examples from the Florida Escarpment. Palaios 7:361–375
Google Scholar
Pfennig N, Biebl H (1981) The dissimilatory sulfur-reducing bacteria. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes, 1st edn. Springer, Berlin/Heidelberg, pp 941–942
Google Scholar
Pitts G, Allam AI, Hollis JP (1972) Beggiatoa: occurrence in the rice rhizosphere. Science 178:990–992
PubMed CAS Google Scholar
Polman JK, Larkin JM (1988) Properties of in vivo nitrogenase in Beggiatoa alba. Arch Microbiol 150:126–130
CAS Google Scholar
Prange A, Chauvistré R, Modrow H, Hormes J, Trüper HG, Dahl C (2002) Quantitative speciation of sulfur in bacterial sulfur globules: x-ray absorption spectroscopy reveals at least three different species of sulfur. Microbiology 148:267–276
PubMed CAS Google Scholar
Preisler A, de Beer D, Lichtschlag A, Lavik G, Boetius A, Jørgensen BB (2007) Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. ISME J 1:341–353
PubMed CAS Google Scholar
Prince RC, Stokley KE, Haith CE, Jannasch HW (1988) The cytochromes of a marine Beggiatoa. Arch Microbiol 150:193–196
CAS Google Scholar
Pringsheim EG, Wiessner W (1963) Minimum requirement for heterotrophic growth and reserve substance in Beggiatoa. Nature 197:102
Google Scholar
Pringsheim EG (1964) Heterotrophism and species concepts in Beggiatoa. Am J Bot 51:898–913
Google Scholar
Pringsheim EG (1967) Die Mixotrophie von Beggiatoa. Arch Mikrobiol 59:247–254
PubMed CAS Google Scholar
Prokopenko MG, Hammond DE, Berelson WM, Bernhard JM, Stott L, Douglas R (2006) Nitrogen cycling in the sediments of Santa Barbara Basin and the Eastern Subtropical North Pacific: nitrogen isotopes, diagenesis, and possible chemosymbiosis between two lithotrophs (Thioploca and Anammox)—“riding on a glider”. Earth Planet Sci Lett 242:186–204
CAS Google Scholar
Prokopenko MG, Sigman DM, Berelson WM, Hammond DE, Barnett B, Chong L, Townsend-Small A (2011) Denitrification in anoxic sediments supported by biological nitrate transport. Geochim Cosmochim Acta 75:7180–7199
CAS Google Scholar
Prokopenko MG, Hirst MB, De Brabandere L, Lawrence DJP, Berelson WM, Granger J, Chang BX, Dawson S, Crane EJ III, Chong L, Thamdrup B, Townsend-Small A, Sigman DM (2013) Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia. Nature 500:194–200
PubMed CAS Google Scholar
Reichenbach H, Dworkin M (1981) Introduction to the gliding bacteria. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes, 1st edn. Springer, Berlin/Heidelberg, pp 315–327
Google Scholar
Roa R, Gallardo VA, Ernst B, Baltazar M, Cañete JI, Enríquez-Brionnes S (1995) Nursery ground, age structure and abundance of the juvenile squat lobster Pleuroncodes monodon on the continental shelf off central Chile. Mar Ecol Prog Ser 116:47–54
Google Scholar
Robinow C, Angert ER (1998) Nucleoids and coated vesicles of “Epulopiscium” spp. Arch Microbiol 170:227–253
PubMed CAS Google Scholar
Rosenberg R, Diaz RJ (1993) Sulfur bacteria (Beggiatoa spp.) mats indicate hypoxic conditions in the inner Stockholm archipelago. Ambio 22:32–36
Google Scholar
Salman V, Amann R, Girnth A-C, Polerecky L, Bailey JV, Høgslund S, Jessen G, Pantoja S, Schulz-Vogt HN (2011) A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. Syst Appl Microbiol 34:243–259
PubMed CAS Google Scholar
Salman V, Amann R, Shub DA, Schulz-Vogt HN (2012) Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria. Proc Natl Acad Sci USA 109:4203–4208
PubMed CAS PubMed Central Google Scholar
Salman V, Bailey JV, Teske A (2013) Phylogenetic and morphological complexity of giant sulfur bacteria. Antonie Van Leeuwenhoek 104:169–186
PubMed CAS Google Scholar
Saravanakumar C, Dineshkumar N, Alavandi SV, Salman V, Poornima M, Kalaimani N (2012) Enrichment and identification of large filamentous sulfur bacteria related to Beggiatoa species from brackishwater ecosystems of Tamil Nadu along the southeast coast of India. Syst Appl Microbiol 35:396–403
PubMed CAS Google Scholar
Sassen R, MacDonald IR, Requejo AG, Guinasso NL, Kennicutt MC II, Sweet ST, Brooks JM (1994) Organic geochemistry of sediments from chemosynthetic communities, Gulf of Mexico slope. Geo-Mar Lett 14:110–119
CAS Google Scholar
Sayama M (2001) Presence of nitrate-accumulating sulfur bacteria and their influence on nitrogen cycling in a shallow coastal marine sediment. Appl Environ Microbiol 67:3481–3487
PubMed CAS PubMed Central Google Scholar
Sayama N, Risgaard-Petersen N, Nielsen LP, Fossing H, Christensen PB (2005) Impact of bacterial NO₃ ⁻ transport on sediment biogeochemistry. Appl Environ Microbiol 71:7575–7577
PubMed CAS PubMed Central Google Scholar
Schlösser UG (1982) Sammlung von Algenkulturen. Ber Dtsch Bot Ges 95:181–276
Google Scholar
Schmaljohann R, Drews M, Walter S, Linke P, Von Rad U, Imhoff JF (2001) Oxygen minimum zone sediments in the northeastern Arabian Sea off Pakistan: a habitat for the bacterium Thioploca. Mar Ecol Prog Ser 211:27–42
CAS Google Scholar
Schmidt TM, Vinci VA, Strohl WR (1986) Protein synthesis by Beggiatoa alba B18LD in the presence and absence of sulfide. Arch Microbiol 144:158–162
CAS Google Scholar
Schmidt TM, Arieli B, Cohen Y, Padan E, Strohl WR (1987) Sulfur metabolism of Beggiatoa alba. J Bacteriol 169:5466–5472
PubMed CAS PubMed Central Google Scholar
Schubert CJ, Ferdelman TG, Strotmann B (2000) Organic matter composition and sulfate reduction rates in sediments off Chile. Org Geochem 31:351–361
CAS Google Scholar
Schulz HN (2006) The genus Thiomargarita. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, vol 6, 3rd edn. Springer, New York, pp 1156–1163
Google Scholar
Schulz HN, de Beer D (2002) Uptake rates of oxygen and sulfide measured with individual Thiomargarita namibiensis cells by using microelectrodes. Appl Environ Microbiol 68:5746–5749
PubMed CAS PubMed Central Google Scholar
Schulz HN, Jørgensen BB, Fossing HA, Ramsing NB (1996) Community structure of filamentous, sheath-building sulfur bacteria, Thioploca spp., off the coast of Chile. Appl Environ Microbiol 62:1855–1862
PubMed CAS PubMed Central Google Scholar
Schulz HN, Strotmann B, Gallardo VA, Jørgensen BB (2000) Population study of the filamentous sulfur bacteria Thioploca spp. off the Bay of Concepción, Chile. Mar Ecol Prog Ser 200:117–126
CAS Google Scholar
Schulz HN, Brinkhoff T, Ferdelman TG, Marine MH, Teske A, Jørgensen BB (1999) Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284:493–495
PubMed CAS Google Scholar
Schulz HN, Jørgensen BB (2001) Big bacteria. Annu Rev Microbiol 55:105–137
PubMed CAS Google Scholar
Schulz HN, Schulz HD (2005) Large sulfur bacteria and the formation of phosphorite. Science 307:416–418
PubMed CAS Google Scholar
Schwedt A, Kreutzmann A-C, Polerecky L, Schulz-Vogt HN (2012) Sulfur respiration in a marine chemolithoautotrophic Beggiatoa strain. Front Microbiol 2:276
PubMed PubMed Central Google Scholar
Scotten HL, Stokes JL (1962) Isolation and properties of Beggiatoa. Arch Mikrobiol 42:353–368
Google Scholar
Sekar R, Mills DK, Remily ER, Voss JD, Richardson LL (2006) Microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased Siderastrea siderea. Appl Environ Microbiol 72:5963–5973
PubMed CAS PubMed Central Google Scholar
Skerman VBD, Dementjeva G, Carey BJ (1957) Intracellular deposition of sulfur by Spaerotilus natans. J Bacteriol 73:507–512
Google Scholar
Smith CR, Kukert H, Wheatcroft RA, Jumars PA, Deming JW (1989) Vent fauna on whale remains. Nature 341:27–28
Google Scholar
Stahl DA, Lance DJ, Olsen GJ, Heller DJ, Schmidt TM, Pace NR (1987) Phylogenetic analysis of certain sulfide-oxidizing and related morphologically conspicuous bacteria by 5S ribosomal ribonucleic acid sequences. Int J Syst Bacteriol 37:116–122
CAS Google Scholar
Stierl M, Stumpf P, Udwari D, Güta R, Hagedorn R, Losi A, Gärtner W, Petereit L, Efetova M, Schwarzel M, Örtner TG, Nagel G, Hegemann P (2011) Light modulation of cellular camp by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. J Biol Chem 286:1181–1188
PubMed CAS PubMed Central Google Scholar
Strohl WR, Schmidt TM, Lawry NH, Mezzino MJ, Larkin JM (1986) Characterization of Vitreoscilla beggiatoides and Vitreoscilla filiformis sp. nov., nom. rev., and comparison with Vitreoscilla stercoraria and Beggiatoa alba. Int J Syst Bacteriol 36:302–313
CAS Google Scholar
Strohl WR, Larkin JM (1978a) Enumeration, isolation, and characterization of Beggiatoa from freshwater sediments. Appl Environ Microbiol 36:755–770
PubMed CAS PubMed Central Google Scholar
Strohl WR, Larkin JM (1978b) Cell division and trichome breakage in Beggiatoa. Curr Microbiol 1:151–155
PubMed CAS Google Scholar
Strohl WR, Howard KS, Larkin JM (1982) Ultrastructure of Beggiatoa alba strain B15LD. J Gen Microbiol 128:73–84
Google Scholar
Strohl WR, Cannon GC, Shively JM, Gude H, Hook LA, Lane CM, Larkin JM (1981a) Heterotrophic carbon metabolism by Beggiatoa alba. J Bacteriol 148:572–583
PubMed CAS PubMed Central Google Scholar
Strohl WR, Geffers I, Larkin JM (1981b) Structure of the sulfur inclusion envelopes from four Beggiatoas. Curr Microbiol 6:75–79
Google Scholar
Strohl WR, Schmidt TM (1984) Mixotrophy of colorless, sulfide-oxidizing gliding bacteria Beggiatoa and Thiothrix. In: Strohl WR, Tuovinen OH (eds) Microbial chemoautotrophy. Ohio University Press, Columbus, pp 79–95
Google Scholar
Strohl WR (1989) Family I. Beggiatoaceae. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 3, 1st edn. Williams & Wilkins, Baltimore, pp 2089–2106
Google Scholar
Sweerts JPRA, Beer DD, Nielsen LP, Verdouw H, Heuvel JCV, Cohen Y, Cappenberg TE (1990) Denitrification by sulfur oxidizing Beggiatoa app. mats on freshwater sediments. Nature 334:762–763
Google Scholar
Teske A, Ramsing NB, Küver J, Fossing H (1995) Phylogeny of Thioploca and related filamentous sulfide-oxidizing bacteria. Syst Appl Microbiol 18:517–526
Google Scholar
Teske A, Sogin ML, Nielsen LP, Jannasch HW (1999) Phylogenetic position of a large marine Beggiatoa. Syst Appl Microbiol 22:39–44
PubMed CAS Google Scholar
Teske A, Stahl DA (2002) Microbial mats and biofilms: evolution, structure and function of fixed microbial communities. In: Staley JT, Schleifer K-H (eds) Biodiversity of microbial life: foundation of earth’s biosphere. Wiley-Liss, New York, pp 49–100
Google Scholar
Teske A, Nelson DC (2006) The genera Beggiatoa and Thioploca. In: Dworkin M, Schleifer K-H (eds) The prokaryotes, vol 6, 3rd edn. Springer, New York, pp 784–810
Google Scholar
Teske A, Jørgensen BB, Gallardo VA (2009) Filamentous bacteria inhabiting the sheaths of marine Thioploca spp. on the Chilean continental shelf. FEMS Microbiol Ecol 68:164–172
PubMed CAS Google Scholar
Thamdrup B, Canfield DE (1996) Pathways of carbon oxidation in continental margin sediments off central Chile. Limnol Oceanogr 41:1629–1650
PubMed CAS Google Scholar
Trevisan V (1842) Prospetto della flora Euganea. Coi Tipi del Seminario, Padua, pp 1–68
Google Scholar
Uphof JCT (1927) Zur Ökologie der Schwefelbakterien in den Schwefelquellen Mittelfloridas. Arch Hydrobiol 18:71–84
Google Scholar
Vallius H (2006) Permanent seafloor anoxia in coastal basins of the northwestern Gulf of Finland, Baltic Sea. Ambio 35:105–108
PubMed CAS Google Scholar
Van Gaever S, Raes M, Pasotti F, Vanreusel A (2010) Spatial scale and habitat-dependent diversity patterns in nematode communities in three seepage related sites along the Norwegian Sea margin. Mar Biol 31:66–77
Google Scholar
Van Niel CB (1948) Family A. Achromatiaceae Massart. In: Breed RS, Murray EGD, Hitchens AP (eds) Bergey’s manual of determinative bacteriology, 6th edn. Williams and Wilkins, Baltimore, pp 997–999
Google Scholar
Vargas A, Strohl WR (1985a) Ammonia assimilation and metabolism by Beggiatoa alba. Arch Microbiol 142:275–278
CAS Google Scholar
Vargas A, Strohl WR (1985b) Utilization of nitrate by Beggiatoa alba. Arch Microbiol 142:279–284
CAS Google Scholar
Vaucher JP (1803) Histoire des conferves d’eau douce, contenant leurs différents modes de reproduction, et la description de leurs principales espèces. Paschoud, Geneva
Google Scholar
Weeks SJ, Currie B, Bakun A (2002) Massive emissions of toxic gas in the Atlantic. Nature 415:493–494
PubMed CAS Google Scholar
Weeks SJ, Currie B, Bakun A, Peard KR (2004) Hydrogen sulphide eruptions in the Atlantic Ocean off southern Africa: implications of a new view based on SeaWiFS satellite imagery. Deep-Sea Res I 51:153–172
CAS Google Scholar
Williams LA, Reimers C (1983) Role of bacterial mats in oxygen-deficient marine basins and coastal upwelling regimes: preliminary report. Geology 11:267–269
Google Scholar
Williams TM, Unz RF (1985) Filamentous sulfur bacteria of activated sludge: characterization of Thiothrix, Beggiatoa, and Eikelboom Type 021N strains. Appl Environ Microbiol 49:887–898
PubMed CAS PubMed Central Google Scholar
Winogradsky S (1887) Über Schwefelbakterien. Botanische Zeitung 45:489–507, 529–539, 545–559, 569–575, 585–594, 606–610
Google Scholar
Wirsen CO, Jannasch HW, Molyneaux SJ (1992) Non-symbiotic microbiota as associated with chemosynthetic communities. In: MacDonald IR (ed) Chemosynthetic ecosystems study, vol II: technical report. Prepared by Geochemical and Environmental Research Group. U.S. Department of the Interior, Minerals Management Service, Gulf of Mexico OCS Regional Office, New Orleans, pp 6.1–6.13
Google Scholar
Wislouch SM (1912) Thioploca ingrica nov. sp. Ber Dtsch Bot Ges 30:470–474
Google Scholar
Yekta SS, Rahm L (2011) A model study of the effects of sulfide-oxidizing bacteria (Beggiatoa spp.) on phosphorus retention processes in hypoxic sediments: implications for phosphorus management in the Baltic Sea. Boreal Environ Res 16:167–184
CAS Google Scholar
Zemskaya TI, Namsaraev BB, Dul’tseva NM, Khanaeva TA, Golobokova LP, Dubinina GA, Dulov LE, Wada E (2001) Ecophysiological characteristics of the mat-forming bacterium Thioploca in bottom sediments of the Frolikha Bay, northern Baikal. Microbiology 70:335–341 (Engl. translation of Mikrobiologiya)
CAS Google Scholar
Zemskaya TI, Chernitsyna SM, Dul’tseva NM, Sergeeva VN, Pogodaeva TV, Namsaraev BB (2009) Colorless sulfur bacteria Thioploca from different sites in Lake Baikal. Microbiology 78:117–124 (Engl. translation of Mikrobiologiya)
CAS Google Scholar
Zhang CL, Huang Z, Cantu J, Pancost RD, Brigmon RL, Lyons TW, Sassen R (2005) Lipid biomarkers and carbon isotope signatures of a microbial (Beggiatoa) mat associated with gas hydrates in the Gulf of Mexico. Appl Environ Microbiol 71:2106–2112
PubMed CAS PubMed Central Google Scholar
Zopfi J, Kjaer T, Nielsen LP, Jørgensen BB (2001) Ecology of Thioploca spp.: nitrate and sulfur storage in relation to chemical microgradients and influence of Thioploca spp. on the sedimentary nitrogen cycle. Appl Environ Microbiol 67:5530–5537
PubMed CAS PubMed Central Google Scholar
Zopfi J, Böttcher ME, Jørgensen BB (2008) Biogeochemistry of sulfur and iron in Thioploca-colonized surface sediments in the upwelling areas off central Chile. Geochim Cosmochim Acta 72:827–843
CAS Google Scholar

Download references

Acknowledgments

The authors of this chapter were supported by NSF (OCE 0647633; MO/MIP 0801741) and by the Deutsche Forschungsgemeinschaft (SA 250/1-1). We thank Jake Bailey, Manabu Fukui, Jan Küver, Ian McDonald, Stefanie Meyer, Marc Mussmann, and Thomas R. Neu for generously providing illustrations. We thank Heide Schulz-Vogt and Victor A. Gallardo for careful edits and suggestions that substantially improved this chapter.

Author information

Authors and Affiliations

Department of Marine Sciences, University of North Carolina at Chapel Hill, 3117B Venable Hall, Chapel Hill, NC, 27599-CB 3300, USA
Andreas Teske & Verena Salman

Authors

Andreas Teske
View author publications
You can also search for this author in PubMed Google Scholar
Verena Salman
View author publications
You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andreas Teske .

Editor information

Editors and Affiliations

Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
Eugene Rosenberg
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
Edward F. DeLong
Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
Edward F. DeLong
Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
Stephen Lory
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Erko Stackebrandt
Laboratory of Microbiology, Institute of Biology, Center for Health Sciences, Federal University of Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil
Fabiano Thompson

Rights and permissions

Reprints and permissions

Copyright information

About this entry

Cite this entry

Teske, A., Salman, V. (2014). The Family Beggiatoaceae . In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38922-1_290

Download citation

DOI: https://doi.org/10.1007/978-3-642-38922-1_290
Published: 11 October 2014
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-38921-4
Online ISBN: 978-3-642-38922-1
eBook Packages: Biomedical and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics

The Family Beggiatoaceae

Abstract

Similar content being viewed by others

Large Sulfur-Oxidizing Bacteria at Gulf of Mexico Hydrocarbon Seeps

Blue-Green Algae (Cyanobacteria) in Rivers

Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments

Keywords

Taxonomy, Historical and Current

Molecular Analyses

Genus Beggiatoa

Beggiatoa alba (Vaucher 1803) Trevisan 1842

Genus Thioploca. Lauterborn 1907

Thioploca schmidlei. Lauterborn 1907

Thioploca ingrica. Maier 1984

“Candidatus Marithioploca”. Salman et al. 2011

“Marithioploca araucae”. Salman et al. 2011

“Marithioploca chileae”. This Publication

Genus Thiomargarita. Schulz et al. 1999

Thiomargarita namibiensis Schulz et al. 1999

“Candidatus Thiomargarita joergensenii” Salman et al. 2011

“Candidatus Thiomargarita nelsonii” Salman et al. 2011

“Candidatus Maribeggiatoa” Salman et al. 2011

“Candidatus Maribeggiatoa vulgaris” Salman et al. 2011

“Candidatus Marithrix” Salman et al. 2011

“Candidatus Marithrix sessilis”Salman et al. 2011

“Candidatus Isobeggiatoa” Salman et al. 2011

“Candidatus Isobeggiatoa divolgata” Salman et al. 2011

“Candidatus Parabeggiatoa” Salman et al. 2011

“Candidatus Parabeggiatoa communis” Salman et al. 2011

“Candidatus Allobeggiatoa” Hinck et al. 2011

“Candidatus Allobeggiatoa salina”Hinck et al. 2011

“Candidatus Halobeggiatoa” Grünke et al. 2012

“Candidatus Halobeggiatoa borealis” Grünke et al. 2012

“Candidatus Thiopilula” Salman et al. 2011

“Candidatus Thiopilula aggregata”Salman et al. 2011

“Candidatus Thiophysa” Salman et al. 2011

“Candidatus Thiophysa hinzei”Salman et al. 2011

Phenotypic Analyses

Phenotypic Characteristics of the Beggiatoaceae

Genus Beggiatoa

Beggiatoa alba

Beggiatoa sp. MS-81-6 and MS-81-1c

Strain 35Flor

Comparative Aspects

Photoresponses of Beggiatoa spp.

Genus Thioploca

Genus Thiomargarita

“Candidatus Marithioploca”

“Candidatus Maribeggiatoa”

“Candidatus Marithrix”

“Candidatus Isobeggiatoa”

“Candidatus Parabeggiatoa”

“Candidatus Allobeggiatoa”

“Candidatus Halobeggiatoa”

“Candidatus Thiopilula”

“Candidatus Thiophysa”

Cell Structure

Vacuolation

Cell Envelope

Cell Inclusions

PHA Inclusions

Sulfur Inclusions

Polyphosphate Inclusions

Isolation, Enrichment, and Maintenance Procedures

Enrichments from Natural Environments

Liquid Media

Isolations on Agar Plates

Isolations and Cultivation in Gradient Media

Coculture and Obligate Associations

Cultivation of Thioploca

Strain Maintenance

Ecology

The Oxygen–Sulfide Interface at the Sediment Surface

The Anoxic, Non-sulfidic Surficial Sediment

Hypersaline Cyanobacterial Mats

Hydrothermal Vents

Hydrocarbon Seeps

Mud Volcanoes

Nearshore Upwelling Areas: The Chilean Continental Shelf

Nearshore Upwelling Areas: The Benguela Upwelling System