Abstract
A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8–3.0 µm in length and 0.4–0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3–90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).
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Introduction
The order Rhodospirillales, a member of the class Alphaproteobacteria belonging to the phylum Pseudomonadota, was first proposed by Pfennig and Trüper (Pfennig and Trüper 1971) to replace the name Athiorhodaceae (Molisch 1907), with Rhodospirillum as the type genus (Molisch 1907). It originally comprised three families, named Chlorobiaceae, Chromatiaceae, and Rhodospirillaceae, there are 12 families with validly published names (https://lpsn.dsmz.de/order/rhodospirillales): Acetobacteraceae (Gillis and De Ley 1980), Azospirillaceae (Hördt et al. 2020), Geminicoccaceae (Proença et al. 2018), Kiloniellaceae (Wiese et al. 2009), Reyranellaceae (Hördt et al. 2020), Rhodospirillaceae (Pfennig and Trüper 1971), Rhodovibrionaceae, Stellaceae, Terasakiellaceae, Thalassobaculaceae, Thalassospiraceae and Zavarziniaceae (Hördt et al. 2020). In 2023, Koziaeva et al. (2023) suggested that the order Rhodospirillales should be split into six more new family-level groups according to phylogenomic analyses, including “Magnetospiraceae” and “Magnetovibrionaceae” separated from the family Thalassospiraceae, “Dongiaceae” and “Niveispirillaceae” separated from the family Rhodospirillaceae, “Fodinicurvataceae” from the family Rhodovibrionaceae and “Oceanibaculaceae” from the family Thalassobaculaceae. Rhodospirillales members are widely distributed in freshwater, soil, seawater, plant root and artificial ecosystems. Most members of this order are Gram-stain-negative, spiral or rod-shaped, non-spore-forming, and obligately aerobic or facultatively anaerobic bacteria with ubiquinone Q-10 as the common major respiratory quinone. The order Rhodospirillales is metabolically diverse group, containing chemoorganoheterotrophs, and photoorganoheterotrophs under anoxic conditions in the light (Hördt et al. 2020)
In recent years, it has revealed that Rhodospirillales members present in the oil reservoir related environments, such as oil-contaminated soil and polluted water (Liu et al. 2015; Abbasian et al. 2016; Elumalai et al. 2021). However, just a few of members belonging to Rhodospirillale have the ability to use alkane as energy source (Wu et al. 2021b). The knowledge about ecological roles of Rhodospirillales in oil reservoir is still limited. Elumalai et al. found Rhodospirillales appears in the biofilm on corroded API 5LX carbon steel in produced water of oil reservoir (Elumalai et al. 2021), implying Rhodospirillales probably related with microbially induced corrosion (MIC). Rhodospirillales members including Rhodospirillaceae and Acetobacteraceae were abundant bacteria in the biofilm on corroded steel coupons and Biodiesel Storage Tanks (Procópio 2020; Stamps et al. 2020), populations of these bacteria were accompanied by a continuous corrosion process over the coupons (López et al. 2002; Moura et al. 2018). Corrosion conducted by microorganisms usually influenced through biofilm formation, sulfur metabolism, corrosive metabolites production (such as inorganic or organic acids, and hydrogen sulfide) (Lv and Du 2018; Moura et al. 2018; Elumalai et al. 2021). Several studies have speculated that Rhodospirillales members participate in MIC by producing acetic acid and biofilms, as well as reducing iron (Chen et al. 2019; Chen and Zhang 2019; Procópio 2020; Stamps et al. 2020). Therefore, Rhodospirillales probably link to the corrosion of oil pipelines and storage tanks, suggesting the importance of isolation Rhodospirillales for investigating their ecological functions in oil reservoir environments. Several species have been isolated from the oil production mixture, oil-contaminated soil or oil reservoir water, such as Roseomonas oleicola (Wu et al. 2021a) and Siccirubricoccus phaeus (Li et al. 2021) of the family Acetobacteraceae, Azospirillum oleiclasticum (Wu et al. 2021b) and Azospirillum rugosum (Young et al. 2008) of the family Azospirillaceae, Oleisolibacter albus (Ruan et al. 2019) and Oleiliquidispirillum nitrogeniifigens (Li et al. 2020) of the family Rhodospirillaceae. All these isolates are mesophilic, aerobic or facultatively anaerobic chemoorganoheterotrophs.
In the present study, one strain, designated Y-P2T, was isolated from the oil sludge collected from Shengli oilfield, China. The polyphasic taxonomic analyses revealed strain Y-P2T represents a novel genus in a new family within the order Rhodospirillales.
Materials and methods
Enrichment and isolation
Strain Y-P2T was obtained from the oil sludge of the Shengli oilfield in PR China (37o54’N, 118o33’E). Approximately 10 g of mixture of oil contaminated soil and oily sludge was inoculated into 50 mL of fresh medium for preparation of pre-enrichment culture, which performed as 25 °C. The pre-reduced mineral medium used for enrichment and isolation was prepared with the following components (L−1): 0.5 g NaCl, 0.5 g MgCl2·6H2O, 0.1 g CaCl2·2H2O, 0.3 g NH4Cl, 0.2 g KH2PO4, 0.5 g KCl, 2 ml trace element solution 284 (JCM medium No.284, https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=284&MD_NAME =), 1 mg resazurin, 0.5 g cysteine hydrochloride and 1 L distilled water. The strain Y-P2T was isolated with mixed substrate (short-chain fatty acid, glucose, yeast extract and tryptone mixture) by using the extinction dilution method as described previously (Zhang et al. 2018). Unless otherwise stated, R2A (Reasoner’s 2A) liquid medium was used for subculturing and cultivating the strain Y-P2T. R2A medium contained (L−1): 0.25 g tryptone, 0.5 g casein hydrolysate, 0.5 g yeast extract, 0.5 g soluble starch, 0.3 g K2HPO4, 0.1 g MgSO4, 0.3 g sodium pyruvate, 0.25 g peptone, 0.5 g glucose, and 1L distilled water. All media used in this study were prepared and dispensed under 100% N2, and sterilized at 121 °C for 15 min. Strain Y-P2T was deposited in the China Collection of Anaerobic Microorganisms (CCAM 826 T) and Japan Collection of Microorganisms (JCM 34766 T). Oceanibaculum nanhaiense KCTC 52312 T obtained from Korean Collection for Type Cultures (KCTC) was used as the reference strain.
Morphological, physiological, and biochemical tests
The strain Y-P2T incubated at 25 °C for 5 days was used for morphology tests. Gram-staining, flagellum-staining and spore-staining were determined using commercial Gram Staining Kit, Flagellum Staining Kit and Spore Staining Kit (Solarbio, China) according to the manufacturers’ instructions, respectively. The cell shape and size of strain Y-P2T were examined using a scanning electron microscope (JEM-1400 Plus, JEOL, Japan). 0.1% melted agarose gel spread flat on slide and solidified, then take a drop of strain Y-P2T by microscope (Nikon 80i, Japan) for observing motility.
Growth at different temperatures (15, 20, 25, 30 and 37 °C), pH (5.0–8.5, at 0.5-unit intervals), and salinities (0 – 70 g L−1, at 10 g L−1 intervals) were determined in the R2A medium supplemented 10% (v/v) oxygen in the headspace of Hungate tubes (25 ml). The pH values were adjusted using the sterile and HCl or NaOH solution and were buffered with 20 mM MES (pH 5.5, pH 6.0 and pH 6.5), 20 mM PIPES (pH 7.0 and pH 7.5) and 20 mM Tris (pH 8.0 and pH 8.5).The final pH was determined with a pH meter (HORIBA B-712, LAQUAtwin, Japan). Growth was determined by measuring the optical density (OD) at 600 nm using a spectrophotometer (DU730, Beckman, Germany).
For biochemical tests, cells in R2A medium were collected by centrifuging at 13,000 rpm for 5 min at room temperature. Substrate utilization, nitrate reduction, and H2S production were tested with API 20NE, API ZYM and API 20E (bioMérieux, France) and incubated aerobically at 28 °C and 37 °C, respectively, the color change was checked every 18–24 h. Oxidase activity was determined using an oxidase reagent kit (bioMérieux, France) according to the manufacturer’s instructions. Oxygen requirement of strain Y-P2T was tested under 0%, 2%,10% and 20% oxygen (O2:N2, v/v). The fermentation products were analysed by liquid chromatography (Aglient 1200, USA) using AminexHPX-87H column (300 mm × 7.8 mm, 9 µm), H2SO4 (5 mM) was used as the mobile phase at a flow rate of 0.6 ml min−1. H2 in the overhead of the tubes were analysed by gas chromatography (Shimadzu GC2010, Japan).
Chemotaxonomic analysis
For cellular fatty acids, polar lipids and respiratory quinones analyses, cells of strains Y-P2T and O. nanhaiense KCTC 52312 T incubated in R2A medium at 25 °C for 5 days were collected by centrifugation. The fatty acids were separated using gas chromatography (Aglient 8860, USA) and identified with Sherlock software (version 6.3) according to the instructions of Microbial Identification Inc. (MIDI) protocol (Sasser 1990). Respiratory quinones of strain Y-P2T were detected using the protocol described previously (Komagata and Suzuki 1988; Tindall 1990). Polar lipids were extracted using a chloroform / methanol system and were analysed using one- and two-dimensional thin-layer chromatography (TLC) following the method described by Kates et al. (1986).
16S rRNA gene sequencing and phylogenetic analysis
Cells incubated at 25 °C for 5 d was used for extracting genomic DNA using bacteria DNA extraction kit (DP302, TIANGEN, China) following the manufacture’s instruction. 16S rRNA gene fragments were amplified by PCR using the universal primers 27F (5′AGAGTTTGATCMTGGCTCAG3′) and 1492R (5′TACGGYTACCTTGTTACGACTT3′) and were sequenced by ABI 3730XL DNA anazlyzer. The sequence obtained was compared with the available 16S rRNA sequences in EzBioCloud database (https://www.ezbiocloud.net/identify) and NCBI database with nucleotide Basic Local Alignment Search Tool (blastn, https://blast.ncbi.nlm.nih.gov/Blast.cgi), respectively. 16S rRNA gene sequences of closely related species that validly published were derived from genomes from NCBI database or downloaded from EzBioCloud, and then were multiply aligned through MUSCLE v3 (https://drive5.com/muscle/downloads_v3.htm). The phylogenetic analyses were performed by fasttree and MEGA X using the neighbor-joining method and maximum-likelihood method (Felsenstein 1981), respectively. Bootstrap values were calculated based on 1000 replicates. Evolutionary distances were calculated using the Kimura two-parameter method (Kimura 1980). The phylogenetic tree was modified by Itol (https://itol.embl.de/).
Whole–genome sequencing and phylogenomic analysis
The whole genome of strain Y-P2T was sequenced by Novogene Corporation Inc. (Beijing, China) using NovaSeq 6000 System (Illumina, USA). Phylogenomic analysis based on the GTDB taxonomy database (release r95) was performed by using the method described previously (Parks et al. 2018). Genome assembly and annotation were performed using methods described previously (Fan et al. 2023).
Up-to-date bacterial core gene (UBCG) and GTDB phylogenomic trees were reconstructed by UBCG (https://www.ezbiocloud.net/tools) and GTDB-Tk (https://gtdb.ecogenomic.org/), respectively, and were optimized in Evolview website (https://www.evolgenius.info/evolview/#/treeview). The pairwise genomic average nucleotide identity (ANI) and average amino acid identity (AAI) were calculated using OrthoANIu (https://www.ezbiocloud.net/tools/orthoaniu) and Compare M (https://github.com/dparks1134/CompareM), respectively. Percentage of conserved proteins (POCP) between two microbial genomes was calculated as the following formula: (conserved protein number of genome A + conserved protein number of genome B) / (total number of proteins being compared in genome A + total number of proteins being compared in genome B) (Qin et al. 2014).
Results and discussion
Morphological, physiological, and biochemical characteristics
Cells of strain Y-P2T were Gram-stain-negative, non-spore-forming, straightly rod-shaped or slightly curved with 0.8 – 3.0 × 0.4 – 0.6 µm in length and in width (Fig. 1). Growth occurred at 15–30 °C (optimum at 25 °C) and pH 6.0–7.5 (optimum pH 7.0) in absence of NaCl (Fig. S1). Weak growth was observed under anaerobic conditions, but the optimum growth occurred in the presence of oxygen up to approx. 10% (v/v), no growth was observed when oxygen increase to 20% (v/v) (Fig. S2), indicating that strain Y-P2T was microaerophilic.
According to API 20NE and API 20E tests (Table 1), strain Y-P2T was positive for urease and gelatinase. The results of API 20NE tests revealed that strain Y-P2T was negative for reduction of nitrate or denitrification, was positive for oxidase activity, but negative for catalase activity, Strain Y-P2T was unable to reduce thiosulfate or ferment tested carbohydrates. In API ZYM test, activities of alkaline phosphatase, esterase (C 4), estase lipase (C 8), acid phosphatase and Naphtol-AS-BI-phosphohydrolase were positive. Acetate and H2 were produced from glucose.
The GenBank accession numbers of the 16S rRNA gene sequence for strain Y-P2T was MZ270534. The GenBank accession number of genome sequence for strain Y-P2T was JAOTID000000000.
Chemotaxonomic characteristics
The predominant fatty acids (> 10%) of strain Y-P2T were C16:0 (34.6%), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c, 23.1%), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c,17.3%), which accounted for 75.0% of the total fatty acids (Table S1). Differently, O. nanhaiense KCTC 52312 T contained sum in feature 8 (C18:1ω7c and/or C18:1ω6c, 50.0%) and C16:0 (12.6%). The polar liquids of strain Y-P2T comprised one unidentified aminolipid (AL), one phosphatidylethanolamine (PE), one phosphatidylglycerol (PG), three unidentified phospholipids (PLs) and four unidentified polar lipids (Ls) (Fig. S3). The respiratory quinone was Q-10.
Phylogenetic analyses
The complete 16S rRNA gene sequence analysis performed using blastn at NCBI showed that strain Y-P2T shares the highest 16S rRNA gene sequence similarity with species in the genus Oceanibaculum (90.3–90.6%) which was affiliated to “Oceanibaculaceae” (formerly Thalassobaculaceae) within the order Rhodospirillales, followed by Stella humosa DSM 5900 T (90.0%) in family Stellaceae, Thalassobaculum and Nisaea (≤ 89.9%) in Thalassobaculaceae, Varunaivibrio and Magnetovibrio (≤ 89.8%) in “Magnetovibrionaceae” (formerly Thalassospiraceae), Zavarzinia compransoris LMG-5821 T (89.1%) in Zavarziniaceae (Table S2). These 16S rRNA gene sequence similarities were lower than the 94.5% threshold for the delineation of genera and the median sequence identity for the delineation of families (Yarza et al. 2014), suggesting that strain Y-P2T belongs to a new genus or may represent a higher rank taxon.
To confirm the phylogenetic relationship between strain Y-P2T and Rhodospirillales members, maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences of strain Y-P2T and the representative genera within order Rhodospirillales were constructed. On the phylogenetic tree, strain Y-P2T was placed in the clade with genera Zavarzinia of the family Zavarziniaceae, but formed an independent evolutionary lineage that is distinguishable among Rhodospirillales families (Fig. S4). The phylogenomic trees reconstructed based on bacterial core gene set (Fig. 2) and 120 single copy genes (Fig. 3) both indicated that strain YP2T clusters with members of “Magnetospiraceae” (Magnetospira), “Magnetovibrionaceae” (Magnetovibrio, Varunaivibrio), and Geminicoccaceae (Defluviicoccus), and formed a clade with Defluviicoccus vanus Ben 114 T.
To further figure out the taxonomic rank of strain Y-P2T, reanalysis of pairwise 16S rRNA gene sequence similarity and indices of pairwise genomic relatedness including ANI, AAI and POCP were performed. Strain Y-P2T had 89.2 ± 0.8% of 16S rRNA sequence similarities to representative species of the family “Oceanibaculaceae” and Thalassobaculaceae (Fig. 4), which were close to the minimum sequence similarity for defining a novel family (Yarza et al. 2014). Meanwhile, the ANI and POCP values between strain Y-P2T and these members were ≤ 69.8 and 43.0% (Table S2), respectively, far lower than the cutoff values for distinguishing genera (83 and 50%, respectively) (Luo et al. 2014; Qin et al. 2014; Jain et al. 2018), and were in the range of relevant inter-family values (ANI 63.7–70.7 and POCP 25.3–49.9%) (Fig. 4); the AAI values were all ≤ 57.8% (Table S2), which were lower the boundary (approximately 60%) for Rhodospirillales families proposed by Koziaeva et al. (2023). In addition, strain Y-P2T was separated from other Rhodospirillales families with the average values of 16S rRNA gene sequence similarity and AAI (86.0 ± 2.0 and 55.3 ± 1.5%, respectively) below the thresholds for family delineation (Fig. 4) (Yarza et al. 2014). All these results suggested strain Y-P2T could be distinguished from families in Rhodospirillales and represents a novel family within Rhodospirillales.
Genomic characteristics
The genome of strain Y-P2T had a total length of 5,388,487 bp, and contained 5053 ORFs, 49 tRNA genes, one 5 s rRNA, one 16 s rRNA and one 23 s rRNA (Table S3). The G + C content was 66.0%. 2314, 3540 and 3592 genes were annotated in KEGG, Swiss and GO database, respectively (Table S3).
Glycan biosynthesis pathways
Extracellular polymeric substance (EPS) is a key component of biofilm causing processes of MIC. Strain Y-P2T was able to form EPS when grown under microaerobic condition (Fig. S5). Results based on KEGG annotation showed that 66 genes associated with glycan biosynthesis and metabolism are identified in the genome of strain Y-P2T (Table S4), 20 of which (more than 30%) involved in the biosynthesis of lipopolysaccharide (LPS) which may effect on the Co-Cr and Ti alloys corrosion (Yu et al. 2016). Genes lpxA, lpxCD, lpxI, lpxB and lpxK encoding homologs that consist of pathway synthesizing lipid IVA from UDP-N-acetyl-α-d-glucosamin or a (3R)-3-hydroxytetradecanoyl-[acp] (Table S5). Meanwhile, homologs encoded by genes kdsD, kdsA, kdsC and kdsB formed a pathway for synthesizing CMP-3-deoxy-β-d-manno-octulosonate from d-ribulose 5-phosphate, providing an essential substrate for generating Kdo2-lipid A via the pathway comprised of integral membrane proteins encoded by kdtA, lpxL, IpxK and lpxM (Wang et al. 2015). However, lpxM was not found in genome of strain Y-P2T. In addition, an ADP-l-glycero-β-d-manno-heptose biosynthesis pathway containing enzymes encoded by gmhAC, gmhB and gmhD was employed by Y-P2T to produce the precursor for the inner core region of LPS, but only one gene (gtrB) related to O-antigen repeat unit synthesis was identified. We also found strain Y-P2T had a complete pathway (rmlADBC) to synthesize dTDP-l-rhamnose which is the precursor of l-rhamnose. l-rhamnose and GDP-d-glycero-d-manno-heptose that generated via enzymes encoded by gmhA, hhdA (absent), gmhB, and hhdC are sugar components of bacterial S-layer glycoproteins (Kneidinger et al. 2001; Graninger et al. 2002). It has been demonstrated that S-layer proteins are associated with cells aggregation, bacterial adherence to substrates and surfaces, as well as biofilm formation (Gerbino et al. 2015).
Sulfur metabolism
Sulfur-cycling microorganisms are commonly considered the key players of MIC, and can participate in the process of MIC through sulfate reduction and sulfur disproportionation (Rajala et al. 2022). The genome of strain Y-P2T contained 24 genes for sulfur metabolism (Table S6). Gene sta, and the operons aprAB and dsrAB comprised a complete dissimilatory sulfate reduction and oxidation pathway for the conversion between sulfate and sulfide, which has been described in Dsr-dependent sulphate-reducing bacteria and sulphur-oxidizing bacteria (Neukirchen and Sousa 2021). SOX system oxidizing thiosulfate to sulfate via enzymes encoded by soxDCBAZYX operon was identified in strain Y-P2T. In addition, a flavocytochrome c sulfide dehydrogenase was presented in genome of Y-P2T by fccA and fccB, it has been reported that this enzyme can oxidize self-produced sulfide or exogenous sulfide to sulfite and thiosulfate under aerobic condition in Pseudomonas aeruginosa (Lü et al. 2017).
Conclusion
Physiological comparison revealed that strain Y-P2T shares several common phenotypic features with Rhodospirillales members, such as mesophilic, Gram-stain-negative and major respiratory quinone, but is different to its phylogenetically close relatives in morphological and physiological traits (Table 2). Thalassobaculaceae members are motile, grow with salinity, positive for oxidase activity; “Magnetospiraceae” and “Magnetovibrionaceae” are magnetotactic; while Geminicoccaceae and Stellaceae are aerobic, having different cell shapes, Geminicoccaceae also has abilities to reduce nitrate and hydrolyze gelatin. Meanwhile, values of the 16S rRNA gene sequence similarity, AAI ANI and POCP between strain Y-P2T and published members of Rhodospirillales families were all lower than boundaries for separating Rhodospirillales families. On the basis of the distinct phenotypic and chemotaxonomic characteristics, phylogenetic and genomic evidence mentioned above, strain Y-P2T is proposed as the type strain of a novel species of a new genus, for which the name Shumkonia mesophila gen. nov., sp. nov. is proposed, within a new family Shumkoniaceae fam. nov.
Description of Shumkoniaceae fam. nov.
Shumkoniaceae (Shum.ko.ni.a.ce’ae. N.L. fem. n. Shumkonia a bacterial genus; aceae suffix to denote a family; N.L. fem. pl. n. Shumkoniaceae the Shumkonia family).
The description of Shumkoniaceae is the same as for the genus Shumkonia. The type genus is Shumkonia.
Description of Shumkonia gen.nov.
Shumkonia (Shum.ko’ni.a. N.L. fem. n. Shumkonia named in honour of ShumKo (1031–1095) who found and used oil in the eleventh century in China).
Microaerophilic, mesophilic, chemoorganoheterotrophic bacterium. Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved rod. Acetate and H2 are the fermentation products of glucose. The predominant cellular fatty acid is C16:0, and the quinone is Q-10. The type species is Shumkonia mesophila.
Description of Shumkonia mesophila sp. nov.
Shumkonia mesophila (me.sophi.la. N.L. fem. adj. mesophila, middle temperature loving).
Microaerophilic, mesophilic, chemoorganoheterotrophic bacterium. Cells are Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved, 0.8–3.0 µm in width and 0.4–0.6 µm in length. Growth occurs optimally under the conditions of 25 °C, pH 7.0 without NaCl. Urease and oxidase positive. Acetate and H2 are the fermentation products of glucose. Catalase, nitrate reduction and denitrification negative. Major cellular fatty acids are C16:0, sum in feature 3 (C16:1 ω7c and/or C16:1 ω6c), sum in feature 8 (C18:1 ω7c and/or C18:1 ω6c). The polar lipids comprise phosphatidylethanolamine (PE), phosphatidylglycerol (PG), one unidentified aminolipid (AL), three unidentified phospholipid (PL) and four unidentified polar lipids (L). Respiratory quinone is Q-10. The genomic DNA G + C content was 66.0%.
The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T) isolated from oil sludge, Shengli, China.
Abbreviations
- AAI:
-
Average amino acid identity
- ANI:
-
Average nucleotide identity
- ANI:
-
Average nucleotide identity
- AL:
-
Aminolipid
- CHES:
-
N-cyclohexyl-2-aminoethanesulfonic acid
- GL:
-
Glycolipids
- L:
-
Lipids
- MES:
-
2-(N-morpholino) ethanesulfonic acid
- PE:
-
Phosphatidylethanolamine
- PG:
-
Phosphatidylglycerol
- PL:
-
Phospholipid
- POCP:
-
Percentage of conserved proteins
- R2A:
-
Reasoner's 2A
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Acknowledgements
We thank Professor Paul A. Lawson at University of Oklahoma (Norman, OK 73019, USA) and Professor Aharon Oren at the Hebrew University of Jerusalem for help with checking the derivation of the names.
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This study was supported by Agricultural Science and Technology Innovation Project of the Chinese Academy of Agriculture Science (CAASASTIP-2016-BIOMA), Central Public-interest Scientific Institution Basal Research Fund (1610012023002, 1610012023003 and 1610012023004), and National Natural Science Foundation of China (no. 92051108).
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Min Yang: Physiological and Biochemical experiment, data analysis and article writing ; Xue Zhang: Enrichment and isolation; Shichun Ma: Project guidance and promotion, data analysis and article revision; Qiumei Zhang: Genomic Data Analysis and phylogenetic analysis; Chenghui Peng: Physiological data collection; Hui Fan: Electron acceptor and substrate experimen; Jiang Li: Genomic Data Analysis; Lirong Dai: Strain preservation and activation; Lei Cheng: Funding support and guidance. All authors reviewed the manuscript.
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Yang, M., Zhang, X., Ma, S. et al. Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis. Antonie van Leeuwenhoek 116, 1359–1374 (2023). https://doi.org/10.1007/s10482-023-01878-1
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DOI: https://doi.org/10.1007/s10482-023-01878-1