Introduction

Members of the genus Streptomyces has been extensively studied for their capacity to produce numerous natural products (Nimaichand et al. 2013; Tamreihao et al. 2016; Nithya et al. 2018). While the genus is ubiquitous in nature, its study has been mostly limited to soil (Goodfellow and Fiedler 2010; Katz and Baltz 2016). Unlike other environments, deserts provide a unique ecosystem in that they are characterised by an arid environment, with water and nutrients being their limiting factors (Andrew et al. 2012). A study on microbial diversity in the Atacama Desert has revealed the dominance of Streptomyces among other actinobacteria (Okoro et al. 2009). This was further illustrated by the isolation of several novel Streptomyces species from the Atacama Desert including Streptomyces asenjonii, Streptomyces atacamensis and Streptomyces deserti (Santhanam et al. 2012a, b; Goodfellow et al. 2017).

The genus Streptomyces was first introduced by Waksman and Henrici (1943) and, at the time of writing, there are more than 800 validly named species (http://www.bacterio.net/streptomyces.html). A major characteristic of the members of the genus Streptomyces is the presence of LL-diaminopimelic acid in the cell wall peptidoglycan, along with an absence of characteristic cell wall sugars (Lechevalier and Lechevalier 1970).

This paper describes another member of the genus Streptomyces isolated from a desert sample.

Materials and methods

Isolation and preservation

Sand samples were collected from Gurbantunggut desert (44°39′N, 87°11′E) located in China. Isolation of strain SYSU D8023T was based on the method described by Yang et al. (2017). Following purification, pure cultures was maintained on Reasoner’s 2A (R2A) agar and preserved as glycerol suspensions (20%, v/v) at − 80 °C. The basal growth condition of the strain for all experiments was maintained at pH 7.0 and 28 °C, unless otherwise stated.

S. barkulensis DSM 42082T was obtained from DSMZ, Germany and cultured under comparable conditions as a reference strain.

Phenotypic characteristics

For phenotypic characteristics, strain SYSU D8023T was cultured on R2A agar. Morphological characteristics were observed using a light microscope (BH2; Olympus) and a scanning electron microscope (JSM-6330F, JOEL), following 7 days of incubation. Growth conditions, colours of the mycelia and pigment formation were recorded after 2 weeks growth on International Streptomyces Project (ISP) media, Czapek’s agar, Gause’s agar, R2A agar, nutrient agar and Potato Dextrose Agar. Gram reaction was tested using a Gram Stain Solution Kit (Shanghai Yeasen Biotechnology Co., Ltd.) and confirmed by a non-staining procedure (Buck 1982). Growth temperature range (0, 4, 14, 28, 37, 45, 50, 55, 60 and 65 °C) and NaCl tolerance (media supplemented with NaCl up to 30% w/v concentration) were observed on R2A agar after 2 weeks of incubation. For pH tolerance, R2A broth was prepared between pH 4.0–10.0 (with interval of 1.0 pH unit, using the buffer system described by Nie et al. 2012) and growth observed after 2 weeks of incubation. Oxidase and catalase activities were determined by assessing the oxidation of 1% (w/v) tetramethyl-p-phenylenediamine (Kovacs 1956) and the formation of bubbles on addition of 3% H2O2, respectively. Cellulose, gelatin and starch hydrolysis, H2S production, milk coagulation and peptonisation, nitrate reduction, degradation of Tweens (20, 40, 60 and 80) and urease activity were tested as previously described (McFaddin 1976; Gonzalez et al. 1978). Utilisation of carbon and nitrogen sources were examined by using the medium of Smibert and Krieg (1994).

Chemotaxonomy

Biomass for chemical studies of strain SYSU D8023T was obtained from cultures grown in R2A broth for 7 days, unless otherwise mentioned. Respiratory quinones were extracted from lyophilised cells (Collins et al. 1977), purified and analysed by HPLC (Tamaoka et al. 1983). Polar lipids were extracted, separated and examined by two-dimensional TLC procedure on silica gel G60 plates (Merck) (Minnikin et al. 1979). Cells for cellular fatty acid analysis were obtained by culturing strain SYSU D8023T and S. barkulensis DSM 42082T on tryptic soy agar (TSA, Difco) for 7 days. Cellular fatty acids were extracted, methylated and analysed following the instructions of the Sherlock Microbial Identification System (MIDI) version 6.1 and the TSBA6 database (Sasser 1990). Diaminopimelic acid was analysed according to the procedures developed by Hasegawa et al. (1983). Whole cell sugars were analysed as described by Lechevalier and Lechevalier (1980). The genomic DNA G + C content was determined by HPLC after enzymatic degradation (Mesbah et al. 1989).

Molecular characterisation

Extraction of chromosomal DNA, PCR amplification of 16S rRNA gene and sequencing of the purified products were carried out as described by Li et al. (2007). The phylogenetic relationships of strain SYSU D8023T were determined after BLAST (Altschul et al. 1990) searches of the 16S rRNA gene sequences in NCBI and the EzBioCloud databases (Yoon et al. 2017). 16S rRNA gene sequences of closely related type strains were retrieved for multiple alignments (CLUSTAL X software package, Thompson et al. 1997) and generation of phylogenetic dendrograms (MEGA version 7.0, Kumar et al. 2016). Algorithms based on the neighbour-joining (Saitou and Nei 1987), maximum-parsimony (Fitch 1971) and maximum-likelihood (Felsenstein 1981) methods were used for generation of phylogenetic trees. Evolutionary distances in the neighbour-joining and maximum likelihood trees were calculated using Kimura two-parameter model (Kimura 1980, 1984). The topology of each tree was evaluated by bootstrap analysis of 1000 replications (Felsenstein 1985).

Results and discussion

Phenotypic characteristics

Strain SYSU D8023T was observed to grew well on ISP 3, ISP 4, ISP 6, ISP 7, Czapeks’ agar, nutrient agar and Gause’s agar, moderately on ISP 5 and poorly on ISP 2 and Potato Dextrose agar. The colour of the aerial mycelia on the above media were white while the substrate mycelia on ISP 3, ISP 4, ISP 7 and NA showed a gray colour. No soluble pigments were produced on the media tested. The aerial mycelia were observed to bear rectiflexibles spore chains (see supplementary Fig. S1). Strain SYSU D8023T was observed to grow at 14–50 °C, pH 6.0–9.0 and in the presence of up to 7% NaCl, Optimum growth was observed at 28 °C, pH 7.0 and in the absence of NaCl. Phenotypic properties distinguishing strain SYSU D8023T from the closely related strain S. barkulensis DSM 42082T are listed in Table 1. Other detailed phenotypic characteristics of strain SYSU D8023T are provided in the species description below.

Table 1 Differential phenotypic characteristics between strain SYSU D8023T and the closely related type strain S. barkulensis DSM 42082T
Full size table

Chemotaxonomic characteristics

The respiratory quinones of strain SYSU D8023T were found to be MK-9(H6) (83.0%) and MK-9(H8) (17.0%). The polar lipid profile of strain SYSU D8023T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phospholipid and an unidentified glycolipid (Fig. S2). Strain SYSU D8023T was found to contain LL-diaminopimelic acid as cell wall diamino acid. The whole cell sugars were identified as glucose and fucose. The major cellular fatty acids (> 5%) detected were anteiso-C15:0 (20.3%), iso-C16:0 (17.8%), anteiso-C17:0 (16.2%) and C12:0 (6.2%). Detailed fatty acid profiles of the strain SYSU D8023T and the closely related type strain S. barkulensis DSM 42082T are given in Table 2. The genomic DNA G + C content of strain SYSU D8010T was determined to be 70.1 mol%.

Table 2 Complete fatty acid profiles of strains SYSU D8023T and Streptomyces barkulensis DSM 42082T
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Molecular characteristics

On pairwise comparison with the 16S rRNA gene sequences available in the EzBioCloud database, strain SYSU D8023T showed highest 16S rRNA gene sequence identity with S. barkulensis RC 1831T (97.9%). This relationship was further supported by the phylogenetic trees (Figs. 1, S3, S4). Since the 16S rRNA gene sequence identities of strain SYSU D8023T with all current validly named Streptomyces strains were below 98.65%, DNA-DNA hybridization experiments were not performed with the related strains (Chun et al. 2018).

Fig. 1
figure 1

Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain SYSU D8023T among related members of the genus Streptomyces. Bootstrap values (≥ 50%) based on 1000 resamplings are given at the nodes. Bar, 0.005 substitutions per nucleotide position

Full size image

On the basis of 16S rRNA gene sequence analysis and chemotaxonomic features, strain SYSU D8023T can be considered to be a member of the genus Streptomyces. The strain can, however, be differentiated from the closely related type strain S. barkulensis DSM 42082T (= RC 1831T) by several characteristics as listed in Table 1. For example, strain SYSU D8023T can grow at 14 °C and 45 °C, but could not tolerate NaCl above 8%, unlike the reference strain S. barkulensis DSM 42082T. Furthermore, strain SYSU D8023T contained phosphatidylethanolamine as one of its polar lipid, unlike S. barkulensis DSM 42082T. Based on these characteristics and phylogenetic analyses, strain SYSU D8023T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces desertarenae sp. nov. is proposed. The Digital Protologue database (Rosselló-Móra et al. 2017) TaxoNumber for strain SYSU D8023T is TA00589.

Description of Streptomyces desertarenae sp. nov.

Streptomyces desertarenae (de.sert.a.re’nae. L. neut. n. desertum desert; L. fem. n. arena sand; N.L. gen. n. desertarenae of desert sand, referring to the source of the type strain).

Aerobic, Gram-positive, halotolerant actinomycete. Forms well-developed and extensively branched substrate mycelia. Aerial mycelia form rectiflexibles spore chains; spores are non-motile, rough and short rod shaped. Shows good growth on ISP 3, ISP 4, ISP 6, ISP 7, Czapek’s agar, nutrient agar and Gause’s agar, moderate growth on ISP 5 and poor growth on ISP 2 and Potato Dextrose agar. Growth occurs at 14–50 °C (optimum, 28 °C), pH 6–9 (optimum, pH 7) and in the presence of up to 7% (w/v) NaCl. Positive for nitrate reduction but negative for oxidase, catalase and urease activities, milk coagulation and peptonisation, and H2S production. Hydrolyses Tweens 20 and 40 but not cellulose, gelatin, starch or Tweens 60 and 80. Utilises arabinose, galactose, glycerol, inositol, mannitol, melitriose, rhamnose, sodium pyruvate, sodium succinate, sorbitol and trehalose as sole carbon sources but not cellobiose, fructose, glucose, lactose, maltose, mannose, ribose, saccharose, sodium fumarate, sorbose, xylitol or xylose. Utilises alanine, arginine, aspartic acid, glutamine, hypoxanthine, lysine, methionine, ornithine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine as sole nitrogen source but not adenine, cysteine, glycine or histidine. The diagnostic cell wall diamino acid is LL-diaminopimelic acid. Contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phospholipid and an unidentified glycolipid as polar lipids. MK-9(H6) and MK-9(H8) are the respiratory quinones. Major cellular fatty acids are C12:0, anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The DNA G + C content of the type strain is 70.1 mol%.

The type strain, SYSU D8023T (= KCTC 49023T = CGMCC 4.7455T), was isolated from a sample collected from Gurbantunggut desert in China. The GenBank accession number for the 16S rRNA gene sequence of strain SYSU D8023T is MH518265.