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Streptomyces albicerus sp. nov., a novel actinomycete isolated from the sediments of the Tailan River in Xinjiang, China

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Abstract

A novel actinomycete, designated TRM68295T, was isolated from the sediments of the Tailan River, Xinjiang, northwest China. The study of the polyphasic approach showed that the characteristics of the strain were consistent with the genus Streptomyces. Phylogenetic analysis indicated that the strain had a high sequence similarity with Streptomyces phaeochromogenes ATCC 3338T (97.9%). The diagnostic diamino acid of cell walls was identified as ll-diaminopimelic acid. The whole cell sugars were identified as ribose, xylose, glucose and galactose. The major fatty acids were iso-C14:0, iso-C15:0, anteiso-C15:0, iso-C16:0, C16:1ω9c, C16:0 and anteiso-C17:0. The major menaquinones were MK-9 (H10), MK-9 (H6) and MK-9 (H2). The polar lipids were composed of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylinositol (PI) and phosphatidylinositol mannoside (PIM). The G+C content in the draft genome sequence of the strain was identified as 70.0 mol%. The average nucleotide identity (ANI) between strains TRM68295T and S. phaeochromogenes ATCC 3338T was 88.1%. Digital DNA-DNA hybridization (dDDH) value between strain TRM68295T and S. phaeochromogenes ATCC 3338T was 40.7%. The multilocus sequence analysis of five house-keeping genes (atpD, gyrB, recA, rpoB, and trpB) indicated that the MLSA distances between the strain and similar species were greater than the threshold of 0.007. Based on the above studies, strain TRM68295T is considered as a novel species of the genus Streptomyces, for which the name Streptomyces albicerus sp. nov. is proposed. The type strain is TRM68295T (= CCTCC AA 2018085T = KCTC 49272T).

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References

  • Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134

    Article  PubMed  PubMed Central  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) Spades: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Calasanz M, Göker M, Pötter G, Rohde M, Spröer C, Schumann P, Klenk HP, Gorbushina AA (2013) Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand. Int J Syst Evol Microbiol 63:2254–2259

    Article  Google Scholar 

  • Chun JS, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    Article  CAS  PubMed  Google Scholar 

  • Deshpande BS, Ambedkar SS, Shewale JG (1988) Biologically active secondary metabolites from Streptomyces. Enzyme Microb Tech 10:455–473

    Article  CAS  Google Scholar 

  • Encheva M, Zaharieva N, Kenarova A, Chipev N, Chipeva V, Hristova P, Ivanova I, Moncheva P (2013) Abundance and activity of soil actinomycetes from Livingston Island, Antarctica. Bulg J Agric Sci 19:68–71

    Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–789

    Article  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Sys Zool 20:406–416

    Article  Google Scholar 

  • Gerhardt P, Murray RGE, Wood WA, Smibert RM, Krieg NR (1994) Methods for general and molecular bacteriology. American Society for Microbiology, Washington

    Google Scholar 

  • Gordon RA (1974) Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119

    Article  Google Scholar 

  • Jose PA, Jebakumar SRD (2012) Phylogenetic diversity of actinomycetes cultured from coastal multipond solar saltern in Tuticorin. India Aquat Biosyst 8:23

    Article  CAS  PubMed  Google Scholar 

  • Kelly KL (1964) Inter-Society Color Council—National Bureau of Standards Color Name Charts illustrated with centroid colors. US Government Printing Office, Washington

    Google Scholar 

  • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee I, Kim YO, Park SC, Chun J (2015) Orthoani: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    Article  PubMed  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meier-Kolthoff PJ, Alexander FA, Klenk HP, Göker M (2013) Genome sequence based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933–2935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 43:130–137

    Article  Google Scholar 

  • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Piao C, Zheng W, Li Y, Liu C, Jin L, Song W, Yan K, Wang X, Xiang W (2017) Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr. Arch Microbiol 199:963–970

    Article  CAS  PubMed  Google Scholar 

  • Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) J SpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931

    Article  CAS  PubMed  Google Scholar 

  • Rong X, Huang Y (2012) Taxonomic evaluation of the Streptomyces hygroscopicus clade using multi-locus sequence analysis and DNA–DNA hybridization, validating the MLSA scheme for the systematics of the whole genus. Syst Appl Microbiol 35:7–18

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425

    CAS  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Technical note 101. Microbial ID, Newark

  • Shirling EB, Gottlieb D (1966) Methods for characterization of streptomyces species. Int J Sys Bacteriol 16:313–340

    Article  Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang SK, Wang Y, Chen Y, Lou K, Cao LL, Xu LH, Li WJ (2009) Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 59:2025–2031

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian XP, Long LJ, Li SM, Zhang J, Xu Y, He J, Li J, Wang FZ, Li WJ, Zhang CS, Zhang S (2013) Pseudonocardia antitumoralis sp. nov., a deoxynyboquinone-producing actinomycete isolated from a deep-sea sediment. Int J Syst Evol Microbiol 63:893–899

    Article  CAS  PubMed  Google Scholar 

  • Waksman SA (1967) The actinomycetes a summary of current knowledge. Ronald Press, New York

    Google Scholar 

  • Waksman SA, Henrici AT (1943) The nomenclature and classification of the actinomycetes. J Bacteriol 46:337–341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang C, Xu XX, Qu Z, Wang HL, Lin HP, Xie QY, Ruan JS, Hong K (2011) Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 61:320–324

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Tian J, Li X, Gan L, He L, Chu Y, Tian Y (2018) Streptomyces dioscori sp. nov., a novel endophytic actinobacterium isolated from bulbil of Dioscorea bulbifera L. Curr Microbiol 75:1384–1390

    Article  CAS  PubMed  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:237–243

    Article  Google Scholar 

  • Xu P, Li W, Tang S, Zhang Y, Chen G, Chen H, Xu L, Jiang C (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  CAS  PubMed  Google Scholar 

  • Yokota A, Tamura T, Hasegawa T, Huang LH (1993) Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order actinomycetales. Int J Syst Bacteriol 43:805–812

    Article  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–2161

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang R, Han X, Xia Z, Luo X, Wan C, Zhang L (2017) Streptomyces luozhongensis sp. nov., a novel actinomycete with antifungal activity and antibacterial activity. Antonie Van Leeuwenhoek 110:195–203

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Thanks to Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Tarim Basin of Xinjiang Production & Construction Corps for providing research facilities.

Funding

This research was supported by the National Natural Science Foundation of China-Xinjiang Joint Fund Key Project (project no. U1703236) and Tarim University graduate research and innovation projects (project no. XJ2019G270).

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Authors and Affiliations

  1. College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar, 843300, People’s Republic of China

    Beibei Sun, Linlin Yuan, Zhanfeng Xia, Chuanxing Wan & Lili Zhang

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  1. Beibei Sun
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Contributions

BS contributed to performing the experiments and writing the initial draft. LY, ZX and CW contributed to the guidance of experimental operations. LZ contributed to reagents, instrumentation and the financial support for this work.

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Correspondence to Lili Zhang.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Communicated by Erko Stackebrandt.

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The GenBank/EMBL/DDBJ accession number for the genome and 16S rRNA gene sequence of strain TRM68295T is VWMY00000000 and MK795696.

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Sun, B., Yuan, L., Xia, Z. et al. Streptomyces albicerus sp. nov., a novel actinomycete isolated from the sediments of the Tailan River in Xinjiang, China. Arch Microbiol 202, 1639–1646 (2020). https://doi.org/10.1007/s00203-020-01871-6

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