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Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil

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Abstract

A novel pink-pigmented bacterium, designated strain 3D7T, was isolated during an investigation of potential psychrotolerant species from Antarctic soil. Cells of the isolate were observed to be rod-shaped (0.7–0.9 × 1.0–2.2 µm), Gram-stain negative and non-motile. It was able to grow at 4–32  °C, pH 7.0–10.0 and in the presence of 0–3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 3D7T belongs to the genus Microvirga and was most closely related to ‘Microvirga brassicacearum’ CDVBN77T (98.3%), Microvirga subterranea DSM 14364 T (96.8%), Microvirga guangxiensis 25BT (96.5%) and Microvirga aerophila DSM 21344 T (96.5%). The predominant quinone was ubiquinone 10 (Q-10), and the major fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G + C content of strain 3D7T was 63.5 mol%. Its genome sequence showed genes encoding phosphatases and lipases. Genetic machinery related to carbohydrate-active enzymes and secondary metabolites were also observed. The average nucleotide identity and digital DNA–DNA hybridization values based on whole genome sequences of strain 3D7T and its closely related species were below the threshold range for species determination. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain 3D7T represents a novel species of the genus Microvirga, for which the name Microvirga antarctica sp. nov. is proposed. The type strain is 3D7T (= CGMCC 1.13821T = KCTC 72465T).

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References

  • Ardley JK, Parker MA, De Meyer SE, Trengove RD, O’Hara GW, Reeve WG, Yates RJ, Dilworth MJ, Willems A, Howieson JG (2012) Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts. Int J Syst Evol Microbiol 62:2579–2588

    CAS  PubMed  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25–29

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bernardet JF, Nakagawa Y, Holmes B, Flavobacteri ST (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    CAS  PubMed  Google Scholar 

  • Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Weber T (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:81–87

    Google Scholar 

  • Caputo A, Lagier JC, Azza S, Robert C, Mouelhi D, Fournier PE, Raoult D (2016) Microvirga massiliensis sp. nov., the human commensal with the largest genome. Microbiologyopen 5:307–322

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu X-W, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    CAS  PubMed  Google Scholar 

  • Collins MD (1985) Isoprenoid quinone analysis in classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical Methods in Bacterial Systematics. Academic Press, London, pp 267–287

    Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    CAS  Google Scholar 

  • Dahal RH, Kim J (2017) Microvirga soli sp. nov., an alphaproteobacterium isolated from soil. Int J Syst Evol Microbiol 67:127–132

    CAS  PubMed  Google Scholar 

  • Desper R, Gascuel O (2004) Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol Biol Evol 21:587–598

    CAS  PubMed  Google Scholar 

  • Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Scientific Press, Beijing

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    PubMed  Google Scholar 

  • Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:261–269

    Google Scholar 

  • Jiménez-Gómez A, Saati-Santamaría Z, Igual JM, Rivas R, Mateos PF, García-Fraile P (2019) Genome insights into the novel species Microvirga brassicacearum, a rapeseed endophyte with biotechnological potential. Microorganisms 7(9):354

    PubMed Central  Google Scholar 

  • Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005

    Google Scholar 

  • Kanso S, Patel BK (2003) Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 53:401–406

    CAS  PubMed  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

    CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accu rate, and fast distance-based phylogeny inference program: table 1. Mol Biol Evol 32:2798–2800

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li WJ, Zhang YQ, Schumann P, Chen HH, Hozzein WN, Tian XP, Xu LH, Jiang CL (2006) Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt. Int J Syst Evol Microbiol 56:733–737

    CAS  PubMed  Google Scholar 

  • Li R, Li Y, Kristiansen K, Wang J (2008) Soap: short oligonucleotide align ment program. Bioinformatics 24:713–714

    CAS  PubMed  Google Scholar 

  • Li R, Zhu HM, Ruan J, Qian WB, Fang XD, Shi ZB, Li YR, Li ST, Shan G, Kristiansen K, Li SG, Yang HM, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu ZT, Xian WD, Li MM, Liu L, Ming YZ, Jiao JY, Fang BZ, Xiao M, Li WJ (2020) Microvirga arsenatis sp. nov., an arsenate reduction bacterium isolated from Tibet hot spring sediments. Antonie Van Leeuwenhoek 113:1147–1153

    CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60

    PubMed  PubMed Central  Google Scholar 

  • Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    CAS  Google Scholar 

  • Minoru K, Yoko S, Masayuki K, Miho F, Mao T (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 1:457–462

    Google Scholar 

  • Niederberger TD, Mcdonald IR, Hacker AL, Soo RM, Barrett JE, Wall DH, Cary SC (2008) Microbial community composition in soils of Northern Victoria Land, Antarctica. Enviro Microbiol 10:1713–1724

    CAS  Google Scholar 

  • Ohta H, Hattori T (1983) Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie Van Leeuwenhoek 49:429–446

    CAS  PubMed  Google Scholar 

  • Radl V, Simões-Araújo JL, Leite J, Passos SR, Martins LM, Xavier GR, Rumjanek NG, Baldani JI, Zilli JE (2017) Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil. Int J Syst Evol Microbiol 64:725–730

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9:945–967

    CAS  Google Scholar 

  • Safronova VI, Kuznetsova IG, Sazanova AL, Belimov AA, Andronov EE, Chirak ER, Osledkin YS, Onishchuk OP, Kurchak ON, Shaposhnikov AI, Willems A, Tikhonovich IA (2017) Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven. Int J Syst Evol Microbiol 67:94–100

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. MIDI Inc, Newark, DE

    Google Scholar 

  • Tapase SR, Mawlankar RB, Sundharam SS, Krishnamurthi S, Dastager SG, Kodam KM (2017) Microvirga indica sp. nov., an arsenite-oxidizing Alphaproteobacterium, isolated from metal industry waste soil. Int J Syst Evol Microbiol 67:3525–3531

    CAS  PubMed  Google Scholar 

  • Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. Am Soci Microbiol. https://doi.org/10.1128/9781555817497.ch15

    Article  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E (1987) Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464

    Google Scholar 

  • Weon HY, Kwon SW, Son JA, Jo EH, Kim SJ, Kim YS, Kim BY, Ka JO (2010) Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov. isolated from air, reclassification of Balneimonas flocculans Takeda et al 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga. Int J Syst Evol Microbiol, 60:2596–2600

  • Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (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

    CAS  PubMed  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286

    CAS  PubMed  Google Scholar 

  • Zhang BT, Miao JL, Li GY, Cui KY (2004) Research progress of polar microbial active substances. Mar Sci 28:58–63

    Google Scholar 

  • Zhang J, Song F, Xin YH, Zhang J, Fang C (2009) Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga. Int J Syst Evol Microbiol 59:1997–2001

    PubMed  Google Scholar 

  • Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Yin Y (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46:95–101

    Google Scholar 

  • Zhang XJ, Zhang J, Yao Q, Feng GD, Zhu HH (2019a) Microvirga flavescens sp. nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga. Int J Syst Evol Microbiol 69:667–671

    CAS  PubMed  Google Scholar 

  • Zhang Y, Zhuang JL, Pang HC, Wang YN, Li YY, Zhang JL (2019b) Paenibacillus lutes sp. nov., isolated from soil. Int J Syst Evol Microbiol 69:2354–2359

    CAS  PubMed  Google Scholar 

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Funding

This research was supported by the National Key Research and Development Program of China (2016YFC0501302) and by the National Natural Science Foundation of China (NSFC, Grant No. 31070002).

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ZJL and ZL designed research and project outline. ZL and ZY performed isolation, deposition and polyphasic taxonomy. ZL, CY and PWW performed genome analysis. ZL, PWW and ZSY drafted the manuscript. ZJL revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Jianli Zhang.

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Zhu, L., Ping, W., Zhang, S. et al. Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil. Antonie van Leeuwenhoek 114, 2219–2228 (2021). https://doi.org/10.1007/s10482-021-01674-9

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