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Microvirga pakistanensis sp. nov., a novel bacterium isolated from desert soil of Cholistan, Pakistan

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Abstract

A Gram-negative, non-spore-forming, non-pigmented, strictly aerobic and non-motile short rod bacterium, designated NCCP-1258T, was isolated from Cholistan desert soil, Bahawalpur, Pakistan. Growth of strain NCCP-1258T was observed at pH range 6.5–9.5 (optimum 7.5–8.5) and temperature range 20–45 °C (optimum 40 °C), and it tolerated 0–2 % NaCl (optimum 0.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain NCCP-1258T belongs to genus Microvirga and is most closely related to Microvirga lotononidis (98.0 %), Microvirga vignae (97.4 %), Microvirga lupini (97.2 %), Microvirga zambiensis (97.2 %) and Microvirga flocculans (97.1 %). Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA and rpoB) also confirmed the placement of strain NCCP-1258T within the genus Microvirga. DNA–DNA relatedness values of NCCP-1258T with above-mentioned type strains were less than 42 %. The DNA G+C content of strain NCCP-1258T was 64.3 mol%. Chemotaxonomic data (predominant menaquinone system was Q-10; major fatty acids were C16:0, C18:1 ω7c and C19:0 cyclo ω8c; the polar lipid profile contained diphosphatidylglycerol, phosphatidylcholine, phosphatidyl dimethyl ethanolamine and phosphatidyl ethanolamine) also supported the affiliation of strain NCCP-1258T to the genus Microvirga. On the basis of physiological and biochemical characteristics, phylogenetic analyses and DNA–DNA relatedness, strain NCCP-1258T can be distinguished from the closely related taxa and thus represents a novel species of the genus Microvirga, for which the name Microvirga pakistanensis sp. nov. is proposed with the type strain NCCP-1258T (=CGMCC 1.15074T = KCTC 42496T).

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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

    Article  CAS  PubMed  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  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 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  • Goris J, K-i Suzuki, Vos PD, Nakase T, Kersters K (1998) Evaluation of a microplate DNA–DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:1148–1153

    Article  CAS  Google Scholar 

  • Gregersen T (1978) Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5:123–127

    Article  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

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703

    Article  CAS  PubMed  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    Article  CAS  Google Scholar 

  • Li WJ, Zhang YG, Zhang YQ, Tang SK, Xu P, Xu LH, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  PubMed  Google Scholar 

  • Marmur J (1963) A procedure for the isolation of deoxyribonucleic acid from microorganisms. Method Enzymol 6:726–738

    Article  CAS  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic-acid by high-performance liquid-chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Radl V, Simões-Araújo JL, Leite J, Passos SR, Martins LM, Xavier GR, Rumjanek NG, Baldani JI, Zilli JE (2014) 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

    Article  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI Inc, Newark

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: A place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849

    Article  CAS  Google Scholar 

  • Takeda M, Suzuki I, Koizumi J (2004) Balneomonas flocculans gen. nov., sp. nov., a new cellulose-producing member of the alpha-2 subclass of Proteobacteria. Syst Appl Microbiol 27:139–145

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA 6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  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 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  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

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the Key Project of International Cooperation of Ministry of Science and Technology (MOST) (No. 2013DFA31980) and the Deanship of Scientific Research at King Saud University for funding this work through the research group no. RGP-1436–27. W.-J. Li was also supported by the Hundred Talents Program of Chinese Academy of Sciences and Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014). We are greatly thankful to Dr Julie K. Ardley from Centre for Rhizobium Studies, Murdoch University Australia for providing us type strains M. lotononidis WSM3557T, M. lupini Lut6T and M. zambiensis WSM3693T.

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Authors and Affiliations

  1. Yunnan Institute of Microbiology, Yunnan University, Kunming, People’s Republic of China

    Arshia Amin, Neeli Habib & Wen-Jun Li

  2. Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan

    Arshia Amin, Iftikhar Ahmed & Saira Abbas

  3. Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan

    Arshia Amin & Fariha Hasan

  4. PARC Institute of Advance Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan

    Iftikhar Ahmed & Saira Abbas

  5. State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Min Xiao & Wen-Jun Li

  6. Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, People’s Republic of China

    Wen-Jun Li

  7. Bioproducts Research Chair (BRC), College of Science, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia

    Wael N. Hozzein

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  1. Arshia Amin
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  2. Iftikhar Ahmed
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  3. Neeli Habib
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  5. Fariha Hasan
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  6. Min Xiao
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  7. Wael N. Hozzein
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  8. Wen-Jun Li
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Corresponding authors

Correspondence to Iftikhar Ahmed or Wen-Jun Li.

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Communicated by Erko Stackebrandt.

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Amin, A., Ahmed, I., Habib, N. et al. Microvirga pakistanensis sp. nov., a novel bacterium isolated from desert soil of Cholistan, Pakistan. Arch Microbiol 198, 933–939 (2016). https://doi.org/10.1007/s00203-016-1251-3

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  • DOI: https://doi.org/10.1007/s00203-016-1251-3

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