1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 12

gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil No Access

Abstract

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640, isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640 were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °С and pH 7. Strain CC-CFT640 showed highest 16S rRNA gene sequence similarity to members of the genus (90.0 %, =1) followed by (89.4–90.0 %, =2), (88.8–89.8 %, =5) and (89.2–89.4 %, =2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % (=1), 74.0–74.6 % (=2), 67.5–68.3 % (=2) when compared within the type strains of the genera , and , respectively. The dominant cellular fatty acids (>5 %) included C, iso-C 10, C cyclo 8, C 2-OH and C 7/C 6. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA–DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640 is considered to represent a novel genus and species of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is CC-CFT640 (=BCRC 81219=JCM 33507).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ammonium assimilation , average nucleotide identity , denitrification , dissimilatory nitrate reduction and Rhodospirillaceae
Funding
This study was supported by the:
  • Ministry of Science and Technology, Taiwan
    • Principle Award Recipient: Chiu-ChungYoung
  • Ministry of Science and Technology, Taiwan (Award MOST 109-2634-F-005-002)
    • Principle Award Recipient: Shih-YaoLin
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005111
2021-12-08
2024-04-26
Loading full text...

Full text loading...

References

  1. Pfennig N, Trüper HG. The phototrophic bacteria. In Buchanan RE, Gibbons NE. eds Bergey’s Manual of Determinative Bacteriology, 8th edn. edn Baltimore: Williams & Wilkins; 1974 pp 24–75
     [Google Scholar]
  2. Imhoff JF. Quinones of phototrophic purple bacteria. FEMS Microbiol Lett 1984; 25:85–89 [View Article]
     [Google Scholar]
  3. Noviana Z, Vieira S, Pascual J, Fobofou SAT, Rohde M et al. Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum. Int J Syst Evol Microbiol 2020; 70:1850–1860 [View Article] [PubMed]
     [Google Scholar]
  4. Wang Z, Zhang Z, Li C, Zhang M, Zhao D et al.. Algihabitans albus gen. nov., sp. nov., isolated from a culture of the green alga Ulva prolifera. Int J Syst Evol Microbiol 2019; 69:828–832 [View Article] [PubMed]
     [Google Scholar]
  5. Wang S, Ye Z-H, Wang N-N, Mu D-S, Du Z-J. Ferruginivarius sediminum gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2019; 69:3056–3061 [View Article]
     [Google Scholar]
  6. Kim J, Jeong SE, Khan SA, Jeon CO. Hwanghaeella grinnelliae gen. nov., sp. nov., isolated from a marine red alga. Int J Syst Evol Microbiol 2019; 69:3544–3550 [View Article] [PubMed]
     [Google Scholar]
  7. Chen R-W, Wang K-X, Zhou X-F, Long C, Tian X-P et al. Indioceanicola profundi gen. nov., sp. nov., isolated from Indian Ocean sediment. Int J Syst Evol Microbiol 2018; 68:3707–3712 [View Article] [PubMed]
     [Google Scholar]
  8. Lin S-Y, Hameed A, Shen F-T, Liu Y-C, Hsu Y-H et al. Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov. Antonie van Leeuwenhoek 2014; 105:1149–1162 [View Article] [PubMed]
     [Google Scholar]
  9. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  10. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852
     [Google Scholar]
  11. Murray RGE, Doetsch RN, Robinow CF. Determination and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 32–34
     [Google Scholar]
  12. Pagnier I, Raoult D, La Scola B. Isolation and characterization of Reyranella massiliensis gen. nov., sp. nov. from freshwater samples by using an amoeba co-culture procedure. Int J Syst Evol Microbiol 2011; 61:2151–2154 [View Article]
     [Google Scholar]
  13. Lee H, Kim DU, Lee S, Park S, Yoon JH et al. Reyranella terrae sp. nov., isolated from an agricultural soil, and emended description of the genus Reyranella. Int J Syst Evol Microbiol 2017; 67:2031–2035
     [Google Scholar]
  14. Staley JT, Irgens RL, Brenner DJ. Enhydrobacter aerosaccus gen. nov., sp. nov., a gas-vacuolated, facultatively anaerobic, heterotrophic rod. Int J Syst Bacteriol 1987; 37:289–291 [View Article]
     [Google Scholar]
  15. Liu Y, Jin JH, Liu YH, Zhou YG, Liu ZP. Dongia mobilis gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a sequencing batch reactor for treatment of malachite green effluent. Int J Syst Evol Microbiol 2010; 60:2780–2785
     [Google Scholar]
  16. Lin S-Y, Liu Y-C, Hameed A, Hsu Y-H, Lai W-A et al. Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter. Int J Syst Evol Microbiol 2013; 63:3762–3768 [View Article] [PubMed]
     [Google Scholar]
  17. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H et al. Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. Int J Syst Evol Microbiol 2014; 64:138–145 [View Article] [PubMed]
     [Google Scholar]
  18. Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 1995; 45:500–506 [View Article] [PubMed]
     [Google Scholar]
  19. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 1998; 8:557–561 [View Article] [PubMed]
     [Google Scholar]
  20. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849
     [Google Scholar]
  21. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
     [Google Scholar]
  22. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  23. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  24. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  25. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  28. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  29. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian Protein Metabolism 1969; 3:21–32
     [Google Scholar]
  30. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  31. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  33. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  34. de Lajudie PM, Young JPW. ternational Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium minutes of the meeting, Budapest, 25 August 2016. Int J Syst Evol Microbiol 2017; 67:2485–2494 [View Article] [PubMed]
     [Google Scholar]
  35. Strope PK, Nickerson KW, Harris SD, Moriyama EN. Molecular evolution of urea amidolyase and urea carboxylase in fungi. BMC Evol Biol 2011; 11:80 [View Article] [PubMed]
     [Google Scholar]
  36. Anderson PM, Sung YC, Fuchs JA. The cyanase operon and cyanate metabolism. FEMS Microbiol Rev 1990; 7:247–252 [View Article] [PubMed]
     [Google Scholar]
  37. Rekha PD, Hameed A, Manzoor MAP, Suryavanshi MV, Ghate SD et al. First report of pathogenic bacterium Kalamiella piersonii isolated from urine of a kidney stone patient: draft genome and evidence for role in struvite crystallization. Pathogens 2020; 9:E711 [View Article] [PubMed]
     [Google Scholar]
  38. Haine V, Dozot M, Dornand J, Letesson J-J, De Bolle X. NnrA is required for full virulence and regulates several Brucella melitensis denitrification genes. J Bacteriol 2006; 188:1615–1619 [View Article] [PubMed]
     [Google Scholar]
  39. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  40. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  41. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
     [Google Scholar]
  42. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual. Newark, DE: MIDI; 1996
  43. Sasser M, Newark DE. MIDI Inc Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 1990; 101:
     [Google Scholar]
  44. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [View Article] [PubMed]
     [Google Scholar]
  45. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  46. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
  47. Chung EJ, Park TS, Kim KH, Jeon CO, Lee H-I et al. Erratum to: Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of iris and emended description of the genus Nitrospirillum. Antonie van Leeuwenhoek 2015; 108:1495–1496 [View Article] [PubMed]
     [Google Scholar]
  48. Kim S-J, Ahn J-H, Lee T-H, Weon H-Y, Hong S-B. Reyranella soli sp. nov., isolated from forest soil, and emended description of the genus Reyranella Pagnier et al. 2011. Int J Syst Evol Microbiol 2013; 63:3164–3167
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005111
Loading
Vineibacter terrae gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil
Int J Syst Evol Microbiol 71, 005111 (2021); https://doi.org/10.1099/ijsem.0.005111
/content/journal/ijsem/10.1099/ijsem.0.005111
/content/journal/ijsem/10.1099/ijsem.0.005111
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error