1887

Abstract

Thirty-nine denitrifying bacterial strains closely related to one another, represented by strains TSA40 and TSA66, were isolated from rice paddy soils. Strains TSA40 and TSA66 were Gram-stain-negative, slightly curved rod-shaped, and motile by means of polar flagella. They were able to reduce nitrate, nitrite and nitrous oxide, but unable to fix atmospheric N. While strain TSA66 was able to grow autotrophically by H-dependent denitrification, strain TSA40 could not. Phylogenetic analysis suggested that they belong to the family , the order s in the class . Major components in the fatty acids (C, C cyclo, Cω7 and summed feature 3) and quinone (Q-8) also supported the affiliation of strains TSA40 and TSA66 to the family . Based on 16S rRNA gene sequence comparisons, strains TSA40 and TSA66 showed the greatest degree of similarity to JC206, CC-AFH3, U15, Z67 and LMG 2207, and lower similarities to the members of other genera. Average nucleotide identity values between the genomes of strain TSA40, TSA66 and JC206 were 75–77 %, which was lower than the threshold value for species discrimination (95–96 %). Based on the 16S rRNA gene sequence analysis in combination with physiological, chemotaxonomic and genomic properties, strains TSA40 (=JCM 17722=ATCC TSD-69) and TSA66 (=JCM 17723=DSM 25787) are the type strains of two novel species within the genus , for which the names sp. nov. and sp. nov. are proposed, respectively. We also propose the reclassification of as comb. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001875
2017-06-01
2020-01-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/6/1841.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001875&mimeType=html&fmt=ahah

References

  1. Ashida N, Ishii S, Hayano S, Tago K, Tsuji T et al. Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria. Appl Microbiol Biotechnol 2010;85:1211–1217 [CrossRef][PubMed]
    [Google Scholar]
  2. Ishii S, Ashida N, Otsuka S, Senoo K. Isolation of oligotrophic denitrifiers carrying previously uncharacterized functional gene sequences. Appl Environ Microbiol 2011;77:338–342 [CrossRef][PubMed]
    [Google Scholar]
  3. Ishii S, Ohno H, Tsuboi M, Otsuka S, Senoo K. Identification and isolation of active N2O reducers in rice paddy soil. ISME J 2011;5:1936–1945 [CrossRef][PubMed]
    [Google Scholar]
  4. Ishii S, Yamamoto M, Kikuchi M, Oshima K, Hattori M et al. Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. Appl Environ Microbiol 2009;75:7070–7078 [CrossRef][PubMed]
    [Google Scholar]
  5. Saito T, Ishii S, Otsuka S, Nishiyama M, Senoo K. Identification of novel Betaproteobacteria in a succinate-assimilating population in denitrifying rice paddy soil by using stable isotope probing. Microbes Environ 2008;23:192–200 [CrossRef][PubMed]
    [Google Scholar]
  6. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009;75:7537–7541 [CrossRef][PubMed]
    [Google Scholar]
  7. Weber KA, Hedrick DB, Peacock AD, Thrash JC, White DC et al. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002. Appl Microbiol Biotechnol 2009;83:555–565 [CrossRef][PubMed]
    [Google Scholar]
  8. Elbeltagy A, Nishioka K, Sato T, Suzuki H, Ye B et al. Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 2001;67:5285–5293 [CrossRef][PubMed]
    [Google Scholar]
  9. Baldani J, Baldani V, Döbereiner J. Herbaspirillum Baldani, Baldani, Seldin and Döbereiner 1986a, 90VP emend. Baldani, Pot, Kirchhof, Falsen, Baldani, Olivares, Hoste, Kersters, Hartmann, Gillis and Döbereiner 1996, 808. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 2 New York: Springer; 2005; pp.629–636[CrossRef]
    [Google Scholar]
  10. Tago K, Ishii S, Nishizawa T, Otsuka S, Senoo K. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields. Microbes Environ 2011;26:30–35 [CrossRef][PubMed]
    [Google Scholar]
  11. Caccavo F, Lonergan DJ, Lovley DR, Davis M, Stolz JF et al. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 1994;60:3752–3759[PubMed]
    [Google Scholar]
  12. 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 [CrossRef]
    [Google Scholar]
  13. Komagata K, Suzuki K-I. 4 Lipid and cell-wall analysis in bacterial systematics. In Colwell RR, Grigorova R. (editors) Methods in Microbiology Academic Press; 1988; pp.161–207
    [Google Scholar]
  14. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983;154:1315–1322[PubMed]
    [Google Scholar]
  15. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  16. Lu H, Fujimura R, Sato Y, Nanba K, Kamijo T et al. Characterization of Herbaspirillum- and Limnobacter-related strains isolated from young volcanic deposits in Miyake-jima Island, Japan. Microbes Environ 2008;23:66–72 [CrossRef][PubMed]
    [Google Scholar]
  17. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  18. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  19. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821–829 [CrossRef][PubMed]
    [Google Scholar]
  20. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012;7:1–14 [CrossRef][PubMed]
    [Google Scholar]
  21. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  22. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210–2215 [CrossRef][PubMed]
    [Google Scholar]
  23. Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA et al. Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 2011;7:e1002064 [CrossRef][PubMed]
    [Google Scholar]
  24. Jendrossek D. Transfer of [Pseudomonas] lemoignei, a gram-negative rod with restricted catabolic capacity, to Paucimonas gen. nov. with one species, Paucimonas lemoignei comb. nov. Int J Syst Evol Microbiol 2001;51:905–908 [CrossRef]
    [Google Scholar]
  25. Lin SY, Hameed A, Arun AB, Liu YC, Hsu YH et al. Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis. Int J Syst Evol Microbiol 2013;63:4100–4107 [CrossRef][PubMed]
    [Google Scholar]
  26. Straub D, Rothballer M, Hartmann A, Ludewig U. The genome of the endophytic bacterium H. frisingense GSF30T identifies diverse strategies in the Herbaspirillum genus to interact with plants. Front Microbiol 2013;4:168 [CrossRef]
    [Google Scholar]
  27. Aragno M, Schlegel HG. Aquaspirillum autotrophicum, a new species of hydrogen-oxidizing, facultatively autotrophic bacteria. Int J Syst Evol Bacteriol 1978;28:112–116 [CrossRef]
    [Google Scholar]
  28. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  29. Kim SJ, Moon JY, Weon HY, Hong SB, Seok SJ et al. Noviherbaspirillum suwonense sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2014;64:1552–1558 [CrossRef][PubMed]
    [Google Scholar]
  30. Sundararaman A, Srinivasan S, Lee SS. Noviherbaspirillum humi sp. nov., isolated from soil. Antonie van Leeuwenhoek 2016;109:697–704 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001875
Loading
/content/journal/ijsem/10.1099/ijsem.0.001875
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

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