1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 9

sp. nov., a methylotrophic nitrogen-fixing species isolated from raised bog Free

Abstract

Nitrogen-fixing bacterial strain, designated B2, was isolated from methane-oxidation enrichment originating from a -dominated raised peatland in Tver region, Russia, and its phenotypic, chemotaxonomic and genomic characteristics were investigated. Cells of isolate were Gram-negative, aerobic, rod or spiral-shaped, with motility provided by a single polar flagellum in liquid media and peritrichous flagella on solid media. Strain was able to grow at 15–40 °C, pH 5.5–8.5 and tolerated NaCl to 2.0 % (w/v). Strain B2 gave positive amplification for dinitrogen reductase ( gene) and acetylene reduction activity was recorded up to 1250 nmol ethylene h (mg protein). Analysis of 16S rRNA showed that B2 represents a member of the genus and had the highest sequence similarity with SgZ-5 (97.92 %). The predominant quinone system was ubiquinone Q-10 and the major fatty acids were Cω7, Cω7 and C. The strain was facultative methylotrophic and used methanol and formate for the growth. Genome sequencing revealed a genome size of 8.0 Mbp and a G+C content of 67.8 mol%. The aFI genes encoding methanol dehydrogenase were absent, but a homologous F gene was detected. The genes encoding enzymes involved in the biosynthesis of tetrahydromethanopterin (HMPT) (formaldehyde oxidation) and NAD-linked formate dehydrogenase () were identified. Pairwise determined whole genome average nucleotide identity (gANI) values confirmed that strain B2 represents a novel species, for which we propose the name sp. nov. with the type strain B2 (VKM B-3233, КСТС 62613).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Azospirillum , genome , methylotrophy , raised bog and Rhodospirillaceae
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003560
2019-09-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/9/2787.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003560&mimeType=html&fmt=ahah

References

  1. Tarrand JJ, Krieg NR, Döbereiner J. A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Can J Microbiol 1978; 24:967–980 [View Article][PubMed]
     [Google Scholar]
  2. Cassán F, Diaz-Zorita M. Azospirillum sp. in current agriculture: From the laboratory to the field. Soil Biology and Biochemistry 2016; 103:117–130 [View Article]
     [Google Scholar]
  3. Cassán F, Maiale S, Masciarelli O, Vidal A, Luna V et al. Cadaverine production by Azospirillum brasilense and its possible role in plant growth promotion and osmotic stress mitigation. Eur J Soil Biol 2009; 45:12–19 [View Article]
     [Google Scholar]
  4. Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA et al. Azospirillum soli sp. nov., a nitrogen-fixing species isolated from agricultural soil. Int J Syst Evol Microbiol 2015; 65:4601–4607 [View Article][PubMed]
     [Google Scholar]
  5. Young CC, Hupfer H, Siering C, Ho MJ, Arun AB et al. Azospirillum rugosum sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2008; 58:959–963 [View Article][PubMed]
     [Google Scholar]
  6. Lin SY, Young CC, Hupfer H, Siering C, Arun AB et al. Azospirillum picis sp. nov., isolated from discarded tar. Int J Syst Evol Microbiol 2009; 59:761–765 [View Article][PubMed]
     [Google Scholar]
  7. Lavrinenko K, Chernousova E, Gridneva E, Dubinina G, Akimov V et al. Azospirillum thiophilum sp. nov., a diazotrophic bacterium isolated from a sulfide spring. Int J Syst Evol Microbiol 2010; 60:2832–2837 [View Article][PubMed]
     [Google Scholar]
  8. Zhou S, Han L, Wang Y, Yang G, Zhuang L et al. Azospirillum humicireducens sp. nov., a nitrogen-fixing bacterium isolated from a microbial fuel cell. Int J Syst Evol Microbiol 2013; 63:2618–2624 [View Article][PubMed]
     [Google Scholar]
  9. Young CC, Lin SY, Shen FT, Lai WA. Molecular tools for identification and characterization of plant growth promoting rhizobacteria with emphasis in Azospirillum spp. In Cassa´n FD, Okon Y, Creus CM. (editors) In Handbook for Azospirillum New York: 2015 pp. 27–44
     [Google Scholar]
  10. Anandham R, Heo J, Krishnamoorthy R, Senthilkumar M, Gopal NO et al. Azospirillum ramasamyi sp. nov., a novel diazotrophic bacterium isolated from fermented bovine products. Int J Syst Evol Microbiol 2019; 69:1369–1375 [View Article][PubMed]
     [Google Scholar]
  11. Yang Y, Zhang R, Feng J, Wang C, Chen J. Azospirillum griseum sp. nov., isolated from lakewater. Int J Syst Evol Microbiol 2019; 28: [View Article][PubMed]
     [Google Scholar]
  12. Maroniche GA, García JE, Salcedo F, Creus CM. Molecular identification of Azospirillum spp.: Limitations of 16S rRNA and qualities of rpoD as genetic markers. Microbiol Res 2017; 195:1–10 [View Article][PubMed]
     [Google Scholar]
  13. Sirin AA, Vompersky SE, Nazarov NA. Influence of forest drainage on river runoff regime: main concepts and examples from Central part of the USSR European territory. Ambio 1991; 20:334–339
     [Google Scholar]
  14. Kravchenko I, Kizilova A, Menko E, Sirin A. Methane cycling microbial communities in natural and drained sites of Taldom Peatland, Moscow Region, Russia. Annu Res Rev Biol 2015; 6:121–132 [View Article]
     [Google Scholar]
  15. Glukhova TV, Sirin AA. Losses of soil carbon upon a Fire on a drained forested raised bog. Eurasian Soil Science 2018; 51:542–549 [View Article]
     [Google Scholar]
  16. Slobodova NV, Kolganova TV, Boulygina ES, Kuznetsov BB, Tourova TP et al. Comparative characterization of methanotrophic enrichments by serological and molecular methods. Microbiology 2006; 75:336–342 [View Article]
     [Google Scholar]
  17. Eckert B, Weber OB, Kirchhof G, Halbritter A, Stoffels M et al. Azospirillum doebereinerae sp. nov., a nitrogen-fixing bacterium associated with the C4-grass Miscanthus. Int J Syst Evol Microbiol 2001; 51:17–26 [View Article][PubMed]
     [Google Scholar]
  18. Cáceres EA. Improved Medium for Isolation of Azospirillum spp. Appl Environ Microbiol 1982; 44:990–991[PubMed]
     [Google Scholar]
  19. Grouzdev DS, Tikhonova EN, Krutkina MS, Kravchenko IK. Genome sequence of methylotrophic Azospirillum sp. Strain B2, isolated from a raised Sphagnum Bog. Genome Announc 2018; 6:e0049218 [View Article][PubMed]
     [Google Scholar]
  20. Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001; Chapter 2:2.4.1–2.4.2 [View Article][PubMed]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2016; 33:1870–1874
     [Google Scholar]
  23. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article][PubMed]
     [Google Scholar]
  24. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:243–273 [View Article][PubMed]
     [Google Scholar]
  25. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article][PubMed]
     [Google Scholar]
  26. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
     [Google Scholar]
  27. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article][PubMed]
     [Google Scholar]
  28. Minh BQ, Nguyen MA, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 2013; 30:1188–1195 [View Article][PubMed]
     [Google Scholar]
  29. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High-throughput ANI analysis of 90 K prokaryotic genomes reveals clear species boundaries. bioRxiv 2017225–342
     [Google Scholar]
  30. 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]
  31. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. Peng G, Wang H, Zhang G, Hou W, Liu Y et al. Azospirillum melinis sp. nov., a group of diazotrophs isolated from tropical molasses grass. Int J Syst Evol Microbiol 2006; 56:1263–1271 [View Article][PubMed]
     [Google Scholar]
  34. Marusina AI, Boulygina ES, Kuznetsov BB, Tourova TP, Kravchenko IK et al. A system of oligonucleotide primers for the amplification of nifH genes of different taxonomic groups of prokaryotes. Microbiology 2001; 70:73–78 [View Article]
     [Google Scholar]
  35. Slobodkina GB, Panteleeva AN, Kostrikina NA, Kopitsyn DS, Bonch-Osmolovskaya EA et al. Tepidibacillus fermentans gen. nov., sp. nov.: a moderately thermophilic anaerobic and microaerophilic bacterium from an underground gas storage. Extremophiles 2013; 17:833–839 [View Article][PubMed]
     [Google Scholar]
  36. Xie CH, Yokota A. Azospirillum oryzae sp. nov., a nitrogen-fixing bacterium isolated from the roots of the rice plant Oryza sativa . Int J Syst Evol Microbiol 2005; 55:1435–1438 [View Article][PubMed]
     [Google Scholar]
  37. Doroshenko EV, Boulygina ES, Spiridonova EM, Tourova TP, Kravchenko IK. Isolation and characterization of nitrogen-fixing bacteria of the genus Azospirillum from the soil of a Sphagnum peat bog. Microbiology 2007; 76:93–101 [View Article]
     [Google Scholar]
  38. Ben Dekhil S, Cahill M, Stackebrandt E, Sly LI. Transfer of Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum as Azospirillum largomobile comb. nov., and Elevation of Conglomeromonas largomobilis subsp. parooensis to the new type species of Conglomeromonas, Conglomeromonas parooensis sp. nov. Syst Appl Microbiol 1997; 20:72–77 [View Article]
     [Google Scholar]
  39. Spiridonova EM, Berg IA, Kolganova TV, Ivanovskiĭ RN, Kuznetsov BB et al. [An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups]. Mikrobiologiia 2004; 73:316–325 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003560
Loading
Azospirillum palustre sp. nov., a methylotrophic nitrogen-fixing species isolated from raised bog
Int J Syst Evol Microbiol 69, 2787 (2019); https://doi.org/10.1099/ijsem.0.003560
/content/journal/ijsem/10.1099/ijsem.0.003560
/content/journal/ijsem/10.1099/ijsem.0.003560
Loading

Data & Media loading...

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