1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 3

sp. nov., isolated from a root nodule of No Access

Abstract

Strain UY79 was isolated from a root nodule of , collected at the Esteros de Farrapos National Park, Río Negro, Uruguay. Cells were non-motile Gram-variable rods with central to subterminal oval to ellipsoidal endospores that swell the sporangia. Growth was observed in the range of 15–42 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0–8.0) and with up to 3 % (w/v) NaCl (optimum, 1–2 %). Strain UY79 was facultative anaerobic, catalase-positive and oxidase-negative. According to the results of 16S rRNA gene sequence analysis, UY79 belongs to the genus and is closely related to MS2379, BD-57, ATCC 842 and PB172, exhibiting 99.4, 99.0, 99.0 and 98.9% sequence identity, respectively. Average nucleotide identity and digital DNA–DNA hybridization values with the most closely related type strains were 74.3–88.6% and 38.2–48.7 %, respectively. Major fatty acids (>10 %) were anteiso-C, iso-C and C. Menaquinones MK-7 and MK-6 were the only isoprenoid quinones detected. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. Spermidine was the predominant polyamine. The DNA G+C content based on the draft genome sequence was 46.34 mol%. Based on the current polyphasic study, UY79 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is UY79 (=CCM 9147=CGMCC 1.19038).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biocontrol , Paenibacillus , Paenibacillus polymyxa complex , root colonization and root nodule bacteria
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005294
2022-03-24
2024-05-01
Loading full text...

Full text loading...

References

  1. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 1993; 64:253–260 [View Article] [PubMed]
     [Google Scholar]
  2. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 1997; 47:289–298 [View Article] [PubMed]
     [Google Scholar]
  3. Behrendt U, Schumann P, Stieglmeier M, Pukall R, Augustin J et al. Characterization of heterotrophic nitrifying bacteria with respiratory ammonification and denitrification activity-description of Paenibacillus uliginis sp. nov., an inhabitant of fen peat soil and Paenibacillus purispatii sp. nov., isolated from a spacecraft assembly clean room. Syst Appl Microbiol 2010; 33:328–336 [View Article] [PubMed]
     [Google Scholar]
  4. Huang Z, Zhao F, Li YH. Isolation of Paenibacillus tumbae sp. nov., from the tomb of the emperor Yang of the Sui dynasty, and emended description of the genus Paenibacillus. Antonie van Leeuwenhoek 2017; 110:357–364 [View Article] [PubMed]
     [Google Scholar]
  5. Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. Bergey’s Manual of Systematics of Archaea and Bacteria Hooken, UK: John Wiley & Sons, Ltd; 2015 pp 1–40
     [Google Scholar]
  6. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  7. De Meyer SE, De Beuf K, Vekeman B, Willems A. A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium). Soil Biol Biochem 2015; 83:1–11 [View Article]
     [Google Scholar]
  8. Ali MA, Lou Y, Hafeez R, Li X, Hossain A et al. Functional analysis and genome mining reveal high potential of biocontrol and plant growth promotion in nodule-inhabiting bacteria within Paenibacillus polymyxa complex. Front Microbiol 2020; 11:1–16 [View Article] [PubMed]
     [Google Scholar]
  9. Pereira-Gómez M, Ríos C, Zabaleta M, Lagurara P, Galvalisi U et al. Native legumes of the Farrapos protected area in Uruguay establish selective associations with rhizobia in their natural habitat. Soil Biol Biochem 2020; 148:107854 [View Article]
     [Google Scholar]
  10. Taulé C, Zabaleta M, Mareque C, Platero R, Sanjurjo L et al. New betaproteobacterial Rhizobium strains able to efficiently nodulate Parapiptadenia rigida (Benth.) Brenan. Appl Environ Microbiol 2012; 78:1692–1700 [View Article] [PubMed]
     [Google Scholar]
  11. Platero R, James EK, Rios C, Iriarte A, Sandes L et al. Novel Cupriavidus strains isolated from root nodules of native Uruguayan Mimosa species. Appl Environ Microbiol 2016; 82:3150–3164 [View Article] [PubMed]
     [Google Scholar]
  12. Vincent JM. A Manual for the Practical Study of the Root-Nodule Bacteria Oxford, U.K: International Biological Programme, Blackwell Scientific; 1970
     [Google Scholar]
  13. Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB et al. Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2021; 71:1–9 [View Article]
     [Google Scholar]
  14. 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]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  21. Costa A, Corallo B, Amarelle V, Stewart S, Pan D et al. Paenibacillus sp. Strain UY79, isolated from a root nodule of Arachis villosa, displays a broad spectrum of antifungal activity. Appl Environ Microbiol 2022; 88:e0164521 [View Article] [PubMed]
     [Google Scholar]
  22. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Syst Appl Microbiol 1988; 10:99–100 [View Article]
     [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  27. 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 [View Article] [PubMed]
     [Google Scholar]
  28. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  29. Lefort V, Desper R, Gascuel O. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  30. Farris JS. Estimating phylogenetic trees from distance matrices. The American Naturalist 1972; 106:645–668 [View Article]
     [Google Scholar]
  31. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article] [PubMed]
     [Google Scholar]
  32. Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res 2020; 48:8883–8900 [View Article] [PubMed]
     [Google Scholar]
  33. Schumann P. Peptidoglycan Structure. In Rainey F, Oren A. eds Methods in Microbiology vol 38 Cambridge, USA: Academic Press; pp 101–129
     [Google Scholar]
  34. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Tech Note 101 1990 pp 1–6
     [Google Scholar]
  35. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202
     [Google Scholar]
  36. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  37. Altenburgera P, Kämpferb P, Makristathisc A, Lubitza W, Bussea H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
     [Google Scholar]
  38. Velazquez LF, Rajbanshi S, Guan S, Hinchee M, Welsh A. Paenibacillus ottowii sp. nov. isolated from a fermentation system processing bovine manure. Int J Syst Evol Microbiol 2020; 70:1463–1469 [View Article] [PubMed]
     [Google Scholar]
  39. Kämpfer P, Rosselló-Mora R, Falsen E, Busse HJ, Tindall BJ. Cohnella thermotolerans gen. nov., sp. nov., and classification of “Paenibacillus hongkongensis” as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 2006; 56:781–786 [View Article]
     [Google Scholar]
  40. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
     [Google Scholar]
  41. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [View Article]
     [Google Scholar]
  42. Hamana K, Akiba T, Uchino F, Matsuzaki S. Distribution of spermine in bacilli and lactic acid bacteria. Can J Microbiol 1989; 35:450–455 [View Article] [PubMed]
     [Google Scholar]
  43. Kämpfer P, Falsen E, Lodders N, Martin K, Kassmannhuber J et al. Paenibacillus chartarius sp. nov., isolated from a paper mill. Int J Syst Evol Microbiol 2012; 62:1342–1347 [View Article] [PubMed]
     [Google Scholar]
  44. Glaeser SP, Falsen E, Busse HJ, Kämpfer P. Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 2013; 63:777–782 [View Article] [PubMed]
     [Google Scholar]
  45. Kämpfer P, Busse H-J, Kloepper JW, Hu C-H, McInroy JA et al. Paenibacillus cucumis sp. nov., isolated from a cucumber plant. Int J Syst Evol Microbiol 2016; 66:2599–2603 [View Article] [PubMed]
     [Google Scholar]
  46. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for Identification of Medical Bacteria Cambridge: Cambridge University Press; 2003
     [Google Scholar]
  47. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds Methods for General and Molecular Microbiology, 3rd edn. Washington, DC: ASM; 2014 pp 330–393
     [Google Scholar]
  48. Murphy JA, Campbell LL. Surface features of Bacillus polymyxa spores as revealed by scanning electron microscopy. J Bacteriol 1969; 98:737–743 [View Article] [PubMed]
     [Google Scholar]
  49. Elo S, Suominen I, Kämpfer P, Juhanoja J, Salkinoja-Salonen M et al. Paenibacillus borealis sp. nov., a nitrogen-fixing species isolated from spruce forest humus in Finland. Int J Syst Evol Microbiol 2001; 51:535–545 [View Article] [PubMed]
     [Google Scholar]
  50. Langendries S, Goormachtig S. Paenibacillus polymyxa, a Jack of all trades. Environ Microbiol 2021; 23:5659–5669 [View Article] [PubMed]
     [Google Scholar]
  51. Montefusco A, Nakamura LK, Labeda DP. Bacillus peoriae sp. nov. Int J Syst Bacteriol 1993; 43:388–390 [View Article]
     [Google Scholar]
  52. von der Weid I, Duarte GF, van Elsas JD, Seldin L. Paenibacillus brasilensis sp. nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil. Int J Syst Evol Microbiol 2002; 52:2147–2153 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005294
Loading
Paenibacillus farraposensis sp. nov., isolated from a root nodule of Arachis villosa
Int J Syst Evol Microbiol 72, 005294 (2022); https://doi.org/10.1099/ijsem.0.005294
/content/journal/ijsem/10.1099/ijsem.0.005294
/content/journal/ijsem/10.1099/ijsem.0.005294
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

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