Skip to content
1887

Abstract

A strain, namely Oc8, was isolated from a root nodule of in Uruguay. This strain induced effective nodules in roots of , , and . Oc8 belongs to the genus according to the results of the 16S rRNA gene sequence analysis, and it forms an independent lineage within a cluster encompassing 13 described species of this genus. From them, the type strains closest related to the strain Oc8 with more than 99.5% similarity in 16S rRNA gene sequence were those of , , and (99.71%, 99.65%, 99.60% and 99.57%, respectively). A genome-based phylogeny showed that JCM 19881, CTAW11 and CTAW71 were the closest type strains to the strain Oc8. Values lower than the species cutoff of 95% and 70% were found after average nucleotide identity and digital DNA–DNA hybridization calculation between the genome of the strain Oc8 and those available genomes of the closest related species. These results, together with those of the symbiotic gene analysis, support the affiliation of this strain to the symbiovar cyanophyllae of a new species of for which the name sp. nov. is proposed. The type strain is Oc8 (=LMG 33261=CECT 30885).

Funding
This study was supported by the:
  • Instituto Nacional de Investigacion Agropecuaria, Uruguay (Award INIA L-1)
    • Principal Award Recipient: NotApplicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006973
2025-11-19
2025-12-16

Metrics

Loading full text...

Full text loading...

References

  1. Mosjidis JA. Crotalaria. In Kole C. eds Wild Crop Relatives: Genomic and Breeding Resources: Industrial Crops Berlin: Springer; 2011 pp 63–69
    [Google Scholar]
  2. Soares MB, Tavanti RFR, Rigotti AR, de Lima JP, da Silva Freddi O. Use of cover crops in the southern amazon region: what is the impact on soil physical quality. Geoderma 2021; 384:114796
    [Google Scholar]
  3. Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., erythrina brucei and glycine max growing in Ethiopia. Mol Phylogenet Evol 2012; 65:595–609 [View Article] [PubMed]
    [Google Scholar]
  4. Berriel V, Morel MA, Filippi CV, Monza J. Draft genome sequence of Bradyrhizobium sp. strain Oc8 isolated from Crotalaria ochroleuca nodule. Curr Res Microb Sci 2021; 2:100074 [View Article]
    [Google Scholar]
  5. Beukes CW, Stępkowski T, Venter SN, Cłapa T, Phalane FL et al. Crotalarieae and genisteae of the South African great escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci. Mol Phylogenet Evol 2016; 100:206–218 [View Article] [PubMed]
    [Google Scholar]
  6. Huang CT, Hish KT, Wang CN, Liu CT, Kao WY. Phylogenetic analyses of Bradyrhizobium symbionts associated with invasive Crotalaria zanzibarica and its coexisting legumes in Taiwan. Syst Appl Microbiol 2018; 41:619–628 [View Article] [PubMed]
    [Google Scholar]
  7. 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]
  8. Martinez-Romero E, Peix A, Hungria M, Mousavi SA, Martinez-Romero J et al. Guidelines for the description of rhizobial symbiovars. Int J Syst Evol Microbiol 2024; 74:006373 [View Article]
    [Google Scholar]
  9. Vincent JM. A Manual for the Practical Study of the Root-Nodule Bacteria IBP Handbook 15 Oxford: Black Well Scientific Publications; 1970
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. Rogers JS, Swofford DL. A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst Biol 1998; 47:77–89 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Fitlong WR. Fitlong. Quality filtering tool for long reads [Software] 2021 https://github.com/rrwick/Filtlong
  17. Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 2016; 32:2103–2110 [View Article] [PubMed]
    [Google Scholar]
  18. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  19. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  20. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 2015; 31:3350–3352 [View Article] [PubMed]
    [Google Scholar]
  21. Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom 2021; 7:000685 [View Article]
    [Google Scholar]
  22. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucl Acids Res 2014; 42:D206–D214 [View Article]
    [Google Scholar]
  23. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [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]
    [Google Scholar]
  25. Pourmohsenin B, Wiese A, Ziemert N. AutoMLST2: a web server for phylogeny and microbial taxonomy. Nucleic Acids Res 2025; 53:W45–W50 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  28. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
    [Google Scholar]
  29. Delamuta JRM, Menna P, Ribeiro RA, Hungria M. Phylogenies of symbiotic genes of Bradyrhizobium symbionts of legumes of economic and environmental importance in Brazil support the definition of the new symbiovars pachyrhizi and sojae. Syst Appl Microbiol 2017; 40:254–265 [View Article] [PubMed]
    [Google Scholar]
  30. Hsouna J, Gritli T, Ilahi H, Ellouze W, Mansouri M et al. Genotypic and symbiotic diversity studies of rhizobia nodulating Acacia saligna in Tunisia reveal two novel symbiovars within the Rhizobium leguminosarum complex and Bradyrhizobium. Syst Appl Microbiol 2022; 45:126343 [View Article] [PubMed]
    [Google Scholar]
  31. Hsouna J, Zouagui H, Gritli T, Ilahi H, Han J-C et al. Bradyrhizobium tunisiense sp. nov., a novel rhizobial species isolated from Acacia saligna nodules. Int J Syst Evol Microbiol 2025; 75:006807 [View Article]
    [Google Scholar]
  32. Rejili M, Bouznif B, Benabderrahim MA, Mars M. Multilocus sequencing analysis of the rhizobial symbionts isolated from Acacia salicina (Lindl.) grown in different regions in Tunisia reveals putative novel Bradyrhizobium species. World J Microbiol Biotechnol 2025; 41: [View Article]
    [Google Scholar]
  33. Morel Revetria MA, Berais-Rubio A, Giménez M, Sanjuán J, Signorelli S et al. Competitiveness and phylogenetic relationship of rhizobial strains with different symbiotic efficiency in Trifolium repens: conversion of parasitic into non-parasitic rhizobia by natural symbiotic gene transfer. Biology (Basel) 2023; 12:243 [View Article] [PubMed]
    [Google Scholar]
  34. Arnon DI, Hoagland DR. A comparison of water culture and soil as media for crop production. Science 1939; 89:512–514 [View Article] [PubMed]
    [Google Scholar]
  35. Somasegaran P, Hoben HJ. Handbook for Rhizobia Methods in Legume-Rhizobium Technology NY (USA): Springer Verlag; 1994 [View Article]
    [Google Scholar]
  36. Doetsch RN. Determinative Methods of Light Microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. eds Manual of Methods for General Bacteriology Washington: American Society for Microbiology; 1981 pp 21–33
    [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  38. Lu JK, Dou YJ, Zhu YJ, Wang SK, Sui XH et al. Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules. Int J Syst Evol Microbiol 2014; 64:1900–1905 [View Article] [PubMed]
    [Google Scholar]
  39. Chahboune R, Carro L, Peix A, Barrijal S, Velázquez E et al. Bradyrhizobium cytisi sp. nov., isolated from effective nodules of Cytisus villosus. Int J Syst Evol Microbiol 2011; 61:2922–2927 [View Article] [PubMed]
    [Google Scholar]
  40. Chahboune R, Carro L, Peix A, Ramírez-Bahena M-H, Barrijal S et al. Bradyrhizobium rifense sp. nov. isolated from effective nodules of Cytisus villosus grown in the Moroccan Rif. Syst Appl Microbiol 2012; 35:302–305 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006973
Loading
/content/journal/ijsem/10.1099/ijsem.0.006973
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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