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A Bradyrhizobium isolate from a marine diatom induces nitrogen-fixing nodules in a terrestrial legume

Nature Microbiology volume 10, pages 2486–2497 (2025) Cite this article

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Abstract

Biological nitrogen fixation converts atmospheric nitrogen into ammonia, essential to the global nitrogen cycle. While cyanobacterial diazotrophs are well characterized, recent studies have revealed a broad distribution of non-cyanobacterial diazotrophs (NCDs) in marine environments, although their study is limited by poor cultivability. Here we report a previously uncharacterized Bradyrhizobium isolated from the marine diatom Phaeodactylum tricornutum. Phylogenomic analysis places the strain within photosynthetic Bradyrhizobium, suggesting evolutionary adaptations to marine and terrestrial niches. Average nucleotide identity supports its classification as a previously undescribed species. Remarkably, inoculation experiments showed that the isolate induced nitrogen-fixing nodules in the Aeschynomene indica legume, pointing to symbiotic capabilities across ecological boundaries. Pangenome analysis and metabolic predictions indicate that this isolate shares more features with terrestrial photosynthetic Bradyrhizobium than with marine NCDs. Overall, these findings suggest that symbiotic interactions could evolve across different ecological niches, and raise questions about the evolution of nitrogen fixation and microbe–host interactions.

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Fig. 1: Bradyrhizobium genome features and comparative genome analysis.
The alternative text for this image may have been generated using AI.
Fig. 2: Maximum likelihood phylogenomic tree showing the positioning of the marine Bradyrhizobium sp. phaeo 1521 within the diversity of terrestrial Bradyrhizobium.
The alternative text for this image may have been generated using AI.
Fig. 3: Pangenome analysis of Bradyrhizobium sp. phaeo 1521.
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Fig. 4: Photosynthesis assay of Bradyrhizobium sp. phaeo 1521.
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Fig. 5: The marine Bradyrhizobium sp. phaeo 1521 nodulates the A. indica legume species.
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Data availability

Data are available under BioProject PRJNA923279 and BioSample SAMN33017024. Requests for access to the isolate should be directed to the corresponding author (tirichine-l@univ-nantes.fr), please note, however, that the isolate is the property of the CNRS and any transfer must be handled through the appropriate institutional channels and with a Material Transfer Agreement. The authors are not authorized to distribute the isolate independently.

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  • 02 March 2026

    In the version of this article initially published, the data availability section did not include details on authorized access and materials transfer agreements, as are now amended in the HTML and PDF versions of the article.

References

  1. Falkowski, P. G. Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature 387, 272–275 (1997).

    Article  CAS  Google Scholar 

  2. Davies-Barnard, T. & Friedlingstein, P. The global distribution of biological nitrogen fixation in terrestrial natural ecosystems. Global Biogeochem. Cycles https://doi.org/10.1029/2019GB006387Received (2020).

  3. Mus, F., Alleman, A. B., Pence, N., Seefeldt, L. C. & Peters, J. W. Exploring the alternatives of biological nitrogen fixation. Metallomics 10, 523–538 (2018).

    Article  CAS  PubMed  Google Scholar 

  4. Ureta, A. & Nordlund, S. Evidence for conformational protection of nitrogenase against oxygen in Gluconacetobacter diazotrophicus by a putative FeSII protein. J. Bacteriol. 184, 5805–5809 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Munoz-Marin, M. D. C. et al. The Transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A). mBio https://doi.org/10.1128/mBio.02495-18 (2019).

  6. Grosskopf, T. et al. Doubling of marine dinitrogen-fixation rates based on direct measurements. Nature 488, 361–364 (2012).

    Article  CAS  PubMed  Google Scholar 

  7. Delmont, T. O. et al. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME J. 16, 927–936 (2022).

    Article  CAS  PubMed  Google Scholar 

  8. Delmont, T. O. et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat. Microbiol. 3, 804–813 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Chakraborty, S. et al. Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles. Nat. Commun. 12, 4085 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Harding, K. J. et al. Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre. Nat. Commun. 13, 6979 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Chandola, U. et al. Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment. Genome Biol. 26, 146 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chaumier, T. et al. Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum. ISME Commun. 4, ycad008 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Avontuur, J. R. et al. Genome-informed Bradyrhizobium taxonomy: where to from here? Syst. Appl. Microbiol. 42, 427–439 (2019).

    Article  PubMed  Google Scholar 

  14. Kojadinovic-Sirinelli, M. et al. Exploring the microbiome of the “star” freshwater diatom Asterionella formosa in a laboratory context. Environ. Microbiol. 20, 3601–3615 (2018).

    Article  CAS  PubMed  Google Scholar 

  15. Ciufo, S. et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int. J. Syst. Evol. Microbiol. 68, 2386–2392 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Richter, M. & Rossello-Mora, R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl Acad. Sci. USA 106, 19126–19131 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Ling, L. et al. Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup. ISME J. 19, wraf030 (2025).

  18. Salazar, E. et al. Characterization of the NifA-RpoN regulon in Rhizobium etli in free life and in symbiosis with Phaseolus vulgaris. Appl. Environ. Microbiol. 76, 4510–4520 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tao, J., Wang, S., Liao, T. & Luo, H. Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages. ISME J. 15, 3195–3206 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Schubert, K. R. & Evans, H. J. Hydrogen evolution: a major factor affecting the efficiency of nitrogen fixation in nodulated symbionts. Proc. Natl Acad. Sci. USA 73, 1207–1211 (1976).

    Article  CAS  PubMed  Google Scholar 

  21. Albrecht, S. L. et al. Hydrogenase in Rhizobium japonicum increases nitrogen fixation by nodulated soybeans. Science 203, 1255–1257 (1979).

    Article  CAS  PubMed  Google Scholar 

  22. Huichalaf, C. et al. In vivo overexpression of frataxin causes toxicity mediated by iron–sulfur cluster deficiency. Mol. Ther. Methods Clin. Dev. 24, 367–378 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sauer, M., Hantke, K. & Braun, V. Sequence of the fhuE outer-membrane receptor gene of Escherichia coli K12 and properties of mutants. Mol. Microbiol. 4, 427–437 (1990).

    Article  CAS  PubMed  Google Scholar 

  24. Sauer, M., Hantke, K. & Braun, V. Feric-coprogen receptor FhuE of Escherichia coli: processing and sequence common to all TonB-dependent outer membrane receptor proteins. J. Bacteriol. 169, 2044–2049 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Oldroyd, G. E. Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat. Rev. Microbiol. 11, 252–263 (2013).

    Article  CAS  PubMed  Google Scholar 

  26. Giraud, E. et al. Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria. Nature 417, 202–205 (2002).

    Article  CAS  PubMed  Google Scholar 

  27. Giraud, E. et al. Two distinct crt gene clusters for two different functional classes of carotenoid in Bradyrhizobium. J. Biol. Chem. 279, 15076–15083 (2004).

    Article  CAS  PubMed  Google Scholar 

  28. Okazaki, S. et al. Rhizobium–legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS. ISME J. 10, 64–74 (2016).

    Article  CAS  PubMed  Google Scholar 

  29. Czernic, P. et al. Convergent evolution of endosymbiont differentiation in dalbergioid and inverted repeat-lacking clade legumes mediated by nodule-specific cysteine-rich peptides. Plant Physiol. 169, 1254–1265 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  30. Bonaldi, K. et al. Nodulation of Aeschynomene afraspera and A. indica by photosynthetic Bradyrhizobium Sp. strain ORS285: the nod-dependent versus the nod- independent symbiotic interaction. Mol. Plant Microbe Interact. 24, 1359–1371 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Rosselli, R. et al. Pangenomics of the symbiotic Rhizobiales. Core and accessory functions across a group endowed with high levels of genomic plasticity. Microorganisms https://doi.org/10.3390/microorganisms9020407 (2021).

  32. Gourion, B. et al. Bacterial RuBisCO is required for efficient Bradyrhizobium/Aeschynomene symbiosis. PLoS ONE 6, e21900 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hall, J. P. J., Brockhurst, M. A. & Harrison, E. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. Phil. Trans. R. Soc. Lond. B https://doi.org/10.1098/rstb.2016.0424 (2017).

  34. Yurkov, V. V. & Beatty, J. T. Aerobic anoxygenic phototrophic bacteria. Microbiol. Mol. Biol. Rev. 62, 695–724 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Molouba, F. et al. Photosynthetic bradyrhizobia from Aeschynomene spp. are specific to stem-nodulated species and form a separate 16S ribosomal DNA restriction fragment length polymorphism group. Appl. Environ. Microbiol. 65, 3084–3094 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Giraud, E., Hannibal, L., Fardoux, J., Vermeglio, A. & Dreyfus, B. Effect of Bradyrhizobium photosynthesis on stem nodulation of Aeschynomene sensitiva. Proc. Natl Acad. Sci. USA 97, 14795–14800 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. John, N. & Thangavel, M. Isolation, screening and identification of marine bacteria for the plant growth promoting activities. Global J. Res. Anal. https://doi.org/10.36106/gjra (2015).

  38. Duarte, B. et al. Marine Plant Growth Promoting Bacteria (PGPB) inoculation technology: testing the effectiveness of different application methods to improve tomato plants tolerance against acute heat wave stress. Plant Stress https://doi.org/10.1016/j.stress.2024.100434 (2024).

  39. Vincent, J. A Manual for the Practical Study of Root-nodule Bacteria (Blackwell Scientific, 1970).

  40. Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016).

    Article  CAS  PubMed  Google Scholar 

  42. Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience https://doi.org/10.1093/gigascience/giab008 (2021).

  43. Sant’Anna, F. H. et al. Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy. Crit. Rev. Microbiol. 45, 182–200 (2019).

    Article  Google Scholar 

  44. Eren, A. M. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat. Microbiol. 6, 3–6 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Camuel, A. et al. Widespread Bradyrhizobium distribution of diverse Type III effectors that trigger legume nodulation in the absence of Nod factor. ISME J. 17, 1416–1429 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Lee, M. D. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 35, 4162–4164 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Vallenet, D. et al. MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Res. 48, D579–D589 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Rasko, D. A. et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. 190, 6881–6893 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Marcais, G. et al. MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Delmont, T. O. & Eren, A. M. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 6, e4320 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

    Article  CAS  PubMed  Google Scholar 

  55. Ehrhardt, D. W., Atkinson, E. M. & Long, S. R. Depolarization of alfalfa root hair membrane potential by Rhizobium meliloti Nod factors. Science 256, 998–1000 (1992).

    Article  CAS  PubMed  Google Scholar 

  56. Songwattana, P. et al. Identification of type III effectors modulating the symbiotic properties of Bradyrhizobium vignae strain ORS3257 with various Vigna species. Sci. Rep. 11, 4874 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Tanaka, A. et al. Ultrastructure and membrane traffic during cell division in the marine pennate diatom Phaeodactylum tricornutum. Protist 166, 506–521 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Maillard, M., Stephant, N., Tanaka, A. & Tirichine, L. Comprehensive protocol for preparing diatom cell samples and associated bacterial consortia for scanning electron microscopy. STAR Protoc. 5, 103380 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank C. Pruvost for technical assistance in routine laboratory procedures. L.T. acknowledges support from the region of Pays de la Loire (ConnecTalent EPIALG project), Epicycle ANR project (ANR-19-CE20- 0028-02) and µAlgaNIF France–Japan International Research Project. U.C. was supported by grant 998UMR6286 Connect Talent EpiAlg from Région Pays de la Loire to L.T. E.G. and A.C. were supported by a grant from the French National Research Agency (‘ET-Nod’; ANR-20-CE20-0012-01). We thank the bioinformatics core facility of Nantes University (BiRD Biogenouest) for technical support.

Author information

Authors and Affiliations

  1. Nantes Université, CNRS, US2B, UMR 6286, Nantes, France

    Udita Chandola, Eric Manirakiza, Margaux Maillard, Louis Josselin Lavier Aydat, Camille Trottier, Timothée Chaumier & Leïla Tirichine

  2. PHIM Plant Health Institute of Montpellier, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France

    Alicia Camuel & Eric Giraud

  3. Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, Japan

    Atsuko Tanaka

  4. Institute for Marine and Antarctic Studies (IMAS), Ecology and Biodiversity Centre, University of Tasmania, Hobart, Tasmania, Australia

    Leïla Tirichine

Authors
  1. Udita Chandola
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  2. Eric Manirakiza
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  3. Margaux Maillard
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Contributions

L.T. conceived and designed the study. U.C. contributed to the study design, conducted most of the experiments and performed the ANI analysis, pangenome analyses, metabolite predictions, annotation of the Bradyrhizobium genome and phylogenetic analyses shown in Extended Data Figs. 1 and 3. A.C. carried out the inoculation experiments, the photosynthetic assay and the phylogenetic analysis presented in Fig. 2. M.M. performed the SEM analysis. A.T. conducted the TEM analysis. L.J.L.A. assisted with experimental work. C.T. generated the initial assembly of the Bradyrhizobium genome. T.C. and E.M. performed the genome assembly, annotation and contributed to the overall bioinformatic analysis. E.G. supervised the inoculation experiments and the Bradyrhizobium phylogeny. U.C., E.G. and L.T. analysed and interpreted the data. U.C. drafted the manuscript. L.T. wrote the manuscript with input from all authors. L.T. supervised and coordinated the study. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Eric Giraud or Leïla Tirichine.

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The authors declare no competing interests.

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Nature Microbiology thanks Tom O. Delmont and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Whole genome phylogeny of B. sp. phaeo 1521 with closest marine and terrestrial NCDs.

Anvi’o based 71 single copy core gene phylogenetic representation of Bradyrhizobium sp. phaeo 1521 (indicated in bold) in comparison to closest terrestrial Bradyrhizobium selected from MicroScope Platform, 1888 TARA MAGs and two non-diazotrophic Bradyrhizobium genera used as outliers. The phylogenetic tree was constructed using Geneious 11.0.5 and visualised in iTOL.

Extended Data Fig. 2 High resolution electron microscopy images of Bradyrhizobium sp. phaeo 1521 bacterial cells.

a,b, scanning electron microscopy showing rod shaped B. sp. phaeo 1521 cells with a subpolar flagellum. Micrographs in Extended Data Fig. 2a, b are representative of results obtained from 30 independent observations, showing consistent outcomes. c,d, Transmission electron microscopy of B. sp. phaeo 1521 representing bacterial cells with clearly defined cell wall (inverted triangle), with granules (black asterisk) localized at the capsule (black triangle) and presence of ribosomes as dark grainy entities (black arrow) and large bubble-like vacuoles/vesicles (blue asterisk) in some cells.

Extended Data Fig. 3 Phylogenetic analysis of Bradyrhizobium sp. phaeo 1521 fra gene identified through pangenome analysis.

NCBI BLAST output of closely related bacterial sequences from the fra gene of Bradyrhizobium sp. phaeo 1521 were used for phylogenetic analysis. Geneious platform with parameters, MUSCLE for sequence alignment and Neighbor-joining for tree building were used. The bootstrap values represented from 0–1 with replicates of 100. The tree was visualized in Itol.

Extended Data Fig. 4 Phylogenetic analysis of Bradyrhizobium sp. phaeo 1521 fhuE gene identified through pangenome analysis.

NCBI BLAST output of closely related bacterial sequences from the fhuE gene of Bradyrhizobium sp. phaeo 1521 were used for phylogenetic analysis. Geneious platform with parameters, MUSCLE for sequence alignment and Neighbor-joining for tree building were used. The bootstrap values represented from 0–1 with replicates of 100. The tree was visualized in Itol.

Supplementary information

Supplementary Information (download PDF )

Extended File 1. List of 71 single-copy genes used for phylogeny.

Reporting Summary (download PDF )

Supplementary Data 1 (download XLSX )

Selected genes description.

Supplementary Data 2 (download XLSX )

Tab 1: genes specific to Bradyrhizobium sp. Phaeo 1521 and not shared with terrestrial and marine bacteria. Tab 2: genes specifically present in Bradyrhizobium sp. Phaeo 1521 for analysis with Bradyrhizobium sp. Btai and Bradyrhizobium denitrificans LMG8443 (Terrestrial genome). Tab 3: genes specifically present in Bradyrhizobium sp. Phaeo 1521 for analysis with TARA_ARC_108_MAG_00008 and TARA_MED_95_MAG_00018 (marine MAGs).

Supplementary Data 3 (download XLSX )

Combined data for Fig. 3b–d indicating genome/MAG size, total number of genes annotated for each bacterium using COG20 and percentage of genes shared by each bacterium with Bradyrhizobium sp. phaeo 1521.

Supplementary Data 4 (download XLSX )

Tab 1: Fra and Tab 2: FhuE sequence information used to build phylogenetic tree for genes specifically present in Bradyrhizobium sp. Phaeo 1521 for pangenomic analysis with terrestrial (Bradyrhizobium sp. Btai and Bradyrhizobium denitrificans LMG8443) and marine (TARA_ARC_108_MAG_00008 and TARA_MED_95_MAG_00018) bacteria.

Supplementary Data 5 (download PDF )

Anvi’o -7.1-based metabolic pathway prediction for Bradyrhizobium sp. phaeo 1521: 253 complete/absolute true (green), partial/significantly true (yellow) or incomplete/false (red) pathways were detected.

Supplementary Data 6 (download XLSX )

Selected KEGG modules were used to assess pathway completeness. A completeness value of 1.0 indicates a fully complete pathway. Modules with 75-99% completeness are considered significant (TRUE) predictions, while those below 75% are considered insignificant (FALSE).

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Chandola, U., Manirakiza, E., Maillard, M. et al. A Bradyrhizobium isolate from a marine diatom induces nitrogen-fixing nodules in a terrestrial legume. Nat Microbiol 10, 2486–2497 (2025). https://doi.org/10.1038/s41564-025-02105-5

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