# Complete genome sequence of Bradyrhizobium sp. 62B, a native nitrogen-fixing rhizobium isolated from peanut nodules

Fiorela Nievas, Santiago Revale, Sacha Cossovich, Emiliano Foresto, María Evangelina Carezzano, Pedro Alzari, Mariano Martinez, Mathilde Ben-Assaya, Damien Mornico, Maricel Santoro, et al.

<figure><img src="image_1.png" /></figure>

► To cite this version:

Fiorela Nievas, Santiago Revale, Sacha Cossovich, Emiliano Foresto, María Evangelina Carezzano, et al. Complete genome sequence of Bradyrhizobium sp. 62B, a native nitrogen-fixing rhizobium isolated from peanut nodules. Microbiology Resource Announcements, 2024, 13 (3), pp.e009282. 10.1128/mra.00928-23. pasteur-04567351

HAL Id: pasteur-04567351

https://pasteur.hal.science/pasteur-04567351

Submitted on 3 May 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Complete genome sequence of *Bradyrhizobium* sp. 62B, a native nitrogen-fixing rhizobium isolated from peanut nodules

Fiorela Nievas,¹ Santiago Revale,² Sacha Cossovich,¹ Emiliano Foresto,¹ María Evangelina Carezzano,¹ Pedro Alzari,³ Mariano Martínez,³ Mathilde Ben-Assaya,³ Damien Mornico,⁴ Maricel Santoro,⁵ Francisco Martínez-Abarca,⁶ Walter Giordano,¹ Pablo Bogino¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 2.

**ABSTRACT** We present the complete genome sequence of *Bradyrhizobium* sp. 62B, a strain isolated from the root nodules of peanut plants that grow in central Argentina. The genome consists of 8.15 Mbp, distributed into a chromosome of 7.29 Mbp and a plasmid of 0.86 Mbp.

**KEYWORDS** *Bradyrhizobium*

The genus *Bradyrhizobium* (1) comprises genetically diverse rhizobia, which can establish symbiosis with different legumes (2), including peanut (*Arachis hypogaea* L.) (3–5). The isolation and characterization of native nitrogen-fixing strains may be key for the development of sustainable agriculture models (6–10).

Here, we announce the complete annotated genome of *Bradyrhizobium* sp. 62B, a native strain isolated from peanut grown in central Argentina (33°06'27"S, 64°17'60"W). The strain was isolated from a single root nodule, which was sterilized, stabbed, and aerobically cultivated on YEM agar plates (11) for 7 days at 28°C (7). After restreaking to obtain a single colony, a pure culture grown on YEM liquid for 7 days at 28°C was used to confirm the symbiotic ability on peanut plants (7), and was the source of total gDNA for sequencing. DNA was obtained either with a DNeasy Blood & Tissue kit (Qiagen, MD, USA) for Illumina sequencing (P2M platform, Institut Pasteur, France), or a Wizard HMW DNA extraction kit (Promega, WI, USA) for Oxford Nanopore Tech (Oxford Genomic Centre Services, UK). The Illumina library was prepared using a Nextera XT DNA Library Preparation kit and then sequenced on an Illumina NextSeq 500 instrument with a paired-end 150 bp read configuration. Two libraries were prepared for Nanopore sequencing: one with an Oxford Nanopore Technologies Rapid Barcoding sequencing kit (SQK-RBK004, transposase fragmentation) and the other with a Native Barcoding Genomic DNA sequencing kit (SQK-LSK109 with EXP-NBD104, mechanical fragmentation). Each library was individually sequenced in two Flongle flow cells. Data were basecalled with Guppy v4.2.2, using the high-accuracy model and the --trim_barcodes option. We obtained a combination of Illumina PE reads and Nanopore long reads (Table 1). All bioinformatic analyses were performed using default parameters unless otherwise specified. Hybrid genome assembly was performed using all the libraries together with the nf-core/bacass pipeline (commit date 2021-03-23) (12). QC filtering and trimming were performed on both read sets as part of the nf-core/bacass pipeline. The assembly resulted in two contigs that were closed by manually analyzing the overlapping ends on Geneious version 2019 2.1 (13). Replicons were rotated based on the fixstart method, with *dnaA* and *repA* as the start positions for chromosome and plasmid, respectively (14), and annotated with Prokaryotic Genome Annotation Pipeline v6.6 (15–17). The whole

**Editor** Leighton Pritchard, University of Strathclyde, United Kingdom

Address correspondence to Walter Giordano, wgiordano@exa.unrc.edu.ar, or Pablo Bogino, pbogino@exa.unrc.edu.ar.

Fiorela Nievas and Santiago Revale contributed equally to this article. Author order was determined by seniority in working with peanut rhizospheric strains.

The authors declare no conflict of interest.

See the funding table on p. 3.

Received 30 September 2023

Accepted 13 February 2024

Published 22 February 2024

Copyright © 2024 Nievas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
# Complete genome sequence of *Bradyrhizobium* sp. 62B, a native nitrogen-fixing rhizobium isolated from peanut nodules

Fiorela Nievas,¹ Santiago Revale,² Sacha Cossovich,¹ Emiliano Foresto,¹ María Evangelina Carezzano,¹ Pedro Alzari,³ Mariano Martínez,³ Mathilde Ben-Assaya,³ Damien Mornico,⁴ Maricel Santoro,⁵ Francisco Martínez-Abarca,⁶ Walter Giordano,¹ Pablo Bogino¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 2.

**ABSTRACT** We present the complete genome sequence of *Bradyrhizobium* sp. 62B, a strain isolated from the root nodules of peanut plants that grow in central Argentina. The genome consists of 8.15 Mbp, distributed into a chromosome of 7.29 Mbp and a plasmid of 0.86 Mbp.

**KEYWORDS** *Bradyrhizobium*

The genus *Bradyrhizobium* (1) comprises genetically diverse rhizobia, which can establish symbiosis with different legumes (2), including peanut (*Arachis hypogaea* L.) (3–5). The isolation and characterization of native nitrogen-fixing strains may be key for the development of sustainable agriculture models (6–10).

Here, we announce the complete annotated genome of *Bradyrhizobium* sp. 62B, a native strain isolated from peanut grown in central Argentina (33°06'27"S, 64°17'60"W). The strain was isolated from a single root nodule, which was sterilized, stabbed, and aerobically cultivated on YEM agar plates (11) for 7 days at 28°C (7). After restreaking to obtain a single colony, a pure culture grown on YEM liquid for 7 days at 28°C was used to confirm the symbiotic ability on peanut plants (7), and was the source of total gDNA for sequencing. DNA was obtained either with a DNeasy Blood & Tissue kit (Qiagen, MD, USA) for Illumina sequencing (P2M platform, Institut Pasteur, France), or a Wizard HMW DNA extraction kit (Promega, WI, USA) for Oxford Nanopore Tech (Oxford Genomic Centre Services, UK). The Illumina library was prepared using a Nextera XT DNA Library Preparation kit and then sequenced on an Illumina NextSeq 500 instrument with a paired-end 150 bp read configuration. Two libraries were prepared for Nanopore sequencing: one with an Oxford Nanopore Technologies Rapid Barcoding sequencing kit (SQK-RBK004, transposase fragmentation) and the other with a Native Barcoding Genomic DNA sequencing kit (SQK-LSK109 with EXP-NBD104, mechanical fragmentation). Each library was individually sequenced in two Flongle flow cells. Data were basecalled with Guppy v4.2.2, using the high-accuracy model and the --trim_barcodes option. We obtained a combination of Illumina PE reads and Nanopore long reads (Table 1). All bioinformatic analyses were performed using default parameters unless otherwise specified. Hybrid genome assembly was performed using all the libraries together with the nf-core/bacass pipeline (commit date 2021-03-23) (12). QC filtering and trimming were performed on both read sets as part of the nf-core/bacass pipeline. The assembly resulted in two contigs that were closed by manually analyzing the overlapping ends on Geneious version 2019 2.1 (13). Replicons were rotated based on the fixstart method, with *dnaA* and *repA* as the start positions for chromosome and plasmid, respectively (14), and annotated with Prokaryotic Genome Annotation Pipeline v6.6 (15–17). The whole

**Editor** Leighton Pritchard, University of Strathclyde, United Kingdom

Address correspondence to Walter Giordano, wgiordano@exa.unrc.edu.ar, or Pablo Bogino, pbogino@exa.unrc.edu.ar.

Fiorela Nievas and Santiago Revale contributed equally to this article. Author order was determined by seniority in working with peanut rhizospheric strains.

The authors declare no conflict of interest.

See the funding table on p. 3.

**Received** 30 September 2023

**Accepted** 13 February 2024

**Published** 22 February 2024

Copyright © 2024 Nievas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
<table><caption>TABLE 1 Main metric data associated with the sequenced *Bradyrhizobium* sp. 62B strain</caption><thead><tr><th>Accession</th><th>Technology</th><th>Number of reads</th><th>Total sequencing data (Mbp)</th><th>GC content (%)</th><th>Coverage</th><th>Average length (bp)</th><th>Longest sequence (bp)</th><th>N50 (bp)</th></tr></thead><tbody><tr><td>SRR17042237</td><td>Nanopore</td><td>39,581</td><td>164.5</td><td>63.61</td><td>20</td><td>4,156</td><td>48,037</td><td>7,771</td></tr><tr><td>SRR17042238</td><td>Nanopore</td><td>5,560</td><td>24.8</td><td>63.27</td><td>3</td><td>4,453</td><td>67,593</td><td>12,925</td></tr><tr><td>SRR17042239</td><td>Nanopore</td><td>10,135</td><td>53.3</td><td>63.31</td><td>7</td><td>5,257</td><td>70,559</td><td>12,787</td></tr><tr><td>SRR17042240</td><td>Nanopore</td><td>6,531</td><td>34.6</td><td>63.73</td><td>4</td><td>5,296</td><td>66,708</td><td>12,464</td></tr><tr><td></td><td>Total Nanopore</td><td>61,807</td><td>277.2</td><td>63.54</td><td>34</td><td>4,484</td><td>70,559</td><td>8,926</td></tr><tr><td>SRR17042241</td><td>Illumina</td><td>6,537,438</td><td>965.1</td><td>63.7</td><td>119</td><td>151</td><td></td><td></td></tr></tbody></table>

genome consists of one chromosome (7,289,796 bp, G + C content 64.5%) containing a single ribosomal operon and 48 tRNAs, and a repABC plasmid (859,431 bp, G + C content 60%) (18), encoding a total of 7,518 proteins across both replicons. Average nucleotide identity analysis (ANI calculator on line version) (19) revealed taxonomic identification of 62B at the genus level, being the closest genome (97.63%) *Bradyrhizobium* sp. CCBAU 53351 (NZ_CP030059.1).

In contrast to other *Bradyrhizobium*, which generally harbor genes involved in symbiosis on chromosomic islands, the *Bradyrhizobium* sp. 62B genome contains them in the plasmid (20, 21). It also carries genes predicted to be related to conjugative transfer proteins and the type three secretion system (22), features related to broader host specificity and putative plasmid transfer toward other strains (23).

## ACKNOWLEDGMENTS

The authors thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z) for the sequencing data. The authors are also grateful to Vincent Enouf from Unité de Génétique Moléculaire des Virus à ARN - UMR3569 CNRS, Université de Paris, Centre National de Référence Virus des Infections Respiratoires (dont la grippe); to Plateforme de Microbiologie Mutualisée (P2M) and Pasteur International Bioresources network (PIBnet); to Institut Pasteur Paris for providing the resources for Illumina sequencing; and finally to Ms. F. Sgarlatta for proofreading the manuscript.

This work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT); and the Spanish Ministerio de Ciencia e Innovación research grant PID2020-113207GB-I00, including the ERDF (European Regional Development Funds) and the Biotechnology and Biosciences Research Council (BBSRC). It was also supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z and the NIHR Oxford BRC. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health.

## AUTHOR AFFILIATIONS

<footnote n="1">¹Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina</footnote>

<footnote n="2">²Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom</footnote>

<footnote n="3">³Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France</footnote>

<footnote n="4">⁴Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France</footnote>

<footnote n="5">⁵Department of Biochemistry, Max Planck for Chemical Ecology, Jena, Germany</footnote>

<footnote n="6">⁶Department of Plant and Soil Microbiology, Structure, Dynamics, and Function of Rhizobacterial Genomes, Estación Experimental del Zaidín-CSIC, Granada, Spain</footnote>
<table><caption>TABLE 1 Main metric data associated with the sequenced *Bradyrhizobium* sp. 62B strain</caption><thead><tr><th>Accession</th><th>Technology</th><th>Number of reads</th><th>Total sequencing data (Mbp)</th><th>GC content (%)</th><th>Coverage</th><th>Average length (bp)</th><th>Longest sequence (bp)</th><th>N50 (bp)</th></tr></thead><tbody><tr><td>SRR17042237</td><td>Nanopore</td><td>39,581</td><td>164.5</td><td>63.61</td><td>20</td><td>4,156</td><td>48,037</td><td>7,771</td></tr><tr><td>SRR17042238</td><td>Nanopore</td><td>5,560</td><td>24.8</td><td>63.27</td><td>3</td><td>4,453</td><td>67,593</td><td>12,925</td></tr><tr><td>SRR17042239</td><td>Nanopore</td><td>10,135</td><td>53.3</td><td>63.31</td><td>7</td><td>5,257</td><td>70,559</td><td>12,787</td></tr><tr><td>SRR17042240</td><td>Nanopore</td><td>6,531</td><td>34.6</td><td>63.73</td><td>4</td><td>5,296</td><td>66,708</td><td>12,464</td></tr><tr><td></td><td>Total Nanopore</td><td>61,807</td><td>277.2</td><td>63.54</td><td>34</td><td>4,484</td><td>70,559</td><td>8,926</td></tr><tr><td>SRR17042241</td><td>Illumina</td><td>6,537,438</td><td>965.1</td><td>63.7</td><td>119</td><td>151</td><td></td><td></td></tr></tbody></table>

genome consists of one chromosome (7,289,796 bp, G + C content 64.5%) containing a single ribosomal operon and 48 tRNAs, and a repABC plasmid (859,431 bp, G + C content 60%) (18), encoding a total of 7,518 proteins across both replicons. Average nucleotide identity analysis (ANI calculator on line version) (19) revealed taxonomic identification of 62B at the genus level, being the closest genome (97.63%) *Bradyrhizobium* sp. CCBAU 53351 (NZ_CP030059.1).

In contrast to other *Bradyrhizobium*, which generally harbor genes involved in symbiosis on chromosomic islands, the *Bradyrhizobium* sp. 62B genome contains them in the plasmid (20, 21). It also carries genes predicted to be related to conjugative transfer proteins and the type three secretion system (22), features related to broader host specificity and putative plasmid transfer toward other strains (23).

## ACKNOWLEDGMENTS

The authors thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z) for the sequencing data. The authors are also grateful to Vincent Enouf from Unité de Génétique Moléculaire des Virus à ARN - UMR3569 CNRS, Université de Paris, Centre National de Référence Virus des Infections Respiratoires (dont la grippe); to Plateforme de Microbiologie Mutualisée (P2M) and Pasteur International Bioresources network (PIBnet); to Institut Pasteur Paris for providing the resources for Illumina sequencing; and finally to Ms. F. Sgarlatta for proofreading the manuscript.

This work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT); and the Spanish Ministerio de Ciencia e Innovación research grant PID2020-113207GB-I00, including the ERDF (European Regional Development Funds) and the Biotechnology and Biosciences Research Council (BBSRC). It was also supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z and the NIHR Oxford BRC. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health.

## AUTHOR AFFILIATIONS

<footnote n="1">¹Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina</footnote>

<footnote n="2">²Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom</footnote>

<footnote n="3">³Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France</footnote>

<footnote n="4">⁴Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France</footnote>

<footnote n="5">⁵Department of Biochemistry, Max Planck for Chemical Ecology, Jena, Germany</footnote>

<footnote n="6">⁶Department of Plant and Soil Microbiology, Structure, Dynamics, and Function of Rhizobacterial Genomes, Estación Experimental del Zaidín-CSIC, Granada, Spain</footnote>
## AUTHOR ORCIDs

Pedro Alzari http://orcid.org/0000-0002-4233-1903

Walter Giordano http://orcid.org/0000-0002-2436-922X

Pablo Bogino http://orcid.org/0000-0001-7841-6119

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s)</td><td>Author(s)</td></tr></thead><tbody><tr><td>MINCyT | Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT)</td><td>PICT-2018-01727</td><td>Pablo Bogino</td></tr></tbody></table>

## DATA AVAILABILITY

The complete genome sequence of *Bradyrhizobium* sp. 62B is available at NCBI Gen-Bank under accession CP092841 for the chromosome and CP092842 for the plasmid with BioProject ID PRJNA782308 and BioSample accession SAMN23371906. Raw data reads are available at NCBI's Sequence Read Archive under accessions SRR17042237, SRR17042238, SRR17042239, SRR17042240, and SRR17042241.

## REFERENCES

1. Jordan DC. 1982. Transfer of *Rhizobium japonicum* Buchanan 1980 to *Bradyrhizobium* gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. *Int J Syst Bacteriol* 32:136-139. https://doi.org/10.1099/00207713-32-1-136

2. Ormeño-Orrillo E, Martínez-Romero E. 2019. A genomotaxonomy view of the *Bradyrhizobium* genus. *Front Microbiol* 10:1334. https://doi.org/10.3389/fmicb.2019.01334

3. Lanier JE, Jordan DL, Spears JF, Wells R, Johnson PD. 2005. Peanut response to inoculation and nitrogen fertilizer. *Agronomy Journal* 97:79-84. https://doi.org/10.2134/agronj2005.0079a

4. Shang JY, Wu Y, Huo B, Chen L, Wang ET, Sui Y, Chen WF, Tian CF, Chen WX, Sui XH. 2021. Potential of Bradyrhizobia inoculation to promote peanut growth and beneficial Rhizobacteria abundance. *J Appl Microbiol* 131:2500-2515. https://doi.org/10.1111/jam.15128

5. Jovino RS, da Silva TR, Rodrigues RT, de Sá Carvalho JR, Cunha J de A, de Lima LM, Dos Santos RC, Santos C de R, Ribeiro P de A, de Freitas ADS, Martins LMV, Fernandes-Júnior PL. 2022. Elite *Bradyrhizobium* strains boost biological nitrogen fixation and peanut yield in tropical drylands. *Braz J Microbiol* 53:1623-1632. https://doi.org/10.1007/s42770-022-00792-4

6. Bogino P, Banchio E, Rinaudi L, Cerioni G, Bonfiglio C, Giordano W. 2006. Peanut (*Arachis hypogaea*) response to inoculation with *Bradyrhizobium* sp. in soils of Argentina. *Ann App Biol* 148:207-212. https://doi.org/10.1111/j.1744-7348.2006.00055.x

7. Bogino P, Banchio E, Bonfiglio C, Giordano W. 2008. Competitiveness of a *Bradyrhizobium* sp. strain in soils containing indigenous rhizobia. *Curr Microbiol* 56:66-72. https://doi.org/10.1007/s00284-007-9041-4

8. Bogino P, Nievas F, Banchio E, Giordano W. 2011. Increased competitiveness and efficiency of biological nitrogen fixation in peanut via in-furrow inoculation of rhizobia. *Eur J Soil Biol* 47:188-193. https://doi.org/10.1016/j.ejsobi.2011.01.005

9. Bogino P, Banchio E, Giordano W. 2010. Molecular diversity of peanut-nodulating rhizobia in soils of Argentina. *J Basic Microbiol* 50:274-279. https://doi.org/10.1002/jbm.200900245

10. Nievas F, Bogino P, Nocelli N, Giordano W. 2012. Genotypic analysis of isolated peanut-nodulating rhizobial strains reveals differences among populations obtained from soils with different cropping histories. *Appl Soil Ecol* 53:74-82. https://doi.org/10.1016/j.apsoil.2011.11.010

11. Somasegaran PH, Hoben H. 1994. Appendix 3: media and staining solutions, p 383-384. Appendix 24: source of rhizobia strains, p 454-460, p 450. In Handbook for Rhizobia: Methods in legume-Rhizobium technology. xvi. Springer, New York, NY.

12. Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. 2020. The nf-core framework for community-curated bioinformatics pipelines. *Nat Biotechnol* 38:276-278. https://doi.org/10.1038/s41587-020-0439-x

13. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. *Bioinformatics* 28:1647-1649. https://doi.org/10.1093/bioinformatics/bts199

14. Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, Dudek MR, Cebrat S. 2004. Where does bacterial replication start? rules for predicting the oriC region. *Nucleic Acids Res* 32:3781-3791. https://doi.org/10.1093/nar/gkh699

15. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. *Nucleic Acids Res* 44:6614-6624. https://doi.org/10.1093/nar/gkw569

16. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD. 2018. RefSeq: an update on prokaryotic genome annotation and curation. *Nucleic Acids Res* 46:D851-D860. https://doi.org/10.1093/nar/gkx1068

17. Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. 2021. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. *Nucleic Acids Res* 49:D1020-D1028. https://doi.org/10.1093/nar/gkaa1105

18. Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM. 2008. The repABC plasmid family. *Plasmid* 60:19-37. https://doi.org/10.1016/j.plasmid.2008.03.001

19. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. *Anton Leeuw Int J G* 110:1281-1286. https://doi.org/10.1007/s10482-017-0844-4

20. Okubo T, Piromyou P, Tittabutr P, Teaumroong N, Minamisawa K. 2016. Origin and evolution of nitrogen fixation genes on symbiosis Islands and plasmid in *Bradyrhizobium*. *Microbes Environ* 31:260-267. https://doi.org/10.1264/jsme2.ME15159

21. Teamtisong K, Songwattana P, Noisangiam R, Piromyou P, Boonkerd N, Tittabutr P, Minamisawa K, Nantagij A, Okazaki S, Abe M, Uchiumi T, Teaumroong N. 2014. Divergent nod-containing *Bradyrhizobium* sp.
## AUTHOR ORCIDs

Pedro Alzari http://orcid.org/0000-0002-4233-1903

Walter Giordano http://orcid.org/0000-0002-2436-922X

Pablo Bogino http://orcid.org/0000-0001-7841-6119

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s)</td><td>Author(s)</td></tr></thead><tbody><tr><td>MINCyT | Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT)</td><td>PICT-2018-01727</td><td>Pablo Bogino</td></tr></tbody></table>

## DATA AVAILABILITY

The complete genome sequence of *Bradyrhizobium* sp. 62B is available at NCBI Gen-Bank under accession CP092841 for the chromosome and CP092842 for the plasmid with BioProject ID PRJNA782308 and BioSample accession SAMN23371906. Raw data reads are available at NCBI's Sequence Read Archive under accessions SRR17042237, SRR17042238, SRR17042239, SRR17042240, and SRR17042241.

## REFERENCES

1. Jordan DC. 1982. Transfer of *Rhizobium japonicum* Buchanan 1980 to *Bradyrhizobium* gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. *Int J Syst Bacteriol* 32:136-139. https://doi.org/10.1099/00207713-32-1-136

2. Ormeño-Orrillo E, Martínez-Romero E. 2019. A genomotaxonomy view of the *Bradyrhizobium* genus. *Front Microbiol* 10:1334. https://doi.org/10.3389/fmicb.2019.01334

3. Lanier JE, Jordan DL, Spears JF, Wells R, Johnson PD. 2005. Peanut response to inoculation and nitrogen fertilizer. *Agronomy Journal* 97:79-84. https://doi.org/10.2134/agronj2005.0079a

4. Shang JY, Wu Y, Huo B, Chen L, Wang ET, Sui Y, Chen WF, Tian CF, Chen WX, Sui XH. 2021. Potential of Bradyrhizobia inoculation to promote peanut growth and beneficial Rhizobacteria abundance. *J Appl Microbiol* 131:2500-2515. https://doi.org/10.1111/jam.15128

5. Jovino RS, da Silva TR, Rodrigues RT, de Sá Carvalho JR, Cunha J de A, de Lima LM, Dos Santos RC, Santos C de R, Ribeiro P de A, de Freitas ADS, Martins LMV, Fernandes-Júnior PL. 2022. Elite *Bradyrhizobium* strains boost biological nitrogen fixation and peanut yield in tropical drylands. *Braz J Microbiol* 53:1623-1632. https://doi.org/10.1007/s42770-022-00792-4

6. Bogino P, Banchio E, Rinaudi L, Cerioni G, Bonfiglio C, Giordano W. 2006. Peanut (*Arachis hypogaea*) response to inoculation with *Bradyrhizobium* sp. in soils of Argentina. *Ann App Biol* 148:207-212. https://doi.org/10.1111/j.1744-7348.2006.00055.x

7. Bogino P, Banchio E, Bonfiglio C, Giordano W. 2008. Competitiveness of a *Bradyrhizobium* sp. strain in soils containing indigenous rhizobia. *Curr Microbiol* 56:66-72. https://doi.org/10.1007/s00284-007-9041-4

8. Bogino P, Nievas F, Banchio E, Giordano W. 2011. Increased competitiveness and efficiency of biological nitrogen fixation in peanut via in-furrow inoculation of rhizobia. *Eur J Soil Biol* 47:188-193. https://doi.org/10.1016/j.ejsobi.2011.01.005

9. Bogino P, Banchio E, Giordano W. 2010. Molecular diversity of peanut-nodulating rhizobia in soils of Argentina. *J Basic Microbiol* 50:274-279. https://doi.org/10.1002/jbm.200900245

10. Nievas F, Bogino P, Nocelli N, Giordano W. 2012. Genotypic analysis of isolated peanut-nodulating rhizobial strains reveals differences among populations obtained from soils with different cropping histories. *Appl Soil Ecol* 53:74-82. https://doi.org/10.1016/j.apsoil.2011.11.010

11. Somasegaran PH, Hoben H. 1994. Appendix 3: media and staining solutions, p 383-384. Appendix 24: source of rhizobia strains, p 454-460, p 450. In Handbook for Rhizobia: Methods in legume-Rhizobium technology. xvi. Springer, New York, NY.

12. Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. 2020. The nf-core framework for community-curated bioinformatics pipelines. *Nat Biotechnol* 38:276-278. https://doi.org/10.1038/s41587-020-0439-x

13. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. *Bioinformatics* 28:1647-1649. https://doi.org/10.1093/bioinformatics/bts199

14. Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, Dudek MR, Cebrat S. 2004. Where does bacterial replication start? rules for predicting the oriC region. *Nucleic Acids Res* 32:3781-3791. https://doi.org/10.1093/nar/gkh699

15. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. *Nucleic Acids Res* 44:6614-6624. https://doi.org/10.1093/nar/gkw569

16. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD. 2018. RefSeq: an update on prokaryotic genome annotation and curation. *Nucleic Acids Res* 46:D851-D860. https://doi.org/10.1093/nar/gkx1068

17. Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. 2021. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. *Nucleic Acids Res* 49:D1020-D1028. https://doi.org/10.1093/nar/gkaa1105

18. Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM. 2008. The repABC plasmid family. *Plasmid* 60:19-37. https://doi.org/10.1016/j.plasmid.2008.03.001

19. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. *Anton Leeuw Int J G* 110:1281-1286. https://doi.org/10.1007/s10482-017-0844-4

20. Okubo T, Piromyou P, Tittabutr P, Teaumroong N, Minamisawa K. 2016. Origin and evolution of nitrogen fixation genes on symbiosis Islands and plasmid in *Bradyrhizobium*. *Microbes Environ* 31:260-267. https://doi.org/10.1264/jsme2.ME15159

21. Teamtisong K, Songwattana P, Noisangiam R, Piromyou P, Boonkerd N, Tittabutr P, Minamisawa K, Nantagij A, Okazaki S, Abe M, Uchiumi T, Teaumroong N. 2014. Divergent nod-containing *Bradyrhizobium* sp.
DOA9 with a megaplasmid and its host range. Microbes Environ 29:370-376. https://doi.org/10.1264/jsme2.ME14065

22. Okazaki S, Noisangiam R, Okubo T, Kaneko T, Oshima K, Hattori M, Teamtisong K, Songwattana P, Tittabutr P, Boonkerd N, Saeki K, Sato S, Uchiumi T, Minamisawa K, Teaumroong N. 2015. Genome analysis of a novel *Bradyrhizobium* sp. DOA9 carrying a symbiotic plasmid. PLoS One 10:e0117392. https://doi.org/10.1371/journal.pone.0117392

23. Wulandari D, Tittabutr P, Songwattana P, Piromyou P, Teamtisong K, Boonkerd N, Boonchuen P, Teaumroong N. 2022. Symbiosis contribution of non-nodulating *Bradyrhizobium cosmicum* S23321 after transferal of the symbiotic plasmid pDOA9. Microbes Environ 37:ME22008. https://doi.org/10.1264/jsme2.ME22008
DOA9 with a megaplasmid and its host range. Microbes Environ 29:370-376. https://doi.org/10.1264/jsme2.ME14065

22. Okazaki S, Noisangiam R, Okubo T, Kaneko T, Oshima K, Hattori M, Teamtisong K, Songwattana P, Tittabutr P, Boonkerd N, Saeki K, Sato S, Uchiumi T, Minamisawa K, Teaumroong N. 2015. Genome analysis of a novel *Bradyrhizobium* sp. DOA9 carrying a symbiotic plasmid. PLoS One 10:e0117392. https://doi.org/10.1371/journal.pone.0117392

23. Wulandari D, Tittabutr P, Songwattana P, Piromyou P, Teamtisong K, Boonkerd N, Boonchuen P, Teaumroong N. 2022. Symbiosis contribution of non-nodulating *Bradyrhizobium cosmicum* S23321 after transferal of the symbiotic plasmid pDOA9. Microbes Environ 37:ME22008. https://doi.org/10.1264/jsme2.ME22008