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Brazilian Journal of Microbiology

Print version ISSN 1517-8382On-line version ISSN 1678-4405

Braz. J. Microbiol. vol.48 no.1 São Paulo Jan./Mar. 2017 

Genome Announcements

Genome sequence of Bradyrhizobium embrapense strain CNPSo 2833T, isolated from a root nodule of Desmodium heterocarpon

Jakeline Renata Marçon Delamutaa  b 

Renan Augusto Ribeiroc 

Douglas Fabiano Gomesa  b 

Renata Carolini Souzaa  b 

Ligia Maria Oliveira Chueirec 

Mariangela Hungriaa  b  * 

aEmbrapa Soja, Londrina, PR, Brazil

bCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Brasília, DF, Brazil

cCNPq, Brasília, DF, Brazil


Bradyrhizobium embrapense CNPSo 2833T is a nitrogen-fixing symbiont of the legume pasture Desmodium. Its draft genome contains 8,267,832 bp and 7876 CDSs. The symbiotic island includes nodulation and nitrogen fixation genes resembling the operon organization of B. japonicum. Several CDSs related to secretion proteins and stress tolerance were also identified.

Keywords: Biological nitrogen fixation; Genome; Nodulation; Symbiosis

Genome announcement

The nitrogen-fixing symbioses of bacteria collectively called as “rhizobia” and plants of the family Leguminosae (=Fabaceae) can contribute with high amounts of nitrogen to agronomic crops, forests and pastures. Selection programs to identify elite rhizobial strains for each legume and the practice of inoculation can greatly impact agronomic and environmental sustainability, decreasing the use of chemical N fertilizers.1,2

The genus Bradyrhizobium occupies a variety of ecosystems and is enriched in living styles,2,3 representing the most abundant rhizobial group in tropical soils.1 In the past few years, our group has reported large genetic diversity among Brazilian Bradyrhizobium strains,4-6 and has also described new Bradyrhizobium species.7-9

Here we report the draft genome of the new species Bradyrhizobium embrapense strain CNPSo 2833T (=CIAT 2372T = BR 2212T = SEMIA 6208T = U674T), an important symbiont of the tropical legume pasture Desmodium heterocarpon (former D. ovalifolium). The strain has been successfully used in commercial inoculants for this legume in Brazil since 1988.8

To access the bacterial genome sequence, total DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) and processed on the MiSeq plataform (Illumina) at Embrapa Soja, Londrina, Brazil. Shotgun sequencing generated 646,023 paired-end reads (2× 300 bp), corresponding to approximately 21.5-fold coverage. The FASTQ files were de novo assembled by A5-miseq pipeline, which performs read trimming, contig assembly, misassembly correction and final scaffolding.10

Sequences were submitted to RAST,11 and the genome estimated at 8,267,832 bp, with one circular chromosome assembled in 36 contigs. Annotation identified 7876 CDSs (coding DNA sequences). This number of predicted genes is lower than in B. japonicum and B. diazoefficiens.12 The analysis at the SEED system13 allowed the classification of 40% of the CDSs in 505 subsystems. The major categories of putative genes were of the metabolism of carbohydrates (14.4%) and amino acids and derivatives (12.9%). A symbiotic island was identified resembling that of B. japonicum,12 with two copies of the regulatory nodD gene, the operon nodABCSUIJ and also nolYK, nolNO and nodZ; some of these genes play important roles in host specificity.14 The island also carries the genes coding for the nitrogenase. The genome is enriched in genes of the Type I, II, III and IV secretion systems and carries 206 CDSs related to stress response.

The information obtained with genome of B. embrapense contributes to our still poor knowledge of the diversity of tropical rhizobia.

Nucleotide sequence accession number. The whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number SUBID (SUB985051), BioProject (PRJNA287423), BioSample (SAMN03782074), Accession (LFIP00000000). The version described in this paper is LFIP02000000.


Funded by Embrapa ( and CNPq (470515/2012-0).


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2 Ormeño-Orrillo E, Hungria M, Martínez-Romero E. Dinitrogen-fixing prokaryotes. In: Rosemberg E, de Long EF, Lory S, Stackebrandt E, Thompson F, eds. The prokaryotes-prokaryotic physiology and biochemistry. Berlin, Heidelberg: Springer-Verlag; 2013:427–451. [ Links ]

3 Eaglesham ARJ, Ellis JM, Evans WR, Fleischman DE, Hungria M, Hardy RWF. The first photosynthetic N2-fixing Rhizobium: characteristics. In: Gresshoff PM, Roth LE, Stacey G, Newton WE, eds. Nitrogen fixation: achievements and objectives. New York: Chapman and Hall; 1990:805–811. [ Links ]

4 Germano MG, Menna P, Mostasso FL, Hungria M. RFLP analysis of the RNA operon of a Brazilian collection of bradyrhizobial strains from thirty-three legume species. Int J Syst Evol Microbiol. 2006;56:217-229. [ Links ]

5 Menna P, Hungria M, Barcellos FG, Bangel EV, Hess PN, Martínez-Romero E. Molecular phylogeny based on the 16S rRNA gene of elite rhizobial strains used in Brazilian commercial inoculants. Syst Appl Microbiol. 2006;29:315-332. [ Links ]

6 Menna P, Barcellos FG, Hungria M. Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of 16S rRNA, ITS, glnII, recA, atpD and dnaK genes. Int J Syst Evol Microbiol. 2009;59:2934-2950. [ Links ]

7 Delamuta JRM, Ribeiro RA, Ormeño-Orrilo E, Melo IS, Martínez-Romero E, Hungria M. Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum Group Ia strains as Bradyrhizobium diazoefficiens sp. nov. Int J Syst Evol Microbiol. 2013;63:3342-3351. [ Links ]

8 Delamuta JRM, Ribeiro RA, Ormeño-Orrillo E, Parma MM, Melo IS, Martínez-Romero E, Hungria M. Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes. Int J Syst Evol Microbiol. 2015;65:4424-4433. [ Links ]

9 Helene LCF, Delamuta JRM, Ribeiro RA, Ormeño-Orrillo E, Rogel MA, Martínez-Romero E, Hungria M. Bradyrhizobium viridifuturi sp. nov., encompassing nitrogen-fixing symbionts of legumes used for green manure and environmental services. Int J Syst Evol Microbiol. 2015;65:4441-4448. [ Links ]

10 Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2015;31:587-589. [ Links ]

11 Aziz RK, Bartels D, Best AA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75. [ Links ]

12 Siqueira AF, Ormeño-Orrillo E, Souza RC, Rodrigues EP, Almeida LGP, Barcellos FG, Batista JSS, Nakatani AS, Martínez-Romero E, Vasconcelos ATR, Hungria M. Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean. BMC Genomics. 2014;15:420. [ Links ]

13 Overbeek R, Olson R, Pusch GD, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:D206-D214. [ Links ]

14 Menna P, Hungria M. Phylogeny of nodulation and nitrogen fixation genes in Bradyrhizobium: support for the theory of monophyletic origin and spread and maintenance by both horizontal and vertical transference. Int J Syst Evol Microbiol. 2011;61:3052-3057. [ Links ]

Received: April 14, 2016; Accepted: June 23, 2016

*Corresponding author at: Embrapa Soja, C. P. 231, 86001-970 Londrina, Paraná, Brazil. E-mails:,, (M. Hungria).

Conflicts of interest

The authors declare no conflicts of interest.

Creative Commons License This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivative License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium provided the original work is properly cited and the work is not changed in any way.