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Occurrence of diverse Bradyrhizobium spp. in roots and rhizospheres of two commercial Brazilian sugarcane cultivars

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Abstract

The genus Bradyrhizobium harbors many endosymbionts of legumes, but recent research has shown their widespread presence in soils and in non-legumes, notably in roots of sugarcane. This study aimed to investigate the Bradyrhizobium sp. community density in the endosphere and the rhizosphere of two commercial sugarcane cultivars. Samples of the rhizosphere and root endosphere of two Brazilian sugarcane cultivars (RB867515 and IACSP95-5000) were collected, serially diluted, and inoculated on axenic cowpea (Vigna unguiculata) and the induction of nodules was evaluated. Based on the results, a density was estimated of at least 1.6 × 104 rhizobia g root−1 in rhizosphere samples and up to 105 rhizobia g root −1 in endosphere. BOX-PCR profiling of 93 Bradyrhizobium isolates revealed genetic variability, with some dominant (up to 18 representants) and less dominant genotypes. 16S rRNA and ITS sequence analyses confirmed nine phylotypes, six of which pertained to the B. elkanii clade and three to the B. japonicum clade. Five isolates were genetically similar to the recently described species B. sacchari. There was no effect of the factors “plant cultivar” and “root compartment” on Bradyrhizobium sp. community composition and the most abundant genotypes occurred both in rhizosphere and endosphere of both cultivars. Therefore, this study confirms the natural presence of diverse Bradyrhizobium spp. in sugarcane root systems (mainly the rhizosphere) and indicates that certain Bradyrhizobium phylotypes have a special affinity for sugarcane root colonization.

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Funding

This study was financially supported by the Brazilian Agricultural Research Corporation (Embrapa, project 0216050170002003) and by the Brazilian National Research Council (CNPq, processes 420746/2016-1 and 308898/2017-6). The first author received a post-graduate grant from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).

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Authors and Affiliations

  1. Programa de Pós-graduação em Fitossanidade e Biotecnologia Aplicada, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, RJ, Brazil

    Ivan de Alencar Menezes Júnior

  2. Programa de Pós-graduação em Fitotecnia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, RJ, Brazil

    Gustavo Feitosa de Matos

  3. Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, RJ, Brazil

    Karine Moura de Freitas, Ederson da Conceição Jesus & Luc Felicianus Marie Rouws

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  1. Ivan de Alencar Menezes Júnior
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  2. Gustavo Feitosa de Matos
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  3. Karine Moura de Freitas
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  4. Ederson da Conceição Jesus
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  5. Luc Felicianus Marie Rouws
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Correspondence to Luc Felicianus Marie Rouws.

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Figure S1

16S rRNA-based phylogenetic relationships among selected isolates from rhizosphere and endosphere samples of sugarcane cultivars RB867515 and IACSP95-5000 and Bradyrhizobium type strains. a) detailed view of the B. elkanii and b) detailed view of the B. japonicum clade. The phylogeny is based on 1197 nucleotide positions. Evolutionary history was inferred using the maximum likelihood method, with 500 replications based on the Tamura 3-parameter model. [35] Numbers next to branches represent the percentage of trees in which the shown topology occurred. Genbank accession numbers are given between parentheses. (PDF 321 KB)

Table S1

- Sequential numbers attributed to cowpea plants inoculated with sugarcane root endosphere and rhizosphere samples from sugarcane cultivars RB867515 and IACSP95–5000 obtained from a field experiment with three experimental blocks (replicates). (DOCX 19.6 kb)

Table S2

– Number of bacterial isolates obtained from cowpea nodules after inoculation with different dilution levels of endosphere and rhizosphere samples from sugarcane cultivars RB867515 and IACSP95–5000. (DOCX 15.8 kb)

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de Alencar Menezes Júnior, I., Feitosa de Matos, G., Moura de Freitas, K. et al. Occurrence of diverse Bradyrhizobium spp. in roots and rhizospheres of two commercial Brazilian sugarcane cultivars. Braz J Microbiol 50, 759–767 (2019). https://doi.org/10.1007/s42770-019-00090-6

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