Abstract
Bradyrhizobia are Gram-negative soil bacteria that regroup a growing number of species. They are widespread in nature and recovered from various biomes that may be explained by a high genetic diversity in this genus. Among the numerous metabolic properties they can harbor, the nitrogen fixation resulting from the association with plants among which important crop legumes (soya bean, peanut, cowpea …) is of great interest, notably in a context of sustainable development. Metabarcoding is widely applied to study biodiversity from complex microbial communities. Here, we demonstrate that using a new species-specific and highly polymorphic 16S-23S rRNA intergenic spacer barcode, we could rapidly estimate the diversity of bradyrhizobial populations that associate with cowpea and peanut plants, two crop legumes of major interest in Senegal. Application of the method on indigenous bradyrhizobia associated with peanut and cowpea grown in soils collected in the center of the peanut basin shows that Bradyrhizobium vignae is a dominant symbiont. We also showed that the two plant species associate with distinct community profiles and that strains introduced by inoculation significantly modified the population structure with these two plants suggesting that application of elite strains as inoculants may well ensure optimized symbiotic performance. This approach may further be used to study the diversity of bradyrhizobia from contrasting agro-eco-climatic zones, to test whether the plant genotype influences the association outputs as well as to estimate the competitiveness for nodule occupancy and the fate of elite strains inoculated in the field.
Key points
• An amplicon sequencing approach targeting the Bradyrhizobium genus was developed.
• Diversity of cowpea and peanut bradyrhizobia from cultivated soils was identified.
• The method is well suited to test the competitiveness of defined Bradyrhizobium inoculants.
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Data availability
The datasets generated during the current study are available in GenBank repository under the accession number PRJNA661308.
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Acknowledgements
The authors would like to acknowledge Olivier Zemb and his team from the GeT-PlaGe sequencing platform of Toulouse for sequencing and Patricia Moulin and her team of the LAMA for chemical analyses and we would like to thank Mariama Gueye and the LMI IESOL for assistance and access to MP BIO instruments.
Funding
The study was funded by the French Institute of Research for the Development (Grant Coup de Pouce IRD 2018–2020).
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A.L.Q. and T.K.W. conceived and designed research. A.L.Q., S.D., D.N., F.D.R., and N.D. conducted experiments. A.L.Q. and N.D. contributed analytical tools. A.L.Q., N.D., and T.K.W. analyzed data. A.L.Q., N.D., S.F., M.N., and T.K.W. wrote the manuscript. All authors read and approved the manuscript.
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Le Quéré, A., Diop, S., Dehaene, N. et al. Development of an Illumina-based analysis method to study bradyrhizobial population structure—case study on nitrogen-fixing rhizobia associating with cowpea or peanut. Appl Microbiol Biotechnol 105, 6943–6957 (2021). https://doi.org/10.1007/s00253-021-11525-2
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DOI: https://doi.org/10.1007/s00253-021-11525-2