Abstract
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.
Highlights
Since the advent of sequencing technologies, the determination of microbial diversity has become a major topic of interest [1]
In an attempt to assign the 77 rhizobial amplicon sequence variants (ASVs) detected from the savannah soils in Northern Côte d’Ivoire to the 18 genera of rhizobia validly published to date, we found that some genera type species, including Aminobacter aminovorans DSM 7048T and Mesorhizobium loti DSM 2626T, had identical 16S rRNA gene V4-V5 region (Figure 2)
A few studies reporting a characterization of soil rhizobial communities using the high-throughput amplicon sequencing (HTAS) of 16S rDNA variable regions were carried out in temperate arable soils in East
Summary
Since the advent of sequencing technologies, the determination of microbial diversity has become a major topic of interest [1]. This unique multi-national project, implemented in a dozen SSA countries, is the first such study to ever be undertaken in Africa at this scale [9,10] It was launched in 2016 to provide new insights into the presence and the distribution of key groups of soil bacteria, including the rhizobia, by using the high-throughput amplicon sequencing (HTAS) and phylogeny of the 16S rRNA gene [9,10]. Rhizobia are Gram-negative saprophytic Alpha- and Beta-proteobacteria that play a key role in nitrogen biochemical cycling [11,12] They form a polyphyletic group of bacteria among the lineages of prokaryotes capable of reducing atmospheric dinitrogen (N2 )
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