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.
Description:
SUPPLEMENTARY MATERIAL : FIGURE S1: Covering area of each sampling site and its corresponding features, FIGURE S2: Rarefaction curve of the seven samples, indicated by the number of ASVs depending on the size of the sequence sample, FIGURE S3: 16S rDNA V4-V5 phylogenetic tree showing the relationship between all selected reference alpha and beta-rhizobia strains and the 77 ASVs detected in savannah soils of Northern Côte d’Ivoire, TABLE S1: Physico-chemical properties of samples soils, TABLE S2: Levels of similarity between the V4-V5 sequences of the 77 ASVs of rhizobia and all 18 alphaproteobacterial and betaproteobacterial genera harboring rhizobia strains, TABLE S3: Major characteristics of the 77 ASVs of rhizobia detected in savannah soils of Northern Côte d’Ivoire, TABLE S4: ASVs and their corresponding md5_hash identities, TABLE S5: ASVs richness, cumulative relative abundance of sequences and prevalence of ASVs per soil, TABLE S6: Measure of the richness and the alpha diversity per savannah zone.
