Archaea and bacteria communities play pivotal roles in tropical forest ecosystems’ functioning, especially nutrient cycling, plant phenology, and health. The objective of this study was to explore the diversity of archaeal and bacterial communities in forest soil ecosystem of Côte d’Ivoire and to identify abiotic factors that influence their composition. Using high-throughput amplicon sequencing targeting the V4V5 hypervariable region of the 16S ribosomal RNA gene, we analyzed 22 soil samples taken from the 2 main forest areas of Côte d’Ivoire, namely the semi-deciduous moist forest and the evergreen moist forest, both of which are located in the humid and sub-humid areas of the country. The analysis revealed that the biodiversity at the phyla level was congruent with previous studies. Richness and Shannon diversity indices revealed the dominance of bacteria over archaea in all studied soils. Moreover, the predominant bacterial community consisted of Proteobacteria (29.8%), Acidobacteria (15.5%), and Actinobacteria (14.2%), while the archaeal community was dominated by Thaumarchaeota (1.93%). However, at the genus level, patterns emerged. The most abundant and ubiquitous members at the genus level included Bradyrhizobium, Rhodoplanes, Bacillus (bacteria), and Nitrosophaera (archaea). While bacterial core microbiome members were found in almost all soils, Nitrososphaera genus were selective to sub-humid bioclimate and cropland land use. These patterns were correlated to the soils’ physicochemical characteristics, bioclimate, and land use. This study sheds light on the intricate relationships between abiotic factors and microbial communities in Côte d’Ivoire’s forest soils and helps to identify keys species for future soil management.

Soybean (Glycine max) is a protein-rich legume crop that plays an important role in achieving food security. The aim of this study was to isolate soybean-nodulating rhizobia from Côte d’Ivoire soils and evaluate their potential as efficient strains in order to develop local bioinoculants. For this objective, 38 composite soil samples were collected from Côte d’Ivoire’s five major climatic zones. These soils were used as substrate to trap the nodulating rhizobia using the promiscuous soybean variety R2-231. A total of 110 bacterial strains were isolated and subsequently identified. The analysis of ITS (rDNA16S-23S), glnII and recA sequences revealed a relatively low genetic diversity of these native rhizobia. Moreover, the ITS phylogeny showed that these were scattered into two Bradyrhizobium clades dominated by the B. elkanii supergroup, with ca. 75% of all isolates. Concatenated glnII-recA sequence phylogeny confirmed that the isolates belong in the majority to ‘B. brasilense’, together with B. vignae and some putative genospecies of Bradyrhizobium that needs further elucidation. The core gene phylogeny was found to be incongruent with nodC and nifH phylogenies, probably due to lateral gene transfer influence on the symbiotic genes. The diversity and composition of the Bradyrhizobium species varied significantly among different sampling sites, and the key explanatory variables identified were carbon (C), magnesium (Mg), nitrogen (N), pH, and annual precipitation. Based on both shoot biomass and leaf relative chlorophyll content, three isolates consistently showed a higher symbiotic effectiveness than the exotic inoculant strain Bradyrhizobium IRAT-FA3, demonstrating their potential to serve as indigenous elite strains as bioinoculants.