Côte d’Ivoire has the largest cashew tree cultivation area in the world, but the cashew apple produced is still underutilized despite its potential for industrial use. The present study aimed to isolate and identify acetic acid bacterial strains and assess their potential use for cashew apple-based vinegar production. Vinegar mother from fermented juice was used to isolate acetic acid bacteria on a standard glucose-based medium. Physiological and biochemical tests followed by 16S rRNA gene analysis and phylogeny were used for isolate characterization. Moreover, their acetic acid production capacity was assessed. As results, five strains of the Acetobacter genus were isolated. Phenotypic and phylogenetic analysis revealed that four of them, namely OYA2, OYA6, OYA9, and OYA10, belong to the A. tropicalis/A. senegalensis species complex with 99.7% or 100% similarity. The fifth strain, OYA7, being similar (99.7%) to A. syzygii. All the isolates were resistant to alcohol 15% (v/v) and grew well between pH 5.0 and 6.5. Their optimal growth temperatures varied between 27 °C and 37 °C, and only isolate OYA6 grew at a temperature of up to 40 °C. They produced vinegar with a yield (Y_p/s, g/g) varying from 0.82 to 0.92, and acetic acid contents (g/L) of 80.67, 70.26, 70.11, 68.70 and 67.22 were obtained with OYA6, OYA7, OYA2, OYA10, and OYA9, respectively. Thus, the isolate OYA6 appeared as the best candidate for vinegar production, owing to its superior yield and thermotolerance abilities that need to be further explored for industry use.

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.

The emergence and dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria pose a major public health threat, necessitating a One Health approach to addressing this threat. Thus, the diversity, ESBL production, and potential public health implications of Gram-negative bacteria recovered from man-made lakes and surrounding lettuce in Yamoussoukro, Côte d’Ivoire were assessed in this study. Also, the lakes’ physicochemical parameters were assessed and correlated with bacteria community using Pearson correlation. A total of 68 Gram-negative bacterial isolates were recovered from the samples and identified via 16S rDNA gene sequencing. Phylogenetic analysis suggested multiple genus-/species-level variations within the isolates. Escherichia coli was the most prevalent in lake water (39.5%), while Acinetobacter was the dominant genus in lettuce (30%). E. coli isolates showed high resistance to ampicillin (90.9%), cefepime (72.7%), cefotaxime (68.2%), and aztreonam (63.6%). Moreover, ESBL production was confirmed in E. coli isolates (22.05%), predominantly mediated by the bla_CTX-M gene. Multidrug-resistant phenotypes were widespread, yielding similar multiple antibiotic resistance index (MARI) values in water (0.27–0.63) and lettuce (0.27–0.81). These data indicate high environmental contamination, which unfortunately is not being taken into account by lettuce producers according to an interview. Statistical analyses showed a significant relationship between bacterial diversity and lakes’ physicochemical parameters, including dissolved oxygen, pH, and turbidity. The basic education level of farmers, the prevalence of ESBL-producing E. coli, and the high prevalence of MDR Gram-negative bacteria in both environmental and crop sources in Yamoussoukro underscore the need for both integrated surveillance and management strategies to mitigate potential microbial public health risks within a One Health framework.

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.

Microorganisms provide numerous ecosystem services to humans, allowing natural systems to benefit from a genetic reservoir essential for their fundamental functioning and sustainability (Rodrigues-Filho et al. 2023). They also play pivotal roles in the functioning of global ecosystems (Li et al. 2023;Liu et al. 2019). The advancement of microbial OMICS has enabled accurate elucidation of microbial functions across diverse ecosystems (Kaur et al. 2023), resulting in the identification and characterization of numerous provisioning services, biological processes, and supporting services (Beale et al. 2022). Moreover, microbial OMICS research has contributed to the advancement of applied biotechnologies and innovations in domains such as food security, agriculture, aquaculture, human health, animal health, and environmental protection (Su et al. 2024;Natnan et al. 2021;Chen et al. 2023;Goossens et al. 2022). The knowledge generated by microbial OMICS technologies, along with the development of related applied biotechnology, represents significant progress in sustainable agriculture and environmental management (Hijri 2023).The use of OMICS technologies enables the monitoring of soil health and productivity within agroecosystems. It has been reported that the utilization of specific microbes within agroecosystems, along with the type of soil management, can influence soil microbial community structure and function, consequently impacting soil health and crop productivity (Bertola et al. 2021). In a review, Adedayo and Babalola (2023) highlighted the significance of plant genomics in promoting the bioeconomy and the potential offered by advances in plant breeding techniques. Along with persisting challenges of underdevelopment and shifts in average weather conditions, the issue of food scarcity remains unresolved. Consequently, advances in crop production offer potential solutions to tackle these challenges. Furthermore, their review discussed the benefits of beneficial microbes in promoting crop growth and outlined the use of OMICS techniques to characterize plant-microbe interactions (Figure 1). Using 16S rRNA gene metabarcoding targeting bacterial communities, Duan et al. (2023b) demonstrated that the cultivation of Morchella esculenta in fallow paddy fields and drylands can alter the diversity of soil bacteria, affecting soil health and rice productivity. Their findings suggested that M. esculenta cultivation may enhance bioavailability of soil phosphorus and potassium in paddy fields, and potassium in dryland soil. M. esculenta cultivation had a modest impact on alpha diversity, and it influenced the abundance of certain genera of soil bacteria. Their functional annotation analysis indicated that M. esculenta cultivation might reduce methane production potential in paddy field soil and enhance nitrogen cycling in dryland soil. They performed a network analysis and correlation analysis, which revealed that Gemmatimonas, Bryobacter, and Anaeromyxobacter were key bacterial genera regulating soil chemical properties in paddy field soil under M. esculenta cultivation, while Bryobacter, Bacillus, Streptomyces, and Paenarthrobacter were key taxa associated with potassium accumulation in dryland soil. Arunrat et al. (2023) compared the variability of soil bacterial communities in maize monoculture and the fallow phase of rotational shifting cultivation fields in Northern Thailand. They selected a continuous 5-year fallow field (CF-5Y) and a continuous 5-year maize cultivation field (M-5Y) with similar microclimate, topography, and duration of field activities. Soil samples were collected from the surface layer at both sites every 3 months for one year. Analysis of soil bacterial diversity and composition was conducted using 16S rRNA gene amplicon sequencing. They observed that CF-5Y soil maintained greater stability in bacterial richness and diversity across seasons than M-5Y soil. Notably, fertilization and tillage practices in M-5Y were found to enhance both the diversity and richness of soil bacteria. The study concluded that changes in soil bacterial diversity may result from multifactorial conditions such as land management practices, soil physicochemical properties, weather conditions, and vegetation cover (Arunrat et al. 2023).Another finding relates to how soil health and crop productivity can be impacted by organic amendment into plant-fungus intercropping systems. Duan et al. (2023a) assessed the impact of bagasse amendment in a sugarcane -Dictyophora indusiata intercropping system on soil health through a field experiment comprising three treatments: bagasse amendment alone, (2) sugarcane amended with bagasse, and the control. Soil chemistry, soil bacterial and fungal diversity using amplicon sequencing, and metabolite composition were analyzed to elucidate the mechanisms underlying the effects of this intercropping system on soil properties. Soil chemistry analyses revealed higher levels of several soil nutrients such as nitrogen and phosphorus in the bagasse application compared to the control. Bacterial diversity was greater in the bagasse application than other treatments, while fungal diversity was lower in the bagasse-amended sugarcane than in other treatments. Soil metabolome analysis revealed significantly lower abundance of carbohydrate metabolites in the bagasse application compared to the control and the bagasse-amended sugarcane. They suggested that the sugarcane amended with bagasse can improve soil health in this intercropping system.Two studies on microbial genome sequencing revealed new species. A Bradyrhizobium . isolated from polluted sediments of a lake in China was identified as a new free-living species Bradyrhizobium roseus (Zhang et al. 2023). B. roseus displays considerable heterogeneity, exhibiting several functional distinctions from previously described Bradyrhizobium genomes. Another study reported a new endophytic fungus, Cladosporium angulosum,...

Rhizobia are a polyphyletic group of Proteobacteria comprising approximately 700 different species. Despite significant advancements in their taxonomy, evolutionary history, and ecological importance, substantial knowledge gaps remain regarding a detailed understanding of rhizobial biodiversity in a geographical context and the interest in studying and valorizing native rhizobial strains. This bibliometric study used data from the last four decades (1985–2025) to review the taxonomic and functional diversity of the documented novel taxa of rhizobia described from African ecosystems, as well as their valorization status as biofertilizers. It aims to discuss the interest in knowing, preserving, and valorizing native rhizobial resources in the global context of climate change and biodiversity erosion. The study revealed that the first African indigenous novel species of rhizobia was published in 1988, although research on rhizobia dates back to the 1950s in Africa. To date, ~63 species (approximately 9% of the total in the world) and two genera of rhizobia have been described using native isolates from 11 African countries, with substantial discoveries from the Succulent Karoo hotspot of biodiversity in South Africa. Approximately 51% of species are affiliated with Bradyrhizobium and Mesorhizobium, with Vachellia karroo and Senegalia spp. (formerly Acacia spp.) as their primary hosts. Most species-type strains (~89%) were found to be infective on legumes and are good candidates for biofertilizer development. However, there is a limited level of commercial valorization of indigenous isolates as inoculants, mainly because the production of biological intrants is still at the experimental stage in Africa. Interestingly, important breaking point discoveries have been made using native rhizobial strains from Africa, including the pioneering demonstration in 2001 that Burkholderia (beta-rhizobia) is a symbiotic genus with legumes. It also includes the discovery of stem-nodulating rhizobia and Nod factor-independent symbiotic processes in some rhizobia. Together, this review highlights the importance of native African rhizobial strains. This underscores the need to accelerate their agronomic valorization to better support the transition to more resilient and sustainable legume-based farming systems in African countries.