Soil hosts diverse microbial communities including bacteria, fungi, archaea, protozoans and nematodes among others, which are fundamental to sustainable agriculture and drive essential processes that underpin soil fertility, plant health, and ecosystem resilience. They promote plant growth through mechanisms like nitrogen fixation, phosphorus solubilization, production of growth-promoting substances, enhancement of nutrient uptake, improvement of soil structure and detoxification of harmful substances. Recently, there has been increasing interest in utilizing microorganisms to improve soil health and boost plant growth and efficiency, despite limited understanding of microbial diversity, microbe-plant interactions, and translating laboratory findings to field conditions. This interest is driven by the urgent need to feed the growing global population, placing pressure on arable land to produce high-quality yields. Conventionally, synthetic fertilizers have been extensively used to provide nutrients, promote plant growth, and increase crop productivity. Although synthetic fertilizers have revolutionized agriculture since the green revolution, their overuse has significantly harmed soil health, and reduced crop productivity. This review synthesizes the current knowledge on the mechanisms by which soil microbes influence sustainable agricultural practices, with a focus on soil nutrient cycling and plant–microbe interactions. We discuss the functions and mechanisms of important microbial groups, such as nitrogen-fixing bacteria, phosphorus-solubilizing bacteria (PSB), and fungi. Furthermore, we discuss the factors that influence soil microbial communities and highlight gaps in future research to maximize their potential use in agriculture. Understanding the significance and key mechanisms of microbial communities increases the potential of harnessing soil microbes as vital contributors to soil health and sustainable agriculture.

Phosphorus solubilizing bacteria (PSB) are a category of microbes that transform insoluble phosphates in soil into soluble forms that crops can utilize. Phosphorus in natural soils is abundant but poorly soluble. Hence, introducing PSB is a safer way of improving its solubility. The aim of this study was to genetically characterize and determine the mineralization capability of selected PSB colonizing rhizospheres of common beans in Western Kenya. Seven potential phosphorus solubilizing bacteria (PSB) were isolated from various subregions of Western Kenya. 16S ribosomal RNA gene sequencing and National Center for Biotechnology Information (NCBI), Basic Local Alignment Search Tool (BLAST) identified the isolates. The phosphate solubilization potential of the isolates was evaluated under agar and broth medium of National Botanical Research Institute’s phosphate (NBRIP) supplemented with tricalcium calcium phosphate (TCP). Identified isolates were as follows: KK3 as Enterobacter mori, B5 (KB5) as Pseudomonas kribbensis, KV1 as Enterobacter asburiae, KB3 as Enterobacter mori, KK1 as Enterobacter cloacae, KBU as Enterobacter tabaci, and KB2 as Enterobacter bugandensis. The strains B5 and KV1 were the most effective phosphorus solubilizers with 4.16 and 3.64 indices, respectively. The microbes converted total soluble phosphate concentration in broth medium which was 1395 and 1471 P μg/mL, respectively. The least performing isolate was KBU with a 2.34 solubility index. Significant ( ≤ 0.05) differences in plant biomass for Rose coco and Mwitemania bean varieties were observed under inoculation with isolates B5 and KV1. PSB isolates found in common bean rhizospheres exhibited molecular variations and isolates B5 and KV1 are the potential in solving the insufficiency of phosphorus for sustainable crop production.

Lake Victoria, the second‐largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far‐reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole‐genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate‐active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.

Background: A diverse range of pollutants, including heavy metals, agrochemicals, pharmaceutical residues, illicit drugs, personal care products, and other anthropogenic contaminants, pose a significant threat to aquatic ecosystems. The Winam Gulf of Lake Victoria, heavily impacted by surrounding human activities, faces potential contamination from these pollutants. However, studies exploring the presence of antibiotic resistance genes (ARGs) in the lake remain limited. In the current study, a shotgun metagenomics approach was employed to identify ARGs and related pathways. Genomic DNA was extracted from water and sediment samples and sequenced using the high‐throughput Illumina NovaSeq platform. Additionally, phenotypic antibiotic resistance was assessed using the disk diffusion method with commonly used antibiotics.Results: The analysis of metagenomes sequences from the Gulf ecosystem and Comprehensive Antibiotic Resistance Database (CARD) revealed worrying levels of ARGs in the lake. The study reported nine ARGs from the 37 high‐risk resistant gene families previously documented by the World Health Organization (WHO). Proteobacteria had the highest relative abundance of antibiotic resistance (53%), Bacteriodes (4%), Verrucomicrobia (2%), Planctomycetes Chloroflexi, Firmicutes (2%), and other unclassified bacteria (39%). Genes that target protection, replacement, change, and antibiotic‐resistant efflux were listed in order of dominance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed antibiotic resistance to beta‐lactamase and vancomycin. Phenotypic resistance to vancomycin, tetracycline, sulfamethoxazole, erythromycin, trimethoprim, tetracycline, and penicillin was reported through the zone of inhibition.Conclusions: This study highlights that the Winam Gulf of Lake Victoria in Kenya harbors a diverse array of antibiotic‐resistant genes, including those conferring multidrug resistance. These findings suggest that the Gulf could be serving as a reservoir for more antibiotic‐resistant genes, posing potential risks to both human health and aquatic biodiversity. The insights gained from this research can guide policy development for managing antibiotic resistance in Kenya.

Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.

Aim: Tungiasis caused by Tunga penetrans is a neglected tropical disease that majorly affects children, the elderly and persons living with disabilities in rural homes in sub-Saharan Africa. The disease is characterized by swelling and inflammation symptoms, especially on the hands and feet. However, it is unclear whether inflammatory responses induced by T. penetrans may be associated with alterations of cytokine and antibody profiles. The study evaluated the immunological changes: cytokine and antibody profiles of experimentally raised guinea pigs exposed to T. penetrans. Methods: A total of 24 guinea pigs were experimented on; 16 were exposed to T. penetrans while 8 were controls. Blood samples were collected before and after exposure. Enzyme-linked immunosorbent assay (ELISA) technique was used to quantify cytokines and antibodies. Data analysis was performed using GraphPad Prism 10.4. Results: At day 10 of post-infection, guinea pigs showed significant elevation (p < 0.05) of pro-inflammatory cytokines, tumor necrosis factor alpha (TNF-α) (235 pg/mL), and interferon gamma (IFN-γ) (425 pg/mL) in the serum. Anti-inflammatory cytokine had a delayed elevation, with interleukin-4 (IL-4) peaking to 357 pg/mL by day 15, while IL-10 rose to 367 pg/mL by day 15 of post-infection. Total systemic circulating levels of antibodies in serum were significantly elevated (p < 0.05), with immunoglobulin E (IgE) elevating to 232 ng/mL while IgG peaking at 272 ng/mL on day 15 post-infection. Conclusions: Pro-inflammatory cytokines elevated during the early stages of infection may serve as early markers for the infection, and their potential role in the pathogenesis of tungiasis needs to be explored further. The study has established that IgE and IgG are important antibodies that are produced in response to tungiasis, and their efficacy in controlling the infection needs to be further explored for potential alleviation of severe forms of the infection.