Root-associated microbial communities have strong influences on the health and development of plants. Through the secretion of root exudates, the soil microbiome is impacted by plants, thereby steering plant-soil reactions. Considering the importance of root exudates in the establishment of symbiotic associations in the rhizosphere, it is quite clear that understanding the interaction between plant roots and the soil microbiome may prove beneficial. Here, we review the interaction between plant root exudates and microbial communities in the soil. The influence of these bioactive molecules on the structure and function of soil microbes is also considered. We additionally, deliberate on how plants determine the soil microbiome and how they extract nutrients from endophytes for the augmentation of their growth and development. A good perspective of the communication between plant roots and the soil microbiome could lead to increased crop production, thereby limiting the need for synthetic fertilizers.

Plant rhizosphere zones are hotspots for microbial diversity consisting of different communities when contrasted with surrounding bulk soils. Rhizosphere microorganisms play significant roles in plant development. We investigated the bacterial community and metabolic potentials of maize rhizosphere and bulk soils at two distant geographical locations in the North West Province of South Africa using shotgun metagenomics. We further characterized bacterial genes contributing to plant-beneficial functions present in the soils. Genes involved in plant-beneficial functions like nitrogen fixation and potassium transport were uncovered. Overall, 51 OTUs were identified in the soils. Shared OTUs between soils were 10.9% and 17.2% at Ventersdorp and Mafikeng, respectively. Significant differences in bacterial taxonomic composition and functional categories between soils (P < 0.05) were revealed. Acidobacteria and Firmicutes dominated the rhizosphere soils while Actinobacteria and Gemmatimonadetes were predominant in bulk soils. Proper understanding of soil indigenous microbiome can help ascertain prospective targets for imminent crop breeding and management.

Soil microbial communities are an important part of ecosystems that possess the capability to improve ecosystem services; however, several aspects of the ecology of forest soil bacterial communities are still unknown. Here, we investigated the impact of land-use change on soil bacterial communities and the soil characteristics. High-throughput sequencing was used to ascertain the bacterial diversity and canonical correspondence analysis was used to determine relationships between the bacterial communities and environmental variables. Our results show spatial heterogeneity in the distribution of the microbial communities and significant relationships between the microbes and soil characteristics (axis 1 of the canonical correspondence analysis (CCA) plot explained 64.55% of the total variance while axis 2 described 24.49%). Knowledge of this is essential as it has direct consequences for the functioning of the soil ecosystem.

Recent studies involving microbial communities in termite mounds have been more focused on bacteria and fungi with little attention given to archaea, which play significant roles in nutrient cycling. Thus, we aimed at characterizing the archaeal taxonomic and functional diversity in two termite mound soils using the shotgun sequencing method with the assumption that termite activities could promote archaeal diversity. Our findings showed that termite mound soils have archaeal groups that are taxonomically different from their surrounding soils, with Euryarchaeota, Korarchaeota, and Nanoarchaeota being predominant while Thaumarchaeota and Crenarchaeota were predominant in the surrounding soils. Additionally, the observed nutrient pathways: phosphorus, nitrogen, and sulfur were all significantly more predominant in termite mound soils than in their comparative surrounding soils. Alpha diversity showed that archaea were not significantly different within termite mound soils and the surrounding soils. The beta diversity revealed significant differences in the archaeal taxonomic composition and their functional categories between the termite mounds and surrounding soils. Our canonical correspondence analysis revealed that the distribution of archaeal communities was likely dependent on the soil properties. Our results suggested that termite activities may promote the diversity of archaea; with some of our sequences grouped as unclassified archaea, there is a need for further research to unveil their identity.

We conducted shotgun metagenomics sequencing of the maize rhizosphere and bulk soils in Ventersdorp, South Africa. Information on the structural composition and functional capabilities of microbial communities in the maize rhizosphere are provided by the data. Characterising the functional potentials of rhizosphere microbiomes gives an opportunity to link the microbiome to plant growth and health and provides the possibility of discovering new plant-beneficial genes that could enhance agricultural sustainability.