Exploring microbial soil communities structure, functions and dynamics in a commercial paddy field in Colombian Eastern Llanos

The Eastern Llanos of Colombia is a region characterized by rice production; but the crops face challenges like poor soil conditions, leading to a heavy reliance on inorganic inputs of fertilizers to achieve optimal yields. However, the role of soil microbial communities, essential for soil health and productivity, remains poorly understood in Colombian paddy fields. This study aimed to explore the microbial dynamics in composition, structure and functional potential in bulk and rhizosphere soils from a commercial paddy field categorized by yield zones during two crop stages, employing a combination of amplicon sequencing and shotgun metagenomics. The samples were dominated by Acidobacteria, Myxococcota, and Proteobacteria phylum, and the composition varied by the yield zone and across the sampling times. There were differences in microbial diversity between bulk and rhizosphere communities, with the rhizosphere exhibiting greater functional potential enrichment. Additionally, using a co-assembly approach to reconstruct Metagenome Assembled Genomes (MAGs) and its functional annotation, we identified Acidobacteriota, Actinomycetota, Proteobacteria, and Nitrospirota phyla, discovering their contribution in the nitrogen, sulfur, and methane cycles. The above results suggest that these phyla could influence the soil health through nutrient cycling, enabling a potential link of soil microbial diversity and the development of future sustainable differential management practices in rice crop.