Organic Amendments Shape the Microbial Community Structure Throughout the Soil Profile in Tropical Agriculture

Microorganisms play a crucial role in soils by driving biochemical reactions. They facilitate nutrient availability to plants by interacting with roots, decomposing soil organic matter, and releasing essential nutrients. Despite their diminishing abundance with soil depth, microorganisms are present in the subsoil and their interaction with deeper roots could potentially facilitate crop productivity. Subsoil microorganisms are also involved in organic carbon sequestration, soil development, prevention of nutrient losses through leaching, and degradation of pollutants. Application of organic residues (ORs) is a common agricultural practice to enhance soil fertility, yet little is known about how different types of OR affect microbial communities throughout the soil profile. The composition and quality of OR can significantly influence nutrient release and decomposition rate of organic matter, which consequently shape the microbial community structure. This study investigated the impact of the application of different ORs (manure, tithonia (Tithonia diversifolia) biomass, and maize stover) on the microbial diversity along the soil depth profile down to 70 cm of a tropical long-term field trial. Soil depth significantly influenced alpha and beta diversity of both bacteria and fungi. The effect of OR treatment on the alpha diversity was limited to the topsoil (0-30 cm depth). Bacterial richness was higher in manure-treated soils at 0-5 cm and 15-20 cm depth and in stover-treated soils at 15-20 cm depth than in the control treatment. In contrast to alpha diversity, the application of different ORs significantly affected microbial beta diversity throughout the soil profile down to 70 cm. Manure application had a more pronounced effect on bacterial and fungal community composition in the top 30 cm compared to other OR treatments, while its effect in subsoil layers (30-70 cm depth) was similar to the other OR treatments. Our findings reveal that soil microbial communities are different across depths, while ORs of varying quality distinctly influence microbial communities throughout the entire soil profile down to 70 cm. These findings highlight the importance of considering the entire soil profile when evaluating organic amendments for sustainable soil management, as their effects on microbial communities extend well beyond the topsoil and may influence key ecosystem services such as nutrient cycling, carbon storage, and crop productivity.