Bacterial interference competition and environmental filtering reduce the fungal taxonomic and functional contribution to plant residue decomposition in anoxic paddy soils

Plant residue decomposition is central to soil organic matter formation. Fungi, bacteria, and archaea are all well-known agents of residue decomposition. However, their relative taxonomic and functional contributions to plant residue decomposition in anoxic paddy soils are not well understood, and neither are the factors that govern these contributions. Here, a series of microcosms inoculated with two distinct paddy soils and amended with 13C-labeled rice straw was set up. DNA stable-isotope probing (DNA-SIP) based shotgun metagenomic sequencing was performed to reveal the relative contributions of bacteria, archaea, and fungi in rice straw degradation. Furthermore, the possible underlying mechanisms were investigated, focusing on microbial interspecies interference competition. We found that bacteria and archaea collectively accounted for 96.2∼99.5% (in CS anoxic paddy soil) and 81.7∼96.0% (in YT anoxic paddy soil) of the total abundance, while fungi accounted for only 0.5∼3.8% and 4.0∼18.3%, respectively. Phylogenetic distribution of functional genes encoding the carbohydrate-active enzyme (CAZyme) revealed that 87.7% (in CS anoxic paddy soil) and 80.9% (in YT anoxic paddy soil) of these genes were derived from bacteria and archaea, the remainder (12.3% and 19.1%) coming from fungi. The bacteria-fungi antagonism experiment indicated that fungal growth was indeed markedly inhibited by members of the two well-known antimicrobial compounds producing bacterial groups present, the Actinobacteria and the Bacilli. This study indicates that bacterial interference competition and environmental filtering (i.e., low redox/oxygen conditions) may reduce the contribution of fungi to plant residue decomposition in anoxic paddy field environments. These outcomes are important when constructing models to forecast and/or quantitative the microbial contributions to the global carbon dynamics in anoxic paddy soils.