Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil

Forest soils represent important terrestrial carbon (C) pools, where C is primarily fixed in plant biomass and then is incorporated in the biomass of fungi and bacteria. Although classical concepts assume that fungi are the main decomposers of the recalcitrant organic matter within plant and microbial biomass, whereas bacteria are considered to mostly utilize simpler compounds, recent studies have shown that fungi and bacteria overlap in substrate utilization. Here, we studied the microbial contribution to the recycling of dead biomass by analyzing the bacterial and fungal communities in soil microcosms supplemented with 13C-labeled biomass of plant, fungal, and bacterial origin using a combination of DNA-stable isotope probing and metagenomics. Both fungi and bacteria contributed actively to the degradation of complex components of plant and microbial biomass. Specific families of carbohydrate-active enzymes (CAZyme) were involved in the degradation of each biomass type. Moreover, the analysis of five bacterial metagenome-assembled genomes indicated the key role of some bacterial genera in the degradation of plant biomass (Cytophaga and Asticcacaulis) and microbial biomass (Herminiimonas). The enzymatic systems utilized by bacteria are highly complex and complementary but also highly diverse among taxa. The results confirm the importance of bacteria, in addition to fungi, as decomposers of complex organic matter in forest soils.