Linking microbial community composition and their functions in the course of cellulose degradation in arable soil

Soil microorganisms utilize organic carbon (C) through catabolic processes to produce the energy required for their metabolic needs and to synthesize microbial biomass via anabolic processes. The fraction of C retained in microbial biomass relative to the total amount of metabolized C is usually termed carbon use efficiency (CUE), which is a key metric for carbon turnover processes in soil. The input of fresh labile substrate in soil typically activates fast-growing microorganisms which are often less efficient than their slow-growing counterparts. However, the microbial succession may differ when utilizing less degradable organic compounds such as plant residues. In addition to the primary C source, newly-formed microbial biomass can subsequently act as a secondary source of C, nutrients, and energy for soil microorganisms. Therefore, the degradation of more complex organic compounds might be sequentially performed by different microbial taxa. However, knowledge of the microbial succession that occurs in the course of degradation of such complex organic compounds remains elusive.

To explore the microbial community changes during the degradation of complex C compounds, we conducted an incubation experiment using arable soil amended with ¹³C-labeled cellulose as a carbon and energy source. Microbial activity, estimated by respiration and heat release, was continuously determined for 56 days. To calculate CUE, the fraction of ¹³C transformed into CO₂ was quantified via isotope probing techniques. Following DNA extraction at specific time points, 16S rRNA and ITS amplicon sequencing were performed to determine successions in bacterial and fungal community composition. Finally, kinetic parameters of cellobiohydrolase, ß-glucosidase, and phosphatase were measured destructively at specific time points during the incubation. Heat and CO₂ release indicated an intensive degradation phase in the first 14 days of incubation. While the V_max of the enzymes slightly changed during the incubation period, essential changes in bacterial and fungal communities were observed. This study provides insights into the dynamics of microbial communities and their functional roles during cellulose degradation in soils.