Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing

Soils represent one of the largest and most active pools of C in the biosphere, and soil respiration represents a major component of global C flux. Fungi are essential to soil carbon cycling due to their propensity for decomposing organic polymers such as cellulose. We performed high throughput sequencing enabled stable isotope probing (HTS-SIP) with 13C-cellulose to characterize the dynamics of fungi and bacteria during cellulose degradation in an agricultural soil. A total of 1900 fungal taxa were observed and 190 of these assimilated 13C-cellulose during a 30-day incubation. A majority of 13C-labeled fungi belonged to Ascomycota, Basidiomycota, and Mucoromycota. However, most 13C-labeled fungi could not be annotated at the species (71%, n = 134), or genus (49%, n = 93) level. Mucoromycota were 13C-labeled early, and by day 3 the most abundant 13C-labeled organism belonged to Mortierella. In contrast, 13C-labeled Ascomycota increased in diversity through day 14 and their relative abundance comprised more than 40% of fungal ITS sequences by day 30. These results show that: i) the majority of fungal taxa that assimilated 13C from 13C-cellulose are uncultivated and poorly characterized, ii) the beta-diversity of 13C-labeled fungi changed significantly over time during cellulose degradation, iii) a relatively small number of the 13C-labeled taxa dominated the community response to cellulose, and iv) fungi incorporated cellulose into DNA more rapidly and in greater numbers than did bacteria. These results show that fungi in a tilled agricultural field respond rapidly to new cellulose inputs, exhibiting complex temporal dynamics that likely drive carbon flow into diverse taxa within the soil community.