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. Here, 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. Furthermore, 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.