TM Soil microbial catabolic structure Soil fungal catabolic structure a b s t r a c t Soil ecosystem services need to monitor soil quality in terms of soil functions. This need in turn requires functional indicators. Microbial functional diversity offers a way to characterize soil quality and any changes to it. Among soil microbial communities, fungi play a critical role in organic matter decomposition and nutrient cycling in soil by decomposing complex substrates, but only a few studies have focused on the function of soil fungal communities. We have developed a protocol based on substrate-induced respiration using the MicroResp TM technique combined with a selective inhibition (SI) procedure to characterize the fungal biomass and catabolic profiles for soil microbial and fungal communities: the FungiResp method. After comparisons with oxytetracycline, we chose bronopol as a bactericide to extend the FungiResp protocol. An optimal bronopol concentration of 78 ␮g g −1 soil was selected for the four soils tested to minimize the risk of inhibiting non-target communities (fungi). We used this convenient, miniaturized method to compare different soils and different perturbations (drought and heat). The FungiResp method gave further data on the fungal part of the microbial substrate-induced respiration in these different contexts. Also, the catabolic structure of microbial and fungal communities measured as pattern of substrate utilization (CLPPs) enabled us to contrast the functional contributions of the decomposer groups in the different soils studied and highlight the functional impacts of the different perturbations applied to them.