Joint species distribution modelling of multiple taxonomic groups shows that water quality explains most of the variation in aquatic community composition along a lake trophic gradient

A key component of conservation biology is understanding how community composition responds to environmental conditions, including stressors (e.g., eutrophication). However, this is complicated by the accompanying shifts in taxa co-occurrence due to taxa interactions (e.g., competition, predation). Thus, we need to consider both taxa co-occurrence and abiotic conditions simultaneously to understand the relative influence of these factors on community composition. In this study, we aimed to elucidate the relative role of water quality and taxa co-occurrence in determining phytoplankton, zooplankton, and macroinvertebrate communities in a set of lakes varying in trophic status from oligotrophic to meso-eutrophic. We built joint species distribution models (JSDMs) using a generalized linear latent variable modelling approach to isolate the influence of abiotic variables and taxa co-occurrence for each level of the food web. We found that water quality explained most of the variation in community composition for all groups, especially for zooplankton (78%) and macroinvertebrate (62%) communities. Additionally, total phosphorus was a significant driver of many taxa in these groups. These findings indicate a strong “bottom-up” control of the lower aquatic food web in these lakes and signify an important role of phosphorus across a distinct trophic gradient. Overall, we demonstrate the effectiveness of JSDMs for determining the relative impacts of abiotic variables on community composition which can provide key insights for lake management.