Environmental changes associated with drying climate are expected to affect functional groups of pro- and microeukaryotes differently in temporary saline waters

Temporary ponds are one of the most sensitive aquatic habitats to climate change. Their microbial communities have crucial roles in food webs and biogeochemical cycling, yet how their communities are assembled along environmental gradients is still understudied. This study aimed to reveal the environmental drivers of the microbial diversity and phylogenetic diversity patterns from a network of saline temporary ponds (soda pans in Austria) in two consecutive spring seasons characterized by contrasting weather conditions (one dry, one wetter). These habitats exhibit multiple environmental stress gradients and are therefore a highly suitable model system to understand the responses of microbial communities. We used DNA-based molecular methods (16S rRNA, 18S rRNA) to investigate the microbial community composition. We tested the effect of environmental variables on the diversity of prokaryotic and microeukaryotic functional groups (Bacteria, Cyanobacteria, Ciliates, heterotrophic flagellates and nanoflagellates, Fungi, phytoplankton) within and across the years. Conductivity and the concentration of total suspended solids and phosphorus were the most important environmental variables affecting all six functional groups. Environmental conditions were harsher and they also had a stronger impact on community composition in the dry spring. Our results imply that harsher environmental conditions, which are becoming more frequent with climate change, have a negative effect on most levels of microbial diversity in temporary saline ponds. At the same time, not all microbial functional groups responded the same way to harsher environmental conditions. This eventually might translate into community-level shifts across trophic groups with changing local conditions with implications for ecosystem functioning. This is the first regional-level study to properly assess how microbial diversity of these rare and threatened ecosystems is shaped by environmental gradients based on amplicon sequencing. We encourage further long-term monitoring studies of these ponds, in order to specifically link changes in the local conditions to the changing climatic parameters. Graphical abstract Highlights Microbial diversity of temporary saline ponds is still largely unknown We studied six functional groups in a habitat network applying amplicon sequencing We compared environmental drivers of diversity during a dry and wet spring Conductivity was the most important environmental gradient shaping diversity patterns Environmental drivers overall played a stronger role in a dry spring