Multiple stressors affect function rather than taxonomic structure of freshwater microbial communities

Microbial community responses to environmental stressors are often characterised by assessing changes in taxonomic structure, but such changes, or lack thereof, may not accurately reflect functional changes that are critical to ecosystem processes. While community-level functional responses have been studied, these are often done under highly controlled, single-stressor scenarios that fail to reflect the complexities of multiple interacting environmental stressors in field conditions. We conducted a manipulative experiment to investigate the individual and combined effects of nutrient enrichment and salinisation – two key, interacting stressors in freshwater systems – on the taxonomic structure and metabolic function of benthic microbial communities using 1,000 L open freshwater ponds established >10 years ago in the field. Microbial communities were pre-established on tiles under ambient conditions for 30 days, and then transferred to ponds with elevated nutrients (+10mg/L N, +1mg/L P), elevated salinity (+15g/L NaCl), both stressors combined, or to ambient ponds, and community structure and function were measured over 90 days. We found that both stressors individually impacted community-level metabolic function, with distinct differences in the direction and timing of these effects. Salinisation decreased metabolic rates within seven days before recovering, nutrient enrichment increased metabolic rates after 30 days, and both stressors combined drove strong decreases in metabolic rates and shifted community metabolic profiles independent of time. Notably, functional changes occurred without significant alterations in bacterial community structure, underscoring the importance of measuring functional responses to environmental stressors. These results imply that critical microbial functions, including decomposition and organic carbon release, are likely to be impaired in freshwater systems under multiple stressors, even when taxonomic structure remains relatively stable. This dataset contains the raw sequences, environmental metadata, absorbance values from the metabolic assay, and the functional metrics from the experiment.