Fine sediment and flow velocity impact bacterial community and functional profile more than nutrient enrichment

Freshwater ecosystems face many simultaneous pressures due to human activities. Consequently, there has been a rapid loss of freshwater biodiversity and an increase in biomonitoring programs. Our study assessed the potential of benthic stream bacterial communities as indicators of multiple‐stressor impacts associated with urbanization and agricultural intensification. We conducted a fully crossed four‐factor experiment in 64 flow‐through mesocosms fed by a pristine montane stream (21 d of colonization, 21 d of manipulations) and investigated the effects of nutrient enrichment, flow‐velocity reduction and added fine sediment after 2 and 3 weeks of stressor exposure. We used high‐throughput sequencing and metabarcoding techniques (16S rRNA genes), as well as curated biological databases (METAGENassit, MetaCyc), to identify changes in bacterial relative abundances and predicted metabolic functional profile. Sediment addition and flow‐velocity reduction were the most pervasive stressors. They both increased α‐diversity and had strong taxon‐specific effects on community composition and predicted functions. Sediment and flow velocity also interacted frequently, with 88% of all bacterial response variables showing two‐way interactions and 33% showing three‐way interactions including nutrient enrichment. Changes in relative abundances of common taxa were associated with shifts in dominant predicted functions, which can be extrapolated to underlaying stream‐wide mechanisms such as carbon use and bacterial energy production pathways. Observed changes were largely stable over time and occurred after just 2 weeks of exposure, demonstrating that bacterial communities can be well‐suited for early detection of multiple stressors. Overall, added sediment and reduced flow velocity impacted both bacterial community structure and predicted function more than nutrient enrichment. In future research and stream management, a holistic approach to studying multiple‐stressor impacts should include multiple trophic levels with their functional responses, to enhance our mechanistic understanding of complex stressor effects and promote establishment of more efficient biomonitoring programs.