Identifying Early Ecological Disturbance Signals through Functional Shifts in Freshwater Microbial Communities

Freshwater systems face multiple coexisting stressors, but typical monitoring programs will not identify degradation until water chemistry falls outside set standards or changes have occurred in macroinvertebrate and fish communities. The microbes respond quickly (from hours to weeks) to environmental disturbances and facilitate key biogeochemical processes in freshwaters. This makes them promising indicators for early warning assessments. The current study investigates whether changes in functional attributes of freshwater microbial communities may act as an early signal of ecological disturbance before any structural and taxonomic change takes place. A systematic review of the literature on microbial resistance, resilience, functional redundancy, community assembly, and critical transition theories was coupled with a comparison of eight different functional indicators, from functional genes and enzymes to predicted metagenomic functionality. A simple simulation of indicator response to disturbance intensity was done afterwards. The synthesis shows that functional traits, especially the relative abundance of genes associated with nitrogen cycling and stress responses and the proportion of enzymes for acquisition of carbon, nitrogen, and phosphorus, respond more quickly and consistently to nutrient addition, pollution, warming, and changes in water flow regimes compared to taxonomic composition. In this experiment, functional gene indicators reached the level of detection 8.5 weeks prior to the macroinvertebrate indicator and four weeks prior to taxonomic community changes. Functional redundancy may obscure disturbances; therefore, increases in variation and delay in the recovery of functional indicators should be considered along with average values. A hierarchical approach to monitoring is suggested, which includes microbial functional assessment together with traditional biomonitoring.