Microbial communities underpin nearly all biogeochemical processes within an ecosystem. Recent studies, however, have revealed tremendous variability in the contribution of individuals and populations to microbial metabolism. Such results suggest that many microbes in natural systems may be dead or dormant. Fluctuations in environmental conditions may serve as metabolic “wake up” calls that have implications for the maintenance of microbial diversity and ecosystem functioning. To address this theme, we conducted a survey of ten north temperate lakes (Michigan, USA) and used the ratio of RNA to DNA as a simple index to quantify the metabolic activity of bacteria and eukaryotes in aquatic ecosystems. In addition, we characterized the composition of “present” and “active” communities by fingerprinting DNA and cDNA, respectively, of both bacterial and eukaryotic microbes. We hypothesized that bacterial and eukaryotic metabolic activity would be coupled, and that any pattern of decoupling would result from local environmental conditions.
The activity of bacteria and eukaryotes among our lakes was only weakly coupled, suggesting that these two microbial domains responded differently to the same set of environmental conditions captured in our survey. Specifically, RNA:DNA ratios of bacteria increased with indicators of ecosystem productivity (i.e., chlorophyll a), while the RNA:DNA ratios of eukaryotes were sensitive to pH. Similarly, results from the fingerprinting of “present” and “active” communities support the notion that bacteria and eukaryotes respond differently to environmental variability. For example, T-RFLP profiles for the DNA and cDNA of eukaryotes were similar suggesting that populations within a given lake were mostly active. In contrast, T-RFLP profiles for bacteria clustered by DNA and cDNA. In other words, the “active” bacterial communities among lakes were more similar to one another than the “active” and “present” bacteria within any given lake. Together, our results suggest that microbes from different domains (bacteria vs. eukaryotes) may have unique life history strategies (e.g., dormancy) that help them contend with environmental variability. These differences may be important for explaining patterns of microbial diversity in a variety of habitats, and should be considered when attempting to link the structure and function of microbial communities.