Leveraging DNA and RNA oscillatory dynamics to investigate the ecology and physiology of a freshwater microbial community

Microbial ecological dynamics in temporally varying environments are often mediated by the physiological responses of community members. Linking physiological responses to ecological dynamics remains challenging and ultimately limits our ability to understand the response of microbial communities to environmental change. Here, we evaluated the physiological response of microorganisms to changing conditions by applying a macroecological approach to a multi-year timeseries of paired ribosomal RNA and DNA measurements from a freshwater microbial community. We found that the dynamics of both microbial RNA and DNA displayed strong seasonal oscillations, with phylogenetically distant species oscillating on similar timescales with varying amplitudes. Despite this variation, several fundamental macroecological patterns displayed the same regularities observed in other biomes, while others clearly deviated due to the sustained oscillations. These deviations motivated the development of a minimal ecological model that accounts for oscillations, with seasonal dynamics captured by a time-dependent carrying capacity. Based on previous studies, we interpreted the ratio of RNA and DNA (RNA:DNA) as a proxy of ribosome concentration and evaluated two physiological hypotheses. First, we tested whether RNA:DNA explained changes in DNA over time within a given community member, finding that the commonly-used ratio had a limited predictive capacity. However, RNA:DNA across community members was predictive of proxies of growth, a result consistent with the interpretation that RNA:DNA reflects growth. By examining environmental variables with similar seasonality, we found that temperature provided a reasonable explanation for dynamics of both RNA and DNA, though not RNA:DNA. The results of this work provide a macroecological understanding of ribosomal RNA barcoding and identify the limitations of RNA:DNA as a measure of microbial physiology.