UC San Diego

Microbes contribute to aquatic ecosystem functioning and fitness of macroscopic organisms such as freshwater zooplankton. Many factors affect the taxonomic compositions of zooplankton-associated and free-living microbial communities in lakes, yet how these communities change seasonally in lakes remains poorly understood. In this study, we investigate how free-living microbial communities and those associated with different zooplankton host species change in response to fluctuations in their natural environment across time and space. We repeatedly sampled zooplankton and water from six lakes in the eastern Sierra Nevada mountains of California, USA across a summer season. Analysis of 16S rRNA gene sequencing found marginal differences in the compositions of the free-living and zooplankton-associated microbial communities; however, they shared the same dominant classes of bacteria suggesting that horizontal transmission is a main mechanism driving the assembly of freshwater zooplankton microbiomes. The free-living and zooplankton-associated microbial communities significantly changed across the five sampling time points. Out of all measured environmental variables, lake temperature and dissolved organic carbon concentrations were the strongest predictors of microbial community composition. We did not find significant differences in the microbial communities across the six lakes, despite geographical separation, as well as differences in elevation, environmental conditions, and zooplankton community composition. Our results suggest that temporal variation plays a stronger role than spatial variation in shaping zooplankton-associated and free-living microbial communities of alpine lakes.