Strategies to Map the Microbiome of Freshwater Lakes: Sampling and Context

Abstract

Freshwater lakes are indispensible resources for humankind and as such also exposed to significant pressure from anthropogenic activities and environmental change. Organic matter holds a central role in these ecosystems, both in providing energy for the food web and in modifying water quality. The transformation, degradation, and internal production of organic matter is largely mediated by microorganisms and there is hence great interest in learning more about the ecology and function of these microscopic but abundant key players in lake ecosystems. The focus of this chapter is thus on strategies to study the spatial and temporal organization of the freshwater lake microbiome, with special attention to representative and rational sampling of freshwater lakes for subsequent analyses of microbial process or community features. Within-system heterogeneity across spatial and temporal scales will be presented and linkages between the physical structure, chemical gradients, and microbial distribution patterns will be discussed. Useful practical considerations to sample water for experiments or cells for biomolecular analyses will be presented along with recommendations regarding how to collect and compile basic but critically important contextual information. It is evident that the long-standing myth of freshwater lakes as homogenous systems delimited by defined shoreline boundaries is incorrect and that heterogeneity should be considered already in designing sampling strategies.