Sofia Papadopoulou: Microbial diversity and activity across connected freshwater habitats

Abstract

Freshwater habitats are often organized into hydrologically connected networks of alternating lentic and lotic environments, in which microorganisms are dispersed from upstream to downstream sites via water flow. Along this aquatic continuum, microbial communities undergo compositional shifts, receiving cells from both terrestrial and aquatic sources. This thesis investigated microbial diversity, activity and community assembly across hydrological networks, focusing on the connections between lakes and their inflowing and outflowing streams or rivers. Field studies in two lake networks (Papers I, III) demonstrated that inflowing streams and rivers are important reservoirs of bacterial and protist diversity, harboring higher alpha and beta diversity than lakes. Lakes, in turn, function as ecological filters, retaining only a subset of the taxa arriving from upstream lotic habitats. Hydrological connectivity shaped outlet community composition, with outlet communities resembling lake habitats under high flow conditions. Outlet communities also reflected upstream dispersal processes, with water flow changes influencing the proportion of taxa shared with upstream sites. The consistency of these diversity patterns across systems differing in hydrology, spatial scale and trophic status suggests that they may represent common features of connected freshwater habitats. Paper II experimentally tested whether abiotic conditions constrain the establishment of stream bacterial communities following dispersal into pelagic environments. Stream communities were incubated in downstream lake water, while physically separated from resident lake bacteria. Environmental filtering restructured stream communities toward a more lake-like composition, driven by an abundant pool of taxa shared between streams and lakes. Notably, this restructuring occurred over a shorter timescale than the lake water residence time. Paper IV was an application of quantitative stable isotope probing in a grazing experiment, examining whether the richness and taxonomic composition of protists actively grazing on bacteria differed between a lake and its main inlet stream. The study showed that a similar number of taxa incorporated prey biomass at the two sites, including abundant and rare taxa, while grazers comprised both heterotrophic and mixotrophic protists. Collectively, these findings demonstrate that lake networks function as dynamic microbial landscapes rather than simple transport continua, with lakes shaping the persistence of taxa locally and their potential for downstream transport.