Seasonal dynamics in microbial plankton reveals the ecological importance of fungi in shallow lake food webs

Abstract Introduction: High-trophy shallow lakes, both natural and artificial, have become the most common type of lentic waterbodies worldwide. They are key for maintaining landscape ecological stability; however, we still have very limited understanding of processes driven by the microbes at the lowest trophic levels in these systems, especially fungi, or drivers that shape them under conditions of extreme eutrophication. This makes predicting the behavior or resilience of shallow lakes under ongoing climate-related changes in nutrient and organic matter inputs difficult. Methods We attempted to fill in some of the knowledge gaps regarding the diversity, function, biotic interactions, and environmental drivers affecting planktonic microbial communities (bacteria and fungi) in hypertrophic shallow lakes in the context of seasonal changes, by combining amplicon sequencing data, co-occurrence network analyses, information on zooplankton and phytoplankton composition, abundance, and activity, as well as detailed chemical analyses, including characterization of dissolved organic matter. As experimental locations, we selected nine artificial hypertrophic ponds in the Czechia. Results Planktonic bacterial and fungal diversity was found to be relatively high, although most fungal sequences could not be identified at the phylum level. Fish biomass and activity (bioturbation) was found to have an overriding effect on microbial assemblage structure. The chemical characteristics of DOM, including its estimated complexity/bioavailability, phytoplankton abundance and composition, as well as the abundance of grazing zooplankton, were significant drivers affecting the composition and relative abundance of microbes. The effect was highly species and sampling time specific. Actinomycetota dominated the cross-domain co-occurrence networks, however fungal taxa (predominantly Basidiomycota and Ascomycota) constituted a significant proportion of nodes (up to 28%). The positive correlation observed between specific yeast genera and rotifer abundance points to a grazing association, which represents a potentially important, but so far unexplored trophic link. Conclusions Given the prevalence of the potentially significant ecological interactions between fungi, organic matter characteristics and degradation, bacteria, phytoplankton, and grazers found in this study, we believe that aquatic fungal biomass and activity, coupled with isolation and characterization efforts, should become one of the priorities in the research of shallow lake ecology, as well as aquatic microbial ecology in general.