Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within seven different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not correlated with the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO 2 + NO 3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) correlated to some extent with the water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. Significantly more data, including time-series measurements of land use and water chemical properties, are needed to fully understand the interaction between the environment and the organization of microbial communities.

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Toxic cyanobacterial blooms are a growing threat to freshwater bodies worldwide. In order for a toxic bloom to occur, a population of cells with the genetic capacity to produce toxins must be present together with the appropriate environmental conditions. In this study, we investigated the distribution patterns and phylogeny of potentially-toxic Microcystis (indicated by the presence and/or phylogeny of the mcyD and mcyA genes). Samples were collected from the water column of almost 60 water bodies across widely differing gradients of environmental conditions and land use in Israel. Potentially, toxic populations were common but not ubiquitous, detected in ~65% of the studied sites. Local environmental factors, including phosphorus and ammonia concentrations and pH, as well as regional conditions such as the distance from built areas and nature reserves, were correlated with the distribution of the mcyD gene. A specific phylogenetic clade of Microcystis, defined using the sequence of the mcyA gene, was preferentially associated with aquaculture facilities but not irrigation reservoirs. Our results reveal important environmental, geospatial, and land use parameters affecting the geographic distribution of toxinogenic Microcystis, suggesting non-random dispersal of these globally abundant toxic cyanobacteria.

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors.

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over three years. The system comprised two fishponds, where fish are grown, and a "control" operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects if aquaculture-related factors.