Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.

Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages – a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013–2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.

Cyanobacterial blooms in lakes frequently display high spatial heterogeneity, which may drive temporal changes in microbial community structure. Here we report on the spatial (horizontal and vertical) structure of the cyanobacteria community and of the co‐occurring heterotroph microbial community during a major lake‐wide bloom event at Lake Kinneret (Sea of Galilee, Israel). We sampled the upper water layer (0, 1 and 5 m depths) at five locations across the lake, spatially representing north, south, east, west and centre of the lake, on two dates during winter 2016 when the Microcystis biomass was high. We aimed to characterise the spatial distribution of the bloom and the associated microbiota, as well as testing the extent to which variation in the structure of the microbial community could be associated with Microcystis biomass. During the winter 2016 bloom, Microcystis biomass was spatially heterogeneous, but the Microcystis population structure was rather homogenous, dominated by a single genotype (ITS sequence variant). By contrast, the composition of the bacterial community, assessed using 16S rRNA gene sequencing, was spatially heterogeneous, differing between depths, sampling locations and time. The largest difference in microbial community structure was between particle‐associated (PA) and free‐living (FL) fractions. The PA community was characterised by a relatively lower diversity, and dominated by Proteobacteria, whereas the FL community was significantly more diverse and dominated by members of Proteobacteria, Bacteroidetes and Actinobacteria. Variation in the microbial community was significantly correlated with geographical location and sampling depth. However, there was no clear relationship between the Microcystis biomass density (cells biovolume) and the structure of the microbial communities. These results suggest that the structure of the bacterial community is partly decoupled from Microcystis population density, and potentially more affected by other environmental factors such as temperature and/or physicochemical conditions. Our study highlights the importance of spatial information on bloom composition and intensity in clarifying the factors affecting the progression of cyanobacterial harmful algal blooms and how this impacts their microbial counterparts.