Differences in salinity are boundaries that act as barriers for the dispersal of most aquatic organisms. This creates distinctive biota in freshwater and brackish water (mesohaline) environments. To test how saline boundaries influence the diversity and composition of host-associated microbiota, we analyzed the microbiome within the digestive tract of Theodoxus fluviatilis, an organism able to cross the freshwater and mesohaline boundary. Alpha-diversity measures of the microbiome in freshwater and brackish water were not significantly different. However, the composition of the bacterial community within freshwater T. fluviatilis differed significantly compared with mesohaline T. fluviatilis and typical bacteria could be determined for the freshwater and the mesohaline digestive tract microbiome. An artificial increase in salinity surrounding these freshwater snails resulted in a strong change in the bacterial community and typical marine bacteria became more pronounced in the digestive tract microbiome of freshwater T. fluviatilis. However, the composition of the digestive tract microbiome in freshwater snails did not converge to that found within mesohaline snails. Within mesohaline snails, no cardinal change was found after either an increase or decrease in salinity. In all samples, Pseudomonas, Pirellula, Flavobacterium, Limnohabitans, and Acinetobacter were among the most abundant bacteria. These bacterial genera were largely unaffected by changes in environmental conditions. As permanent residents in T. fluviatilis, they may support the digestion of the algal food in the digestive tract. Our results show that freshwater and mesohaline water host-associated microbiomes respond differently to changes in salinity. Therefore, the salinization of coastal freshwater environments due to a rise in sea level can influence the gut microbiome and its functions with currently unknown consequences for, e.g., nutritional physiology of the host.

The community composition of bacteria with highly dynamic abundance and activity was observed to be with low variability in a shallow lake sediment with frequent physical disturbance. This suggests that physical disturbance did not create more niches and did not lead to highly variable bacterial community. The major part of the bacterial community was homogeneous, with 40% of phylotypes being ubiquitous and present in all samples. A minor part was responding to two contrasting periods - permanent ice cover and open lake. During the period of ice cover the total number of phylotypes decreased by ∼ 10%, the productivity of sediment bacteria varied by 15-fold (decreased by 40% under ice) and the abundance of bacteria by up to sixfold (decreased by 20%), suggesting that community of sediment bacteria with stable species composition might be highly dynamic in numbers and activity. Phylotypes identified by 16S rRNA gene sequencing were close to those observed in similar environments. All sequences were closely related only to uncultured phylotypes. Proteobacteria, particularly of the Beta subgroup, were the most common identified species in Lake Võrtsjärv sediment samples. A few other phylotypes, mostly those typical of anoxic sediments, were observed, but were uncommon.

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Bacterioplankton abundance and production were followed during one decade (1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001) in the hypertrophic and steeply stratified small Lake Verevi (Estonia). The lake is generally dimictic. However, a partly meromictic status could be formed in specific meteorological conditions as occurred in springs of 2000 and 2001. The abundance of bacteria in Lake Verevi is highly variable (0.70 to 22 · 10 6 cells ml )1 ) and generally the highest in anoxic hypolimnetic water. In 2000-2001, the bacterial abundance in the hypolimnion increased probably due to meromixis. During a productive season, heterotrophic bacteria were able to consume about 10-40% of primary production in the epilimnion. Our study showed that bacterioplankton in the epilimnion was top-down controlled by predators, while in metalimnion bacteria were dependent on energy and carbon sources (bottom-up regulated). Below the thermocline hypolimnetic bacteria mineralized organic matter what led to the depletion of oxygen and created anoxic hypolimnion where rich mineral nutrient and sulphide concentrations coexisted with high bacterial numbers.