Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water.

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

Prediction of COVID-19 positive cases, a nation-wide SARS-CoV-2 wastewater-based epidemiology study.

Taking advantage of Estonia's small size and population, we have employed wastewater-based epidemiology approach to monitor the spread of SARS-CoV-2, releasing weekly nation-wide updates. In this study we report results obtained between August 2020 and December 2021. Weekly 24 h composite samples were collected from wastewater treatment plants of larger towns already covered 65% of the total population that was complemented up to 40 additional grab samples from smaller towns/villages and the specific sites of concern. The N3 gene abundance was quantified by RT-qPCR. The N3 gene copy number (concentration) in wastewater fluctuated in accordance with the SARS-CoV-2 spread within the total population, with N3 abundance starting to increase 1.25 weeks (9 days) (95% CI: [1.10, 1.41]) before a rise in COVID-19 positive cases. Statistical model between the load of virus in wastewater and number of infected people validated with the Alpha variant wave (B.1.1.17) could be used to predict the order of magnitude in incidence numbers in Delta wave (B.1.617.2) in fall 2021. Targeted testing of student dormitories, retirement and nursing homes and prisons resulted in successful early discovery of outbreaks. We put forward a SARS-CoV-2 Wastewater Index (SARS2-WI) indicator of normalized virus load as COVID-19 infection metric to complement the other metrics currently used in disease control and prevention: dynamics of effective reproduction number (Re), 7-day mean of new cases, and a sum of new cases within last 14 days. In conclusion, an efficient surveillance system that combines analysis of composite and grab samples was established in Estonia. There is considerable discussion how the viral load in wastewater correlates with the number of infected people. Here we show that this correlation can be found. Moreover, we confirm that an increased signal in wastewater is observed before the increase in the number of infections. The surveillance system helped to inform public health policy and place direct interventions during the COVID-19 pandemic in Estonia via early warning of epidemic spread in various regions of the country.

Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system.

The gut microbiome is one of the most important sites of host-microbe interactions, however, mechanisms governing the responses of host-associated microbes to changing environmental conditions are poorly understood. To address this, we investigated individual and combined effects of dietary changes and increase in salinity (from freshwater to salinity 3) or antibiotic concentration on the gastrointestinal bacterial community of the aquatic snail Ampullaceana balthica. In parallel, the energy reserves of the host were quantified. A change of natural food source to biofilm forming green algae Scenedesmus obliquus as well as the combined treatment of salinity and S. obliquus decreased the richness and changed the composition of the A. balthica gastrointestinal bacterial community. In these treatments Pseudomonas became the dominant bacterium. However, energy reserves of the host were higher in these treatments compared to the reference aquaria specimens and the combined treatment of antibiotics with S. obliquus. The presence of antibiotics inhibited the dominance of Pseudomonas and resulted in lower energy reserves despite S. obliquus feeding. Therefore the host seems to be able to adapt and replace its bacterial community composition to respond to mild changes in salinity and food source. Antibiotics in the water can disturb this self-regulating mechanism. Our study underlines the ability of aquatic macroinvertebrates to respond to sudden changes in food source and mild shifts in salinity. Moreover, it emphasizes the strong impact of the food source on the gastrointestinal microbiome and the importance of generalists during disturbance.

Bacterial communities in ballast tanks of cargo vessels - Shaped by salinity, treatment and the point of origin of the water but "hatch" its typical microbiome.

Ballast water is a main vector of introduction of potentially harmful or pathogenic aquatic organisms. The development of genetic tools for ballast water monitoring has been underway and highlighted as a source for accurate and reliable data for decision making. We used 16S rRNA gene amplicon sequencing to analyze the microbial communities found in the ballast water of fifteen commercial ships routed through two Estonian ports. In parallel, samples from the port area were collected at the same time each ship visited. Fluorescence microscopy was utilized to assess the effectiveness of the treatment applied to ballast water. In addition, supplemental samples were collected from Hamburg Port (Germany) and a ballast tank decontamination system used at this port. The composition and diversity of bacterial communities varied greatly between obtained samples. The application of UV treatment did not demonstrate significant reduction in species richness estimates. The composition of microbial communities was significantly influenced by salinity, treatment (mainly untreated or UV treated) and the point of origin of the ballast water. Over a hundred potentially pathogenic bacterial taxa were found in relatively high abundance, including in ballast water that had received UV treatment. These shortcomings of stand-alone UV treatment of ballast water, especially when weak treatment is applied insufficiently, highlight the danger of possible harmful effects arising over time and the need for genetic tools for ballast water monitoring and management.

Distinct stages of the intestinal bacterial community of Ampullaceana balthica after salinization.

Environmental disturbances influence bacterial community structure and functioning. To investigate the effect of environmental disturbance caused by changes in salinity on host-protected bacterial communities, we analyzed the microbiome within the gastrointestinal tract of Ampullaceana balthica in different salinities. A. balthica is a benthic gastropod found in fresh- and mesohaline waters. Whereas the total energy reserves of A. balthica were unaffected by an increase of salinity to 3, a high mortality rate was detected after a shift from freshwater to salinity 6 suggesting a major disruption of energy homeostasis. The shift to salinity 6 also caused a change in the gastrointestinal bacterial community composition. At salinity 3, the bacterial community composition of different host individuals was related either to the freshwater or salinity 6 gastrointestinal bacterial community, indicating an ambivalent nature of salinity 3. Since salinity 3 represents the range where aquatic gastropods are able to regulate their osmolarity, this may be an important tipping point during salinization. The change in the intestinal microbiome was uncoupled from the change in the water bacterial community and unrelated to the food source microbiome. Our study shows that environmental disturbance caused by salinity acts also on the host-protected microbiome. In light of the sea-level rise, our findings indicate that salinization of the near-shore freshwater bodies will cause changes in organisms' intestinal microbiomes if a critical salinity threshold (presumably ∼3) is exceeded.

Impact of Salinity on the Gastrointestinal Bacterial Community of Theodoxus fluviatilis.

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 influence of zooplankton enrichment on the microbial loop in a shallow, eutrophic lake.

With increasing primary productivity, ciliates may become the most important members of the microbial loop and form a central linkage in the transformation of microbial production to upper trophic levels. How metazooplankters, especially copepods, regulate ciliate community structure in shallow eutrophic waters is not completely clear. We carried out mesocosm experiments with different cyclopoid copepod enrichments in a shallow eutrophic lake to examine the responses of ciliate community structure and abundance to changes in cyclopoid copepod biomass and to detect any cascading effects on bacterioplankton and edible phytoplankton. Our results indicate that an increase in copepod zooplankton biomass favours the development of small-sized bacterivorous ciliates. This effect is unleashed by the decline of predaceous ciliate abundance, which would otherwise graze effectively on the small-sized ciliates. The inverse relationship between crustacean zooplankton and large predaceous ciliates is an important feature adjusting not only the structure of the ciliate community but also the energy transfer between meta- and protozooplankton. Still we could not detect any cascading effects on bacterio- or phytoplankton that would be caused by the structural changes in the ciliate community.

Low seasonal variability in community composition of sediment bacteria in large and shallow lake.

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.