Search Results (69)

Holomictic mesotrophic lakes, characterized by oxygenated hypolimnion due to seasonal mixing of their water layers, host microbial assemblages with diversity and community compositions strongly shaped by the constant recycling of nutrients. However, other studies showed occurrences of hypolimnion-specific lineages, distinct from adjacent epilimnion in such lakes. The study focused on Lake Biwa, a tectonic mesotrophic lake in Japan, to spatially elucidate bacterial assemblages between the epilimnion and oxygenated hypolimnion. 16S rRNA gene analysis revealed dominance of bacterial members belonging to Pseudomonadota, Bacillota and Bacteroidota throughout the water column, while other lineages such as Bdellovibrionota, Kapabacteria and WGS were not detected in the epilimnion and were solely hypolimnion-specific in their occurrences. This study serves to further corroborate earlier investigations that have shown bacterioplankton community differences in the vertical distribution of deep-water lakes. Full article

One of the global issues concerning aquatic environments is the increasing frequency of cyanobacterial blooms. These blooms can lead to oxygen depletion and the release of potent toxins, potentially disrupting the bacterial communities responsible for organic matter transformation and mineralization. This study aimed to examine the structural and functional diversity of bacterioplankton in three eutrophic lakes during periods of cyanobacterial bloom. The microbial communities were analyzed using high-throughput sequencing of the 16S rRNA gene, and the abundance and activity of bacterioplankton were assessed with fluorescent markers. The findings revealed that dead bacterial cells predominated in the water samples (61.16%). Taxonomic profiling identified Cyanobacteria (45.38%), Proteobacteria (20.99%), Bacteroidetes (11.37%), Actinobacteria (8.08%), and Verrucomicrobia (4.04%) as the dominant phyla. Additionally, the structure of the bacterial communities (β-diversity) showed significant variation across the lakes, but this variation did not correlate with seasonal changes. No marked effect of abiotic factors on the structural or functional diversity of the bacterioplankton was observed. These results suggest that, despite the presence of cyanobacterial dominance, microbial community structure is more closely tied to the type of lake rather than seasonal or abiotic factors. Further studies are needed to better understand the factors driving these community patterns. Full article

Ocean Alkalinity Enhancement (OAE) is a promising carbon dioxide removal strategy, but its ecological impacts on marine microbial communities under varying nutrient conditions remain poorly understood. We conducted laboratory incubations using a natural North Atlantic microbial assemblage to investigate the response to OAE under both natural and nutrient-enriched regimes. We tracked phytoplankton and bacterioplankton dynamics, biomass, and leucine aminopeptidase (LAP) and alkaline phosphatase (ALP) activity as indicators of organic matter remineralization. OAE consistently reduced phytoplankton abundance in both nutrient regimes, potentially due to CO₂ limitation, resulting in lower production of phytoplankton-derived organic matter. This reduction was reflected in decreased LAP activity and shifts in the relative abundance of phytoplankton-associated bacterial taxa. These findings indicate that OAE can directly affect phytoplankton through carbonate chemistry alterations, with potential microbial responses largely mediated by changes in organic matter availability. While short-term microbial disruptions were modest, the ecological consequences of altered bloom dynamics should be carefully considered in future OAE deployment strategies. Full article

Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. Limnohabitans, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting Limnohabitans have been reported to date. Here, we describe, for the first time, three phages infecting Limnohabitans, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on Limnohabitans in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding Limnohabitans–phage interactions. Full article

Kuibyshev Reservoir, the largest in the Volga basin, is poorly covered by modern molecular studies. The results of a metabarcoding study of pro- and eukaryotic microbial plankton in its lower section during the summer period are presented. Bacterioplankton composition was typical for most temperate freshwater bodies and characterized by the dominance of cyanobacteria, Pseudomonadota, Bacteroidota, Actinomycetota, and PVC superphylum (Verrucomicrobiota and Planctomycetota), with a somewhat increased proportion of the latter. The protist community was dominated by Cryptista, principally phototrophic, and various ciliates. Several picoeukaryotic groups were newly detected in the reservoir. A relationship between the composition of both bacterioplankton and protist communities and the stage of phytoplankton succession, including the cyanobacterial bloom, was observed. Some inconsistency between the cyanobacterial bloom phase and the structure of other parts of the microbial plankton is obviously due to some temporal delay, spatial station position, and inflow from tributaries. Heterotrophic bacterioplankton indicator species of the main bloom stage include OTUs representing both the phycosphere of colonial cyanobacteria and free-living species. Among the protists, sessile ciliates benefit most from plenty of substrates for colonization, while cyanobacterial grazers and parasites were minor. Overall, the cyanobacterial bloom creates new niches for the plankton community and significantly modifies its structure. Full article

Artificial reservoirs formed by hydroelectric dams are young ecosystems requiring water quality monitoring, as they often serve local populations. Traditionally, this is performed through hydrochemical and sanitary assessments, alongside phytoplankton composition analysis. This study aimed to assess the seasonal dynamics of microbial communities—both bacterioplankton and microeukaryotes including phytoplankton—in the Irkutsk Reservoir (IR), which is fed by the cold oligotrophic waters of Southern Baikal (SB). Using parallel metabarcoding of 16S and 18S rRNA gene fragments, we analyzed community composition during the open-water season and evaluated the ecological connectivity between these two freshwater systems. We demonstrated that seasonal changes in microeukaryotic communities were closely linked between SB and IR, with the greatest divergence observed in early summer and progressive convergence by autumn. Metabarcoding confirmed microscopy-based observations while providing higher taxonomic resolution and detecting otherwise overlooked groups. Bacterioplankton communities also exhibited seasonal variation and were shaped by environmental gradients and reservoir characteristics. Cyanobacteria peaked in SB in late summer but did not dominate communities, unlike in mesotrophic lowland reservoirs. These findings demonstrate the value of metabarcoding for freshwater monitoring and provide new insights into microbial community dynamics in river–reservoir systems influenced by oligotrophic lake inflow. Full article

The structure and density of plankton communities greatly influence carbon and nutrient cycling as well as the environmental status of lake ecosystems. This community can respond to a range of environmental drivers, including those influenced by human perturbations on local and regional scales, causing abrupt changes and imbalances. While the implications of climate and land-use changes are evident for a range of tropical lake conditions, their impacts on planktonic population dynamics are less understood. In this study, we aimed to investigate how distinctive levels of nutrients, allochthonous organic matter (OM), and sunlight availability change phytoplankton and zooplankton density and structure in a natural tropical lake. Using an in situ mesocosm facility, we manipulated the addition of nutrients and OM, in addition to sunlight availability and a combination of these treatments. We monitored limnological parameters, plankton count, and identification for 12 days. The mesocosms included eight different combinations in a 2 × 2 × 2 factorial design, each with two replicates. Inorganic nutrient addition reduced phytoplankton species richness, favoring the dominance of opportunistic species such as Chlorella sp. at much higher densities. Organic matter also increased light attenuation and caused the substitution of species and changes in dominance from Pseudanabaena catenata to Aphanocapsa elachista. On the other hand, physical shading had less influence on these communities, presenting densities similar to those found in the control mesocosms. Zooplankton presented a group dominance substitution in all mesocosms from copepod to rotifer species, and copepod growth seemed to be negatively affected by Chlorella sp. density increase. Furthermore, this community was associated with the light attenuation indices and bacterioplankton. These results indicate that tropical planktonic responses to environmental changes can effectively occur in just a few days, and the responses can be quite different depending on the nutritional source added. The punctual nutrient addition was sufficient to provide changes in this community, evidencing the strength of anthropic events associated with strong nutrient input. Understanding tropical plankton dynamics in response to environmental changes, such as those simulated in this work, is important for understanding the effects of climate and anthropogenic changes on tropical lake functioning. This knowledge can strengthen measures for the conservation of freshwater systems by allowing predictions of plankton community changes and the possible consequences for the aquatic food chain and water quality. Full article

Marine bacterioplankton perform a very important role in the cycles of carbon, nitrogen, phosphorus, and other elements in coastal waters. The impacts of environmental factors on bacterial community structure are dynamic and ongoing. This study investigated the spatiotemporal distributions of elements and their influences on bacterioplankton communities in the coastal waters around the Changli Gold Coast National Nature Reserve in northern China. The results demonstrate the significant temporal variability of phosphorus, nitrogen, and carbon in spring and summer, influenced by natural environmental factors and anthropogenic activities. In spring, increased biological activity, particularly phytoplankton growth, may elevate TOC and POC levels near the river estuaries, while in summer, microbial decomposition likely stabilized carbon concentrations. The seasonal variation in the bacterioplankton community was obvious. Bacteroidetes were enriched in spring samples and Cyanobacteriota proliferated in summer. The dominated genera in the spring, including Planktomarina, an unclassified NS5_marine_group (belonging to Flavobacteriaceae), and the OM43_clade (Methylophilaceae), showed significant positive correlation with salinity, TDP, TOC, POP, and DO levels, while Synechococcus_CC9902 (Synechococcus), PeM15_unclassified (Actinobacteria), and HIMB11 (Rhodobacteraceae), which all dominate in summer samples, are significantly positively correlated with TN, TDN, temperature, and ammonium levels. In summer in particular, the increase in human activities and river inputs greatly improves nutrient levels and promotes the propagation of photosynthetic microorganisms. These results indicate that the nutrient elements and environmental physical conditions are affected by seasonal changes and human activities, which have significant effects on the community structure of bacterioplankton. This study highlights the importance of ongoing monitoring in estuarine coastal areas, especially in protected areas like the Changli Reserve, to manage eutrophication risks and maintain ecological balance. Full article

As global food security issues become increasingly severe, an important innovation in agricultural production patterns, namely integrated rice–fish farming, has been widely implemented around the world, especially in Asia. To assess the impact of integrated rice–crayfish (Procambarus clarkii) farming (IRCF) on agricultural ecosystems, we used Illumina high-throughput 16S rRNA gene sequencing to analyze differences in diversity, composition, co-occurrence network, and assembly process of planktonic bacterial communities in paddy water between traditional rice farming (TRM) and IRCF. Environmental factors and planktonic bacterial communities were evaluated during the tillering, jointing, flowering, and grain-filling stages on August 24, September 5, September 24, and October 16, respectively. Our findings revealed that, throughout the entire cultivation period, IRCF had no notable impacts on bacterioplankton community diversity in paddy water, but it changed the composition and relative abundance of the dominant bacterioplankton. Specifically, IRCF promoted the Chloroflexota during the tillering stage but reduced its presence during the grain-filling stage. It also significantly decreased the Bacillota during the jointing stage while notably enhancing Actinomycetota during the flowering stage. Furthermore, IRCF markedly improved the robustness and negative/positive cohesion within bacterioplankton co-occurrence networks during jointing and grain-filling stages. IRCF altered the assembly processes shaping planktonic bacterial communities, promoting a greater dominance of stochastic processes during the tillering, jointing, and flowering stages and a diminished dominance during the grain-filling stage. IRCF dramatically changed aquatic environmental factors, particularly during the jointing stage, by substantially increasing the TN, ammonium, nitrate, and phosphate levels in paddy water. These nutrient levels were closely correlated with the dynamics of the planktonic bacterial communities. Our findings underscore the considerable potential of IRCF in enhancing the stability of bacterioplankton communities and promoting rice growth while also providing valuable data and theoretical insights into the microbiological ecological impacts of IRCF on the agroecosystem. Full article

To investigate the hypothesis of top-down control by viruses and heterotrophic nanoflagellates on bacterial-mediated carbon fluxes in freshwater systems, a year-long study (2023–2024) was conducted in the pelagic zone of Lake Saint-Gervais (France). The variability in BGE (9.9% to 45.5%) was attributed to the decoupling of production and respiration, providing bacterioplankton communities with a competitive advantage in adapting to fluctuating environmental disturbances in freshwater systems. The high nucleic acid (HNA) bacterial community, the active fraction, contributed the most to bacterial production and was linked to BGE estimates. Weak bottom-up controls (nutrient concentrations and stoichiometry) on BGE suggested a stronger role for mortality forces. Among viral subgroups (VLP1–VLP4) identified via flow cytometry, the dominant low-fluorescence DNA VLP1 subgroup (range = 0.7 to 3.1 × 10⁸ VLP mL⁻¹) accounting for the majority of viral production was closely linked to the HNA population. Both top-down forces exerted antagonistic effects on BGE at the community level. The preferential lysis and grazing of the susceptible HNA population, which stimulated bacterial community respiration more than production in the non-target population, resulted in reduced BGE. These results underscore the key role of top-down processes in shaping carbon flux through bacterioplankton in this freshwater system. Full article

The rice–fish co-culture is an important model of carp farming in China; however, research on the dynamics and assembly of water bacterial communities in this system remains limited. Therefore, this study aimed to explore the dynamics and assembly of bacterial communities, as well as their correlation with environmental factors in paddy water. For these purposes, this study was divided into two groups: a rice–carp co-culture (WRC) group and a rice monoculture (WRM) group, with 20 rice fields in each group. After 60 days of farming, the concentrations of NH₄⁺-N, NO₂⁻-N, TN, and PO₄³⁻ were significantly higher in the WRC group than those in the WRM group. Alpha diversity analysis showed that the Shannon index in the WRC group was significantly decreased compared with the WRM group. At the phylum level, the relative abundance of Actinobacteria significantly increased, while the relative abundance of Proteobacteria and Bacteroidetes significantly decreased in the paddy water of the WRC group. The neutral community model (NCM) indicated that a random process played a dominant role in the construction of bacterial communities in the two groups, and common carp cultivation increased migration rates, thereby affecting community assembly. The co-occurrence network displayed that common carp cultivation led to looser interactions between bacterial communities. In addition, the contents of nutrients significantly affected the abundance of bacteria in paddy water. In summary, carp cultivation decreased the diversity of bacteria and changed the relative abundance of dominant bacteria, thereby affecting the stability and assembly of bacterial communities. Full article

Climate change may increase the vulnerability of aquifers to contamination through extreme precipitation and extended drought periods. Therefore, the understanding of groundwater ecosystem dynamics is crucial, with bacterial assemblages playing a major role in biogeochemical cycles. The present research describes a geospatial study targeting the bacterial community structure of groundwaters from the largest karst aquifer in Portugal (the Maciço Calcário Estremenho), integrating hydrogeochemical and bacterial diversity data. A total of 22 samples were analyzed from a set of 11 geographically sparsely distributed groundwater sources in dry vs. wet seasons. The 16S rRNA gene barcoding data revealed bacterial community variability across samples in space and time. The phylum Proteobacteria was dominant across all samples (from 44 to 92% of total sequence reads), mainly represented by the classes Alphaproteobacteria (orders Sphingomonadales, BD7–3, Rhizobiales and Rhodospirillales), Betaproteobacteria (orders Burkholderiales, Rhodocyclales, Nitrosomonadales), Gammaproteobacteria (orders Pseudomonadales, Xanthomonadales, Alteromonadales, Legionellales) and Deltaproteobacteria (orders Myxococcales, Spirobacillales). Variation in the bacterial community was primarily attributed to parameters such as redox conditions (DO, ORP), Fe, Mn, SO₄, PO₄, Sr and Cl, but also some minor and trace elements (Al, V, Cr, Cu, Pb). Our results provide novel insights into bacterial diversity in relation to groundwater hydrogeochemistry. The strong dominance of OTUs related to bacterial taxa associated with nitrification/denitrification also highlights a potentially important role of these assemblages on nutrients (nitrogen sources) and groundwater quality dynamics at this karstic aquifer system. Moreover, the integration of bacterial assemblages information is emphasized as central for water quality monitoring programs. Full article

Constructing underground reservoirs has emerged as a crucial strategy to address the shortage of fresh water in Rizhao, Shandong Province, China. However, the water quality, microbial community composition, and biogeochemical cycling of nutrients in underground reservoirs compared to raw water remain unknown. To unveil the characteristics of microbial community structures and their nitrogen cycling metabolic potential in coastal underground reservoirs, we utilized a functional gene array (GeoChip 5.0) in conjunction with high-throughput sequencing of 16S rRNA and 18S rRNA genes. Our findings indicate that the water quality in the underground reservoir exhibits a certain degree of eutrophication compared to raw water, with higher concentrations of TN, TP, NO₃⁻N, NO₂⁻-N, and Chl a, but lower concentrations of DO and NH₄⁺-N. The alpha diversity of bacterial and microeukaryotic communities was significantly lower in the underground reservoir. The bacterial community presented a stronger correlation with environmental factors than the microeukaryotic community. Regarding the relative abundance of bacterial communities, Gammaproteobacteria dominated the bacterial community in raw water, while Gammaproteobacteria and Alphaproteobacteria dominated the bacterial community in underground reservoir water. Additionally, the relative abundance of Nitrospirae was noticeably higher in the underground reservoir water. Moreover, we found significantly higher sequence abundance of the archaea Thaumarchaeota in the underground reservoir. Furthermore, our analysis revealed that, except for the amoA functional gene, which significantly increased the metabolic potential of nitrification, the metabolic potential of other microbial nitrogen functional genes was significantly reduced. This reduction may contribute to the lower concentration of NH₄⁺-N in the underground reservoir. This study provides a comprehensive understanding of the microbial community characteristics and their nitrogen cycling metabolic potential in underground reservoirs. It serves as a valuable reference for water source selection, the formulation of water quality assurance measures, and the construction and management of underground reservoirs for subsequent impounding. Full article

Intensive shrimp farming may lead to adverse environmental consequences due to discharged water effluent. Inoculation of microalgae can moderate the adverse effect of shrimp-farming water. However, how bacterial communities with different lifestyles (free-living (FL) and particle-attached (PA)) respond to microalgal inoculation is unclear. In the present study, we investigated the effects of two microalgae (Nannochloropsis oculata and Thalassiosira weissflogii) alone or in combination in regulating microbial communities in shrimp-farmed water and their potential applications. PERMANOVA revealed significant differences among treatments in terms of time and lifestyle. Community diversity analysis showed that PA bacteria responded more sensitively to different microalgal treatments than FL bacteria. Redundancy analysis (RDA) indicated that the bacterial community was majorly influenced by environmental factors, compared to microalgal direct influence. Moreover, the neutral model analysis and the average variation degree (AVD) index indicated that the addition of microalgae affected the bacterial community structure and stability during the stochastic process, and the PA bacterial community was the most stable with the addition of T. weissflogii. Therefore, the present study revealed the effects of microalgae and nutrient salts on bacterial communities in shrimp aquaculture water by adding microalgae to control the process of community change. This study is important for understanding the microbial community assembly and interpreting complex interactions among zoo-, phyto-, and bacterioplankton in shrimp aquaculture ecosystems. Additionally, these findings may contribute to the sustainable development of shrimp aquaculture and ecosystem conservation. Full article

Bacterioplankton communities are critical components of varied ecosystems in the oceans. Their occurrences represent a variety of connections between environmental and ecological elements. However, our current knowledge about the shaping factors of surface bacterioplankton communities in the eastern East China Sea (ECS) is still limited. In this study, we reveal the spatial patterns of the taxonomic and functional profiles of the surface bacterioplankton communitiesies in the nearshore and offshore areas in the eastern ECS, based on 16S rRNA gene pyrosequencing and functional annotation analysis. The obtained results show that the surface bacterioplankton communities in the nearshore areas are mainly dominated by the firmicutes (85.9%), actinobacteria (8.1%), and proteobacteria (5.4%), which are mainly involved in organic compound metabolism. Meanwhile, different bacteria predominate the composition of the offshore group, namely proteobacteria (71.1%) and bacteroidetes (22.0%) responsible for nitrogen and sulfur metabolism. Furthermore, their distribution pattern is shown to be spatially determined, along with a modest finding of functional diversity when comparing the bacterial species. The primary two shaping factors of bacterioplankton diversity are found to be the offshore distance and temperature. Overall, these findings add to those previously published on bacterial species and offer up functional information on the surface bacterioplankton communities in the eastern ECS. To extend our research, we propose that, in the future, it may be beneficial to monitor the dynamics of the ecosystem in this sea area. Full article