Bacterioplankton Metacommunity Processes across Thermal Gradients: Weaker Species Sorting but Stronger Niche Segregation in Summer than in Winter in a Subtropical Bay

Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant

As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.

Planktonic and early-stage biofilm microbiota respond contrastingly to thermal discharge-created seawater warming

Thermal-discharges from power plants highly disturb the biological communities of the receiving water body and understanding their influence is critical, given the relevance to global warming. We employed 16 S rRNA gene sequencing to examine the response of two dominant marine bacterial lifestyles (planktonic and biofilm) against elevated seawater temperature (+5 ℃). Obtained results demonstrated that warming prompted high heterogeneity in diversity and composition of planktonic and biofilm microbiota, albeit both communities responded contrastingly. Alpha diversity revealed that temperature exhibited positive effect on biofilm microbiota and negative effect on planktonic microbiota. The community composition of planktonic microbiota shifted significantly in warming area, with decreased abundances of Bacteroidetes, Cyanobacteria, and Actinobacteria. Contrastingly, these bacterial groups exhibited opposite trend in biofilm microbiota. Co-occurrence networks of biofilm microbiota displayed higher node diversity and co-presence in warming area. The study concludes that with increasing ocean warming, marine biofilms and biofouling management strategies will be more challenging.

Seasonal succession of microbial community co-occurrence patterns and community assembly mechanism in coal mining subsidence lakes

Coal mining subsidence lakes are classic hydrologic characteristics created by underground coal mining and represent severe anthropogenic disturbances and environmental challenges. However, the assembly mechanisms and diversity of microbial communities shaped by such environments are poorly understood yet. In this study, we explored aquatic bacterial community diversity and ecological assembly processes in subsidence lakes during winter and summer using 16S rRNA gene sequencing. We observed that clear bacterial community structure was driven by seasonality more than by habitat, and the α-diversity and functional diversity of the bacterial community in summer were significantly higher than in winter (p < 0.001). Canonical correspondence analysis indicated that temperature and chlorophyll-a were the most crucial contributing factors influencing the community season variations in subsidence lakes. Specifically, temperature and chlorophyll-a explained 18.26 and 14.69% of the community season variation, respectively. The bacterial community variation was driven by deterministic processes in winter but dominated by stochastic processes in summer. Compared to winter, the network of bacterial communities in summer exhibited a higher average degree, modularity, and keystone taxa (hubs and connectors in a network), thereby forming a highly complex and stable community structure. These results illustrate the clear season heterogeneity of bacterial communities in subsidence lakes and provide new insights into revealing the effects of seasonal succession on microbial assembly processes in coal mining subsidence lake ecosystems.

Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake

In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.

Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay

Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.

Metagenomics reveals bacterioplankton community adaptation to long-term thermal pollution through the strategy of functional regulation in a subtropical bay

Thermal effluents from coastal nuclear power plants have led to undesirable pollution and subsequent ecological impacts on local marine ecosystems. However, despite the ecological importance, we know little about the impacts on functionality of bacterioplankton subjected in systems with long-term thermal pollution. We used metagenomic sequencing to study of the effect of thermal pollution on bacterioplankton community metagenomics in summer in a subtropical bay located on the northern coast of the South China Sea. Thermal pollution (>15 y), which resulted in an increase in the summer seawater temperature around 8°C and caused seawater temperature up to approximate 39°C, significantly decreased bacterioplankton metabolic potentials in photosynthesis, organic carbon synthesis, and energy production. The bacterioplankton community metagenomics underwent a significant change in its structure from Synechococcus-dominant autotrophy to Alteromonas, Vibrio, and Pseudoalteromonas-dominated heterotrophy, and significantly up-regulated genes involved in organic compound degradation and dissimilatory nitrate reduction for the matter and energy acquisition under thermal pollution. Moreover, the bacterioplankton community metagenomics showed an up-regulation with heating of genes involved in DNA repair systems, heat shock responsive chaperones and proteins, and proteins involved in other biological processes, such as biofilm formation and the biosynthesis of unsaturated fatty acids and glycan, to adapt to the thermal environment. Collectively, it indicates a functional regulation of bacterioplankton adaptation to high-temperature stress, which might advance the understanding of the molecular mechanisms of community adaptation to global extreme warming in aquatic ecosystems.

Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China

It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.

Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea

Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.

Photosynthetic Characteristics of Three Cohabitated Macroalgae in the Daya Bay, and Their Responses to Temperature Rises

Biochemical compositions and photosynthetic characteristics of three naturally cohabitated macroalgae, Ulva fasciata, Sargassum hemiphyllum and Grateloupia livida, were comparably explored in the field conditions in Daya Bay, northern South China Sea, as well as their responses to temperature rise. Chlorophyll a (Chl a) and carotenoids contents of U. fasciata were 1.00 ± 0.15 and 0.57 ± 0.08 mg g^-1 in fresh weight (FW), being about one- and two-fold higher than that of S. hemiphyllum and G. livida; and the carbohydrate content was 20.3 ± 0.07 mg g^-1 FW, being about three- and one-fold higher, respectively. Throughout the day, the maximal photochemical quantum yield (F_V/F_M) of Photosystem II (PS II) of these three macroalgae species decreased from morning to noon, then increased to dusk and kept steady at nighttime. Consistently, the rapid light curve-derived light utilization efficiency (α) and maximum relative electron transfer rate (rETRmax) were lower at noon than that at morning- or night-time. The F_V/F_M of U. fasciata (varying from 0.78 to 0.32) was 38% higher than that of G. livida throughout the day, and that of S. hemiphyllum was intermediate. The superoxide dismutase (SOD) and catalase (CAT) activities in U. fasciata were lower than that in S. hemiphyllum and G. livida. Moreover, the rises in temperature species-specifically mediated the damage (k) caused by stressful high light and the corresponding repair (r) to photosynthetic apparatus, making the r/k ratio increase with the rising temperature in U. fasciata, unchanged in S. hemiphyllum but decreased in G. livida. Our results indicate that U. fasciata may compete with S. hemiphyllum or G. livida and dominate the macroalgae community under aggravatedly warming future in the Daya Bay.

Eutrophication increases deterministic processes and heterogeneity of co-occurrence networks of bacterioplankton metacommunity assembly at a regional scale in tropical coastal reservoirs

Understanding microbial metacommunity assembly and the underlying methanisms are fundamental objectives of aquatic ecology. However, little is known about how eutrophication, the primary water quality issue of aquatic ecosystems, regulates bacterioplankton metacommunity assembly at a regional scale in reservoirs. In this study, we applied a metacommunity framework to study bacterioplankton communities in 210 samples collected from 42 tropical coastal reservoirs in the wet summer season. We found that the spatial pattern of bacterioplankton community compositions (BCCs) at a regional scale was shaped mainly by species sorting. The reservoir trophic state index (TSI) was the key determinant of bacterioplankton metacommunity assembly. BCC turnover increased significantly with the TSI differences between sites (∆TSI) when ∆TSI was < 20, but remained at a level of about 80% when ∆TSI was > 20. Compared to oligo-mesotrophic and mesotrophic reservoirs, increased heterogeneity of co-occurrence bacterioplankton networks and bacterioplankton β-diversity were observed across eutrophic reservoirs. We propose that larger variation in phytoplankton community assembly may play directly or indirectly deterministic processes in controlling the bacterioplankton metacommunity assembly and became the potential mechanisms behind the observed higher BCC heterogeneity across the eutrophic reservoirs. Our research contributes to a broader understanding of the ecological effects of eutrophication on reservoir ecosystems and provides clues to the management of the tropical coastal reservoirs.

Thermal discharge-induced seawater warming alters richness, community composition and interactions of bacterioplankton assemblages in a coastal ecosystem

Despite accumulating evidence on the impact of global climate warming on marine microbes, how increasing seawater temperature influences the marine bacterioplankton communities is elusive. As temperature gradient created by thermal discharges provides a suitable in situ model to study the influence of warming on marine microorganisms, surface seawater were sampled consecutively for one year (September-2016 to August-2017) from the control (unimpacted) and thermal discharge-impacted areas of a coastal power plant, located in India. The bacterioplankton community differences between control (n = 16) and thermal discharge-impacted (n = 26) areas, as investigated using 16S rRNA gene tag sequencing revealed reduced richness and varied community composition at thermal discharge-impacted areas. The relative proportion of Proteobacteria was found to be higher (average ~ 15%) while, Bacteroidetes was lower (average ~ 10%) at thermal discharge-impacted areas. Intriguingly, thermal discharge-impacted areas were overrepresented by several potential pathogenic bacterial genera (e.g. Pseudomonas, Acinetobacter, Sulfitobacter, Vibrio) and other native marine genera (e.g. Marinobacter, Pseudoalteromonas, Alteromonas, Pseudidiomarina, Halomonas). Further, co-occurrence networks demonstrated that complexity and connectivity of networks were altered in warming condition. Altogether, results indicated that increasing temperature has a profound impact on marine bacterioplankton richness, community composition, and inter-species interactions. Our findings are immensely important in forecasting the consequences of future climate changes especially, ocean warming on marine microbiota.

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems

Stream bacterioplankton communities, a crucial component of aquatic ecosystems and surface water quality, are shaped by environmental selection (i.e., changes in taxa abundance associated with more or less favorable abiotic conditions) and passive dispersal (i.e., organisms' abundance and distribution is a function of the movement of the water). These processes are a function of hydrologic conditions such as residence time and water chemistry, which are mediated by human infrastructure. To quantify the role of environmental conditions, dispersal, and human infrastructure (dams) on stream bacterioplankton, we measured bacterioplankton community composition in rivers from sub-alpine to urban environments in three watersheds (Utah, United States) across three seasons. Of the 53 environmental parameters measured (including physicochemical parameters, solute concentrations, and catchment characteristics), trace element concentrations explained the most variability in bacterioplankton community composition using Redundancy Analysis ordination. Trace elements may correlate with bacterioplankton due to the commonality in source of water and microorganisms, and/or environmental selection creating more or less favorable conditions for bacteria. Bacterioplankton community diversity decreased downstream along parts of the stream continuum but was disrupted where large reservoirs increased water residence time by orders of magnitude, potentially indicating a shift in the relative importance of environmental selection and dispersal at these sites. Reservoirs also had substantial effects on community composition, dissimilarity (Bray-Curtis distance) and species interactions as indicated by co-occurrence networks. Communities downstream of reservoirs were enriched with anaerobic Sporichthyaceae, methanotrophic Methylococcaceae, and iron-transforming Acidimicrobiales, suggesting alternative metabolic pathways became active in the hypolimnion of large reservoirs. Our results identify that human activity affects river microbial communities, with potential impacts on water quality through modified biogeochemical cycling.

Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes

Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.

Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest

Using a high-throughput metagenomic approach, we evaluated nifH-harboring bacterial communities and their assembly in the Gotjawal forest, which was naturally formed on basalt rocks with thin layer of soil. Significant differences in soil properties and community structure were observed in comparison with similar communities in various habitats, including other lava-formed forests (on Jeju Island and in Hawaii) and in regions with high humidity (Florida) or low temperatures (Alaska). nifH-harboring bacterial communities were found to assemble along gradients of environmental factors, particularly cation-exchange capacity. Unlike in other regions, in the Gotjawal forest, Paenibacillus and Clostridium, which belong to the phylum Firmicutes, were present in significantly higher proportion than in other regions. Network analysis suggested that much fewer co-occurrence relationships occurred in the Gotjawal forest than in other lava-formed forests. Our results indicate that the unique nifH-harboring bacterial community and its assembly in the Gotjawal forest are due to its distinctive soil properties, which has implications for microbial interactions and functional potentials.