Patterns in the composition of microbial communities from a subtropical river: effects of environmental, spatial and temporal factors

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning

Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.

Diversity and biogeography of bacterial community in the Ili River network varies locally and regionally

Microorganisms in rivers indeed play a crucial role in nutrient cycling within aquatic ecosystems. Understanding the assembly mechanisms of bacterial communities in river networks is essential for predicting their special composition and functional characteristics in natural rivers. This study employed 16S rRNA gene amplicon sequence variation (ASVs) to scrutinize the bacterial community within the uniquely topographical Ili River network. The bacterial community composition varied across the three tributaries with distinct sources and the mainstream. The confluence of various sources diminished the diversity of the bacterial community and altered the functionality of within mainstream. We suggest that strong dispersal limitation predominantly shaped the community at the regional scale (46.6 %), underscoring the significant contribution of headwater sites to bacterial community composition. Contrary to expectation, the bacterial resources in the mainstream were not enriched by the higher diversity in three tributaries. Instead, confluence disturbance potentially increased the undominated processes (36.7 %) and alter the bacterial community composition at the local scale of the mainstream. The intricate coalescence at the confluence could potentially be an intriguing causative factor. Our research indicates that the composition of bacterial communities within intricate river networks exhibits biogeographic patterns, simultaneously influenced by river confluence and geographical features, necessitating multi-scale analysis.

Spatial and temporal characteristics of microbial communities in the Seine river in the greater Paris area under anthropogenic perturbation

Microorganisms play an important role in maintaining the proper functioning of river ecosystems and are promising candidates for environmental indicators. They are also highly sensitive to environmental changes. It is necessary to have basic knowledge about them in order to know the ecological status of river ecosystem. To our knowglege, there is very little information on the status of microorganisms in surface water of the Seine River, although the Seine River is one of the rivers that suffers the greatest impact from humain activities in the world due to a weak dilution effect. It is therefore necessary to carry out a microbial analysis to assess the ecological status of the Seine River and to use it as a reference to compare with the future state when, for instance, new disinfection technologies of wastewater are implemented. To this end, the microbial communities of the Seine surface water were analyzed, taking into account the spatial effect, including the tributaries, and from upstream to downstream of the Paris conurbation and the temporal aspect, with a monitoring over 4 seasons. The results showed that the microbiome of the water is highly diverse and involved a variety of functions. The main phyla making up the surface water microbiome were Proteobacteria, Actinobacteriota, Firmicutes, Bacteroidota, while other minor phyla were Deinococcota, Patescibacteria, Gemmatimonadota, Cyanobacteria, Bdellovibrionota, Acidobacteriota, Campilobacterota, Myxococcota, and Desulfobacterota. Overall, the microbial community did not change spatially (with the exception of some minor differences between upstream and downstream), but did vary seasonally. The main factors influencing this microbiome were temperature, nitrate and orthophosphate concentrations. The main predicted functions were related to cell metabolism, in particular carbohydrates, amino acids, lipids, energy, vitamins and cofactors, and cell mobility. The microbial compositions showed a strong balance between microbial groups and were involved in the degradation of recalcitrant compounds.

The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China

It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.

Human-induced homogenization of microbial taxa and function in a subtropical river and its impacts on community stability

Combination of taxa and function can provide a more comprehensive picture on human-induced microbial homogenization. Here, we obtained 2.58 billion high-throughput sequencing reads and 479 high-quality metagenome-assembled genomes (MAGs) of planktonic microbial communities in a subtropical river for 5 years. We found the microbial taxa homogenization and functional homogenization were uncoupled. Although human activities in downstream sites significantly decreased the taxonomic diversity of non-abundant ASV communities (16S rRNA gene amplicon sequence variants), they did not significantly decrease the taxonomic diversity of abundant ASV and total observed MAG communities. However, the total observed MAG communities in downstream sites tended to homogenize into some specific taxa which encode human-activity-related functional genes, such as nutrient cycles, greenhouse gas emission, antibiotic and arsenic resistance. Those specific MAGs with high taxonomic diversity caused the weak heterogenization of total observed MAG communities in downstream sites. Moreover, functional homogenization promoted the synchrony among downstream MAGs, and these MAGs constructed some specific network modules might to synergistically execute or resist the human-activity-related functions. High synchrony also led to the tandem effects among MAGs and thus decreased community stability. Overall, our findings revealed the links of microbial taxa, functions and stability under human activity impacts, and provided a strong evidence to encourage us re-thinking biotic homogenization based on microbial taxa and their functional attributes.

Spatiotemporal assembly and functional composition of planktonic microeukaryotic communities along productivity gradients in a subtropical lake

Microeukaryotes play crucial roles in the microbial loop of freshwater ecosystems, functioning both as primary producers and bacterivorous consumers. However, understanding the assembly of microeukaryotic communities and their functional composition in freshwater lake ecosystems across diverse environmental gradients remains limited. Here, we utilized amplicon sequencing of 18S rRNA gene and multivariate statistical analyses to examine the spatiotemporal and biogeographical patterns of microeukaryotes in water columns (at depths of 0.5, 5, and 10 m) within a subtropical lake in eastern China, covering a 40 km distance during spring and autumn of 2022. Our results revealed that complex and diverse microeukaryotic communities were dominated by Chlorophyta (mainly Chlorophyceae), Fungi, Alveolata, Stramenopiles, and Cryptophyta lineages. Species richness was higher in autumn than in spring, forming significant hump-shaped relationships with chlorophyll a concentration (Chl-a, an indicator of phytoplankton biomass). Microeukaryotic communities exhibited significant seasonality and distance-decay patterns. By contrast, the effect of vertical depth was negligible. Stochastic processes mainly influenced the assembly of microeukaryotic communities, explaining 63, 67, and 55% of community variation for spring, autumn, and both seasons combined, respectively. Trait-based functional analysis revealed the prevalence of heterotrophic and phototrophic microeukaryotic plankton with a trade-off along N:P ratio, Chl-a, and dissolved oxygen (DO) gradients. Similarly, the mixotrophic proportions were significantly and positively correlated with Chl-a and DO concentrations. Overall, our findings may provide useful insights into the assembly patterns of microeukaryotes in lake ecosystem and how their functions respond to environmental changes.

Ensemble learning model identifies adaptation classification and turning points of river microbial communities in response to heatwaves

Heatwaves are a global issue that threaten microbial populations and deteriorate ecosystems. However, how river microbial communities respond to heatwaves and whether and how high temperatures exceed microbial adaptation remain unclear. In this study, we proposed four types of pulse temperature-induced microbial responses and predicted the possibility of microbial adaptation to high temperature in global rivers using ensemble machine learning models. Our findings suggest that microbial communities in parts of South American (e.g., Brazil and Chile) and Southeast Asian (e.g., Vietnam) countries are likely to change due to heatwave disturbance from 25 to 37°C for consecutive days. Furthermore, the microbial communities in approximately 48.4% of the global river gauge stations are prone to fast stress inadaptation, with approximately 76.9% of these stations expected to exceed microbial adaptation after heatwave disturbances. If emissions of particulate matter with sizes not more than 2.5 μm (PM2.5, an indicator of human activities) increase by twofold, the number of global rivers associated with the fast stress adaptation type will decrease by ~13.7% after heatwave disturbances. Understanding microbial responses is crucially important for effective ecosystem management, especially for fragile and sensitive rivers facing heatwave events.

Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian

The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.

Effects of metal contamination with physicochemical properties on the sediment microbial communities in a tropical eutrophic-hypereutrophic urban reservoir in Brazil

We investigated the effects of metals and physicochemical variables on the microbes and their metabolisms in the sediments of Guarapiranga reservoir, a tropical eutrophic-hypereutrophic freshwater reservoir located in a highly urbanized and industrialized area in Brazil. The metals cadmium, copper, and chromium showed minor contribution to changes in the structure, composition, and richness of sediment microbial communities and functions. However, the effects of metals on the microbiota are increased when taken together with physicochemical properties, including the sediment carbon and sulfur, the bottom water electrical conductivity, and the depth of the water column. Clearly, diverse anthropic activities, such as sewage discharge, copper sulfate application to control algal growth, water transfer, urbanization, and industrialization, contribute to increase these parameters and the metals spatially in the reservoir. Microbes found especially in metal-contaminated sites encompassed Bathyarchaeia, MBG-D and DHVEG-1, Halosiccatus, Candidatus Methanoperedens, Anaeromyxobacter, Sva0485, Thermodesulfovibrionia, Acidobacteria, and SJA-15, possibly showing metal resistance or acting in metal bioremediation. Knallgas bacteria, nitrate ammonification, sulfate respiration, and methanotrophy were inferred to occur in metal-contaminated sites and may also contribute to metal removal. This knowledge about the sediment microbiota and metabolisms in a freshwater reservoir impacted by anthropic activities allows new insights about their potential for metal bioremediation in these environments.

Responses of the bacterial community of tobacco phyllosphere to summer climate and wildfire disease

Both biotic and abiotic factors continually affect the phyllospheric ecology of plants. A better understanding of the drivers of phyllospheric community structure and multitrophic interactions is vital for developing plant protection strategies. In this study, 16S rRNA high-throughput sequencing was applied to study how summer climatic factors and bacterial wildfire disease have affected the composition and assembly of the bacterial community of tobacco (Nicotiana tabacum L.) phyllosphere. Our results indicated that three time series groups (T1, T2 and T3) formed significantly distinct clusters. The neutral community model (NCM) and beta nearest taxon index (betaNTI) demonstrated that the overall bacterial community assembly was predominantly driven by stochastic processes. Variance partitioning analysis (VPA) further showed that the complete set of the morbidity and climatic variables together could explain 35.7% of the variation of bacterial communities. The node numbers of the molecular ecological networks (MENs) showed an overall uptrend from T1 to T3. Besides, Pseudomonas is the keystone taxa in the MENs from T1 to T3. PICRUSt2 predictions revealed significantly more abundant genes of osmoprotectant biosynthesis/transport in T2, and more genes for pathogenicity and metabolizing organic substrate in T3. Together, this study provides insights into spatiotemporal patterns, processes and response mechanisms underlying the phyllospheric bacterial community.

Distribution of sediment microbial communities and their relationship with surrounding environmental factors in a typical rural river, Southwest China

With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Firmicutes, accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae, Haliangium, and Pseudolabrys, possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola, Nocardioides, Gaiella, Sphingomonas, norank_f_67-14, Subgroup_10, Agromyces, and Lysobacter, with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1, norank_f__Bacteroidetes_vadinHA17, Candidatus_Competibacter, and Methylocystis. Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.

Biogeographical Patterns of Bacterial Communities and Their Antibiotic Resistomes in the Inland Waters of Southeast China

Freshwater ecosystems are important sources of drinking water and provide natural settings for the proliferation and dissemination of bacteria and antibiotic resistance genes (ARGs). However, the biogeographical patterns of ARGs in natural freshwaters and their relationships with the bacterial community at large scales are largely understudied. This is of specific importance because data on ARGs in environments with low anthropogenic impact is still very limited. We characterized the biogeographical patterns of bacterial communities and their ARG profiles in 24 reservoirs across southeast China using 16S rRNA gene high-throughput sequencing and high-throughput-quantitative PCR, respectively. We found that the composition of both bacterial communities and ARG profiles exhibited a significant distance-decay pattern. However, ARG profiles displayed larger differences among different water bodies than bacterial communities, and the relationship between bacterial communities and ARG profiles was weak. The biogeographical patterns of bacterial communities were simultaneously driven by stochastic and deterministic processes, while ARG profiles were not explained by stochastic processes, indicating a decoupling of bacterial community composition and ARG profiles in inland waters under relatively low-human-impact at a large scale. Overall, this study provides an overview of the biogeographical patterns and driving mechanisms of bacterial community and ARG profiles and could offer guidance and reference for the control of ARGs in drinking water sources. IMPORTANCE Antibiotic resistance has been a serious global threat to environmental and human health. The "One Health" concept further emphasizes the importance of monitoring the large-scale dissemination of ARGs. However, knowledge about the geographical patterns and driving mechanisms of bacterial communities and ARGs in natural freshwater environments is limited. This study uncovered the distinct biogeographical patterns of bacterial communities and ARG profiles in inland waters of southeast China under low-anthropogenic impact at a large scale. This study improved our understanding of ARG distribution in inland waters with emphasis on drinking water supply reservoirs, therefore providing the much-needed baseline information for future monitoring and risk assessment of ARGs in drinking water resources.

Adaptations of microbial communities and dissolved organics to seasonal pressures in a mesotrophic coastal Mediterranean lake

In lake ecosystems, changes in eukaryotic and prokaryotic microbes and the concentration and availability of dissolved organic matter (DOM) produced within or supplied to the system by allochthonous sources are components that characterize complex processes in the microbial loop. We address seasonal changes of microbial communities and DOM in the largest Croatian lake, Vrana. This shallow lake is connected to the Adriatic Sea and is impacted by agricultural activity. Microbial community and DOM structure were driven by several environmental stressors, including drought, seawater intrusion, and heavy precipitation events. Bacterial composition of different lifestyles (free-living and particle-associated) differed and only a part of the particle-associated bacteria correlated with microbial eukaryotes. Oscillations of cyanobacterial relative abundance along with chlorophyll a revealed a high primary production season characterized by increased levels of autochthonous DOM that promoted bacterial processes of organic matter degradation. From our results, we infer that in coastal freshwater lakes dependent on precipitation-evaporation balance, prolonged dry season coupled with heavy irrigation impact microbial communities at different trophic levels even if salinity increases only slightly and allochthonous DOM inputs decrease. These pressures, if applied more frequently or at higher concentrations, could have the potential to overturn the trophic state of the lake. This article is protected by copyright. All rights reserved.

Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean

Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton.

IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.

Anthropogenic activities change the relationship between microbial community taxonomic composition and functional attributes

Functional redundancy is considered common in microbial systems, but recent studies have challenged this idea. The mechanism for this contradictory result is not clear. However, in this study, we hypothesize that strong environmental filtering which links to the anthropogenic activities is able to weaken microbial functional redundancy. We used metagenome and 16S rRNA gene high-throughput sequencing to investigate planktonic microbial communities in a subtropical river. We found that the weak anthropogenic activities might result in a low selection pressure in the river upstream area. Therefore, the microbial community functional attributes were stable although the community composition changed with the water temperature and NO₃ -N in upstream area (this indicates functional redundancy). However, the strong anthropogenic activities in river downstream area selected pollutant-degraded functions (e.g. nitrogen metabolism, toluene, xylenes and ethylbenzene degradation) and potentially pollutant-degraded (tolerant) microbes, and therefore caused the microbial community composition synchronously changed with the variation of community functional attributes. Our results reveal that strong environmental filtering which associates with the anthropogenic activities not only has effects on microbial community composition and community functional attributes but also on their relationships. These results provide a new insight to refine the functional redundancy idea.

High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem

Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.

Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence

Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.

The Urban River Syndrome: Achieving Sustainability Against a Backdrop of Accelerating Change

Human activities have been affecting rivers and other natural systems for millennia. Anthropogenic changes to rivers over the last few centuries led to the accelerating state of decline of coastal and estuarine regions globally. Urban rivers are parts of larger catchment ecosystems, which in turn form parts of wider nested, interconnected systems. Accurate modelling of urban rivers may not be possible because of the complex multisystem interactions operating concurrently and over different spatial and temporal scales. This paper overviews urban river syndrome, the accelerating deterioration of urban river ecology, and outlines growing conservation challenges of river restoration projects. This paper also reviews the river Thames, which is a typical urban river that suffers from growing anthropogenic effects and thus represents all urban rivers of similar type. A particular emphasis is made on ecosystem adaptation, widespread extinctions and the proliferation of non-native species in the urban Thames. This research emphasizes the need for a holistic systems approach to urban river restoration.

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir

BACKGROUND

Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity.

RESULTS

Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics.

CONCLUSIONS

Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.

Arsenic speciation, the abundance of arsenite-oxidizing bacteria and microbial community structures in groundwater, surface water, and soil from a gold mine

The arsenic speciation, the abundance of arsenite-oxidizing bacteria, and microbial community structures in the groundwater, surface water, and soil from a gold mining area were explored using the PHREEQC model, cloning-ddPCR of the aioA gene, and high-throughput sequencing of the 16S rRNA gene, respectively. The analysis of the aioA gene showed that arsenite-oxidizing bacteria retrieved from groundwater, surface water, and soil were associated with Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In groundwaters from the mining area, there were relatively high ratios of aioA/total 16S rRNA gene copies and the dominance of As⁵⁺, which suggested the presence and activity of arsenite-oxidizing bacteria. Metagenomic analysis revealed that the majority of the soil and surface water microbiomes were Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi, whereas the groundwater microbiomes were dominated exclusively by Betaproteobacteria and Alphaproteobacteria. Geochemical factors influencing the microbial structure in the groundwater were As, residence time, and groundwater flowrate, while those showing a positive correlation to the microbial structure in the surface water were TOC, ORP, and DO. This study provides insights into the groundwater, surface water, and soil microbiomes from a gold mine and expands the current understanding of the diversity and abundance of arsenite-oxidizing bacteria, playing a vital role in global As cycling.

Bacterial community structure upstream and downstream of cascade dams along the Lancang River in southwestern China

Extensive construction of dams by humans has caused alterations in flow regimes and concomitant alterations in river ecosystems. Even so, bacterioplankton diversity in large rivers influenced by cascade dams has been largely ignored. In this study, bacterial community diversity and profiles of seven cascade dams along the720 km of the Lancang River were studied using Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Spatiotemporal variations of bacterial communities in sediment and water of the Gongguoqiao hydroelectric dam and factors affecting these variations were also examined. Microbial diversity and richness in surface water increased slightly from upstream toward downstream along the river. A significant positive correlation between spatial distance and dissimilarities in bacterial community structure was confirmed (Mantel test, r = 0.4826, p = 0.001). At the Gongguoqiao hydroelectric dam, temporal differences in water overwhelmed spatial variability in bacterial communities. Temperature, precipitation, and nutrient levels were major drivers of seasonal microbial changes. Most functional groups associated with carbon cycling in sediment samples decreased from winter to summer. Our findings improve our understanding of associations, compositions, and predicted functional profiles of microbial communities in a large riverine ecosystem influenced by multiple cascade dams.

High heterogeneity of bacterioplankton community shaped by spatially structured environmental factors in West Lake, a typical urban lake in eastern China

Elucidating the bacterioplankton spatial distribution patterns and its determinants is a central topic in ecological research. However, research on the distribution patterns of bacterioplankton community composition (BCC) within a small-sized, highly dynamic freshwater lake remains unclear. In this study, we collected surface water samples from West Lake to investigate the spatiotemporal variation of BCC by 16S rRNA gene high-throughput sequencing. Clear spatial heterogeneity in BCC was identified both in summer and winter. The relatively high abundant taxa exhibited greater correlations with environmental factors and other abundant species in summer than in winter. Variation partitioning analysis was used to unravel the relative importance of environmental factors and spatial processes and further explore the underlying mechanism of BCC successions. Our results showed the predominant shared effect of environmental and spatial factors on BCC in summer (68.41%) and winter (57.37%), indicating that spatially structured environmental factors were the key determinants of structuring BCC spatial heterogeneity in West Lake in the two seasons. Furthermore, environmental factors alone explained a higher proportion of the variation in summer whereas spatial factors explained a higher proportion in winter. These divergences may be related to seasonal environmental changes and anthropogenic disturbances. Our study provided knowledge on BCC spatial heterogeneity in small freshwater habitats and their underlying determinants in different seasons.

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China

Bacterial communities are sensitive to environmental fluctuations, and a better understanding of the relationships between bacterial community distribution and complex environmental conditions is important for the remediation of lake ecosystems. In this study, bacterial communities from 7 water and 7 sediment samples in 3 different regions (east, the hydrophyte-dominated region; north, the transitional region; west, the highly polluted region) of Lake Taihu were investigated via high-throughput sequencing. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the three lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The Shannon and Simpson values indicated that the diversity of bacterial communities in water was the highest in the eastern region, followed by the northern and western regions, while there was no significant difference in the bacterial community characteristics in sediments among lake regions. We found that the western lake region had the highest Cyanobacteria concentration (34.71%), suggesting that Cyanobacteria may have competitive advantages over the other bacterioplankton in water columns without plants. The abundances of Chlorobi detected in the water samples in the east (2.69%) and north (6.66%) were higher than those in the west because the high turbidity in the western lake region was unsuitable for the growth of Chlorobi. Nitrospirae (average 6.36%) and Chloroflexi (average 11.62%) were more common in the sediments than in the water of Lake Taihu, suggesting that the nutrient level of Lake Taihu sediment was higher than that of water bodies. Welch's t test revealed that there were significant differences in species abundance (such as Microcystis, Synechococcus, Flavobacterium, and hgcI_clade) among the different regions, except that the east was relatively similar to the north. Canonical correspondence analysis demonstrated that TN, TP, and DO showed significant effects on the relative abundance of the dominant bacterial genera in water, while TOC, TP, and TN were positively correlated with TOC, TP and TN. This study provides useful information for understanding the variation in the diversity of bacterial communities in different habitats of Lake Taihu.

Contrasting Patterns in Diversity and Community Assembly of Phragmites australis Root-Associated Bacterial Communities from Different Seasons

The common reed (Phragmites australis), a cosmopolitan aquatic macrophyte, plays an important role in the structure and function of aquatic ecosystems. We compared bacterial community compositions (BCCs) and their assembly processes in the root-associated compartments (i.e., rhizosphere and endosphere) of reed and bulk sediment between summer and winter. The BCCs were analyzed using high-throughput sequencing of the bacterial 16S rRNA gene; meanwhile, null-model analysis was employed to characterize their assembly mechanisms. The sources of the endosphere BCCs were quantitatively examined using SourceTracker from bulk sediment, rhizosphere, and seed. We observed the highest α-diversity and the lowest β-diversity of BCCs in the rhizosphere in both seasons. We also found a significant increase in α- and β-diversity in summer compared to that in winter among the three compartments. It was demonstrated that rhizosphere sediments were the main source (∼70%) of root endosphere bacteria during both seasons. Null-model tests indicated that stochastic processes primarily affected endosphere BCCs, whereas both deterministic and stochastic processes dictated bacterial assemblages of the rhizosphere, with the relative importance of stochastic versus deterministic processes depending on the season. This study suggests that multiple mechanisms of bacterial selection and community assembly exist both inside and outside P. australis roots in different seasons.IMPORTANCE Understanding the composition and assembly mechanisms of root-associated microbial communities of plants is crucial for understanding the interactions between plants and soil. Most previous studies of the plant root-associated microbiome focused on model and economic plants, with fewer temporal or seasonal investigations. The assembly mechanisms of root-associated bacterial communities in different seasons remain poorly known, especially for the aquatic macrophytes. In this study, we compared the diversity, composition, and relative importance of two different assembly processes (stochastic and deterministic processes) of bacterial communities associated with bulk sediment and the rhizosphere and endosphere of Phragmites australis in summer and winter. While we found apparent differences in composition, diversity, and assembly processes of bacterial communities among different compartments, season played important roles in determining BCCs and their diversity patterns and assemblages. We also found that endosphere bacteria mainly originated from the rhizosphere. The results add new knowledge regarding the plant-microbe interactions in aquatic ecosystems.

Biogeography of the free-living and particle-attached bacteria in Tibetan lakes

The free-living (FL) and particle-attached (PA) bacteria have different dispersal potentials and ecological roles in aquatic ecosystems. However, our knowledge of their diversity and regional biogeographic patterns in high-altitude alpine lakes is limited. In this study, to investigate the diversity and geographic patterns of the FL and PA bacterial communities and to quantify the relative influence of environmental filtering and dispersal limitation in shaping the FL and PA bacterial communities, we collected surface water samples from 26 lakes over 1000 kilometers on the Tibetan Plateau. The majority of sequences exclusively in the FL bacteria were Actinobacteria (29.4%), Proteobacteria (27.7%) and Bacteroidetes (21.6%), while sequences exclusively in the PA bacteria were dominated by Proteobacteria (57.9%). The α-diversity indices, including Shannon index and Pielou's evenness, were significantly lower in the FL bacteria than that in PA bacteria. The surrounding soils as an important potential source contributed more to the diversity of the PA bacteria than the FL bacteria. Both of the FL and PA bacterial communities exhibited a significant regional distance-decay pattern. Environmental filtering and dispersal limitation were significantly related to the spatial variation of the FL and PA bacterial communities, whereas the environmental filtering/dispersal limitation effect ratio was higher in the FL bacterial communities. Our study is the first to describe the regional-scale spatial variability and to identify the factors that drive regional variability of the FL and PA bacterial communities in Tibetan lakes.

Hysteretic response of Microbial Eukaryotic Communities to Gradually Decreased Nutrient Concentrations in Eutrophic Water

External environments to microbial eukaryotic communities often change gradually with time. However, whether the responses of microbial eukaryotic communities to these gradually changed environments are continuous or hysteretic and the mechanisms underlying these responses are largely unknown. Here, we used a microcosm to investigate the temporal variation of microbial eukaryotic communities with the gradually decreased nutrient concentrations (nitrogen and phosphorus). We found the differences of microbial eukaryotic community composition and species richness between the control and treatment groups were low during the days 0 to 12, although the nutrient concentrations decreased rapidly during this period in treatment group. However, these differences were clear during the days 14 to 18, although the nutrient concentrations decreased slowly during this period in treatment group. The mechanisms for these results are that the strong homogenous selection (perhaps due to the biotic factors) during the days 8 to 10 in treatment group might enhance the stability of microbial eukaryotic communities. However, the continuously decreased nutrient concentrations weakened the homogenous selection and promoted the strength of environmental filtering, and therefore resulted in the distinct change of microbial eukaryotic communities during the days 14 to 18 in treatment group. Fungi, Chlorophyta and Chrysophyta which associated with the nutrient removal played important roles in this hysteretic change of microbial eukaryotic communities. Overall, our findings suggest that disentangling the non-linear response of communities to gradual environmental changes is essential for understanding ecosystem restoration and degradation in future.

Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake

Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R² ≥ 0.31), except between Fungi and Metazoa (R² = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.

Factors shaping community patterns of protists and bacteria on a European scale

Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.

Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions

Temporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null model approaches (elements of metacommunity structure, Raup-Crick beta-diversity and quantitative process estimates) to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in the case of bacteria and microeukaryotes, respectively. We distinguished these processes from dispersal-related processes using additional tests. Regardless of the applied null model, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.

Geographical Patterns of Algal Communities Associated with Different Urban Lakes in China

Urban lakes play an important role in drainage and water storage, regulating urban microclimate conditions, supplying groundwater, and meeting citizens' recreational needs. However, geographical patterns of algal communities associated with urban lakes from a large scale are still unclear. In the present work, the geographical variation of algal communities and water quality parameters in different urban lakes in China were determined. The water quality parameters were examined in the samples collected from north, central, south, and coastal economic zones in China. The results suggested that significant differences in water quality were observed among different geographical distribution of urban lakes. The highest total phosphorus (TP)(0.21 mg/L) and total nitrogen (TN) (3.84 mg/L) concentrations were found in XinHaiHu (XHH) lake, it also showed highest the nitrate nitrogen (NO3--N) (0.39 mg/L),total organic carbon(TOC) (9.77 mg/L), and COD Mn (9.01 mg/L) concentrations among all samples. Environmental and geographic factors also cause large differences in algal cell concentration in different urban lakes, which ranged from 4,700×104 to 247,800 ×104cell/L. Through light microscopy, 6 phyla were identified, which includes Chlorophyta, Bacillariophyta, Cyanophyta, Dinophyta, Euglenophyta, and Cryptophyta. Meanwhile, the heat map with the total 63 algal community composition at the genus level profile different urban lakes community structures are clearly distinguishable. Further analyses showed that the dominant genera were Limnothrixsp., Synedra sp., Cyclotella sp., Nephrocytium sp., Melosirasp., and Scenedesmussp. among all samples. The integrated network analysis indicated that the highly connected taxa (hub) were Fragilariasp.,Scenedesmus sp., and Stephanodiscus sp. The water quality parameters of NO3--N and NH4+-N had significant impacts on the structural composition of the algal community. Additionally, RDA further revealed distinct algal communities in the different urban lakes, and were influenced by NO2--N, Fe, and algal cell concentrations. In summary, these results demonstrate that the pattern of algal communities are highly correlated with geographic location and water quality on a large scale, and these results also give us further understanding of the complex algal communities and effectively managing eutrophication of urban lakes.

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

BACKGROUND

The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.

RESULTS

Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.

CONCLUSIONS

This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.

Structural Characteristics and Functional Implications of PM2.5 Bacterial Communities During Fall in Beijing and Shanghai, China

Air pollution characterized by fine particulate matter (PM_2.5) frequently has occurred in China, and has posed threats to human health. The physiochemical characteristics of airborne PM_2.5 have been extensively studied, but its bacterial structures and functions have not yet been well studied. Herein, we focused on the structural characteristics and functional implications of airborne bacteria under different pollution levels in Beijing and Shanghai. The α- and β-diversities showed no obvious difference in two cities (p > 0.05). The dominant phyla Proteobacteria, Firmicutes, and Actinobacteria with total abundance of over 92% were found in all PM_2.5 samples. The results of weighted unifrac non-metric multidimensional scaling (NMDS) suggested that air pollution was no obviously correlated with bacterial community but dispersed disorderly. Furthermore, canonical correlation analysis (CCA) and permutation test indicated that NH4+, SO42-, and wind speed were the key factors that associated with airborne bacterial community structure. Chemical components of particulate matter played more important role in structuring bacterial community than meteorological conditions based on the result of partial CCA. In addition, the annotation of metabolic pathway suggested that the predominant genus Pseudomonas was obviously correlated with disease infections. Several dominant species might contribute to organic degradation, nitrogen cycles, and ice-nuclei activities in environments. Overall, this work enhanced our understanding of functions of airborne bacteria and highlighted their potential role in atmospheric chemical progresses.

Bacterial and ciliate biofilm community structure at different spatial levels of a salt lake meta-community

Meta-communities are assembled along an ecological scale that determines local and regional diversity. Spatial patterns have been detected in planktonic bacterial communities at distances <20 m, but little is known about the occurrence of similar variation for other microbial groups and changes in microbial meta-community assembly at different levels of a meta-community. To examine this variation, the biofilm of eight saline ponds were used to investigate processes shaping diversity within ponds (β) and between ponds (δ). Bacterial and ciliate communities were assessed using ARISA and T-RFLP respectively, while diversity partitioning methods were used to examine the importance of taxonomic turnover and variation partitioning was used to distinguish spatial from environmental determinants. The results show that turnover is important for determining β- and δ-diversity of biofilms. Spatial factors are important drivers of bacterial β-diversity but were unimportant for ciliate β-diversity. Environmental variation was a strong determinant of bacterial and ciliate δ-diversity, suggesting sorting processes are important for assembling pond communities. Determinants of diversity in bacteria are not universal for ciliates, suggesting higher functional redundancy of bacteria or the greater niche breadth of ciliates may be important in discriminating assembly processes between the two organisms.

Decoupling the Dynamics of Bacterial Taxonomy and Antibiotic Resistance Function in a Subtropical Urban Reservoir as Revealed by High-Frequency Sampling

Aquatic environments serve as important reservoirs of antibiotic resistance genes (ARGs), but the information on the high-resolution temporal pattern of ARGs in waterbodies is extremely limited. In this study, the weekly dynamics of ARGs and their relationships with microbial taxonomic communities and environmental variables were analyzed in a subtropical urban reservoir over the period of 1 year using high-throughput approaches. In total, 197 ARGs and 10 mobile genetic elements (MGEs) were detected. The results showed that the bacterial community had a seasonal pattern, while ARGs composition did not exhibit seasonality, thereby indicating the asynchrony or decoupling of temporal patterns of microbial taxonomy and function. More importantly, bacterial abundance and community diversity were more strongly correlated with 17 measured environmental variables than ARGs (36 significant correlations for OTUs, 11 for ARGs). However, stochastic processes appeared to have a minor role in the structuring of the ARG profiles, but a more important role in the structuring of bacterial taxonomic communities. Furthermore, we found that precipitation and turbidity were significantly correlated with the richness and diversity of ARGs, suggesting that multiple environmental factors influence the composition and dynamics of ARGs in complex ways. MGEs were abundant and showed significant positive correlations with ARGs, indicating a plausible influence of MGEs on the variation of ARGs. This is the first study which provides an overview of high-resolution dynamics of ARGs in a subtropical waterbody. Our results improve the understanding of microbial processes and mechanisms of ARGs at fine temporal scale, and offer empirical data of use in the monitoring, assessment and management of the urban water environments.

Dynamics of the bacterial community in a channel catfish nursery pond with a cage-pond integration system

The changes in the bacterial community composition in a channel catfish nursery pond with a cage-pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage-pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

The antibiotic resistome of free-living and particle-attached bacteria under a reservoir cyanobacterial bloom

In freshwater systems, both antibiotic resistance genes (ARGs) and cyanobacterial blooms attract global public health concern. Cyanobacterial blooms can greatly impact bacterial taxonomic communities, but very little is known about the influence of the blooms on antibiotic resistance functional community. In this study, the ARGs in both free-living (FL) and particle-attached (PA) bacteria under bloom and non-bloom conditions were simultaneously investigated in a subtropical reservoir using high-throughput approaches. In total, 145 ARGs and 9 mobile genetic elements (MGEs) were detected. The most diverse and dominant of which (68.93%) were multidrug resistance genes and efflux pump mechanism. The richness of ARGs in both FL and PA bacteria was significantly lower during the bloom period compared with non-bloom period. The abundance of ARGs in FL bacteria was significantly lower under bloom condition than in the non-bloom period, but the abundance of ARGs in PA bacteria stayed constant. More importantly, the resistant functional community in PA bacteria was more strongly influenced by the cyanobacterial bloom than in the FL bacteria, although >96% ARGs were shared in both FL and PA bacteria or both bloom and non-bloom periods. We also compared the community compositions between taxonomy and function, and found antibiotic resistant communities were highly variable and exhibited lower similarity between bloom and non-bloom periods than seen in the taxonomic composition, with an exception of FL bacteria. Altogether, cyanobacterial blooms appear to have stronger inhibitory effect on ARG abundance in FL bacteria, and stronger influence on antibiotic resistant community composition in PA bacteria. Our results further suggested that both neutral and selective processes interactively affected the ARG composition dynamics of the FL and PA bacteria. However, the antibiotic resistant community of FL bacteria exhibited a higher level of temporal stochasticity following the bloom event than PA bacteria. Therefore, we emphasized the bacterial lifestyles as an important mechanism, giving rise to different responses of antibiotic resistant community to the cyanobacterial bloom.

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

Plankton communities normally consist of few abundant and many rare species, yet little is known about the ecological role of rare planktonic eukaryotes. Here we used a 18S ribosomal DNA sequencing approach to investigate the dynamics of rare planktonic eukaryotes, and to explore the co-occurrence patterns of abundant and rare eukaryotic plankton in a subtropical reservoir following a cyanobacterial bloom event. Our results showed that the bloom event significantly altered the eukaryotic plankton community composition and rare plankton diversity without affecting the diversity of abundant plankton. The similarities of both abundant and rare eukaryotic plankton subcommunities significantly declined with the increase in time-lag, but stronger temporal turnover was observed in rare taxa. Further, species turnover of both subcommunities explained a higher percentage of the community variation than species richness. Both deterministic and stochastic processes significantly influenced eukaryotic plankton community assembly, and the stochastic pattern (e.g., ecological drift) was particularly pronounced for rare taxa. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species, which may play fundamental roles in network persistence. Importantly, covariations between rare and non-rare taxa were predominantly positive, implying multispecies cooperation might contribute to the stability and resilience of the microbial community. Overall, these findings expand current understanding of the ecological mechanisms and microbial interactions underlying plankton dynamics in changing aquatic ecosystems.

Metagenomic characterization of ambulances across the USA

BACKGROUND

Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals.

RESULTS

We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation).

CONCLUSIONS

While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.

Response of bacterial communities to cyanobacterial harmful algal blooms in Lake Taihu, China

Cyanobacterial harmful algal blooms are prevalent around the world, influencing aquatic organisms and altering the physico-chemical properties in freshwater systems. However, the response of bacterial communities to toxic cyanobacterial blooms and associated microcystins (MC) remain poorly understood even though global concentrations of MC have increased dramatically in the past few decades. To address this issue, the dynamics of bacterial community composition (BCC) in the water column and how BCC is influenced by both harmful cyanobacterial blooms and environmental factors were investigated on a monthly basis from August 2013 to July 2014 in Lake Taihu, China. Non-metric multidimensional scaling (NMDS) revealed that seasonal variation in BCC was significant, and that the succession of BCC greatly depends on changes in environmental conditions. Redundancy analysis (RDA) results showed that the overall variation of BCC was explained mainly by dissolved oxygen (DO), nitrate nitrogen (NO₃^--N), and Microcystis. The alpha biodiversity of the bacterial community was different among months with the highest diversity in February and the lowest diversity in October. Furthermore, significant negative relationships were found between alpha biodiversity indices and Microcystis abundance as well as with intracellular MC concentrations, indicating that Microcystis and associated MC may influence the bacterial community structure by reducing its biodiversity. This study shows that potential associations exist between toxic cyanobacterial blooms and bacterial communities but more investigations are needed to obtain a mechanistic understanding of their complex relationships.

Variation of bacterial communities in water and sediments during the decomposition of Microcystis biomass

The bacterial community composition in water and sediment samples during the decomposition of Microcystis biomass were analyzed using the 454 pyrosequencing technique. We found dramatic shifts in the bacterial community composition of water and sediments after the addition of Microcystis biomass. Among all the detected phyla, only Firmicutes was found to be dominant in both water and sediment samples. The genus Clostridium sensu stricto was the absolutely dominant group in Firmicutes and showed drastic variations with incubation time during the decomposition process. Peak values in relative abundance of Clostridium sensu stricto appeared in the first few days for water and sediment samples. Environmental factors such as pH, dissolved oxygen (DO), and dissolved organic carbon (DOC) in water samples showed drastic variations during the decomposing process, which might be the prominent forces driving the variation of bacterial communities. The abundant genus, Clostridium sensu stricto, were thought to be well adapted to higher DOC and turbidity and lower pH and DO conditions. Compared with the sediment samples, the decomposition of Microcystis biomass had greater influence on the bacterial community composition in water and Clostridium sensu stricto might play important roles in the process of Microcystis biomass decomposition.

DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

Microeukaryotic plankton (0.2-200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve -by using SSU rDNA-based high-throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore-size sieve. We further found that both >0.2 μm and 0.2-200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size-fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.

Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel

Stability of microbial communities can impact the ability of dispersed cells to colonize a new habitat. Saturated brines and their halophile communities are presumed to be steady state systems due to limited environmental perturbations. In this study, the bacteriorhodopsin-containing fraction of the haloarchaeal community from Eilat salt crystallizer ponds was sampled five times over 3 years. Analyses revealed the existence of a constant core as several OTUs were found repeatedly over the length of the study: OTUs comprising 52 % of the total cloned and sequenced PCR amplicons were found in every sample, and OTUs comprising 89 % of the total sequences were found in more than one, and often more than two samples. LIBSHUFF and UNIFRAC analyses showed statistical similarity between samples and Spearman's coefficient denoted significant correlations between OTU pairs, indicating non-random patterns in abundance and co-occurrence of detected OTUs. Further, changes in the detected OTUs were statistically linked to deviations in salinity. We interpret these results as indicating the existence of an ever-present core bacteriorhodopsin-containing Eilat crystallizer community that fluctuates in population densities, which are controlled by salinity rather than the extinction of some OTUs and their replacement through immigration and colonization.

Ammonium and phosphate enrichment across the dry-wet transition and their ecological relevance in a subtropical reservoir, China

Small river reservoirs are widespread and can be ecologically sensitive across the dry-wet transition under monsoon climate with respect to nutrient loading and phenology. Monthly sampling and high-frequency in situ measurements were conducted for a river reservoir (southeast China) in 2013-2014 to examine the seasonal pattern of nutrients and phytoplankton. We found that nutrient concentrations were runoff-mediated and determined by watershed inputs and, in some cases, by internal cycling depending on hydrology and temperature. Ammonium and phosphate were relatively enriched in February-March (a transitional period from dry/cold to wet/hot climate), which can be ascribed to initial flushing runoff from human/animal waste and spring fertilizer use. A phytoplankton bloom (mainly Chlorophyta) occurred during April after a surge of water temperature, probably due to the higher availability of inorganic nutrients and sunlight and suitable hydraulic residence time (medium flow) in the transitional period. The concentration of phytoplankton was low during May-June (wet-hot climate) when the concentrations of total suspended matter (TSM) were highest, likely owing to the "shading" effect of TSM and turbulence of high flow conditions. Nutrient-algae shifts across the dry-wet season and vertical profiles suggested that algal blooms seem to be fueled primarily by phosphate and ammonium rather than nitrate. Current findings of a strong temporal pattern and the relationship between physical parameters, nutrient and biota would improve our understanding of drivers of change in water quality and ecosystem functions with dam construction.

Snowmelt-driven changes in dissolved organic matter and bacterioplankton communities in the Heilongjiang watershed of China

Bacterioplankton plays a significant role in the circulation of materials and ecosystem function in the biosphere. Dissolved organic matter (DOM) from dead plant material and surface soil leaches into water bodies when snow melts. In our study, water samples from nine sampling sites along the Heilongjiang watershed were collected in February and June 2014 during which period snowmelt occurred. The goal of this study was to characterize changes in DOM and bacterioplankton community composition (BCC) associated with snowmelt, the effects of DOM, environmental and geographical factors on the distribution of BCC and interactions of aquatic bacterioplankton populations with different sources of DOM in the Heilongjiang watershed. BCC was measured by denaturing gradient gel electrophoresis (DGGE). DOM was measured by excitation-emission matrix (EEM) fluorescence spectroscopy. Bacterioplankton exhibited a distinct seasonal change in community composition due to snowmelt at all sampling points except for EG. Redundancy analysis (RDA) indicated that BCC was more closely related to DOM (Components 1 and 4, dissolved organic carbon, biochemical oxygen demand and chlorophyll a) and environmental factors (water temperature and nitrate nitrogen) than geographical factors. Furthermore, DOM had a greater impact on BCC than environmental factors (29.80 vs. 15.90% of the variation). Overall, spring snowmelt played an important role in altering the quality and quantity of DOM and BCC in the Heilongjiang watershed.

Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing

The aims of this study were to determine the microbial community in five rivers in the proximity of a city in the Czech Republic using 454-pyrosequencing, as well as to assess seasonal variability over the course of 1 year and to identify the factors influencing the structure of bacterial communities. Samples from five rivers around the city of Brno were obtained during four seasons and analysed using 454 pyrosequencing of the 16S rRNA gene. The core composition of bacterial communities consisted of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, TM7 and others. Our approach enabled us to more closely study the correlation between the abundance of different families and environmental factors. Overall, Actinobacteria negatively correlated with phosphorus, sulphate, dissolved particle and chloride levels. In contrast, Proteobacteria positively correlated with sulphate, dissolved particle, chloride, dissolved oxygen and nitrite levels. Future work should focus on the dynamics of bacterial communities present in river water and their relation to the overall stability of the water ecosystem.

Spatial-Temporal Changes of Bacterioplankton Community along an Exhorheic River

To date, few aquatic microbial ecology studies have discussed the variability of the microbial community in exorheic river ecosystems on both the spatial and seasonal scales. In this study, we examined the spatio-temporal variation of bacterioplankton community composition in an anthropogenically influenced exorheic river, the Haihe River in Tianjin, China, using pyrosequencing analysis of 16S rRNA genes. It was verified by one-way ANOVA that the spatial variability of the bacterioplankton community composition over the whole river was stronger than the seasonal variation. Salinity was a major factor leading to spatial differentiation of the microbial community structure into riverine and estuarial parts. A high temperature influence on the seasonal bacterial community variation was only apparent within certain kinds of environments (e.g., the riverine part). Bacterial community richness and diversity both exhibited significant spatial changes, and their seasonal variations were completely different in the two environments studied here. Furthermore, riverine bacterial community assemblages were subdivided into urban and rural groups due to changes in the nutritional state of the river. In addition, the nutrient-loving group including Limnohabitans, Hydrogenophaga, and Polynucleobacter were abundant in the urbanized Haihe River, indicating the environmental factors in these anthropogenic waterbodies heavily influence the core freshwater community composition.

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system

Dissolved organic matter (DOM) is the main substrate and energy source for heterotrophic bacterioplankton. To understand the interactions between DOM and the bacterial community (BC), it is important to identify the key factors on both sides in detail, chemically distinct moieties in DOM and the various bacterial taxa. Next-generation sequencing facilitates the classification of millions of reads of environmental DNA and RNA amplicons and ultrahigh-resolution mass spectrometry yields up to 10 000 DOM molecular formulae in a marine water sample. Linking this detailed biological and chemical information is a crucial first step toward a mechanistic understanding of the role of microorganisms in the marine carbon cycle. In this study, we interpreted the complex microbiological and molecular information via a novel combination of multivariate statistics. We were able to reveal distinct relationships between the key factors of organic matter cycling along a latitudinal transect across the North Sea. Total BC and DOM composition were mainly driven by mixing of distinct water masses and presumably retain their respective terrigenous imprint on similar timescales on their way through the North Sea. The active microbial community, however, was rather influenced by local events and correlated with specific DOM molecular formulae indicative of compounds that are easily degradable. These trends were most pronounced on the highest resolved level, that is, operationally defined 'species', reflecting the functional diversity of microorganisms at high taxonomic resolution.