Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints

Effects of micro/nano-ozone bubble nutrient solutions on growth promotion and rhizosphere microbial community diversity in soilless cultivated lettuces

Due to its high efficacy as a wide-spectrum disinfectant and its potential for the degradation of pollutants and pesticides, ozone has broad application prospects in agricultural production. In this study, micro/nano bubble technology was applied to achieve a saturation state of bubble nutrient solution, including micro-nano oxygen (O2 group) and micro-nano ozone (O3 group) bubble nutrient solutions. The effects of these solutions on lettuce physiological indices as well as changes in the microbial community within the rhizosphere substrate were studied. The application of micro/nano (O2 and O3) bubble nutrient solutions to substrate-cultured lettuce plants increased the amount of dissolved oxygen in the nutrient solution, increased the lettuce yield, and elevated the net photosynthetic rate, conductance of H2O and intercellular carbon dioxide concentration of lettuce plants. Diversity analysis of the rhizosphere microbial community revealed that both the abundance and diversity of bacterial and fungal communities in the substrate increased after plant cultivation and decreased following treatment with micro/nanobubble nutrient solutions. RDA results showed that the microbial community in the S group was positively associated with EC, that in the CK and O2 groups exhibited a positive correlation with SC, and that in the O3 group displayed a positive correlation with CAT and POD. Overall, the implementation of micro/nanobubble generation technology in soilless substrates can effectively increase the lettuce growth and yield, and O3 had a more pronounced effect on lettuce yield and quality and the microbial community structure in the substrate than O2. Our study would provide a reference and theoretical basis for developing sustainable and green technology for promoting lettuce production and can be a promising alternative to conventional methods for improving crop yields.

Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence

When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.

Effects of Maize-Crop Rotation on Soil Physicochemical Properties, Enzyme Activities, Microbial Biomass and Microbial Community Structure in Southwest China

Introducing cover crops into maize rotation systems is widely practiced to increase crop productivity and achieve sustainable agricultural development, yet the potential for crop rotational diversity to contribute to environmental benefits in soils remains uncertain. Here, we investigated the effects of different crop rotation patterns on the physicochemical properties, enzyme activities, microbial biomass and microbial communities in soils from field experiments. Crop rotation patterns included (i) pure maize monoculture (CC), (ii) maize-garlic (CG), (iii) maize-rape (CR) and (iv) maize-annual ryegrass for one year (Cir1), two years (Cir2) and three years (Cir3). Our results showed that soil physicochemical properties varied in all rotation patterns, with higher total and available phosphorus concentrations in CG and CR and lower soil organic carbon and total nitrogen concentrations in the maize-ryegrass rotations compared to CC. Specifically, soil fertility was ranked as CG > Cir2 > CR > Cir3 > CC > Cir1. CG decreased enzyme activities but enhanced microbial biomass. Cir2 decreased carbon (C) and nitrogen (N) acquiring enzyme activities and soil microbial C and N concentrations, but increased phosphorus (P) acquiring enzyme activities and microbial biomass P concentrations compared to CC. Soil bacterial and fungal diversity (Shannon index) were lower in CG and Cir2 compared to CC, while the richness (Chao1 index) was lower in CG, CR, Cir1 and Cir2. Most maize rotations notably augmented the relative abundance of soil bacteria, including Chloroflexi, Gemmatimonadetes and Rokubacteria, while not necessarily decreasing the abundance of soil fungi like Basidiomycota, Mortierellomycota and Anthophyta. Redundancy analysis indicated that nitrate-N, ammonium-N and microbial biomass N concentrations had a large impact on soil bacterial communities, whereas nitrate-N and ammonium-N, available P, soil organic C and microbial biomass C concentrations had a greater effect on soil fungal communities. In conclusion, maize rotations with garlic, rape and ryegrass distinctly modify soil properties and microbial compositions. Thus, we advocate for garlic and annual ryegrass as maize cover crops and recommend a two-year rotation for perennial ryegrass in Southwest China.

Local eukaryotic and bacterial stream community assembly is shaped by regional land use effects

With anticipated expansion of agricultural areas for food production and increasing intensity of pressures stemming from land-use, it is critical to better understand how species respond to land-use change. This is particularly true for microbial communities which provide key ecosystem functions and display fastest responses to environmental change. However, regional land-use effects on local environmental conditions are often neglected, and, hence, underestimated when investigating community responses. Here we show that the effects stemming from agricultural and forested land use are strongest reflected in water conductivity, pH and phosphorus concentration, shaping microbial communities and their assembly processes. Using a joint species distribution modelling framework with community data based on metabarcoding, we quantify the contribution of land-use types in determining local environmental variables and uncover the impact of both, land-use, and local environment, on microbial stream communities. We found that community assembly is closely linked to land-use type but that the local environment strongly mediates the effects of land-use, resulting in systematic variation of taxon responses to environmental conditions, depending on their domain (bacteria vs. eukaryote) and trophic mode (autotrophy vs. heterotrophy). Given that regional land-use type strongly shapes local environments, it is paramount to consider its key role in shaping local stream communities.

Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition

Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.

Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales

Identifying the main drivers of community assembly remains an open fundamental question in ecology. Dispersal processes introduce randomness in community composition while selection for particular environments creates predictable assemblages. However, the interaction between selection and dispersal processes is still poorly understood. Here, we address this question in bacterial and microeukaryotic communities inhabiting a highly dynamic system of ephemeral (hyper)saline lakes. We show that the combination of beta-diversity decomposition methods and a temporal approach based on colonization and extinction dynamics yields new insights into the relative effect of selection and dispersal along environmental gradients. Selective pressure and dispersal-related processes simultaneously shape each local community with variable strength and effect. The dominance of selection vs. dispersal shifted from stochastic to deterministic assembly as salinity increased along the gradient. This transition also had an impact on the temporal dynamics of the lakes as community turnover decreased at high salinities because both colonization and extinction rates slowed down. Only microeukaryotic richness decreased along the gradient due to lower effective colonization at higher salinities, suggesting that the net effect of selection and dispersal is determined by both environmental conditions and the idiosyncrasy of the different microbial ecologies. Our results emphasize the use of temporal approaches in combination with standard statistical methods for a better understanding of the dynamic processes underlying community assembly.

Environmental filtering and mass effect are two important processes driving lake benthic diatoms: Results of a DNA metabarcoding study in a large lake

Environmental filtering is often found to dominate assembly rules in diatoms. These microalgae are diverse, especially at subspecies level, and tend to exhibit a niche phylogenetic conservatism. Therefore, other rules, such as competition or mass effects, should be detectable when environmental gradients and dispersal barriers are limited. We used metabarcoding to analyse benthic littoral diatom communities in 153 sites in a large lake (Geneva) exhibiting weak geographical barriers and weak environmental gradients outside river estuaries. We assessed assembly rules using variance partitioning, phylogenetic and source tracking analyses. No phylogenetic over-dispersion of communities, indicative of exclusive competition, was detected. Instead, we found these communities to be phylogenetically over-clustered, indicating environmental filtering, which was even stronger near river estuaries where environmental gradients are stronger. Finally, using a Bayesian method (SourceTracker), we found that rivers flowing into the lake bring communities that settle, especially in sites close to estuaries. Rivers with the highest discharges are primarily responsible for immigration, explaining 27% of lake composition. Therefore, despite favourable conditions to observe other rules, our results support that diatom communities are prominently assembled by environmental filtering and immigration processes, in particular from rivers. However, this does not exclude that other assembly rules may be at play at a finer spatial, temporal and/or phylogenetic scale.

Cultivation of different seaweed species and seasonal changes cause divergence of the microbial community in coastal seawaters

Although the effects of certain species of seaweed on the microbial community structure have long been a research focus in marine ecology, the response of the microbial community to seasons and different seaweed species is poorly understood. In the present study, a total of 39 seawater samples were collected during 3 months from three zones: Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G), and control zones (C). These samples were then analyzed using 18S and 16S rRNA gene sequencing to ascertain the fungal and bacterial communities, respectively, along with the determination of environmental factors. Our results showed that increased dissolved oxygen (DO), decreased inorganic nutrients, and released dissolved organic matter (DOM) in seaweed cultivation zone predominantly altered the variability of eukaryotic and prokaryotic microbial communities. Certain microbial groups such as Aurantivirga, Pseudomonas, and Woeseia were stimulated and enriched in response to seaweed cultivation, and the enriched microorganisms varied across seaweed cultivation zones due to differences in the composition of released DOM. In addition, seasonal changes in salinity and temperature were strongly correlated with microbial community composition and structure. Our study provides new insights into the interactions between seaweed and microbial communities.

Stabilizing microbial communities by looped mass transfer

Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.

Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape

In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.

Combined effects of heatwaves and micropollutants on freshwater ecosystems: Towards an integrated assessment of extreme events in multiple stressors research

Freshwater ecosystems are strongly influenced by weather extremes such as heatwaves (HWs), which are predicted to increase in frequency and magnitude in the future. In addition to these climate extremes, the freshwater realm is impacted by the exposure to various classes of chemicals emitted by anthropogenic activities. Currently, there is limited knowledge on how the combined exposure to HWs and chemicals affects the structure and functioning of freshwater ecosystems. Here, we review the available literature describing the single and combined effects of HWs and chemicals on different levels of biological organization, to obtain a holistic view of their potential interactive effects. We only found a few studies (13 out of the 61 studies included in this review) that investigated the biological effects of HWs in combination with chemical pollution. The reported interactive effects of HWs and chemicals varied largely not only within the different trophic levels but also depending on the studied endpoints for populations or individuals. Hence, owing also to the little number of studies available, no consistent interactive effects could be highlighted at any level of biological organization. Moreover, we found an imbalance towards single species and population experiments, with only five studies using a multitrophic approach. This results in a knowledge gap for relevant community and ecosystem level endpoints, which prevents the exploration of important indirect effects that can compromise food web stability. Moreover, this knowledge gap impairs the validity of chemical risk assessments and our ability to protect ecosystems. Finally, we highlight the urgency of integrating extreme events into multiple stressors studies and provide specific recommendations to guide further experimental research in this regard.

Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network

During transit from soils to the ocean, microbial communities are modified and re-assembled, generating complex patterns of ecological succession. The potential effect of upstream assembly on downstream microbial community composition is seldom considered within aquatic networks. Here, we reconstructed the microbial succession along a land-freshwater-estuary continuum within La Romaine river watershed in Northeastern Canada. We captured hydrological seasonality and differentiated the total and reactive community by sequencing both 16 S rRNA genes and transcripts. By examining how DNA- and RNA-based assemblages diverge and converge along the continuum, we inferred temporal shifts in the relative importance of assembly processes, with mass effects dominant in spring, and species selection becoming stronger in summer. The location of strongest selection within the network differed between seasons, suggesting that selection hotspots shift depending on hydrological conditions. The unreactive fraction (no/minor RNA contribution) was composed of taxa with diverse potential origins along the whole aquatic network, while the majority of the reactive pool (major RNA contribution) could be traced to soil/soilwater-derived taxa, which were distributed along the entire rank-abundance curve. Overall, our findings highlight the importance of considering upstream history, hydrological seasonality and the reactive microbial fraction to fully understand microbial community assembly on a network scale.

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)

Flow from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities. IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.

How sediment bacterial community shifts along the urban river located in mining city

Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.

Rhizosphere microbiome dynamics in tropical seagrass under short-term inorganic nitrogen fertilization

Rhizosphere microbes are crucial to seagrass meadows because they promote plant growth and heath. However, information concerning the response of rhizosphere microorganisms in seagrass sediment in the presence of different nitrogen sources is lacking. Here, by means of high-throughput sequencing, we investigated how addition of inorganic nitrogen affects the rhizosphere microbiome of the tropical seagrass Thalassia hemperichii. A seagrass culture system was set up to conduct a nitrogen addition (ammonium and nitrate) simulation experiment. We found that the relative abundance of Proteobacteria and Bacteroidetes was increased in inorganic nitrogen-enriched samples, whereas that of Acidobacteria decreased under ammonium enrichment, especially after 35 days. High levels of inorganic nitrogen addition caused a significant decrease in the relative abundance of Desulfobacteraceae, Sulfurovaceae, and Spirochaetes, which are primarily involved in sulfur cycling. Additionally, the abundance of microbes in the seagrass rhizosphere reached the highest after the ammonium-enrichment treatment. Among the analyzed seagrass photosynthetic characteristics, seagrass leaves presented the highest light utility in treatments receiving nitrate, followed by the control groups and ammonium-enrichment groups. Moreover, 16S rRNA gene-predicted functional analysis suggested that some functions related to metabolism of amino acids and signal transduction were enriched in samples receiving high ammonium, whereas nitrate addition enriched predicted functions related to diseases. These findings provide new insights into the response of microbial communities to different types of nitrogen additions in seagrass ecosystems.

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Aquifer recharge viewed through the lens of microbial community ecology: Initial disturbance response, and impacts of species sorting versus mass effects on microbial community assembly in groundwater during riverbank filtration

Riverbank filtration has gained increasing importance for balancing rising groundwater demands and securing drinking water supplies. While microbial communities are the pillar of vital ecosystem functions in groundwater, the impact of riverbank filtration on these communities has been understudied so far. Here, we followed changes in microbial community composition based on 16S rRNA gene amplicon sequence variants (ASVs) in an initially pristine shallow porous aquifer in response to surface water intrusion during the early stages of induced riverbank filtration over a course of seven weeks. We further analyzed sediment cores for imprints of river-derived ASVs after seven weeks of riverbank filtration. The onset of the surface water intrusion caused loss of taxa and significant changes in community composition, revealing low disturbance resistance of the initial aquifer microbial communities. SourceTracker analysis revealed that proportions of river-derived ASVs in the groundwater were generally <25%, but locally could reach up to 62% during a period of intense precipitation. However, variation partitioning showed that the impact of dispersal of river-derived ASVs on changes in aquifer microbial community composition was overall outweighed by species sorting due to changes in environmental conditions caused by the infiltrating river water. Proportions of river-derived ASVs on aquifer sediments were <0.5%, showing that taxa transported from the river into the aquifer over the course of the study mainly resided as planktonic microorganisms in the groundwater. Our study demonstrates that groundwater microbial communities react sensitively to changes in environmental conditions caused by surface water intrusion, whereas mass effects resulting from the influx of river-derived taxa play a comparatively minor role.

Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream

Water quality monitoring is essential to safeguard human and environmental health. The advent of next-generation sequencing techniques in recent years, which allow a more in-depth study of environmental microbial communities in the environment, could broaden the perspective of water quality monitoring to include impact of faecal pollution bacteria on ecosystem. In this study, 16 S rRNA amplicon sequencing was used to evaluate the impact of wastewater treatment plant (WWTP) effluent on autochthonous microbial communities of a temporary Mediterranean stream characterized by high flow seasonality (from 0.02 m³/s in winter to 0.006 m³/s in summer). Seven sampling campaigns were performed under different temperatures and streamflow conditions (winter and summer). Water samples were collected upstream (Upper) of the WWTP, the secondary effluent (EF) discharge and 75 m (P75) and 1000 m (P1000) downstream of the WWTP. A total of 5,593,724 sequences were obtained, giving rise to 20,650 amplicon sequence variants (ASV), which were further analysed and classified into phylum, class, family and genus. Each sample presented different distribution and abundance of taxa. Although taxon distribution and abundance differed in each sample, the microbial community structure of P75 resembled that of EF samples, and Upper and P1000 samples mostly clustered together. Alpha diversity showed the highest values for Upper and P1000 samples and presented seasonal differences, being higher in winter conditions of high streamflow and low temperature. Our results suggest the microbial ecology re-establishment, since autochthonous bacterial communities were able to recover from the impact of the WWTP effluent in 1 km. Alpha diversity results indicates a possible influence of environmental factors on the bacterial community structure. This study shows the potential of next-generation sequencing techniques as useful tools in water quality monitoring and management within the climate change scenario.

The Role of Land Use Types and Water Chemical Properties in Structuring the Microbiomes of a Connected Lake System

Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within seven different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not correlated with the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO2 + NO3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) correlated to some extent with the water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. Significantly more data, including time-series measurements of land use and water chemical properties, are needed to fully understand the interaction between the environment and the organization of microbial communities.

Distinct Assembly Mechanisms Underlie Similar Biogeographic Patterns of Rare and Abundant Bacterioplankton in Cascade Reservoirs of a Large River

Bacterioplankton communities commonly consist of few highly abundant species and a large number of rare species that play key roles in biogeochemical cycles of aquatic ecosystems. However, little is known about the biogeographic assemblies of these communities, especially in large rivers suffering from cascade dam regulation. Here, we used a 16S rRNA gene amplicon sequencing approach to investigate the biogeographic patterns and underlying assembly mechanisms of abundant and rare bacterioplankton taxa in cascade reservoirs of the Jinsha River in China. The results revealed species loss of bacterioplankton due to dam construction, which was more significant for rare taxa than for abundant ones. The distributions of abundant and rare taxa exhibited similar spatial and temporal patterns, which were significantly distinct between winter and summer and between upstream and downstream reservoirs. Both spatial (dispersal-related process) and environmental (selection process) factors seemed to together govern the assembly and biogeography of abundant and rare taxa, although both factors explained only a small fraction of variation in the rare taxa. More importantly, environmental factors explained more community variation in abundant sub-community than that in rare sub-community. Co-occurrence network analysis revealed that abundant species with closer interactions were more often located in a central position of the network compared with rare species. Nevertheless, half of the keystone species were rare species and may play important roles in maintaining the network stability. Overall, these findings indicate that distinct assembly mechanisms underlie the similar biogeography of rare and abundant bacteria in cascade reservoirs of a large river.

The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension

Lakes are exposed to anthropogenic pollution including the release of allochthonous bacteria into their waters. Antibiotic resistance genes (ARGs) stabilize in bacterial communities of temperate lakes, and these environments act as long-term reservoirs of ARGs. Still, it is not clear if the stabilization of the ARGs is caused by a periodical introduction, or by other factors regulated by dynamics within the water column. Here we observed the dynamics of the tetracycline resistance gene (tetA) and of the class 1 integron integrase gene intI1 a proxy of anthropogenic pollution in the water column and in the sediments of subalpine Lake Maggiore, together with several chemical, physical and microbiological variables. Both genes resulted more abundant within the bacterial community of the sediment compared to the water column and the water-sediment interface. Only at the inset of thermal stratification they reached quantifiable abundances in all the water layers, too. Moreover, the bacterial communities of the water-sediment interface were more similar to deep waters than to the sediments. These results suggest that the vertical distribution of tetA and intI1 is mainly due to the deposition of bacteria from the surface water to the sediment, while their resuspension from the sediment is less important.

Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant

In aerobic granular sludge (AGS) systems, different-sized microbial aggregates having different solids retention time (SRT) coexist in the same reactor compartment and are subjected to the same influent wastewater. Thus, the AGS system provides a unique ecosystem to study the importance of local (species sorting) and regional (immigration) processes in bacterial community assembly. The microbial communities of different-sized aggregates (flocs <0.2 mm, small granules (0.2-1.0 mm) and large granules >1.0 mm), influent wastewater, excess sludge and effluent of a full-scale AGS plant were characterized over a steady-state operation period of 6 months. Amplicon sequencing was integrated with mass balance to determine the SRT and net growth rate of operational taxonomic units (OTUs). We found strong evidence of species sorting as opposed to immigration, which was significantly higher at short SRT (i.e., flocs and small granules) than that at long SRT (large granules). Rare OTUs in wastewater belonging to putative functional groups responsible for nitrogen and phosphorus removal were progressively enriched with an increase in microbial aggregates size. In contrast, fecal- and sewage infrastructure-derived microbes progressively decreased in relative abundance with increase in microbial aggregate size. These findings highlight the importance of AGS as a unique model ecosystem to study fundamental microbial ecology concepts.

Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India

Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.

Freshwater Bacterioplankton Metacommunity Structure Along Urbanization Gradients in Belgium

Urbanization is transforming and fragmenting natural environments worldwide, driving changes in biological communities through alterations in local environmental conditions as well as by changing the capacity of species to reach specific habitats. While the majority of earlier studies have been performed on higher plants and animals, it is crucial to increase our insight on microbial responses to urbanization across different spatial scales. Here, using a metacommunity approach, we evaluated the effects of urbanization on bacterioplankton communities in 50 shallow ponds in Belgium (Flanders region), one of the most urbanized areas in Northwest Europe. We estimated the relative importance of local environmental factors (35 abiotic and biotic variables), regional spatial factors and urbanization (built-up area) quantified at two spatial scales (200 m × 200 m and 3 km × 3 km). We show that urbanization at local or regional scales did not lead to strong changes in community composition and taxon diversity of bacterioplankton. Urbanization at regional scale (3 km × 3 km) explained only 2% of community composition variation while at local scale (200 m × 200 m), no effect was detected. Local environmental factors explained 13% (OTUs with relative abundance ≥ 0.1%) to 24% (12 dominant OTUs -≥ 1%) of community variation. Six local environmental variables significantly explained variation in bacterioplankton community composition: pH, alkalinity, conductivity, total phosphorus, abundance of Daphnia and concentration of copper (Cu), of which pH was partly mediated by urbanization. Our results indicate that environmental rather than spatial factors accounted for the variation in bacterioplankton community structure, suggesting that species sorting is the main process explaining bacterioplankton community assembly. Apparently, urbanization does not have a direct and strong effect on bacterioplankton metacommunity structure, probably due to the capacity of these organisms to adapt toward and colonize habitats with different environmental conditions and due to their fast adaptation and metabolic versatility. Thus, bacterioplankton communities inhabiting shallow ponds may be less affected by environmental conditions resulting from urbanization as compared to the impacts previously described for other taxa.

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity

Selection and dispersal are ecological processes that have contrasting roles in the assembly of communities. Variable selection diversifies and strong dispersal homogenizes them. However, we do not know whether dispersal homogenizes communities directly via immigration or indirectly via weakening selection across habitats due to physical transfer of material, e.g., water mixing in aquatic ecosystems. Here we examine how dispersal homogenizes a simplified synthetic bacterial metacommunity, using a sequencing-independent approach based on flow cytometry and mathematical modeling. We show that dispersal homogenizes the metacommunity via immigration, not via weakening selection, and even when immigration is four times slower than growth. This finding challenges the current view that dispersal homogenizes communities only at high rates and explains why communities are homogeneous at small spatial scales. It also offers a benchmark for sequence-based studies in natural microbial communities where immigration rates can be inferred solely by using neutral models.

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

Thermal effluents from nuclear power plants greatly change the environmental and ecological conditions of the receiving marine water body, but knowledge about their impact on microbial ecology is limited. Here we used high-throughput sequencing of the 16S rRNA gene to examine marine bacterioplankton metacommunity assembly across thermal gradients in two representative seasons (i.e., winter and summer) in a subtropical bay located on the northern coast of the South China Sea. We found high heterogeneity in bacterioplankton community compositions (BCCs) across thermal gradients and between seasons. The spatially structured temperature gradient created by thermal effluents was the key determinant of BCCs, but its influence differed by season. Using a metacommunity approach, we found that in the thermal discharge area, i.e., where water is frequently exchanged with surrounding seawater and thermal effluent water, the BCC spatial patterns were shaped by species sorting rather than by mass effects from surrounding seawater or by dilution of thermal effluent water by surrounding seawater. However, this effect of species sorting was weaker in summer than in winter seawater. In both seasons, the bacterioplankton community structure was predominately determined by niche sharing; however, the relative importance of niche segregation was enhanced in summer seawater. Our findings suggest that for the seasonal differences in metacommunity processes, the BCCs of subtropical summer seawater were more sensitive to temperature and were more difficult to predict than those of winter seawater in the face of different intensities of thermal impacts.IMPORTANCE Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents from two nuclear power plants have been present in the subtropical Daya Bay for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environmental patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale; thus, this is a useful model for the study of the metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to reveal how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future conditions of global warming.

Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

Temporal variability of bacterioplankton is habitat driven

Temporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, nonmetric multidimensional scaling and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to meltwater inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats.

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean

Deep-sea mining of commercially valuable polymetallic nodule fields will generate a seabed sediment plume into the water column. Yet, the response of bacterioplankton communities, critical in regulating energy and matter fluxes in marine ecosystems, to such disturbances is unknown. Metacommunity theory, traditionally used in general ecology for macroorganisms, offers mechanistic understanding on the relative role of spatial differences compared with local environmental conditions (habitat filtering) for community assembly. We examined bacterioplankton metacommunities using 16S rRNA amplicons from the Clarion-Clipperton Zone (CCZ) in the eastern Pacific Ocean and in global ocean transect samples to determine sensitivity of these assemblages to environmental perturbations. Habitat filtering was the main assembly mechanism of bacterioplankton community composition in the epi- and mesopelagic waters of the CCZ and the Tara Oceans transect. Bathy- and abyssopelagic bacterioplankton assemblages were mainly assembled by undetermined metacommunity types or neutral and dispersal-driven patch-dynamics for the CCZ and the Malaspina transect. Environmental disturbances may alter the structure of upper-ocean microbial assemblages, with potentially even more substantial, yet unknown, impact on deep-sea communities. Predicting such responses in bacterioplankton assemblage dynamics can improve our understanding of microbially-mediated regulation of ecosystem services in the abyssal seabed likely to be exploited by future deep-sea mining operations.

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system

It is unknown whether bacterioplankton and biofilm communities are structured by the same ecological processes, and whether they influence each other through continuous dispersal (known as mass effects). Using a hierarchical sampling approach we compared the relative importance of ecological processes structuring the dominant fraction (relative abundance ≥0.1%) of bacterioplankton and biofilm communities from three microhabitats (open water, Nuphar and Phragmites sites) at within- and among-pond scale in a set of 14 interconnected shallow ponds. Our results demonstrate that while bacterioplankton and biofilm communities are highly distinct, a similar hierarchy of ecological processes is acting on them. For both community types, most variation in community composition was determined by pond identity and environmental variables, with no effect of space. The highest β-diversity within each community type was observed among ponds, while microhabitat type (Nuphar, Phragmites, open water) significantly influenced biofilm communities but not bacterioplankton. Mass effects among bacterioplankton and biofilm communities were not detected, as suggested by the absence of within-site covariation of biofilm and bacterioplankton communities. Both biofilm and plankton communities were thus highly structured by environmental factors (i.e., species sorting), with among-lake variation being more important than within-lake variation, whereas dispersal limitation and mass effects were not observed.

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet

Retreating glaciers and ice sheets are among the clearest signs of global climate change. One consequence of glacier retreat is the formation of new meltwater-lakes in previously ice-covered terrain. These lakes provide unique opportunities to understand patterns in community organization during early lake ontogeny. Here, we analyzed the bacterial community structure and diversity in six lakes recently formed by the retreat of the Greenland Ice Sheet (GrIS). The lakes represented a turbidity gradient depending on their past and present connectivity to the GrIS meltwaters. Bulk (16S rRNA genes) and putatively active (16S rRNA) fractions of the bacterioplankton communities were structured by changes in environmental conditions associated to the turbidity gradient. Differences in community structure among lakes were attributed to both, rare and abundant community members. Further, positive co-occurrence relationships among phylogenetically closely related community members dominate in these lakes. Our results show that environmental conditions along the turbidity gradient structure bacterial community composition, which shifts during lake ontogeny. Rare taxa contribute to these shifts, suggesting that the rare biosphere has an important ecological role during early lakes ontogeny. Members of the rare biosphere may be adapted to the transient niches in these nutrient poor lakes. The directionality and phylogenetic structure of co-occurrence relationships indicate that competitive interactions among closely related taxa may be important in the most turbid lakes.

Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River

BACKGROUND

Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, little is presently known about the integrated biogeography of planktonic and sedimentary bacterial communities in large rivers.

RESULTS

This study provides the first spatiotemporal pattern of bacterial communities in the Yangtze River, the largest river in Asia with a catchment area of 1,800,000 km2. We find that sedimentary bacteria made larger contributions than planktonic bacteria to the bacterial diversity of the Yangzte River ecosystem with the sediment subgroup providing 98.8% of 38,906 operational taxonomic units (OTUs) observed in 280 samples of synchronous flowing water and sediment at 50 national monitoring stations covering a 4300 km reach. OTUs within the same phylum displayed uniform seasonal variations, and many phyla demonstrated autumn preference throughout the length of the river. Seasonal differences in bacterial communities were statistically significant in water, whereas bacterial communities in both water and sediment were geographically clustered according to five types of landforms: mountain, foothill, basin, foothill-mountain, and plain. Interestingly, the presence of two huge dams resulted in a drastic fall of bacterial taxa in sediment immediately downstream due to severe riverbed scouring. The integrity of the biogeography is satisfactorily interpreted by the combination of neutral and species sorting perspectives in meta-community theory for bacterial communities in flowing water and sediment.

CONCLUSIONS

Our study fills a gap in understanding of bacterial communities in one of the world's largest river and highlights the importance of both planktonic and sedimentary communities to the integrity of bacterial biogeographic patterns in a river subject to varying natural and anthropogenic impacts.

Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan'ao Island, South China Sea

Seaweed cultivation not only provides economy benefits, but also remediates the environment contaminated by mariculture of animals (e.g., fish, shrimps). However, the response of microbial communities to seaweed cultivation is poorly understood. In this study, we analyzed the diversity, composition, and structure of water and sediment microbial communities at a seaweed, Gracilaria lemaneiformis, cultivation zone and a control zone near Nan'ao Island, South China Sea by MiSeq sequencing of 16S rRNA gene amplicons. We found that large-scale cultivation of G. lemaneiformis increased dissolved oxygen (DO) and pH but decreased inorganic nutrients, possibly due to nutrient uptake, photosynthesis and other physiological processes of G. lemaneiformis. These environmental changes significantly (adonis, P<0.05) shifted the microbial community composition and structure of both water column and sediment samples in the G. lemaneiformis cultivation zone, compared to the control zone. Also, certain microbial taxa associated with seaweed, such as Arenibacter, Croceitalea, Glaciecola, Leucothrix and Maribacter were enriched at the cultivation zone. In addition, we have proposed a conceptual model to summarize the results in this study and guide future studies on relationships among seaweed processes, microbial communities and their environments. Thus, this study not only provides new insights into our understanding the effect of G. lemaneiformis cultivation on microbial communities, but also guides future studies on coastal ecosystems.

Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea

Marine microbes exhibit biogeographical patterns linked with fluxes of matter and energy. Yet, knowledge of the mechanisms shaping bacterioplankton community assembly across temporal scales remains poor. We examined bacterioplankton 16S rRNA gene fragments obtained from Baltic Sea transects to determine phylogenetic relatedness and assembly processes coupled with niche breadth. Communities were phylogenetically more related over time than expected by chance, albeit with considerable temporal variation. Hence, habitat filtering, i.e., local environmental conditions, rather than competition structured bacterioplankton communities in summer but not in spring or autumn. Species sorting (SS) was the dominant assembly process, but temporal and taxonomical variation in mechanisms was observed. For May communities, Cyanobacteria, Actinobacteria, Alpha- and Betaproteobacteria exhibited SS while Bacteroidetes and Verrucomicrobia were assembled by SS and mass effect. Concomitantly, Gammaproteobacteria were assembled by the neutral model and patch dynamics. Temporal variation in habitat filtering and dispersal highlights the impact of seasonally driven reorganization of microbial communities. Typically abundant Baltic Sea populations such as the NS3a marine group (Bacteroidetes) and the SAR86 and SAR11 clade had the highest niche breadth. The verrucomicrobial Spartobacteria population also exhibited high niche breadth. Surprisingly, variation in bacterioplankton community composition was regulated by environmental factors for generalist taxa but not specialists. Our results suggest that generalists such as NS3a, SAR86, and SAR11 are reorganized to a greater extent by changes in the environment compared to specialists and contribute more strongly to determining overall biogeographical patterns of marine bacterial communities.

Relative importance of advective flow versus environmental gradient in shaping aquatic ammonium oxidizers near the Three Gorges Dam of the Yangtze River, China

Construction of a dam in a large river alters its hydrodynamic condition and geochemical gradient, but the effect of such anthropogenic activity on microbial ecology remains poorly understood. To assess this effect, we investigated the relative importance of advective flow versus environmental condition in shaping ammonia oxidizing bacteria (AOB) and archaea (AOA) community from 110 km upstream to the Three Gorges Dam (TGD) of the Yangtze River, China. Water physicochemical conditions, including turbidity, conductivity, redox state and nutrient level, were fairly constant from 110 to 45 km upstream of the TGD, but significantly oscillated near the dam. AOB and AOA in the Yangtze River were dominated by Nitrosospira- and Nitrosopumilus-affiliated clusters, respectively, and these compositions were invariant throughout the sampled 110 km flow path, suggesting that AOB and AOA communities in the river were largely transported from upstream by advection with minor local and transient inputs from surrounding soils and tributaries. However, the abundance of AOB and AOA was influenced by local geochemical conditions, possibly via the growth/decay mechanisms. The source of AOB in the Yangtze River appeared to be derived from soil near the headwater, but its abundance was enhanced during downstream transport, likely due to survival and growth.

Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing

To understand the differences of the bacteria associated with different mosses, a phylogenetic study of bacterial communities in three mosses was carried out based on 16S rDNA and 16S rRNA sequencing. The mosses used were Hygroamblystegium noterophilum, Entodon compressus and Grimmia montana, representing hygrophyte, shady plant and xerophyte, respectively. In total, the operational taxonomic units (OTUs), richness and diversity were different regardless of the moss species and the library level. All the examined 1183 clones were assigned to 248 OTUs, 56 genera were assigned in rDNA libraries and 23 genera were determined at the rRNA level. Proteobacteria and Bacteroidetes were considered as the most dominant phyla in all the libraries, whereas abundant Actinobacteria and Acidobacteria were detected in the rDNA library of Entodon compressus and approximately 24.7% clones were assigned to Candidate division TM7 in Grimmia montana at rRNA level. The heatmap showed the bacterial profiles derived from rRNA and rDNA were partly overlapping. However, the principle component analysis of all the profiles derived from rDNA showed sharper differences between the different mosses than that of rRNA-based profiles. This suggests that the metabolically active bacterial compositions in different mosses were more phylogenetically similar and the differences of the bacteria associated with different mosses were mainly detected at the rDNA level. Obtained results clearly demonstrate that combination of 16S rDNA and 16S rRNA sequencing is preferred approach to have a good understanding on the constitution of the microbial communities in mosses.

Effects of dispersal and selection on stochastic assembly in microbial communities

Stochastic processes can play an important role in microbial community assembly. Dispersal limitation is one process that can increase stochasticity and obscure relationships between environmental variables and microbial community composition, but the relationship between dispersal, selection and stochasticity has not been described in a comprehensive way. We examine how dispersal and its interactions with drift and selection alter the consistency with which microbial communities assemble using a realistic, individual-based model of microbial decomposers. Communities were assembled under different environmental conditions and dispersal rates in repeated simulations, and we examined the compositional difference among replicate communities colonizing the same type of leaf litter ('within-group distance'), as well as between-group deterministic selection. Dispersal rates below 25% turnover per year resulted in high within-group distance among communities and no significant environmental effects. As dispersal limitation was alleviated, both within- and between-group distance decreased, but despite this homogenization, deterministic environmental effects remained significant. In addition to direct effects of dispersal rate, stochasticity of community composition was influenced by an interaction between dispersal and selection strength. Specifically, communities experiencing stronger selection (less favorable litter chemistries) were more stochastic, possibly because lower biomass and richness intensified drift or priority effects. Overall, we show that dispersal rate can significantly alter patterns of community composition. Partitioning the effects of dispersal, selection and drift based on static patterns of microbial composition will be difficult, if not impossible. Experiments will be required to tease apart these complex interactions between assembly processes shaping microbial communities.

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a result of nutrient importation from the surrounding watershed.

Temperature mediates continental-scale diversity of microbes in forest soils

Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial biodiversity, particularly in terrestrial soils. Here we show that, in accordance with metabolic theory of ecology, taxonomic and phylogenetic diversity of soil bacteria, fungi and nitrogen fixers are all better predicted by variation in environmental temperature than pH. However, the rates of diversity turnover across the global temperature gradients are substantially lower than those recorded for trees and animals, suggesting that the diversity of plant, animal and soil microbial communities show differential responses to climate change. To the best of our knowledge, this is the first study demonstrating that the diversity of different microbial groups has significantly lower rates of turnover across temperature gradients than other major taxa, which has important implications for assessing the effects of human-caused changes in climate, land use and other factors.

Climate warming has a wide range of effects on biodiversity. Here, Zhou et al. show that although variation in environmental temperature is a primary driver of soil microbial biodiversity, microbes show much lower rates of turnover across temperature gradients than other major taxa.

Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains

Microbial community assembly and microbial functions are affected by a number of different but coupled drivers such as local habitat characteristics, dispersal rates, and species interactions. In groundwater systems, hydrological flow can introduce spatial structure and directional dependencies among these drivers. We examined the importance of hydrology in structuring bacterial communities and their function within two alpine floodplains during different hydrological states. Piezometers were installed in stream sediments and surrounding riparian zones to assess hydrological flows and also were used as incubation chambers to examine bacterial community structures and enzymatic functions along hydrological flow paths. Spatial eigenvector models in conjunction with models based on physico-chemical groundwater characteristics were used to evaluate the importance of hydrologically-driven processes influencing bacterial assemblages and their enzymatic activities. Our results suggest a strong influence (up to 40% explained variation) of hydrological connectivity on enzymatic activities. The effect of hydrology on bacterial community structure was considerably less strong, suggesting that assemblages demonstrate large functional plasticity/redundancy. Effect size varied between hydrological periods but flow-related mechanisms always had the most power in explaining both bacterial structure and functioning. Changes in hydrology should be considered in models predicting ecosystem functioning and integrated into ecosystem management strategies for floodplains.

Neutral community model explains the bacterial community assembly in freshwater lakes

Over the past decade, neutral theory has gained attention and recognition for its capacity to explain bacterial community structure (BCS) in addition to deterministic processes. However, no clear consensus has been drawn so far on their relative importance. In a metacommunity analysis, we explored at the regional and local scale the effects of these processes on the bacterial community assembly within the water column of 49 freshwater lakes. The BCS was assessed using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes. At the regional scales, results indicated that the neutral community model well predicted the spatial community structure (R(2) mean = 76%) compared with the deterministic factors - which explained only a small fraction of the BCS total variance (less than 14%). This suggests that the bacterial compartment was notably driven by stochastic processes, through loss and gain of taxa. At the local scale, the bacterial community appeared to be spatially structured by stochastic processes (R(2) mean = 65%) and temporally governed by the water temperature, a deterministic factor, even if some bacterial taxa were driven by neutral dynamics. Therefore, at both regional and local scales the neutral community model appeared to be relevant in explaining the bacterial assemblage structure.

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.

Influence of influent wastewater communities on temporal variation of activated sludge communities

Continuously feeding influent wastewater containing diverse bacterial species to a wastewater treatment activated sludge bioreactor may influence the activated sludge bacterial community temporal dynamics. To explore this possibility, this study tracked influent wastewater and activated sludge bacterial communities by pyrosequencing 16S rRNA genes from four full-scale wastewater treatment plants over a 9-month period. The activated sludge communities showed significantly higher richness and evenness than the influent wastewater communities. Furthermore, the two communities were different in composition and temporal dynamics. These results demonstrate that the impact of the influent wastewater communities on the activated sludge communities was weak. Nevertheless, 4.3-9.3% of the operational taxonomic units (OTUs) detected in the activated sludge were shared with the influent wastewater, implying contribution from influent wastewater communities to some extent. However, the relative OTU abundance of the influent wastewater was not maintained in the activated sludge communities (i.e., weak neutral assembly). In addition, the variability of the communities of the shared OTUs was moderately correlated with abiotic factors imposed to the bioreactors. Taken together, temporal dynamics of activated sludge communities appear to be predominantly explained by species sorting processes in response to influent wastewater communities.