Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network

Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study

Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.

Transport and transformations of cadmium in water-biofilm-sediment phases as affected by hydrodynamic conditions

Hydrodynamic conditions play a crucial role in governing the fate, transport, and risks of metal elements. However, the contribution of hydrodynamic conditions to the fate and transport of heavy metals among water, sediment, and biofilm phases is poorly understood. In our study, we conducted experiments in controlled hydrodynamic conditions using a total of 6 two-phase and 9 three-phase mesocosms consisting of water, biofilm, and sediment. We also measured Cd (cadmium) specification in different phases to assess how hydrodynamic forces control Cd bioavailability. We found that turbulent flow destroyed the surface morphology of the biofilm and significantly decreased the content of extracellular polymeric substances (p < 0.05). This led to a decrease in the biofilm's adsorption capacity for Cd, with the maximum adsorption capacity (0.124 mg/g) being one-tenth of that under static conditions (1.256 mg/g). The Cd chemical forms in the biofilm and sediment were significantly different, with the highest amount of Cd in the biofilm being acid-exchangeable, accounting for up to 95.1% of the total Cd content. Cd was more easily released in the biofilm due to its weak binding state, while Cd in the sediment existed in more stable chemical forms. Hydrodynamic conditions altered the migration behavior and distribution characteristics of Cd in the system by changing the adsorption capacity of the biofilm and sediment for Cd. Cd mobility increased in laminar flow but decreased in turbulent flow. These results enhance our understanding of the underlying mechanisms that control the mobility and bioavailability of metals in aquatic environments with varying hydrodynamic conditions.

Connecting thiamine availability to the microbial community composition in Chinook salmon spawning habitats of the Sacramento River basin

Thiamine deficiency complex (TDC) is a major emerging threat to global populations of culturally and economically important populations of salmonids. Salmonid eggs and embryos can assimilate exogenous thiamine, and evidence suggests that microbial communities in benthic environments can produce substantial amounts of thiamine. We therefore hypothesize that natural dissolved pools of thiamine exist in the surface water and hyporheic zones of riverine habitats where salmonids with TDC migrate, spawn, and begin their lives. To examine the relationship between dissolved thiamine-related compounds (dTRCs) and their microbial source, we determined the concentrations of these metabolites and the compositions of microbial communities in surface and hyporheic waters of the Sacramento River, California and its tributaries. Here we determine that all dTRCs are present in femto-picomolar concentrations in a range of critically important salmon spawning habitats. We observed that thiamine concentrations in the Sacramento River system are orders of magnitude lower than those of marine waters, indicating substantial differences in thiamine cycling between these two environments. Our data suggest that the hyporheic zone is likely the source of thiamine to the overlying surface water. Temporal variations in dTRC concentrations were observed where the highest concentrations existed when Chinook salmon were actively spawning. Significant correlations were seen between the richness of microbial taxa and dTRC concentrations, particularly in the hyporheic zone, which would influence the conditions where embryonic salmon incubate. Together, these results indicate a connection between microbial communities in freshwater habitats and the availability of thiamine to spawning TDC-impacted California Central Valley Chinook salmon.IMPORTANCEPacific salmon are keystone species with considerable economic importance and immeasurable cultural significance to Pacific Northwest indigenous peoples. Thiamine deficiency complex has recently been diagnosed as an emerging threat to the health and stability of multiple populations of salmonids ranging from California to Alaska. Microbial biosynthesis is the major source of thiamine in marine and aquatic environments. Despite this importance, the concentrations of thiamine and the identities of the microbial communities that cycle it are largely unknown. Here we investigate microbial communities and their relationship to thiamine in Chinook salmon spawning habitats in California's Sacramento River system to gain an understanding of how thiamine availability impacts salmonids suffering from thiamine deficiency complex.

Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge

The spread of bacteria with antibiotic resistance genes (ARGs) in aquatic ecosystems is of growing concern as this can pose a risk of transmission to humans and animals. While the impact of wastewater treatment plant (WWTP) effluent on ARG abundance in surface waters has been studied extensively, less is known about the fate of ARGs in biofilms. The proximity and dense growth of microorganisms in combination with the accumulation of higher antibiotic concentrations in biofilms might render biofilms a reservoir for ARGs. Seasonal parameters such as water temperature, precipitation, and antibiotic concentrations should be considered as well, as they may further influence the fate of ARGs in aquatic ecosystems. Here we investigated the effect of WWTP effluent on the abundance of the sulfonamide resistance genes sul1 and sul2, and the integrase gene intI1 in biofilm and surface water compartments of a river in Germany with a gradient of anthropogenic impact using quantitative PCR. Furthermore, we analyzed the bacterial community structure in both compartments via 16S rRNA gene amplicon sequencing, following the river downstream. Additionally, conventional water parameters and sulfonamide concentrations were measured, and seasonal aspects were considered by comparing the fate of ARGs and bacterial community diversity in the surface water compartment between the summer and winter season. Our results show that biofilm compartments near the WWTP had a higher relative abundance of ARGs (up to 4.7%) than surface waters (<2.8%). Sulfonamide resistance genes were more persistent further downstream (>10 km) of the WWTP in the hot and dry summer season than in winter. This finding is likely a consequence of the higher proportion of wastewater and thus wastewater-derived microorganisms in the river during summer periods. We observed distinct bacterial communities and ARG abundance between the biofilm and surface water compartment, but even greater variations when considering seasonal and spatiotemporal parameters. This underscores the need to consider seasonal aspects when studying the fate of ARGs in aquatic ecosystems.

Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities

The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure-function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function.

Clogging modulates the copper effects on microbial communities of streambed sediments

The hyporheic zone, i.e. the water-saturated sediment beneath and alongside the riverbed, is exposed to multiple stressors. Agricultural-watershed rivers are frequently exposed to two concomitant stressors: clogging and copper contamination. However, one stressor exposure can increase sensitivity to a second stressor. The aim of this study was to experimentally test the cumulative effects of these two stressors on copper distribution and structural and functional microbial communities responses in the hyporheic zone. A slow filtration column experiment was conducted to compare the effects of 3 treatments of increasing complexity: 'Reference', 'Copper-contaminated' (dissolved copper added at 191 µg L^-1), and 'Clogging+Copper' (dissolved copper + addition of 2 cm of fine sediment). Microbial community structure and activities were studied at 4 column sediment depths. The results showed that clogging did not modify the distribution of copper, which remained fixed in the first few centimetres. In the first few centimetres, clogging had a stimulating effect on microbial activities whereas copper had limited effects mainly on leucine aminopeptidase activity and microbial community tolerance to copper. The subsurface zone thus hosts significant different microbial communities from the communities in the deeper zones that were protected from surface stressors. This experiment confirms the valuable filtering role played by the hyporheic zone and shows that microbial responses are strongly correlated to microhabitat-scale physicochemical conditions in sediment.

Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows

Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems.

Enhanced Cd2+ adsorption and toxicity for microbial biofilms in the presence of TiO2 nanoparticles

Titanium dioxide nanoparticles (TiO₂ NPs) easily combine with other pollutants such as heavy metals because of their excellent physiochemical properties. However, how such an interaction may affect the binding behavior of metals onto biofilms remains largely unclear. This study, examined the effects of TiO₂ NPs on Cd²⁺ accumulation and toxicity for natural periphytic biofilms were examined. The adsorption kinetics showed that adding 0.1 and 1 mg/L TiO₂-NPs increased the Cd²⁺ adsorption of biofilms at equilibrium by 23.5% and 35.8%, respectively. However, adding 10 mg/L TiO₂ NPs increased the Cd²⁺ adsorption of biofilms at equilibrium by only 1.9%. The adsorption isotherms indicate that the presence of TiO₂ NPs considerably increased the Cd²⁺ adsorption capacity of the biofilms; however, this effect became less prominent at high TiO₂ NP concentrations. The optimum pH for Cd²⁺ adsorption increased with increasing Cd²⁺ and TiO₂ NP contents. At low concentrations, the coexistence of Cd²⁺ and TiO₂ NPs may facilitate their respective accumulation by stimulating the secretion of extracellular polymeric substances and enhancing the microbial activity of the biofilm. The presence of TiO₂ NPs increases the surface binding energy between Cd²⁺ and functional groups such as carboxyl groups, enhancing the Cd²⁺ accumulation on the biofilm.

Physiological characteristics, geochemical properties and hydrological variables influencing pathogen migration in subsurface system: What we know or not?

The global outbreak of coronavirus infectious disease-2019 (COVID-19) draws attentions in the transport and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in aerosols, wastewater, surface water and solid wastes. As pathogens eventually enter the subsurface system, e.g., soils in the vadose zone and groundwater in the aquifers, they might survive for a prolonged period of time owing to the uniqueness of subsurface environment. In addition, pathogens can transport in groundwater and contaminate surrounding drinking water sources, possessing long-term and concealed risks to human society. This work critically reviews the influential factors of pathogen migration, unravelling the impacts of pathogenic characteristics, vadose zone physiochemical properties and hydrological variables on the migration of typical pathogens in subsurface system. An assessment algorithm and two rating/weighting schemes are proposed to evaluate the migration abilities and risks of pathogens in subsurface environment. As there is still no evidence about the presence and distribution of SARS-CoV-2 in the vadose zones and aquifers, this study also discusses the migration potential and behavior of SARS-CoV-2 viruses in subsurface environment, offering prospective clues and suggestions for its potential risks in drinking water and effective prevention and control from hydrogeological points of view.

Source apportionment and risk assessment of metal pollution in natural biofilms and surface water along the Lancang River, China

Herein, surface water and periphytic biofilm samples were collected from 16 sites along the Lancang River, China, to assess the spatial distribution, enrichment factor (EF), potential ecological risk index (RI), and associated source-oriented health risks of heavy metal elements (As, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) in the samples. Results showed that the levels of heavy metals were significantly lower in the surface water samples than in the biofilm samples (one-way analysis of variance, p < 0.001). Moreover, 37.50 % of the biofilm samples were significantly polluted by these heavy metals with a mean EF of >5. As and V were the highest polluting metals, and the enrichment of Co and Ni were attributed to natural sources. RI assessment results showed a consistent ecological risk of As. Based on principal component analysis with multiple linear regression (PCA-MLR) and positive matrix factorization (PMF) models, the presence of heavy metal ions in the biofilm samples was largely attributed to industrial activities (PCA-MLR: 68.89 %; PMF: 76.39 %), followed by a mixed source of natural and agricultural activities (PCA-MLR: 18.12 %; PMF: 13.56 %), and traffic emissions (PCA-MLR: 12.99 %; PMF: 10.05 %). Both carcinogenic and noncarcinogenic risks for adults were negligible even though adults tended to be exposed to greater risk through ingestion. Source-specific risk evaluations indicated that industrial pollution was the most important source of health risks. Our findings highlight the potential threat of biofilms to the ecological and human health.

Microbial diversity and geochemistry of groundwater impacted by steel slag leachates

To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m³ steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.

High biodiversity and distinct assembly patterns of microbial communities in groundwater compared with surface water

The differences in bacterial community assembly mechanism between surface water and groundwater, as well as the driving factors of environmental factors, are still unknown. Here we aimed to answer these questions by analyzing microbial community samples from surface water and groundwater. We observed a strong connection between microbial communities in surface water and groundwater and several human pathogens are shared between surface water and groundwater; however, the richness and diversity of groundwater microbial communities were greater than those of surface water, regardless of the season. Additionally, bacterial community compositions of surface water and groundwater differed significantly between seasons. Most importantly, the groundwater community exhibited a highly deterministic assembly process (56% contributed by deterministic process, with neutral community model R² = 0.277) compared with surface water (51% contributed by deterministic process, with R² = 0.526). This study provides a deep understanding of the effects of environmental factors on surface water and groundwater microbial communities, to better protect water resources.

Seasonal Variation Imparts the Shift in Endophytic Bacterial Community Between Mango and its Hemiparasites

The study of community composition and community structure is important to know the ecological behaviour and community dynamics of the participating species and to understand the molecular interplay that lies between them. The community diversity greatly lies in the physiological status of the host and the environmental factors. The present study aims to explore the endophytic bacterial communities and their dynamics in the pre-flowering and post-flowering seasons in the horticulturally important Mango (Mangifera indica L.) and its hemiparasites: Loranthus parasiticus (L.) Marr. and Macrosolen colchinchinensis (Lour.) Tiegh. through a metagenomic approach using the sequence of V3 region of 16S rRNA gene. The genera Bacillus, Acinetobacter and Corynebacterium, under the phyla Firmicutes, Proteobacteria and Actinobacteria, respectively, were found to be the most abundant genera present in mango and its hemiparasites. It was found that during the post-flowering season, the twigs and leaves of mango had lesser endophytes than in other seasons while the alpha-diversity indices of the representative genera were the highest in L. parasiticus during the same seasons. However, in M. colchinchinensis, the alpha diversity was also higher in the post-flowering season similar to another hemiparasite plant L. parasiticus. The ecological, taxonomic and complex correlation studies unravelled that the hemiparasites act as the potent reservoirs of endophytic communities throughout the year and during favourable conditions, these bacterial communities disseminate to the mango plant.

Drying and rewetting induce changes in biofilm characteristics and the subsequent release of metal ions

Drying and rewetting can markedly influence the microbial structure and function of river biofilm communities and potentially result in the release of metal ions from biofilms containing metals. However, little information is available on the response of metal-enriched biofilms to drying and rewetting over time. In this study, natural biofilms were allowed to develop in four rotating annular bioreactors for 2-11 weeks, followed by drying for 5 days and rewetting for another 5 days. Subsequently, we assessed Zn, Cd, and As desorption from the biofilms and other related parameters (microbial community structure, biofilm morphology, enzyme activity, and surface components as well as characteristics). High-throughput sequencing of the 16 S rRNA gene and confocal laser scanning microscopy revealed that the biofilm architecture and bacterial communities were distinct in different growth phases and under drying and rewetting conditions (permutational multivariate analysis of variance; p = 0.001). Proteobacteria was the dominant bacterial phylum, accounting for 69.7-90.1% of the total content. Kinetic experiments revealed that the drying and rewetting process increased metal desorption from the biofilm matrix. The desorption of heavy metals was affected by the age of the biofilm, with the maximum amount of metal ions released from 2-week-old biofilms (one-way ANOVA, Zn: p < 0.001; Cd: p = 0.008; As: p < 0.001). The modifications in biofilm properties and decreased diversity of the bacterial community (paired t-test, p < 0.05) after drying and rewetting decreased the number of specific binding sites for metal ions. In addition, negatively charged arsenate and other anions in the liquid phase could compete with As ions for adsorption sites to promote the release of As(V) and/or reductive desorption of As(III). The results of this study and their interpretation are expected to help refine the behaviors of heavy metals in the aquatic environment.

The Coupling Response between Different Bacterial Metabolic Functions in Water and Sediment Improve the Ability to Mitigate Climate Change

Extreme climatic events, such as heat wave and large temperature fluctuations, are predicted to increase in frequency and intensity during the next hundred years, which may rapidly alter the composition and function of lake bacterial communities. Here, we conducted a year-long experiment to explore the effect of warming on bacterial metabolic function of lake water and sediment. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The results indicated that the increase in temperature changed the structure of bacterial metabolic functional groups in water and sediment. During periods of low temperature, the carbon degradation pathway decreased, and the synthesis pathway increased, under the stimulation of warming, especially under the conditions temperature fluctuation. We also observed that nitrogen fixation ability was especially important in the warming treatments during the summer season. However, an elevated temperature significantly led to reduced nitrogen fixation abilities in winter. Compared with the water column, the most predominant functional groups of nitrogen cycle in sediment were nitrite oxidation and nitrification. Variable warming significantly promoted nitrite oxidation and nitrification function in winter, and constant warming was significantly inhibited in spring, with control in sediments. Co-occurrence network results showed that warming, especially variable warming, made microbial co-occurrence networks larger, more connected and less modular, and eventually functional groups in the water column and sediment cooperated to resist warming. We concluded that warming changed bacterial functional potentials important to the biogeochemical cycling in the experimental mesocosms in winter and spring with low temperature. The effect of different bacteria metabolism functions in water column and sediment may change the carbon and nitrogen fluxes in aquatic ecosystems. In conclusion, the coupling response between different bacterial metabolic functions in water and sediment may improve the ability to mitigate climate change.

Top-down and bottom-up cohesiveness in microbial community coalescence

In the microbial world, it is common for previously isolated communities to come in contact with one another. This phenomenon is known as community coalescence. Despite it being a key process in the assembly of microbial communities, little is known about the mechanisms that determine its outcomes. Here we present an experimental system that allowed us to study over 100 coalescence events between previously segregated microbiomes. Our results, predicted by a mathematical model, provide direct evidence of ecological coselection: the situation where members of a community recruit one another during coalescence. Our combined experimental and theoretical framework represents a powerful tool to predict the outcomes and interrogate the mechanisms of community coalescence.

Microbial communities frequently invade one another as a whole, a phenomenon known as community coalescence. Despite its potential importance for the assembly, dynamics, and stability of microbial consortia, as well as its prospective utility for microbiome engineering, our understanding of the processes that govern it is still very limited. Theory has suggested that microbial communities may exhibit cohesiveness in the face of invasions emerging from collective metabolic interactions across microbes and their environment. This cohesiveness may lead to correlated invasional outcomes, where the fate of a given taxon is determined by that of other members of its community—a hypothesis known as ecological coselection. Here, we have performed over 100 invasion and coalescence experiments with microbial communities of various origins assembled in two different synthetic environments. We show that the dominant members of the primary communities can recruit their rarer partners during coalescence (top-down coselection) and also be recruited by them (bottom-up coselection). With the aid of a consumer-resource model, we found that the emergence of top-down or bottom-up cohesiveness is modulated by the structure of the underlying cross-feeding networks that sustain the coalesced communities. The model also predicts that these two forms of ecological coselection cannot co-occur under our conditions, and we have experimentally confirmed that one can be strong only when the other is weak. Our results provide direct evidence that collective invasions can be expected to produce ecological coselection as a result of cross-feeding interactions at the community level.

Microbial biofilm community dynamics in five lowland streams

Stream biofilms are complex aggregates of diverse organism groups that play a vital role in global carbon and nitrogen cycles. Most of the current studies on stream biofilm focus on a limited number of organism groups (e.g., bacteria and algae), and few have included both prokaryote and eukaryote communities simultaneously. In this study, we incubated artificial substrates in five Danish lowland streams exhibiting different hydrological and physico-chemical conditions and explored the dynamics of community composition and diversity of the benthic biofilm, including both prokaryotes and eukaryotes. We found that few phyla in the prokaryote (Gammaproteobacteria and Bacteroidetes) and eukaryote (Cercozoa) communities accounted for over two-thirds of the total abundance at most of the sites. Both prokaryotic and eukaryotic diversity displayed the same temporal patterns, i.e., diversity peaked in July and January. We also found that hydrological and physico-chemical variables significantly explained the variation in the community composition at phylum level for both prokaryotes and eukaryotes. However, a large proportion of variation remained unexplained, which can be ascribed to important but unmeasured variables like light intensity and biological factors such as trophic and non-trophic interactions as revealed by network analysis. Therefore, we suggest that use of a multitrophic level perspective is needed to study biofilm i.e., the "microbial jungles", where high occurrences of trophic and non-trophic interactions are expected.

The role of competition versus cooperation in microbial community coalescence

New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed "community coalescence". Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because of their superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities.

Human Fecal Contamination Corresponds to Changes in the Freshwater Bacterial Communities of a Large River Basin

Microbial water quality is generally monitored by culturable fecal indicator bacteria (FIB), which are intended to signal human health risk due to fecal pollution. However, FIB have limited utility in most urbanized watersheds as they do not discriminate among fecal pollution sources, tend to make up a small fraction of the total microbial community, and do not inform on pollution impacts on the native ecosystem. To move beyond these limitations, we assessed entire bacterial communities and investigated how bacterial diversity relates to traditional ecological and human health-relevant water quality indicators throughout the Milwaukee River Basin. Samples were collected from 16 sites on 5 days during the summer, including both wet and dry weather events, and were processed by 16S rRNA gene amplicon sequencing. Historical water quality at each sampling location, as opposed to upstream land use, was associated significantly with bacterial community alpha diversity. Source partitioning the sequence data was important for determining water quality relationships. Sewage-associated bacterial sequences were detected in all samples, and the relative abundance of sewage sequences was strongly associated with the human Bacteroides fecal marker. From this relationship, we developed a preliminary threshold for human sewage pollution when using bacterial community sequence data. Certain abundant freshwater bacterial sequences were also associated with human fecal pollution, suggesting their possible utility in water quality monitoring. This study sheds light on how bacterial community analysis can be used to supplement current water quality monitoring techniques to better understand interactions between ecological water quality and human health indicators. IMPORTANCE Surface waters in highly developed mixed-use watersheds are frequently impacted by a wide variety of pollutants, leading to a range of impairments that must be monitored and remediated. With advancing technologies, microbial community sequencing may soon become a feasible method for routine evaluation of the ecological quality and human health risk of a water body. In this study, we partnered with a local citizen science organization to evaluate the utility of microbial community sequencing for identifying pollution sources and ecological impairments in a large mixed-use watershed. We show that changes in microbial community diversity and composition are indicative of both long-term ecological impairments and short-term fecal pollution impacts. By source partitioning the sequence data, we also estimate a threshold target for human sewage pollution, which may be useful as a starting point for future development of sequencing-based water quality monitoring techniques.

Transformations from specialists to generalists cause bacterial communities are more stable than micro-eukaryotic communities under anthropogenic activity disturbance

Different microbial components have different responses to environmental disturbances. Here, we found that the planktonic bacterial and micro-eukaryotic communities had different responses to anthropogenic activity disturbance in a subtropical river, because they had different survival strategies (generalist and specialist). We used nutrients (nitrogen and phosphorus) as indicators of anthropogenic activities. We found that river stretch 1 showed low nutrient concentrations from October 2018 to September 2019. However, a nutrient disturbance was observed in river stretch 2. The nutrient concentrations increased largely in December and January but recovered to low values in June. Bacterial communities had higher resilience under this disturbance than micro-eukaryotic communities in river stretch 2. The bacterial community composition were quite different between the two river stretches in December and January but were similar in June and July. However, the differences of micro-eukaryotic community composition between the two river stretches were always high during the study period. The bacterial communities in river stretch 2 contained more generalists and nutrient tolerant specialists. The bacterial nutrient tolerant specialists rapidly decreased in the low nutrient months and were replaced by the generalists. Bacteria which were involved in this shifts accounted for 29.3% of the total abundance. However, the micro-eukaryotic communities in river stretch 2 contained more moderate generalists. These moderate generalists were insensitive to the variation of nutrients and only 19.56% of the micro-eukaryotes had significant responses to the disturbance. The survival strategies caused bacterial communities had higher adaptability than eukaryotes to environmental fluctuation.

Application of nanofiber carriers for sampling of microbial biomass from contaminated groundwater

Sampling of microbial biomass is crucial for understanding and controlling remediation processes ongoing at contaminated sites in general, particularly when molecular genetic analyses are employed. In this study, fiber-based carriers with a nanofiber layer were developed and tested as a method to sample microbial biomass in groundwater for molecular genetic analysis. Nanofiber carriers, varying in the shape and the linear density of nanofibers, were examined throughout a 27-month monitoring period in groundwater contaminated with benzene, toluene, ethylbenzene and xylene isomers (BTEX), and chlorinated ethenes. The effect of carrier shape and nanofiber layer density on the microbial surface colonization and composition of the microbial biofilm was determined using real-time PCR and next-generation sequencing (NGS) analysis. Differences in microbial community composition between nanofiber carriers, groundwater, and soil samples were also analyzed to assess the applicability of carriers for biomass sampling at contaminated sites. The nanofiber carriers showed their applicability as a sampling tool, particularly because of their easy manipulation that facilitates DNA isolation. The majority of taxa (Proteobacteria, Firmicutes, and Bacteroidetes) present on the carrier surfaces were also detected in the groundwater. Moreover, the microbial community on all nanofiber carriers reflected the changes in the chemical composition of groundwater. Although the carrier characteristics (shape, nanofiber layer) did not substantially influence the microbial community on the carrier surface, the circular and planar carriers with a nanofiber layer displayed faster microbial surface colonization. However, the circular carrier was the most suitable for biomass sampling in groundwater because of its high contact area and because it does not require pre-treatment prior to DNA extraction.

Soil rehabilitation shaped different patterns of bacterial and archaeal community in AMD-irrigated paddy soil

Microorganisms are essential for soil rehabilitation and long-term sustainability of established plants. However, the recovery process of microorganisms in AMD-irrigated paddy soil is poorly understood at present. To verify this, we sampled AMD-irrigated paddy soils before at different rehabilitation stages by characterizing bacteria and archaea community from a chronosequence of AMD-irrigated rehabilitation to pre-disturbance levels from references sites. Next-generation sequencing is used to describe shifts in diversity and taxonomic composition of bacterial and archaeal. Co-occurrence networks are constructed to reveal potential microbial interaction patterns. The result showed bacterial community followed an observable taxonomic transition overtimes, with community structure becoming more similar to that of unmined reference sites. But the archaeal community only showed a seasonal change, which may hint that the archaeal community needs more time in rehabilitation. Both bacterial and archaeal community composition changes were apparent at high taxonomic levels, bacterial communities become dominated by Proteobacteria phylum, and archaeal community was dominated by Crenarchaeota, we proposed the possible reason is bacterial community were mainly derived by soil pH while the archaeal community was impacted by heavy metal. The bacterial co-occurrence networks increased in complexity during succession, improving the community's resistance to environmental disturbance, while the archaeal did not change monotonically with time. This study highlights the distinct recovery pattern of the bacterial and archaeal community during AMD-irrigated paddy soil rehabilitation, which provides a deep understanding of their role in paddy soil, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.