Hyporheic microbial community development is a sensitive indicator of metal contamination

Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China

The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.

A new quantitative insight: Interaction of polyethylene microplastics with soil - microbiome - crop

In this study, the interaction between primary/secondary PE MPs and soil - microbiome - crop complex system and PE MPs enrichment behavior in crops were studied by using the self-developed quantitative characterization method of Eu-MPs and in situ zymography. The results demonstrated for the first time the enrichment effect of micron-sized PE (> 10 µm) in crops, manifested as roots>leaves>stems. Primary PE MPs significantly increased soil TN, TC, SOM and β-glu activity and inhibited Phos activity. Age-PE MPs significantly reduced soil TN, TP, β-glu and Phos activities and also have significant inhibitory effects on plant height, stem diameter, and leaf dry weight of maize. Age-PE MPs significantly affected soil microbial diversity, mainly caused by bacterial genera such as UTCFX1, Sphingomonas, Subgroup-6 and Gemmatimonas. Age-PE MPs also affected some metabolism related to microbial community composition and maize growth, including Glycerolipid, Citrate cycle (TCA cycle), C5-Branched dibasic acid, Arginine and proline, Tyrosine metabolism, pentose phosphate pathway, Valine, leucine and isoleucine biosynthesis. These research results indicated that the PE MPs, which are widely present in farmland soils, can affect crop growth, soil microbial community and metabolic function after aging, thus affecting agroecosystems and terrestrial biodiversity.

Microbial community composition and degradation potential of petroleum-contaminated sites under heavy metal stress

Total petroleum hydrocarbons (n-alkanes), semi-volatile organic compounds, and heavy metals pose major ecological risks at petrochemical-contaminated sites. The efficiency of natural remediation in situ is often unsatisfactory, particularly under heavy metal pollution stress. This study aimed to verify the hypothesis that after long-term contamination and restoration, microbial communities in situ exhibit significantly different biodegradation efficiencies under different concentrations of heavy metals. Moreover, they determine the appropriate microbial community to restore the contaminated soil. Therefore, we investigated the heavy metals in petroleum-contaminated soils and observed that heavy metals effects on distinct ecological clusters varied significantly. Finally, alterations in the native microbial community degradation ability were demonstrated through the occurrence of petroleum pollutant degradation function genes in different communities at the tested sites. Furthermore, structural equation modeling (SEM) was used to explain the influence of all factors on the degradation function of petroleum pollution. These results suggest that heavy metal contamination from petroleum-contaminated sites reduces the efficiency of natural remediation. In addition, it infers that MOD1 microorganisms have greater degradation potential under heavy metal stress. Utilizing appropriate microorganisms in situ may effectively help resist the stress of heavy metals and continuously degrade petroleum pollutants.

Time-dependent effects of microplastics on soil bacteriome

Microplastic threats to biodiversity, health and ecological safety are adding to concern worldwide, but the real impacts on the functioning of organisms and ecosystems are obscure owing to their inert characteristics. Here we investigated the long-lasting ecological effects of six prevalent microplastic types: polyethylene (PE), polypropylene (PP), polyamide (PA), polystyrene (PS), polyethylene terephthalate (PET), and polyvinyl chloride (PVC) on soil bacteria at a 2 % (w/w) level. Due to the inertia and lack of available nitrogen of these microplastics, their effects on bacteriome tended to converge after one year and were strongly different from their short-term effects. The soil volumes around microplastics were very specific, in which the microplastic-adapted bacteria (e.g., some genera in Actinobacteria) were enriched but the phyla Bacteroidetes and Gemmatimonadetes declined, resulting in higher microbial nitrogen requirements and reduced organic carbon mineralization. The reshaped bacteriome was specialized in the genetic potential of xenobiotic and lipid metabolism as well as related oxidation, esterification, and hydrolysis processes, but excessive oxidative damage resulted in severe weakness in community genetic information processing. According to model predictions, microplastic effects are indirectly derived from nutrients and oxidative stress, and the effects on bacterial functions are stronger than on structure, posing a heavy risk to soil ecosystems.

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.

Effects of heavy metals stress on chicken manures composting via the perspective of microbial community feedback

Heavy metal pollution was the main risk during livestock manures composting, in which microorganisms played a vital role. However, response strategies of microbial community to heavy metals stress (HMS) remained largely unclear. Therefore, the objective of this study was to reveal the ecological adaptation and counter-effect of bacterial community under HMS during chicken manures composting, and evaluating environmental implications of HMS on composting. The degradation of organic matters (more than 6.4%) and carbohydrate (more than 19.8%) were enhanced under intense HMS, suggesting that microorganisms could quickly adapt to the HMS to ensure smooth composting. Meanwhile, HMS increased keystone nodes and strengthened significant positive correlation relationships between genera (p < 0.05), indicating that bacteria resisted HMS through cooperating during composting. In addition, different bacterial groups performed various functions to cope with HMS. Specific bacterial groups responded to HMS, and certain groups regulated bacterial networks. Therefore, bacterial community had the extraordinary potential to deal with HMS and guarantee chicken manures composting even in the presence of high concentrations of heavy metals.

Alkaline mine drainage drives stream sediment microbial community structure and function

With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and functional responses of microbial communities in different environmental compartments are not well understood. We investigated sediment microbiomes in mining impacted streams to determine how community composition and function respond to mining and to look for potential microbial bioindicators. Using 16s rRNA gene amplicon sequencing, we found that mining leads to shifts in microbial community structure, with the phylum Planctomycetes enriched by 1-6% at mined sites. We observed ~51% increase in species richness in bulk sediments. In contrast, of the 31 predicted metabolic pathways that changed significantly with mining, 23 responded negatively. Mining explained 15-18% of the variance in community structure and S, Se, %C and %N were the main drivers of community and functional pathway composition. We identified 12 microbial indicators prevalent in the ecosystem and sensitive to mining. Overall, alkaline mountaintop mining drainage causes a restructuration of the sediment microbiome, and our study identified promising microbial indicators for the long-term monitoring of these impacted streams.

Selective pressures of heavy metals on microbial community determine microbial functional roles during composting: Sensitive, resistant and actor

Heavy metals (HM) pollution exerts an effect on microbial community composition and structure during composting, the way how microbial community responses to HM pressure is remain poorly understood though. The aim of this study was to explore functional roles of microorganisms based on selective pressures of HM (Cu, Zn and Cd). The results of microbial resistance showed that the toxicity of metals to microorganisms were Cu > Zn > Cd during composting. Cu and Zn were more toxic for microorganisms during composting when compared with Cd. However, microorganisms had a longer lag period to grow under Zn stress through microbial tolerance determination. In addition, the microbial catalase activity generally decreased and protease activity generally increased, thus microorganisms became more adaptable to HM stress during composting. The experimental results confirmed the existence of sensitive, resistant and actor microorganisms during beef cattle and chicken manures composting. Ultimately, the resistant, sensitive and actor microorganisms at genus level were distinguished under HM pressure based on the network analysis and structural equation models, including 85 resistant microorganisms, 5 sensitive microorganisms and 6 actor microorganisms. This would be helpful to understand the microbial succession process under HM stress and identify functional strains of HM remediation.

Deciphering the toxic effects of metals in gold mining area: Microbial community tolerance mechanism and change of antibiotic resistance genes

Mine tailing dumps represent significant threats to ecological environments due to the presence of toxic substances. The present work investigated the relationship among microbial activity, the community, antibiotic resistance genes (ARGs) and trace metals in soil surrounding gold mine tailings. Using microbial metabolic activity and high-throughput sequencing analysis, we found the trace metals Cd and Hg could be main factors influencing the microbial community. According to bacterial co-occurrence pattern analysis, the effects of total cadmium and total mercury on bacterial diversity are potentially mediated by influencing bacteria community in the keystone module II. Additionally, most of metal-resistant bacteria belong to Actinobacteria and Proteobacteria, and the metal tolerance suggested to be linked with various functions including replication, recombination and repair, as well as inorganic ion transport and metabolism based on PICRUSt2 analysis. We also found that metals generated by mining activity may trigger the co-selection of antibiotic resistance in the phyla Actinobacteria and Proteobacteria due to co-resistance or cross resistance. Additionally, PLS-PM analysis revealed that metals could indirectly affect ARGs by influencing bacterial diversity in gold mining areas.

Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa

Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

Integrating high-throughput sequencing and metagenome analysis to reveal the characteristic and resistance mechanism of microbial community in metal contaminated sediments

Some metallic tailings from closed mines were scattered in upstream of the Miyun Reservoir, Beijing, threatening the ecological environment of rivers due to trace metals. The Liuli River, one of the main rivers affected, was investigated as a typical model in this work. In this study, we selected eight sites to assess interactions among the various geochemical factors especially between trace metals and sediment microbiota. Random forest predicted that low concentrations of Cu, Cd, Cr and Ni (lower than 61.8 mg/kg, 3.2 mg/kg, 173.2 mg/kg and 34.1 mg/kg, respectively) were able to enhance community diversity but generally, trace metals contamination impaired microbial diversity. Environmental factor correlation analysis showed that As, pH and available P were the major factors that shifted the distribution of the microbial communities. Metagenome sequencing revealed that Proteobacteria harbored the vast majority of heavy metal resistance genes followed by Actinobacteria and Bacteroidetes. Metal tolerance of Proteobacteria were achieved by exportation of metals by the corresponding transporters, by pumps and ion channels, or by their reduction via redox reactions. In addition, Proteobacteria harbored a greater ability to repair DNA damage via DNA recombination.

Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments

Benthic Archaea play a crucial role in the biogeochemical cycles and food webs, however, their spatiotemporal distribution and environmental drivers are not well investigated in brackish sediments. The composition and abundances of benthic archaeal communities were examined from a coastal lagoon; Chilika (India) which is experiencing an intense pressure from anthropogenic and natural factors. High-throughput sequencing of 16S rRNA genes revealed that sediment (n = 96) archaeal communities were largely composed of Crenarchaeota (18.76%), Euryarchaeota (18.34%), Thaumarchaeota (13.45%), Woesearchaeota (10.05%), and Pacearchaeota (4.21%). Archaeal taxa affiliated to methanogens, sulfate-reducers, and ammonia-oxidizers were detected suggesting that carbon, sulfur, and nitrogen cycles might be prominent in benthic sediments. Salinity, total organic carbon, available nitrogen, available phosphorus, macrophyte (Phragmites karka) and inter-taxa relationships between community members and with bacterial communities played steering roles in structuring the archaeal communities. Marine sites with mesohaline-polyhaline regime were dominated by Nitrosopumilus and Thaumarchaeota. In contrast, riverine sites with oligohaline regime demonstrated a higher abundance of Thermoprotei. Macrophyte dominated zones were enriched in Methanomicrobia and Methanobacteria in their rhizosphere sediments, whereas, bulk (un-vegetated) sediments were dominated by Nitrosopumilus. Spatial patterns in archaeal communities demonstrated 'distance-decay' patterns which were correlated with changes in physicochemical factors over geographical distances. Heterotrophic microbial communities showed much higher metabolic diversity and activity in their carbon utilization profiles in rhizosphere sediments than the bulk sediments. This baseline information on benthic archaea and their environmental drivers would be useful to assess the impact of anthropogenic and natural pressures on these communities and associated biogeochemical cycles.

Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.

Hyporheic Interactions Increase Zinc Exposure and Effects on Hyalella azteca in Sediments under Flow-Through Conditions

Groundwater-surface water interactions in the hyporheic transition zone can influence contaminant exposure to benthic macroinvertebrates. In streams, hyporheic flows are subject to varying redox conditions, which influence biogeochemical cycling and metal speciation. Despite these relationships, little is known about how these interactions influence the ecological risk of contaminants. The present study investigated the effects of hyporheic flows and zinc (Zn)-contaminated sediments on the amphipod Hyalella azteca. Hyporheic flows were manipulated in laboratory streams during 10-d experiments. Zinc toxicity was evaluated in freshly spiked and aged sediments. Hyporheic flows altered sediment and porewater geochemistry, oxidizing the sediments and causing changes to redox-sensitive endpoints. Amphipod survival was lowest in the Zn sediment exposures with hyporheic flows. In freshly spiked sediments, porewater Zn drove mortality, whereas in aged sediments simultaneously extracted metals (SEM) in excess of acid volatile sulfides (AVS) normalized by the fraction of organic carbon (fOC) [(SEM-AVS)/fOC] influenced amphipod responses. The results highlight the important role of hyporheic flows in determining Zn bioavailability to benthic organisms, information that can be important in ecological risk assessments. Environ Toxicol Chem 2019;38:2447-2458. © 2019 SETAC.

An ecological response index for simultaneous prediction of eutrophication and metal pollution in large rivers

The ecological responses of riverine ecosystems are strongly influenced by anthropogenic perturbations. However, high-resolution quantitative shifts in the 'ecosystem responses' to multiple human pressures in riverine ecosystems are not well understood. Given that, in most of the anthropogenically impacted rivers, eutrophy and metal pollution occur simultaneously, we explored FDAase activity, microbial quotient, and a sum of six heavy metals in an empirical relationship to develop an 'ecological response index' (ERI). The FDAase, a measure of fluorescein diacetate hydrolytic activity, and microbial quotient, the proportion of microbial biomass-C to the total organic carbon (C_mic/TOC) were used to address 'ecosystem responses' to C-eutrophy and metal pollution. We analyzed 1404 water samples and 2808 sediment samples collected from the land-water interface (LWI) and riverbed sediment (50 m reach) of 24 sites along a 528 km main stem and from 30 sites downstream two point sources of the Ganga River. The index was compare to Carlson's trophic state index (TSI) to quantify eutrophy and Håkanson's risk index (RI) and modified ecological risk index (MRI) for metal pollution. The ERI showed strong correlation with TSI (R² = 0.70-0.97; p < 0.001), RI (R² = 0.76-0.94; p < 0.001) and MRI (R² = 0.76-0.96; p < 0.001). The ERI developed here is the first 'response index' against multiple human pressures, able to quantitatively predict C-eutrophication and metal pollution simultaneously in large rivers.

Bacterial community composition and function shift with the aggravation of water quality in a heavily polluted river

Blackening and odorization of heavily polluted rivers has become a vital aquatic environmental problem in developing countries and has threatened river ecosystems. Monitoring the contamination and functional degradation conditions is important for bioremediation of river ecosystems. In this study, the diversity, composition, co-occurrence pattern, and function of bacterial communities collected from a heavily polluted urban river sediment were investigated using 16S rRNA amplicon sequencing analysis. The degree of pollution in the river was divided into three levels, and the clustering result based on the relative abundance of bacterial communities was consistent with the pollution levels in the river. The community assembly analysis further demonstrated that bacterial community assembly was mainly driven by environmental selection (95.84%) in Jinchuan River. Composition of bacterial communities were clearly different at different pollution level sites, although no apparent changes in alpha diversity were observed. The complexity of the bacterial co-occurrence network decreased with aggravation of the pollution level, as indicated by topological features, suggesting that the interactions among bacterial communities were weakened. A phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis predicted that the relative abundance of functional genes was negatively correlated with pollution levels, and those related to energy metabolism as well as xenobiotic biodegradation and metabolism decreased significantly. These results provide an ecological reference for monitoring and bioremediation of aquatic ecosystems.

Variation in microbial community structure in surface seawater from Pearl River Delta: Discerning the influencing factors

Contamination of perfluoroalkyl acids (PFAAs) is ubiquitously detected in various environments. However, their potential effects on microbial communities remain largely unknown. In this study, surface seawater of the Pearl River Delta (PRD) is sampled to measure PFAA concentrations and profile the structure of free-living microbial community. Total PFAAs concentrations range from 131 to 1563 pg L^-1 in surface seawater. PFOS (16-470 pg L^-1), PFOA (27-272 pg L^-1), PFHpA (18-201 pg L^-1) and PFBA (25-152 pg L^-1) are the major homologues, indicating continued industrial application or release of PFOS and a gradual shift towards using shorter-chain PFAAs. Concentrations of PFAAs from this recent cruise are much lower than previous reports, which may be due to the effective management of PFAA usage around PRD region. In addition, the microbial community in PRD surface seawater is predominantly colonized by the Proteobacteria phylum (27.2 to 61.5%) and the Synechococcus genus (5.6 to 38.6%). The structure of the microbial communities varies among stations, mainly resulting from different abundances of Synechococcus, Prochlorococcus and Nitrosopumilus. Geochemical parameters (e.g., nutrients and salinity) and phytoplankton are significantly associated with the microbial community dynamics in surface seawater. In the interactive network of microbiota, a subset of bacteria (i.e., Fluviicola, Nitrosopumilus, Limnohabitans, Sediminibacterium, C39 and Polynucleobacter) shows significantly positive correlations with PFAAs (R > 0.6; P < 0.001). Overall, this study gives a timely monitoring of PFAA pollution around PRD area. Shift in environmental microbiota by geochemical factors and phytoplankton is also observed, which may affect biogeochemical cycling.

Statistical determination of crucial taxa indicative of pollution gradients in sediments of Lake Taihu, China

In order to accurately monitor the changes in a freshwater ecosystem in response to anthropogenic stressors, microbe-environment correlations and microbe-microbe interactions were combined to determine crucial indicator taxa in contaminated sediments. The diversity, composition, and co-occurrence pattern of bacterial communities in 23 sediment samples collected from Lake Taihu were explored using 16S rRNA amplicon sequencing analysis. Fisher's exact test showed that the cluster analyses of samples could show a direct correlation between the relative abundance of bacterial communities and the physicochemical properties of the sediment (P < 0.0001), suggesting that bacterial communities can be used to monitor contamination gradients in freshwater sediments. According to the microbe-environment correlation, 24 orders and 60 families were initially identified via indicator species analysis as indicator taxa of different pollution levels. The co-occurrence network further showed that topological features of bacterial communities were clearly different at different pollution levels, although the diversity and composition of bacterial communities displayed similarities between minimally and moderately polluted sites. Indicator taxa were then screened for keystone species, which co-occurrence relationships showed the high degree and low betweenness centrality values (i.e. degree >5, betweenness centrality <1000) of the network. Nine orders and 13 families were finally extracted as crucial indicator taxa of the different pollution levels in eutrophic Lake Taihu. Obtaining crucial indicator taxa from environmental sequences allows to trace increasing levels of pollution in aquatic ecosystems and provides a novel mean to monitor watersheds sensitive to anthropic influences.

Contamination by perfluoroalkyl substances and microbial community structure in Pearl River Delta sediments

Environmental microbiota play essential roles in the maintenance of many biogeochemical processes, including nutrient cycling and pollutant degradation. They are also highly susceptible to changes in environmental stressors, with environmental pollutants being key disruptors of microbial dynamics. In the present study, a scientific cruise was launched on July 2017 around Pearl River Delta, a suitable studying site for perfluoroalkyl substances (PFASs) in the wake of the severe PFAS pollution. Surface sediment samples were collected from 18 representative stations to assess PFAS accumulation and profile microbial community. PFAS concentrations ranged from 24.2 to 181.4 pg/g dry weight in sediment, and perfluorooctanesulfonic acid (PFOS) was the dominant homologue. The concentrations of PFAS homologues in the current study were much lower than those reported in previous studies, implying effective management and control of pollution from PFAS-related industries. 16S rRNA gene amplicon sequencing revealed that Proteobacteria was the dominant phylum, while nitrogen-metabolizing Nitrosopumilus and sulfate-reducing Desulfococcus genera were the most abundant. Variations in microbial communities among sampling stations were mainly due to the differences in abundances of Escherichia, Nitrosopumilus, and Desulfococcus. The outbreak of Escherichia bacteria at specific coastal stations potentially indicated the discharge of fecal matter into the marine environment. Dissolved oxygen (DO) in bottom seawater significantly influenced the structure of microbial communities in the sediment, while current study failed to observe significant effects from PFAS pollutants. Positive correlations were found between DO and sulfate-reducing bacteria in Desulfococcus and GOUTA19 genera. Overall, this study explored relationships between environmental variables (e.g., PFAS pollutants) and sediment bacteria. Biogeochemical parameters significantly influenced the structure and composition of microbial communities in sediment.

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities

In lotic ecosystems highly susceptible to anthropogenic activities, the influences of environmental variables on microbial communities and their functions remain poorly understood, despite our rapidly increasing sequencing ability. In this study, we profiled the microbial communities in the hyporheic sediments of a watershed undergoing intensive anthropogenic activities via next-generation sequencing of 16S rRNA V4-V5 hypervariable regions on Illumina MiSeq platform. Tidal impacts on microbial communities were investigated via co-occurrence networks. In addition, the influences of physicochemical variables including salinity, and the concentrations of nutrients, organic matter and heavy metals on the microbial communities were explored via canonical correspondence analyses. The sediment samples were collected from 19 sites covering the whole main river stem of the target watershed (n = 19; Maozhou river watershed, Shenzhen, China). The samples were sub-divided in the field for microbiological analyses and measurements of physicochemical variables. The results indicated that core microbiome was associated with archaea methanogens and bacteria members from Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Synergistetes and Firmicutes, among which, gram-negative and anaerobic bacteria genera contributing to the cycling of carbon, nitrogen and sulfur were predominant. Site-specific microbiomes were revealed that may serve as indicators of local environmental conditions (e.g., members affiliated to Oceanospirillales were abundant at sites with salt intrusion). Distinct microbial co-occurrence networks were identified for non-tidal, inter-tidal and tidal sites. Major environmental factors influencing microbial community composition included the concentrations of nitrate and bicarbonate in river water, pore water concentrations of sulfate, dissolved organic carbon and electrical conductivity, as well as manganese concentrations associated with the solid sediment. Collectively, the results of this study provide fundamental insights into the influence of environmental perturbations on microbial community composition in a lotic system, which may aid in the design of effective remediation and/or restoration strategies in the target watershed and beyond.

Do soil bacterial communities respond differently to abrupt or gradual additions of copper?

Many experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.

Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi

Metagenomic analyses of microbial communities from aquatic sediments are relatively few, and there are no reported metagenomic studies on sediment from inland ponds used for aquaculture. Catfish ponds in the southeastern U.S. are eutrophic systems. They are fertilized to enhance algae growth and encourage natural food production, and catfish are fed with commercial feed from spring to fall. As result, catfish pond sediment (CPS) contains a very dense, diverse microbial community that has significant effects on the physiochemical parameters of pond dynamics. Here we conducted an in-depth metagenomic analysis of the taxonomic and metabolic capabilities of a catfish pond sediment microbiome from a southeastern U.S. aquaculture farm in Mississippi using Illumina next-generation sequencing. A total of 3.3 Gbp of sequence was obtained, 25,491,518 of which encoded predicted protein features. The pond sediment was dominated by Proteobacteria sequences, followed by Bacteroidetes, Firmicutes, Chloroflexi, and Actinobacteria. Enzyme pathways for methane metabolism/methanogenesis, denitrification, and sulfate reduction appeared nearly complete in the pond sediment metagenome profile. In particular, a large number of Deltaproteobacteria sequences and genes encoding anaerobic functional enzymes were found. This is the first study to characterize a catfish pond sediment microbiome, and it is expected to be useful for characterizing specific changes in microbial flora in response to production practices. It will also provide insight into the taxonomic diversity and metabolic capabilities of microbial communities in aquaculture. Furthermore, comparison with other environments (i.e., river and marine sediments) will reveal habitat-specific characteristics and adaptations caused by differences in nutrients, vegetation, and environmental stresses.

Anthropogenic Activities Induce Depletion in Microbial Communities at Urban Sites of the River Ganges

The Ganges is the largest river of India, worshiped by Hindus with a belief that bathing in the river causes the remission of sins and is considered very pure. It is heavily polluted by the unrestricted human usage including ritual practices, urbanization, and industrialization. Such perturbations may subsequently influence the bacterial community composition and ecosystem functioning. Here, we applied targeted amplicon sequencing to determine the impact of spatial variation on the microbial community assemblage of the Ganga River. The river bacterial community demonstrates taxonomic variability across the sites with accumulation of Firmicutes (20.9%) Verrucomicrobia (6.09%), Actinobacteria (4.51%), and Synergistetes (1.16%), at rural site while Proteobacteria (49.4%) and Bacteroidetes (12.7%) predominate at urban sites. Furthermore, sites under study establish the unique taxonomic signature which could represent the impact of spatial variation on the microbial community assemblage.

Environmental DNA metabarcoding reveals primary chemical contaminants in freshwater sediments from different land-use types

Land-use intensification threatens freshwater biodiversity. Freshwater eukaryotic communities are affected by multiple chemical contaminants with a land-use specific manner. However, biodiversities of eukaryotes and their associations with multiple chemical contaminants are largely unknown. This study characterized in situ eukaryotic communities in sediments exposed to mixtures of chemical contaminants and assessed relationships between various environmental variables and eukaryotic communities in sediments from the Nanfei River. Eukaryotic communities in the sediment samples were dominated by Annelida, Arthropoda, Rotifera, Ochrophyta, Chlorophyta and Ciliophora. Alpha-diversities (Shannon entropy) and structures of eukaryotic communities were significantly different between land-use types. According to the results of multiple statistical tests (PCoA, distLM, Mantel and network analysis), dissimilarity of eukaryotic community structures revealed the key effects of pyrethroid insecticides, manganese, zinc, lead, chromium and polycyclic aromatic hydrocarbons (PAHs) on eukaryotic communities in the sediment samples from the Nanfei River. Furthermore, taxa associated with land-use types were identified and several sensitive eukaryotic taxa to some of the primary contaminants were identified as potential indicators to monitor effects of the primary chemical contaminants. Overall, environmental DNA metabarcoding on in situ eukaryotic communities provided a powerful tool for biomonitoring and identifying primary contaminants and their complex effects on benthic eukaryotic communities in freshwater sediments.

Microbial communities in riparian soils of a settling pond for mine drainage treatment

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage.

Using in situ bacterial communities to monitor contaminants in river sediments

Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments.

Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams

Microbial community composition and diversity change along chemical gradients, leading to the expectation that microbial community information might provide new gradient characterizations. Here we examine stream bacteria composition and diversity along a strong chemical gradient in Central Appalachian streams. Coal mining in the region generates alkaline mine drainage (AlkMD), causing dramatic increases in conductivity, alkalinity, sulfate and metals sufficient to degrade stream macrobiota communities throughout the ecoregion. In this study, we examined the relationship between water and biofilm chemistry and biofilm bacteria taxonomic composition in streams where active and reclaimed surface coal mines occupied 0-96% of watershed surface area. We incubated wood veneers in each stream site for 4 months to develop biofilms on similar substrates. We sampled water chemistry at the time of deployment and collection, and after 1 month. Following incubation, we collected biofilms for microbial and chemical characterization. Microbial composition was determined by pyrosequencing 16S rRNA amplicons. Biofilm subsamples were analyzed by inductively coupled plasma mass spectrometry to determine metal concentrations. Our results show that microbial community composition differed significantly between AlkMD-exposed and AlkMD-unexposed sites, and that compositional dissimilarity increased with AlkMD loading. Diversity was not correlated with pH or extent of upstream mining, but instead correlated with biofilm concentrations of Cd, Mn, Zn and Ni. Within mined sites, the extent of upstream mining was negatively correlated with taxonomic richness. Despite major compositional shifts, functional capacity predicted with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) correlated with mining in only 3 of 43 level-2 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology groups.

Human and environmental impacts on river sediment microbial communities

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (∼ 65,000 microbial 'species' identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.

Vertical distribution of ammonia-oxidizing archaea (AOA) in the hyporheic zone of a eutrophic river in North China

Nitrification plays a significant role in the global nitrogen cycle, and this concept has been challenged with the discovery of ammonia-oxidizing archaea (AOA) in the environment. In this paper, the vertical variations of the diversity and abundance of AOA in the hyporheic zone of the Fuyang River in North China were investigated by molecular techniques, including clone libraries, phylogenetic analysis and real-time polymerase chain reaction. The archaeal amoA gene was detected in all sediments along the profile, and all AOA fell within marine group 1.1a and soil group1.1b of the Thaumarchaeota phylum, with the latter being the dominant type. The diversity of AOA decreased with the sediment depth, and there was a shift in AOA community between top-sediments (0-5 cm) and sub-sediments (5-70 cm). The abundance of the archaeal amoA gene (1.48 × 10⁷ to 5.50 × 10⁷ copies g⁻¹ dry sediment) was higher than that of the bacterial amoA gene (4.01 × 10⁴ to 1.75 × 10⁵ copies g⁻¹ dry sediment) in sub-sediments, resulting in a log₁₀ ratio of AOA to ammonia-oxidizing bacteria (AOB) from 2.27 to 2.69, whereas AOB outnumbered AOA in top-sediments with a low log10 ratio of (-0.24). The variations in the AOA community were primarily attributed to the combined effect of the nutrients (ammonium-N, nitrate-N and total organic carbon) and oxygen in sediments. Ammonium-N was the major factor influencing the relative abundance of AOA and AOB, although other factors, such as total organic carbon, were involved. This study helps elucidate the roles of AOA and AOB in the nitrogen cycling of hyporheic zone.

Persistent metal contamination limits lotic ecosystem heterotrophic metabolism after more than 100 years of exposure: a novel application of the Resazurin Resorufin Smart Tracer

Persistent stress from anthropogenic metal deposition in lotic ecosystems is a global concern. This long-term selective pressure shapes hyporheic microbial assemblages and influences ecosystem functional integrity. We hypothesized that, even after 100 years of adaptation opportunity, ecosystem function remains inhibited by sediment-associated metal stress and that the Resazurin Resorufin Smart Tracer can be used to quantify this impact. The Resazurin Resorufin Smart Tracer system is applied here in a novel capacity as an indicator of ecosystem function by quantifying ecosystem respiration of microbial communities. Hyporheic microbial communities exposed to differing magnitudes of chronic metal stress were compared to pristine reference sites in controlled column experiments. A Markov chain Monte Carlo technique was developed to solve the inverse smart tracer transport equation to derive community respiration data. Results suggest metals inhibit respiration by 13-30% relative to reference sites and this inhibition is directly related to the level of in situ metal stress. We demonstrate the first application of a hydrologic smart tracer as a functional indicator of ecological integrity within anthropogenically influenced flowing water systems and provide data suggesting resilience is limited in hyporheic ecosystems even after more than a century of microbial adaption to chronic pollutants.

Characteristics of aerobic and anaerobic ammonium-oxidizing bacteria in the hyporheic zone of a contaminated river

Both β-proteobacterial aerobic ammonium-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (ANAMMOX) bacteria were investigated in the hyporheic zone of a contaminated river in China containing high ammonium levels and low chemical oxygen demand. Fluorescence in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and cloning-sequencing were employed in this study. FISH analysis illustrated that AOB (average population of 3.5 %) coexisted with ANAMMOX bacteria (0.7 %). The DGGE profile revealed a high abundance and diversity of bacteria at the water-air-soil interface rather than at the water-soil interface. The redundancy analysis correlated analysis showed that the diversity of ANAMMOX bacteria was positively related to the redox potential. The newly detected sequences of ANAMMOX organisms principally belonged to the genus Candidatus "Brocadia", while most ammonia monooxygenase subunit-A gene amoA sequences were affiliated with Nitrosospira and Nitrosomonas. These results suggest that the water-air-soil interface performs an important function in the nitrogen removal process and that the bioresources of AOB and ANAMMOX bacteria can potentially be utilized for the eutrophication of rivers.

Use of microcalorimetry to determine the costs and benefits to Pseudomonas putida strain KT2440 of harboring cadmium efflux genes

A novel microcalorimetric approach was used to analyze the responses of a metal-tolerant soil bacterium (Pseudomonas putida strain KT2440) to metal resistance gene deletions in cadmium-amended media. As hypothesized, under cadmium stress, the wild-type strain benefited from the resistance genes by entering the exponential growth phase earlier than two knockout strains. In the absence of cadmium, strain KT1, carrying a deletion in the main component (czcA1) of a Cd/Zn chemiosmotic efflux transporter (CzcCBA1), grew more efficiently than the wild type and released ∼700 kJ (per mole of biomass carbon) less heat than the wild-type strain, showing the energetic cost of maintaining CzcCBA1 in the absence of cadmium. A second mutant strain (KT4) carrying a different gene deletion, ΔcadA2, which encodes the main Cd/Pb efflux transporter (a P-type ATPase), did not survive beyond moderate cadmium concentrations and exhibited a decreased growth yield in the absence of cadmium. Therefore, CadA2 plays an essential role in cadmium resistance and perhaps serves an additional function. The results of this study provide direct evidence that heavy metal cation efflux mechanisms facilitate shorter lag phases in the presence of metals and that the maintenance and expression of tolerance genes carry quantifiable energetic costs and benefits.

Bacterial gene abundances as indicators of greenhouse gas emission in soils

Nitrogen fixing and denitrifying bacteria, respectively, control bulk inputs and outputs of nitrogen in soils, thereby mediating nitrogen-based greenhouse gas emissions in an ecosystem. Molecular techniques were used to evaluate the relative abundances of nitrogen fixing, denitrifying and two numerically dominant ribotypes (based on the > or =97% sequence similarity at the 16S rRNA gene) of bacteria in plots representing 10 agricultural and other land-use practices at the Kellogg biological station long-term ecological research site. Quantification of nitrogen-related functional genes (nitrite reductase, nirS; nitrous oxide reductase, nosZ; and nitrogenase, nifH) as well as two dominant 16S ribotypes (belonging to the phyla Acidobacteria, Thermomicrobia) allowed us to evaluate the hypothesis that microbial community differences are linked to greenhouse gas emissions under different land management practices. Our results suggest that the successional stages of the ecosystem are strongly linked to bacterial functional group abundance, and that the legacy of agricultural practices can be sustained over decades. We also link greenhouse gas emissions with specific compositional responses in the soil bacterial community and assess the use of denitrifying gene abundances as proxies for determining nitrous oxide emissions from soils.