Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada

Microbial communities change along the 300 km length of the Grand River for extreme high- and low-flow regimes

The Grand River watershed is the largest catchment in southern Ontario. The river's northern and southern sections are influenced by agriculture, whereas central regions receive wastewater effluent and urban runoff. To characterize in-river microbial communities, as they relate to spatial and environmental factors, we conducted two same-day sampling events along the entire 300 km length of the river, representing contrasting flow seasons (high flow spring melt and low flow end of summer). Through high-throughput sequencing of 16S rRNA genes, we assessed the relationship between river microbiota and spatial and physicochemical variables. Flow season had a greater impact on communities than spatial or diel effects and profiles diverged with distance between sites under both flow conditions, but low-flow profiles exhibited higher beta diversity. High-flow profiles showed greater species richness and increased presence of soil and sediment taxa, which may relate to increased input from terrestrial sources. Total suspended solids, dissolved inorganic carbon, and distance from headwaters significantly explained microbial community variation during the low-flow event, whereas conductivity, sulfate, and nitrite were significant explanatory factors for spring melt. This study establishes a baseline for the Grand River's microbial community, serving as a foundation for modeling the microbiology of anthropogenically impacted freshwater systems affected by lotic processes.

Impact of wastewater treatment upgrade and nitrogen removal on bacterial communities and their interactions in eutrophic prairie streams

Eutrophication can impact bacteria by altering fluxes and processing of nutrients and organic matter. However, relatively little is known of how bacterial communities, diversity, and interactions with phytoplankton might respond to nutrient management. We used 16S rRNA amplicon sequencing to compare bacterial assemblages in the water column upstream (control) and downstream (impact) of a wastewater treatment plant (WWTP) located on a eutrophic prairie stream. Sampling occurred before (2012) and after (2018) the 2016 biological nutrient removal (BNR) upgrade that removed >90% of nitrogen (N, mainly NH4+). Multivariate ordination suggested that effluent-impacted bacterial communities were associated mainly with elevated NH4+ concentrations before the upgrade, whereas those after BNR were characteristic of reference systems (low NO3-, diverse regulation). Genera such as Betaproteobacteria and Rhodocyclacea were abundant at impacted sites in 2012, whereas Flavobacterium and a potential pathogen (Legionella) were common at impacted sites in 2018. Nitrifier bacteria (Nitrospira and Nitrosomonas) were present but rare at all sites in 2012, but recorded only downstream of the WWTP in 2018. Generalized additive models showed that BNR reduced bacterial diversity, with ∼70% of the deviance in diversity explained by hydrology, pH, nutrients, and phytoplankton abundance. Overall, NH4+ removal reduced symptoms of cultural eutrophication in microbe assemblages.

Spatio-temporal variation and hazard assessment of potentially toxic metal element contamination in sediments and water before and after a water-level fluctuation cycle in the Three Gorges Reservoir, Wanzhou, China

Previous investigations on heavy metals in the water-sediment compartment focused on their spatial distribution, and the influence of sediment pH and organic matter (OM) on metal environmental occurrences. However, there are limited studies on the effects of physicochemical properties on the migration and transformation of heavy metals in the water-sediment compartments. This study investigated the relationship between the physicochemical properties of sediments and the distribution and chemical speciation of heavy metals, and the potential environmental risk of heavy metals in water and sediment using Risk Assessment Code (RAC) values and the Tessier five-step extraction method. Adsorption and desorption experiments showed that the sediment had weak adsorption and the strongest desorption capacity for Cd. Results of the pH, OM, surface element content, and X-ray diffraction (XRD) patterns suggested that cadmium (Cd) was more likely to partition into the water phase from the sediment during the flooding and water storage periods. When pH was 7-8 and OM content was 3.6-5.9%, the sediment-water distribution coefficient of Cd was low due to its large ionic radius, and the surface adsorption sites were saturated by other elements. These studies can provide a theoretical basis for the management and pollution control of the Three Gorges Reservoir.

Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event

Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.

Effects of municipal wastewater effluents on the digestive gland microbiome of wild freshwater mussels (Lasmigona costata)

Gut microbial communities are vital for maintaining host health, and are sensitive to diet, environment, and chemical exposures. Wastewater treatment plants (WWTPs) release effluents containing antimicrobials, pharmaceuticals, and other contaminants that may negatively affect the gut microbiome of downstream organisms. This study investigated changes in the diversity and composition of the digestive gland microbiome of flutedshell mussels (Lasmigona costata) from upstream and downstream of two large (service >100,000) WWTPs. Mussel digestive gland microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16 S rRNA gene. Bacterial alpha diversity decreased at sites downstream of the second WWTP and these sites were dissimilar in beta diversity from sites upstream and downstream of the first upstream WWTP. The microbiomes of mussels collected downstream of the first WWTP had increased relative abundances of Actinobacteria, Bacteroidetes, and Firmicutes, with a decrease in Cyanobacteria, compared to upstream mussels. Meanwhile, those collected downstream of the second WWTP increased in Proteobacteria and decreased in Actinobacteria, Bacteroidetes, and Tenericutes. Increased Proteobacteria has been linked to adverse effects in mammals, but their functions in mussels is currently unknown. Finally, effluent-derived bacteria were found in the microbiome of mussels downstream of both WWTPs but not in those from upstream. Overall, results show that the digestive gland microbiome of mussels collected upstream and downstream of WWTPs differed, which has implications for altered host health and the transport of WWTP-derived bacteria through aquatic ecosystems.

Deciphering the influence of multiple anthropogenic inputs on taxonomic and functional profiles of the microbial communities in Yitong River, Northeast China

We conducted the analysis of physicochemical parameters, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nitrate and total phosphorus declined at the reservoir outlet. The WWTP effluent discharge caused a decrease of the relative abundance of Actinobacteria and Cyanobacteria, while the impact on the variation of alpha diversity of river microbial community was slight. Carbon fixation and nitrogen cycle varied with the change of land use type. The rare taxa contributed with a predominant role in the response to environmental variables and NH₃-N as well as NO₃^--N were the main environmental factors that drove the shift in the bacterial community. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the WWTP effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

Study on Influencing Factors and Simulation of Watershed Ecological Compensation Based on Evolutionary Game

In the practice of watershed ecological compensation, due to the inconsistency between the interests of economic development and the objectives of ecological protection, there are typical game characteristics among the relevant stakeholders. Taking the ecological compensation between Henan and Shaanxi in the Yellow River Basin as an example, this paper constructs an evolutionary game model, obtains the external conditions for various stakeholders to achieve stable cooperation from the perspective of the government, and demonstrates the necessity of combining vertical and horizontal ecological compensation. The sensitivity of each party’s decision making to key elements is analyzed through a simulation. The results show that: (1) the optimal strategy is mainly affected by the initial willingness of the upstream government and the central government; the strong regulatory power of the central government can eliminate the influence of the initial will; (2) development opportunity costs and vertical fiscal transfer payments have the most obvious influence on upstream government decision-making; (3) the effect on optimal decision state of downstream paying upstream ecological compensation is higher than that of upstream paying downstream ecological compensation; (4) the punishment of the central government should ensure the binding force on the lower governments, and the revenue and expenditure under its supervision strategy should ensure the effectiveness of the supervision public power. The above conclusions provide support for improving the ecological compensation mechanism of transboundary basins.

Altered microbiomes of aquatic macroinvertebrates and riparian spiders downstream of municipal wastewater effluents

Municipal wastewater treatment plants (WWTPs) contain numerous contaminants, including antimicrobials, that could affect the composition of the beneficial bacterial communities associated with host aquatic organisms. There is also potential for these effects to transfer to terrestrial predators. Riparian spiders and five families of aquatic macroinvertebrates were collected from sites upstream and downstream of two WWTPs, Waterloo and Kitchener, discharging to the Grand River, Ontario, Canada. Whole-body microbiota were analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16S rRNA genetic barcode. Changes in the relative abundance of major microbiome phyla were observed in all downstream aquatic insects except Hydropsychidae caddisflies, which exhibited little site variation. Shannon alpha diversity differed among sites for Tetragnathidae spiders, Perlidae, Hydropsychidae, and Heptageniidae. Downstream of the Waterloo WWTP alpha diversity decreased in spiders, while downstream of the Kitchener WWTP this measure decreased in Perlidae and increased in spiders. Bray-Curtis beta diversity was dissimilar among sites in all invertebrate taxa; upstream sites differed from those downstream of Waterloo in spiders, Perlidae, and Hydropsychidae, and from those downstream of Kitchener in spiders, Perlidae, and Hydropsychidae. Finally, effluent-derived bacteria were found in the microbiomes of downstream spiders and aquatic insects and not upstream. Overall, results indicated that the microbiomes of invertebrates collected downstream differed from those collected upstream of WWTPs, which has implications for altered host health and transport of WWTP-derived bacteria through aquatic ecosystems.

Functional microbial community structures and chemical properties indicated mechanisms and potential risks of urban river eco-remediation

To investigate the mechanisms and potential risks of river eco-remediation, river water, sediment, and biofilms in remediation facilities were sampled from a 2-year full scale eco-remediation site in an urban river in southeastern China. The samples from both remediated and adjacent control areas were analyzed for chemical properties and functional microbial community structures. The eco-remediation significantly changed the community structures in the river and introduced much more diverse functional microorganisms in facility biofilms. Corresponding to effective reduction of organics and ammonium in river water, some labile-organics-degrading and ammonia-oxidizing gene families showed higher abundances in river water of remediated area than control area, and were obviously more abundant in facility biofilms than in river water and sediment. The eco-remediation facilities showed obvious absorption of N, P, and heavy metals (Mn, Cr^VI, Fe, Al, As, Co), contributing to nutrients and metals removal from river water. The eco-remediation also increased transparency and sedimentation of some heavy metals (Cu, Pb, Zn), which probably associated with colloids breakdown. Various metal-resistance microorganisms showed different abundances between facility biofilms and sediment, in accordance with relative metals. Most detected pathogens were not significantly affected by eco-remediation. However, our measurements in sediment and facilities showed heavy metals accumulation and development of some pathogens and several antibiotic-resistance pathogens, alerting us to investigate and control these potential risks to ecosystem and human health.

Impact of nitrogen compound variability of sewage treated water on N2O production in riverbeds

Nitrous oxide (N₂O), a strong greenhouse and ozone depleting gas, is known to be generated in the river environment. However, the impact of sewage treated water on the production mechanism has not been clarified. In this study, N₂O production in the upper reach of a river was evaluated by field survey and activity test. The results demonstrated that the N₂O production activity of the river pebbles increased with the inflow of the sewage treated water, which was supported by field survey results, such as the dissolved N₂O concentrations and water quality. The emission factors of N₂O were determined to be 0.02-0.05% in nitrification and 0.01-0.025% in denitrification. Our study shows that combining a field survey and an activity test improves the reliability of the results and leads to the appropriate quantitative evaluation. From a perspective of controlling the N₂O emissions from the sewage treatment plant, N₂O generation inside the plant is critical. However, appropriate nitrogen removal in the treatment plant is connected to the reduction of N₂O generation in the river environment.

River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs

The sensitivity and spatial recovery of river sediment biofilms along 1 km after the input of two wastewater treatment plants (WWTPs) located in two river reaches with different degrees of anthropogenic influence were investigated. First, at the upper reach, we observed an inhibition of some microbial functions (microbial respiration and extracellular enzyme activities) and strong shifts in bacterial community composition (16S rRNA gene), whereas an increase in microbial biomass and activity and less pronounced effect on microbial diversity and community composition were seen at the lower reach. Second, at the lower reach we observed a quick spatial recovery (around 200 m downstream of the effluent) as most of the functions and community composition were similar to those from reference sites. On the other hand, bacterial community composition and water quality at the upper reach was still altered 1 km from the WWTP effluent. Our results indicate that biofilms in the upstream sites were more sensitive to the effect of WWTPs due to a lower degree of tolerance after a disturbance than communities located in more anthropogenically impacted sites.

Insight into the nitrogen accumulation in urban center river from functional genes and bacterial community

Along with urbanization, the intensified nitrogen pollution in urban rivers and the form of black-odor rivers has become one of the biggest concerns. Better understanding of the nitrogen transformations and microbial mechanisms occurring within urban rivers could help to manage their water quality. In this study, pollution characteristics, potential nitrogen removal rate, composition and function of bacterial community, and abundance of functional genes associated with nitrogen transformation were comparatively investigated in a typical urban river (FC) and a suburban river (LH). Compared with LH, FC was characterized by higher content of nutrients, lower potential nitrogen removal rate and lower abundance of functional genes associated with nitrogen transformation in both overlying water and sediment, especially in summer. Sediment dissolved organic matter characterized by excitation−emission matrix (EEM) showed that FC was more severely polluted by high nitrogen organic matter. Our results revealed that anammox was the main nitrogen removal pathway in both rivers and potential nitrogen removal rates decreased significantly in summer. Bacterial community analysis showed that the benthic communities were more severely influenced by the pollutant than aquatic ones in both rivers. Furthermore, the FC benthic community was dominated by anaerobic respiring, fermentative, sulfate reduction bacteria. Quantitatively, the denitrification rate showed a significant positive correlation with the abundance of denitrification genes, whilst the anammox rate was significantly negatively correlated with bacterial diversity. Meanwhile, NH₄⁺-N had a significant negative correlation to both denitrification and anammox in sediment. Taken together, the results indicated that the increased nitrogen pollutants in an urban river altered nitrogen removal pathways and bacterial communities, which could in turn exacerbate the nitrogen pollution to this river.

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH₄⁺ and NO₂^- biochemically to form N₂ gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams

Through a combined approach using analytical chemistry, real-time quantitative polymerase chain reaction (qPCR), and targeted amplicon sequencing, we studied the impact of wastewater treatment plant effluent sources at six sites on two sampling dates on the chemical and microbial population regimes within the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, Pennsylvania, USA. These water bodies contribute flow to the Schuylkill River, one of the major drinking water sources for Philadelphia, Pennsylvania. Effluent was observed to be a significant source of nutrients, human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources, which we hypothesize is controlled by distance from effluent source. Antecedent moisture conditions were observed to impact overall microbial community diversity, with higher diversity occurring after rainfall. Finally, the efficacy of using a subset of the microbial community including the orders of Bifidobacteriales, Bacteroidales, and Clostridiales to estimate the degree of influence due to sewage and fecal sources was explored and verified.

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage

Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 10⁴ – 4.9 × 10⁷ archaeal amoA copies ∗ μg DNA^-1, 1.5 × 10³ – 5.3 × 10⁵ AOB 16S rRNA copies ∗ μg DNA^-1, and 1.3 × 10⁶ – 7.7 × 10⁷Nitrospira nxrB copies ∗ μg DNA^-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but were correlated to the relative abundances of several individual OTUs. These findings extend our understanding of the distribution of nitrifying microbes in AMD-impacted systems and provide a platform for further research.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

Impact of microbial physiology and microbial community structure on pharmaceutical fate driven by dissolved oxygen concentration in nitrifying bioreactors

Operation at low dissolved oxygen (DO) concentrations (<1 mg/L) in wastewater treatment could save utilities significantly by reducing aeration energy costs. However, few studies have evaluated the impact of low DO on pharmaceutical biotransformations during treatment. DO concentration can impact pharmaceutical biotransformation rates during wastewater treatment both directly and indirectly: directly by acting as a limiting substrate that slows the activity of the microorganisms involved in biotransformation; and indirectly by shaping the microbial community and selecting for a community that performs pharmaceutical biotransformation faster (or slower). In this study, nitrifying bioreactors were operated at low (∼0.3 mg/L) and high (>4 mg/L) DO concentrations to understand how DO growth conditions impacted microbial community structure. Short-term batch experiments using the biomass from the parent reactors were performed under low and high DO conditions to understand how DO concentration impacts microbial physiology. Although the low DO parent biomass had a lower specific activity with respect to ammonia oxidation than the high DO parent reactor biomass, it had faster biotransformation rates of ibuprofen, sulfamethoxazole, 17α-ethinylestradiol, acetaminophen, and atenolol in high DO batch conditions. This was likely because the low DO reactor had a 2x higher biomass concentration, was enriched for ammonia oxidizers (4x higher concentration), and harbored a more diverse microbial community (3x more unique taxa) as compared to the high DO parent reactor. Overall, the results show that there can be indirect benefits from low DO operation over high DO operation that support pharmaceutical biotransformation during wastewater treatment.

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI, and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Anaerobic Disposal of Arsenic-Bearing Wastes Results in Low Microbially Mediated Arsenic Volatilization

The removal of arsenic from drinking water sources produces arsenic-bearing wastes, which are disposed of in a variety of ways. Several disposal options involve anaerobic environments, including mixing arsenic waste with cow dung, landfills, anaerobic digesters, and pond sediments. Though poorly understood, the production of gaseous arsenic species in these environments can be a primary goal (cow dung mixing) or an unintended consequence (anaerobic digesters). Once formed, these gaseous arsenic species are readily diluted in the atmosphere. Arsenic volatilization can be mediated by the enzyme arsenite S-adenosylmethionine methyltransferase (ArsM) or through the enzymes involved in methanogenesis. In this study, methanogenic mesocosms with arsenic-bearing ferric iron waste from an electrocoagulation drinking water treatment system were used to evaluate the role of methanogenesis in arsenic volatilization using methanogen inhibitors. Arsenic volatilization was highest in methanogenic mesocosms, but represented <0.02% of the total arsenic added. 16S rRNA cDNA sequencing, qPCR of mcrA transcripts, and functional gene array-based analysis of arsM expression, revealed that arsenic volatilization correlated with methanogenic activity. Aqueous arsenic concentrations increased in all mesocosms, indicating that unintended contamination may result from disposal in anaerobic environments. This highlights that more research is needed before recommending anaerobic disposal intended to promote arsenic volatilization.

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

BACKGROUND

Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary.

RESULTS

We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels.

CONCLUSION

This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.

Anaerobic microbial community response to methanogenic inhibitors 2-bromoethanesulfonate and propynoic acid

Methanogenic inhibitors are often used to study methanogenesis in complex microbial communities or inhibit methanogens in the gastrointestinal tract of livestock. However, the resulting structural and functional changes in archaeal and bacterial communities are poorly understood. We characterized microbial community structure and activity in mesocosms seeded with cow dung and municipal wastewater treatment plant anaerobic digester sludge after exposure to two methanogenic inhibitors, 2‐bromoethanesulfonate (BES) and propynoic acid (PA). Methane production was reduced by 89% (0.5 mmol/L BES), 100% (10 mmol/LBES), 24% (0.1 mmol/LPA), and 95% (10 mmol/LPA). Using modified primers targeting the methyl‐coenzyme M reductase (mcrA) gene, changes in mcrA gene expression were found to correspond with changes in methane production and the relative activity of methanogens. Methanogenic activity was determined by the relative abundance of methanogen 16S rRNA cDNA as a percentage of the total community 16S rRNA cDNA. Overall, methanogenic activity was lower when mesocosms were exposed to higher concentrations of both inhibitors, and aceticlastic methanogens were inhibited to a greater extent than hydrogenotrophic methanogens. Syntrophic bacterial activity, measured by 16S rRNA cDNA, was also reduced following exposure to both inhibitors, but the overall structure of the active bacterial community was not significantly affected.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors.

Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta

Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms

Streams affected by wastewater treatment plant (WWTP) effluents are hotspots of nitrification. We analyzed the influence of WWTP inputs on the abundance, distribution, and composition of epilithic ammonia-oxidizing (AO) assemblages in five Mediterranean urban streams by qPCR and amoA gene cloning and sequencing of both archaea (AOA) and bacteria (AOB). The effluents significantly modified stream chemical parameters, and changes in longitudinal profiles of both NH(4)(+) and NO(3)(-) indicated stimulated nitrification activity. WWTP effluents were an allocthonous source of both AOA, essentially from the Nitrosotalea cluster, and mostly of AOB, mainly Nitrosomonas oligotropha, Nitrosomonas communis, and Nitrosospira spp. changing the relative abundance and the natural composition of AO assemblages. Under natural conditions, Nitrososphaera and Nitrosopumilus AOA dominated AO assemblages, and AOB were barely detected. After the WWTP perturbation, epilithic AOB increased by orders of magnitude whereas AOA did not show quantitative changes but a shift in population composition to dominance of Nitrosotalea spp. The foraneous AOB successfully settled in downstream biofilms and probably carried out most of the nitrification activity. Nitrosotalea were only observed downstream and only in biofilms exposed to either darkness or low irradiance. In addition to other potential environmental limitations for AOA distribution, this result suggests in situ photosensitivity as previously reported for Nitrosotalea under laboratory conditions.

Acesulfame-K and pharmaceuticals as co-tracers of municipal wastewater in a receiving river

Wastewater treatment plant (WWTP) effluents are important sources of emerging contaminants at environmentally-relevant concentrations. In this study, water samples were collected from a river downstream of two WWTPs to identify practical tracers for tracking wastewater. The results of the study indicate elevated concentrations of Cl(-), nutrients (NH3-N and NO2(-)), the artificial sweetener acesulfame-K (ACE-K), and the pharmaceuticals carbamazepine (CBZ), caffeine (CAF), sulfamethoxazole (SMX), ibuprofen (IBU), gemfibrozil (GEM), and naproxen (NAP) in the river close to the WWTPs that decreased with distance downstream. A correlation analysis using the Spearman Rank method showed that ACE-K, CBZ, GEM, NAP, and Cl(-) were strongly correlated with each other over a 31 km stretch of the river in the study area. The strong correlations of these target compounds indicate that the artificial sweetener ACE-K and the pharmaceuticals CBZ, GEM, and NAP can potentially be used as co-tracers to track wastewater.

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N₂ gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.