The effect of combined sewer overflow (CSO) on the abundance of antibiotic resistant bacteria in the James River

Antibiotics have been used to treat bacterial infections worldwide since their discovery in the early 20th century and are vital to human health. Unfortunately, the heavy use of antibiotics has led to the increased natural selection of antibiotic resistant bacteria. In urban rivers, the spread of resistance resistance is through through the direct acquisition of resistance genes by either either either cell-to -cell contact or DNA uptake via a process called horizontal gene transfer transfer(HGT) 2.HGT, resistance genes, and resistant bacteria are in greater abundance in wastewater systems, and are released into the environment in wastewater plant effluent2,3. One problematic method of wastewater treatment, used in over over 750 cities in the US, is the Combined Sewer System System(CSS) 4.This collects the water from both rainfall and sewage for treatment at a single facility.Occasionally when it rains, the treatment plant exceeds capacity and the combined untreated effluent enters the river in what is called a CSO (Combined Sewer Overflow) event. Some studies have found that antibiotic resistance genes can be more abundant in river water water affected by wastewater treatment effluent and correlated with CSO events events 7

Effect of Tidal Cycling Rate on the Distribution and Abundance of Nitrogen-Oxidizing Bacteria in a Bench-Scale Fill-and-Drain Bioreactor

Most domestic wastewater can be effectively treated for secondary uses by engineered biological systems. These systems rely on microbial activity to reduce nitrogen (N) content of the reclaimed water. Such systems often employ a tidal-flow process to minimize space requirements for the coupling of aerobic and anaerobic metabolic processes. In this study, laboratory-scale tidal-flow treatment systems were studied to determine how the frequency and duration of tidal cycling may impact reactor performance. Fluorescent in situ hybridization and epifluorescence microscopy were used to enumerate the key functional groups of bacteria responsible for nitrification and anaerobic ammonium oxidation (anammox), and N-removal efficiency was calculated via a mass-balance approach. When water was cycled (i.e., reactors were filled and drained) at high frequencies (16–24 cycles day−1), nitrate accumulated in the columns—presumably due to inadequate periods of anoxia that limited denitrification. At lower frequencies, such as 4 cycles day−1, nearly complete N removal was achieved (80–90%). These fill-and-drain systems enriched heavily for nitrifiers, with relatively few anammox-capable organisms. The microbial community produced was robust, surviving well through short (up to 3 h) anaerobic periods and frequent system-wide perturbation

Greenhouse Gas Emissions Over a Tidal Cycle in a Freshwater Wetland

Tidal freshwater wetlands are located at the interface of non-tidal freshwater riverine systems and estuarine tidal systems. These habitats experience freshwater tides, creating unique redoximorphic soil characteristics while simultaneously presenting an opportunity for hydrologic nutrient transport into the system. Because of this periodic flooding and draining, tidal freshwater wetlands are systems of intense biogeochemical transformations, which are microbially mediated. Several microbial transformations (e.g., methanogenesis, incomplete denitrification, and nitrification) result in the production of greenhouse gases (CO2, CH4, and N2O) at globally-significant levels. For example, wetlands are one of the greatest sources of methane on Earth, accounting for 20-33% of the global methane budget (Schlesinger and Bernhardt, 2013). Compared to global methane emission estimates, the global nitrous oxide budget remains largely uncertain (Tian et al. 2015), and the contribution of wetlands is currently unknown (Schlesinger and Bernhardt, 2013). However, given that recent work by Liengaard et al. (2012) estimated that nitrous oxide emissions from the Pantanal wetland system in South America alone represent ~2% of global emissions, it is reasonable to expect wetlands to be major contributors to atmospheric concentrations of this potent greenhouse gas. Despite the growing recognition that wetlands are important sources of greenhouse gases, little research has examined how flux rates vary in response to basic environmental drivers such as tidal cycling Objectives: The main objective of this study is to assess rates of CO2, CH4, and N2O production at high and low tides in a tidal freshwater wetlands. In addition, we sought to determine if pore water ion concentrations and edaphic characteristics fluctuate over a tidal cycle

Evolutionary history influences the salinity preference of bacterial taxa in wetland soils

Salinity is a major driver of bacterial community composition across the globe. Despite growing recognition that different bacterial species are present or active at different salinities, the mechanisms by which salinity structures community composition remain unclear. We tested the hypothesis that these patterns reflect ecological coherence in the salinity preferences of phylogenetic groups using a reciprocal transplant experiment of fresh- and saltwater wetland soils. The salinity of both the origin and host environments affected community composition (16S rRNA gene sequences) and activity (CO2 and CH4 production, and extracellular enzyme activity). These changes in community composition and activity rates were strongly correlated, which suggests the effect of environment on function could be mediated, at least in part, by microbial community composition. Based on their distribution across treatments, each phylotype was categorized as having a salinity preference (freshwater, saltwater, or none) and phylogenetic analyses revealed a significant influence of evolutionary history on these groupings. This finding was corroborated by examining the salinity preferences of high-level taxonomic groups. For instance, we found that the majority of α- and γ-proteobacteria in these wetland soils preferred saltwater, while many β-proteobacteria prefer freshwater. Overall, our results indicate the effect of salinity on bacterial community composition results from phylogenetically-clustered salinity preferences

Assessing how disruption of methanogenic communities and their syntrophic relationships in tidal freshwater marshes via saltwater intrusion may affect CH4 emissions

Tidal freshwater wetlands (TFW), which lie at the interface of saltwater and freshwater ecosystems, are predicted to experience moderate salinity increases due to sea level rise. Increases in salinity generally suppress CH4 production, but it is uncertain to what extent elevated salinity will affect CH4 cycling in TFW. It is also unknown whether CH4 production will resume when freshwater conditions return. The ability to produce CH4 is limited to a monophyletic group of the Euryarchaeota phylum called methanogens (MG), who are limited to a small number of substrates (e.g., acetate, H2, and formate) produced from the breakdown of fermentation products. In freshwater anaerobic soils, the degradation of certain fermentation products (e.g., butyrate, propionate) is only energetically favorable when their catabolic byproduct, H2 or formate, is consumed to low concentrations by MGs. This is considered a form of obligate syntrophy. Sulfate reducing bacteria (SRB) are capable of utilizing a larger variety of substrates than MG, including substrates degraded by methanogenic syntrophy (e.g., butyrate, propionate). The introduction of sulfate (SO4 -2) into TFW via saltwater intrusion events may allow SRB to disrupt syntrophic relationships between hydrogenotrophic MG and syntrophic fermenters. This may select for MG taxa that differ in their rate of CH4 production. The objectives of this study were to determine the effect of oligohaline SO4 -2 concentrations on MG community functions (i.e., CH4 production and syntrophic butyrate degradation); and, to assess whether these functions recover after competition with SRB has been removed

Biological Control on Acid Generation at the Conduit-Bedrock Boundary in Submerged Caves: Quantification through Geochemical Modeling

No-mount Cave, located in Wekiwa Springs State Park in central Florida, USA, is an aphotic, submerged, freshwater cave in which large colonies of sulfur-oxidizing bacteria live in filamentous microbial mats. Upwardly discharging groundwater enters the cave from the Upper Floridan aquifer, specifically the Eocene-aged Ocala Limestone. We undertook a combined field, laboratory, and modeling study in which we sought to determine the amount of calcite dissolution attributable to the generation of protons by microbially mediated sulfide oxidation. The chemical compositions of groundwater within the limestone formation collected through a newly designed sampling device and of water in the cave conduit were used in geochemical modeling. We used the reaction-path model PHREEQCI to quantify the amount of calcite dissolution expected under various plausible scenarios for mixing of formation water with conduit water and extent of bacterial sulfide oxidation. Laboratory experiments were conducted using flow-through columns packed with crushed limestone from the study site. Replicate columns were eluted with artificial groundwater containing dissolved HS- in the absence of microbial growth. Without biologically mediated sulfide oxidation, no measurable calcite dissolution occurred in laboratory experiments and no additional amount of speleogenesis is expected as formation water mixes with conduit water in the field. In contrast, significant calcite dissolution is driven by the protons released in the biological transformation of the aqueous sulfur species. Although a range of results were calculated, a plausible amount of 158 mg Ca2+ released to conduit water per liter of groundwater crossing the formation-conduit boundary and mixing with an equal volume of conduit water was predicted. Our modeling results indicate that significant cave development can be driven by microbially mediated sulfide oxidation under these hydrogeochemical conditions.žKeywords: calcite dissolution, microbial sulfide oxidation, geochemical model.DOI: 10.3986/ac.v42i2-3.66

Trace Metal Availability Affects Greenhouse Gas Emissions and Microbial Functional Group Abundance in Freshwater Wetland Sediments

We investigated the effects of trace metal additions on microbial nitrogen (N) and carbon (C) cycling using freshwater wetland sediment microcosms amended with micromolar concentrations of copper (Cu), molybdenum (Mo), iron (Fe), and all combinations thereof. In addition to monitoring inorganic N transformations (NO3–, NO2–, N2O, NH4+) and carbon mineralization (CO2, CH4), we tracked changes in functional gene abundance associated with denitrification (nirS, nirK, nosZ), dissimilatory nitrate reduction to ammonium (DNRA; nrfA), and methanogenesis (mcrA). With regards to N cycling, greater availability of Cu led to more complete denitrification (i.e., less N2O accumulation) and a higher abundance of the nirK and nosZ genes, which encode for Cu-dependent reductases. In contrast, we found sparse biochemical evidence of DNRA activity and no consistent effect of the trace metal additions on nrfA gene abundance. With regards to C mineralization, CO2 production was unaffected, but the amendments stimulated net CH4 production and Mo additions led to increased mcrA gene abundance. These findings demonstrate that trace metal effects on sediment microbial physiology can impact community-level function. We observed direct and indirect effects on both N and C biogeochemistry that resulted in increased production of greenhouse gasses, which may have been mediated through the documented changes in microbial community composition and shifts in functional group abundance. Overall, this work supports a more nuanced consideration of metal effects on environmental microbial communities that recognizes the key role that metal limitation plays in microbial physiology

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River\u27s planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 106 reads revealed \u3e3 × 106 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 106 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and ‘Vibrionales\u27) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River\u27s planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10 6 reads revealed \u3e3 × 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads.Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax(biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and ‘Vibrionales\u27) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River