Effects of microbiological and geochemical interactions in mine drainage
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The shallow and Memphis aquifers in Shelby County, Tennessee, are valuable natural resources that are used for domestic, public-supply, and agricultural water use. The Memphis aquifer is the primary source for public supply in West Tennessee and provides 170 to 175 million gallons of water per day for more than 900,000 people (Robinson, 2018). The shallow aquifer includes the unconfined water table, provides domestic water supplies in Shelby County, and is susceptible to contamination from urban and industrial activities, underground storage tanks, old dumps, and other sources. Both aquifers are likely to be stressed in the future by factors such as population increase, contaminant migration from historical contamination sites, industrial and agricultural activities, climate change, and other competing demands on the water resources.
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Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.
The Bemidji aquifer in Minnesota, USA is a well-studied site of subsurface petroleum contamination. The site contains an anoxic groundwater plume where soluble petroleum constituents serve as an energy source for a region of methanogenesis near the source and bacterial Fe(III) reduction further down gradient. Methanogenesis apparently begins when bioavailable Fe(III) is exhausted within the sediment. Past studies indicate that Geobacter species and Geothrix fermentens -like organisms are the primary dissimilatory Fe-reducing bacteria at this site. The Fe mineralogy of the pristine aquifer sediments and samples from the methanogenic (source) and Fe(III) reducing zones were characterized in this study to identify microbiologic changes to Fe valence and mineral distribution, and to identify whether new biogenic mineral phases had formed. Methods applied included X-ray diffraction; X-ray fluorescence (XRF); and chemical extraction; optical, transmission, and scanning electron microscopy; and Mössbauer spectroscopy. All of the sediments were low in total Fe content (≈ 1%) and exhibited complex Fe-mineralogy. The bulk pristine sediment and its sand, silt, and clay-sized fractions were studied in detail. The pristine sediments contained Fe(II) and Fe(III) mineral phases. Ferrous iron represented approximately 50% of Fe TOT . The relative Fe(II) concentration increased in the sand fraction, and its primary mineralogic residence was clinochlore with minor concentrations found as a ferroan calcite grain cement in carbonate lithic fragments. Fe(III) existed in silicates (epidote, clinochlore, muscovite) and Fe(III) oxides of detrital and authigenic origin. The detrital Fe(III) oxides included hematite and goethite in the form of mm-sized nodular concretions and smaller-sized dispersed crystallites, and euhedral magnetite grains. Authigenic Fe(III) oxides increased in concentration with decreasing particle size through the silt and clay fraction. Chemical extraction and Mössbauer analysis indicated that this was a ferrihydrite like-phase. Quantitative mineralogic and Fe(II/III) ratio comparisons between the pristine and contaminated sediments were not possible because of textural differences. However, comparisons between the texturally-similar source (where bioavailable Fe(III) had been exhausted) and Fe(III) reducing zone sediments (where bioavailable Fe(III) remained) indicated that dispersed detrital, crystalline Fe(III) oxides and a portion of the authigenic, poorly crystalline Fe(III) oxide fraction had been depleted from the source zone sediment by microbiologic activity. Little or no effect of microbiologic activity was observed on silicate Fe(III). The presence of residual “ferrihydrite” in the most bioreduced, anoxic plume sediment (source) implied that a portion of the authigenic Fe(III) oxides were biologically inaccessible in weathered, lithic fragment interiors. Little evidence was found for the modern biogenesis of authigenic ferrous-containing mineral phases, perhaps with the exception of thin siderite or ferroan calcite surface precipitates on carbonate lithic fragments within source zone sediments.
Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H 2 , which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of other habitats, the study of deep subsurface microbiology is still in its infancy.
Onsite wastewater disposal systems (OWDS) are used extensively in the Black Hills of South Dakota where many of the watersheds and aquifers are characterized by fractured or solution-enhanced bedrock with thin soil cover. A study was conducted during 2006-08 to characterize water-quality effects and indicators of OWDS. Water samples were collected and analyzed for potential indicators of OWDS, including chloride, bromide, boron, nitrite plus nitrate (NO2+NO3), ammonia, major ions, nutrients, selected trace elements, isotopes of nitrate, microbiological indicators, and organic wastewater compounds (OWCs). The microbiological indicators were fecal coliforms, Escherichia coli (E. coli), enterococci, Clostridium perfringens (C. perfringens), and coliphages. Sixty ground-water sampling sites were located either downgradient from areas of dense OWDS or in background areas and included 25 monitoring wells, 34 private wells, and 1 spring. Nine surface-water sampling sites were located on selected streams and tributaries either downstream or upstream from residential development within the Precambrian setting. Sampling results were grouped by their hydrogeologic setting: alluvial, Spearfish, Minnekahta, and Precambrian. Mean downgradient dissolved NO2+NO3 concentrations in ground water for the alluvial, Spearfish, Minnekahta, and Precambrian settings were 0.734, 7.90, 8.62, and 2.25 milligrams per liter (mg/L), respectively. Mean downgradient dissolved chloride concentrations in ground water for these settings were 324, 89.6, 498, and 33.2 mg/L, respectively. Mean downgradient dissolved boron concentrations in ground water for these settings were 736, 53, 64, and 43 micrograms per liter (ug/L), respectively. Mean dissolved surface-water concentrations for NO2+NO3, chloride, and boron for downstream sites were 0.222 mg/L, 32.1 mg/L, and 28 ug/L, respectively. Mean values of delta-15N and delta-18O (isotope ratios of 14N to 15N and 18O to 16O relative to standard ratios) for nitrate in ground-water samples were 10.4 and -2.0 per mil (0/100), respectively, indicating a relatively small contribution from synthetic fertilizer and probably a substantial contribution from OWDS. The surface-water sample with the highest dissolved NO2+NO3 concentration of 1.6 mg/L had a delta-15N value of 12.36 0/100, which indicates warm-blooded animals (including humans) as the nitrate source. Fecal coliforms were detected in downgradient ground water most frequently in the Spearfish (19 percent) and Minnekahta (9.7 percent) settings. E. coli was detected most frequently in the Minnekahta (29 percent) and Spearfish (13 percent) settings. Enterococci were detected more frequently than other microbiological indicators in all four settings. Fecal coliforms and E. coli were detected in 73 percent and 95 percent of all surface-water samples, respectively. Enterococci, coliphages (somatic), and C. perfringens were detected in 50, 70, and 50 percent of surface-water samples, respectively. Of the 62 OWC analytes, 12 were detected only in environmental samples, 10 were detected in at least one environmental and one blank sample (not necessarily companion pairs), 2 were detected only in blank samples, and 38 were not detected in any blank, environmental, or replicate sample from either ground or surface water. Eleven different organic compounds were detected in ground-water samples at eight different sites. The most frequently occurring compound was DEET, which was found in 32 percent of the environmental samples, followed by tetrachloroethene, which was detected in 20 percent of the samples. For surface-water samples, 16 organic compounds were detected in 9 of the 10 total samples. The compound with the highest occurrence in surface-water samples was camphor, which was detected in 50 percent of samples. The alluvial setting was characterized by relatively low dissolved NO2+NO3 concentrations, detection of ammonia nitrogen, and relatively high concentr
Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.
The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.
Rapid population growth and urban development along waterways and coastal areas have led to decreasing water quality. To examine the effects of upstream anthropogenic activities on microbiological water quality, methods for source-specific testing are required. In this study, molecular assays targeting human enteroviruses (HEV), bovine enteroviruses (BEV), and human adenoviruses (HAdV) were developed and used to identify major sources of fecal contamination in the lower Altamaha River, Georgia. Two-liter grab samples were collected monthly from five tidally influenced stations between July and December 2002. Samples were analyzed by reverse transcription- and nested-PCR. PCR results were confirmed by dot blot hybridization. Eleven and 17 of the 30 surface water samples tested positive for HAdV and HEV, respectively. Two-thirds of the samples tested positive for either HEV or HAdV, and the viruses occurred simultaneously in 26% of samples. BEV were detected in 11 of 30 surface water samples. Binary logistic regression analysis showed that the presence of both human and bovine enteric viruses was not significantly related to either fecal coliform or total coliform levels. The presence of these viruses was directly related to dissolved oxygen and streamflow but inversely related to water temperature, rainfall in the 30 days preceding sampling, and chlorophyll-?? concentrations. The stringent host specificity of enteric viruses makes them good library-independent indicators for identification of water pollution sources. Viral pathogen detection by PCR is a highly sensitive and easy-to-use tool for rapid assessment of water quality and fecal contamination when public health risk characterization is not necessary. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.
Monitoring beach waters for human health has led to an increase and evolution of science in the Great Lakes, which includes microbiology, limnology, hydrology, meteorology, epidemiology, and metagenomics, among others. In recent years, concerns over the accuracy of water quality standards at protecting human health have led to a significant interest in understanding the risk associated with water contact in both freshwater and marine environments. Historically, surface waters have been monitored for fecal indicator bacteria (fecal coliforms, Escherichia coli , enterococci), but shortcomings of the analytical test (lengthy assay) have resulted in a re-focusing of scientific efforts to improve public health protection. Research has led to the discovery of widespread populations of fecal indicator bacteria present in natural habitats such as soils, beach sand, and stranded algae. Microbial source tracking has been used to identify the source of these bacteria and subsequently assess their impact on human health. As a result of many findings, attempts have been made to improve monitoring efficiency and efficacy with the use of empirical predictive models and molecular rapid tests. All along, beach managers have actively incorporated new findings into their monitoring programs. With the abundance of research conducted and information gained over the last 25 years, “Beach Science” has emerged, and the Great Lakes have been a focal point for much of the ground-breaking work. Here, we review the accumulated research on microbiological water quality of Great Lakes beaches and provide a historic context to the collaborative efforts that have advanced this emerging science.
Beaches worldwide provide recreational opportunities to hundreds of millions of people and serve as important components of coastal economies. Beach water is often monitored for microbiological quality to detect the presence of indicators of human sewage contamination so as to prevent public health outbreaks associated with water contact. However, growing evidence suggests that beach sand can harbor microbes harmful to human health, often in concentrations greater than the beach water. Currently, there are no standards for monitoring, sampling, analyzing, or managing beach sand quality. In addition to indicator microbes, growing evidence has identified pathogenic bacteria, viruses, and fungi in a variety of beach sands worldwide. The public health threat associated with these populations through direct and indirect contact is unknown because so little research has been conducted relating to health outcomes associated with sand quality. In this manuscript, we present the consensus findings of a workshop of experts convened in Lisbon, Portugal to discuss the current state of knowledge on beach sand microbiological quality and to develop suggestions for standardizing the evaluation of sand at coastal beaches. The expert group at the “Microareias 2012” workshop recommends that 1) beach sand should be screened for a variety of pathogens harmful to human health, and sand monitoring should then be initiated alongside regular water monitoring; 2) sampling and analysis protocols should be standardized to allow proper comparisons among beach locations; and 3) further studies are needed to estimate human health risk with exposure to contaminated beach sand. Much of the manuscript is focused on research specific to Portugal, but similar results have been found elsewhere, and the findings have worldwide implications.
Human sewage contaminates waterways, delivering excess nutrients, pathogens, chemicals, and other toxic contaminants. Contaminants and various sewage indicators are measured to monitor and assess water quality, but these analytes vary in their representation of sewage contamination and the inferences about water quality they support. We measured the occurrence and concentration of multiple microbiological ( n = 21) and chemical ( n = 106) markers at two urban stream locations in Milwaukee, Wisconsin, USA over two years. Five-day composite water samples ( n = 98) were collected biweekly, and sewage influent samples ( n = 25) were collected monthly at a Milwaukee, WI water reclamation facility. We found the vast majority of markers were not sensitive enough to detect sewage contamination. To compare analytes for monitoring applications, five consistently detected human sewage indicators were used to evaluate temporal patterns of sewage contamination, including microbiological (pepper mild mottle virus, human Bacteroides , human Lachnospiraceae ) and chemical (acetaminophen, metformin) markers. The proportion of human sewage in each stream was estimated using the mean influent concentration from the water reclamation facility and the mean concentration of all stream samples for each sewage indicator marker. Estimates of instream sewage pollution varied by marker, differing by up to two orders of magnitude, but four of the five sewage markers characterized Underwood Creek (mean proportions of human sewage ranged 0.0025 % - 0.075 %) as less polluted than Menomonee River (proportions ranged 0.013 % - 0.14 %) by an order of magnitude more. Chemical markers correlated with each other and yielded higher estimates of sewage pollution than microbial markers, which exhibited greater temporal variability. Transport, attenuation, and degradation processes can influence chemical and microbial markers differently and cause variation in human sewage estimates. Given the range of potential human and ecological health effects of human sewage contamination, robust characterization of sewage contamination that uses multiple lines of evidence supports monitoring and research applications.
Drinking water supply wells can be contaminated by a broad range of waterborne pathogens. However, groundwater assessments frequently measure microbial indicators or a single pathogen type, which provides a limited characterization of potential health risk. This study assessed contamination of wells by testing for viral, bacterial, and protozoan pathogens and fecal markers. Wells supplying groundwater to community and noncommunity public water systems in Minnesota, USA (n = 145) were sampled every other month over one or two years and tested using 23 qPCR assays. Eighteen genetic targets were detected at least once, and microbiological contamination was widespread (96% of 145 wells, 58% of 964 samples). The sewage-associated microbial indicators HF183 and pepper mild mottle virus were detected frequently. Human or zoonotic pathogens were detected in 70% of wells and 21% of samples by qPCR, with Salmonella and Cryptosporidium detected more often than viruses. Samples positive by qPCR for adenovirus (HAdV), enterovirus, or Salmonella were analyzed by culture and for genotype or serotype. qPCR-positive Giardia and Cryptosporidium samples were analyzed by immunofluorescent assay (IFA), and IFA and qPCR concentrations were correlated. Comparisons of indicator and pathogen occurrence at the time of sampling showed that total coliforms, HF183, and Bacteroidales -like HumM2 had high specificity and negative predictive values but generally low sensitivity and positive predictive values. Pathogen-HF183 ratios in sewage have been used to estimate health risks from HF183 concentrations in surface water, but in our groundwater samples Cryptosporidium oocyst:HF183 and HAdV:HF183 ratios were approximately 10,000 times higher than ratios reported for sewage. qPCR measurements provided a robust characterization of microbiological water quality, but interpretation of qPCR data in a regulatory context is challenging because few studies link qPCR measurements to health risk.
Inland waters are increasingly recognized as critical sites of methane emissions to the atmosphere, but the biogeochemical reactions driving such fluxes are less well understood. The Prairie Pothole Region (PPR) of North America is one of the largest wetland complexes in the world, containing millions of small, shallow wetlands. The sediment pore waters of PPR wetlands contain some of the highest concentrations of dissolved organic carbon (DOC) and sulfur species ever recorded in terrestrial aquatic environments. Using a suite of geochemical and microbiological analyses, we measured the impact of sedimentary carbon and sulfur transformations in these wetlands on methane fluxes to the atmosphere. This research represents the first study of coupled geochemistry and microbiology within the PPR and demonstrates how the conversion of abundant labile DOC pools into methane results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Abundant DOC and sulfate additionally supported some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments, which we infer to account for a large fraction of carbon mineralization in this system. Methane accumulations in zones of active sulfate reduction may be due to either the transport of free methane gas from deeper locations or the co-occurrence of methanogenesis and sulfate reduction. If both respiratory processes are concurrent, any competitive inhibition of methanogenesis by sulfate-reducing bacteria may be lessened by the presence of large labile DOC pools that yield noncompetitive substrates such as methanol. Our results reveal some of the underlying mechanisms that make PPR wetlands biogeochemical hotspots, which ultimately leads to their critical, but poorly recognized role in regional greenhouse gas emissions.
Septic systems that are built in compliance with regulations are generally not expected to be the cause of groundwater borne disease outbreaks, especially in areas with thick vadose zones. However, this case study demonstrates that a disease outbreak can occur in such a setting and outlines the combination of epidemiological, microbiological, and hydrogeological methods used to confirm the source of the outbreak. In early June 2007, 229 patrons and employees of a new restaurant in northeastern Wisconsin were affected by acute gastroenteritis; 6 people were hospitalized. Epidemiological case-control analysis indicated that drinking the restaurant's well water was associated with illness (odds ratio = 3.2, 95% confidence interval = 0.9 to 11.4, P = 0.06). Microbiological analysis (quantitative reverse transcription-polymerase chain reaction) measured 50 genomic copies per liter of norovirus genogroup I in the well water. Nucleotide sequencing determined the genotype as GI.2 and further showed the identical virus was present in patrons' stool specimens and in the septic tank. Tracer tests using dyes injected at two points in the septic system showed that effluent was traveling from the tanks (through a leaking fitting) and infiltration field to the well in 6 and 15 d, respectively. The restaurant septic system and well (85-m deep, in a fractured dolomite aquifer) both conformed to state building codes. The early arrival of dye in the well, which was 188 m from the septic field and located beneath a 35-m thick vadose zone, demonstrates that in highly vulnerable hydrogeological settings, compliance with regulations may not provide adequate protection from fecal pathogens.
Convective transport of dissolved oxygen (D.O.) from shallow to deeper parts of wells was observed as the shallow water in wells in South Carolina became cooler than the deeper water in the wells due to seasonal changes. Wells having a relatively small depth to water were more susceptible to thermally induced convection than wells where the depth to water was greater because the shallower water levels were more influenced by air temperature. The potential for convective transport of D.O. to maintain oxygenated conditions in a well screened in an anaerobic aquifer was diminished as ground water exchange through the well screen increased and as oxygen demand increased. Transport of D.O. to the screened interval can adversely affect the ability of passive samplers to produce accurate concentrations of oxygen-sensitive solutes such as iron, other redox indicators, and microbiological data. A comparison of passive sampling to low-flow sampling in a well undergoing convection, however, showed general agreement of volatile organic compound concentrations. During low-flow sampling, the pumped water may be a mixture of convecting water from within the well casing and aquifer water moving inward through the screen. This mixing of water during low-flow sampling can substantially increase equilibration times, can cause false stabilization of indicator parameters, can give false indications of the redox state, and can provide microbiological data that are not representative of the aquifer conditions. Data from this investigation show that simple in-well devices can effectively mitigate convective transport of oxygen. The devices can range from inflatable packers to simple, inexpensive baffle systems. ?? 2007 National Ground Water Association.
The American Society for Microbiology (ASM) national conference, Microbe, is the flagship meeting for microbiologists across the globe. The presence of roughly 10,000 attendees provides enormous opportunities for networking and learning. However, such a large meeting can be intimidating to many, especially early career scientists, students, those attending alone, and those from historically underrepresented groups. While mentorship is widely valued by ASM and its members, finding concrete ways to develop new and diverse mentoring opportunities can be a challenge. We recognized the need for an initiative aimed at expanding peer-to-peer mentoring, facilitating networking, and providing support for Microbe attendees; therefore, we created the program Binning Singletons for ASM Microbe 2019. The program consisted of five steps named after tools or phenomena in the profession of microbiology: (i) Identify the Singletons (e.g., individuals attending alone), (ii) Bin the Singletons, (iii) Horizontal Transfer, (iv) Quorum Sensing, and (v) Exponential Growth. These steps resulted in the matching of participants unsure of how to get the most out of their conference experience (e.g., singletons) with mentors who assisted with meeting planning, networking, and/or impostor syndrome. Started on social media only a month before ASM Microbe 2019, the program successfully launched despite limited time and resources. Binning Singletons improved inclusivity and networking opportunities for participants at the conference. Here, we discuss what worked, and what can be improved, with an eye toward development of the Binning Singletons model for future conferences to provide opportunities to increase inclusivity, networking, and accessibility for singletons and build a stronger scientific community.