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Results for “Research in Microbiology”

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At least 73 records · Page 4Linked to original sources

USGS1986

Effects of organic wastes on water quality from processing of oil shale from the Green River Formation, Colorado, Utah, and Wyoming

A series of investigations were conducted during a 6-year research project to determine the nature and effects of organic wastes from processing of Green River Formation oil shale on water quality. Fifty percent of the organic compounds in two retort wastewaters were identified as various aromatic amines, mono- and dicarboxylic acids phenols, amides, alcohols, ketones, nitriles, and hydroxypyridines. Spent shales with carbonaceous coatings were found to have good sorbent properties for organic constituents of retort wastewaters. However, soils sampled adjacent to an in situ retort had only fair sorbent properties for organic constituents or retort wastewater, and application of retort wastewater caused disruption of soil structure characteristics and extracted soil organic matter constituents. Microbiological degradation of organic solutes in retort wastewaters was found to occur preferentially in hydrocarbons and fatty acid groups of compounds. Aromatic amines did not degrade and they inhibited bacterial growth where their concentrations were significant. Ammonia, aromatic amines, and thiocyanate persisted in groundwater contaminated by in situ oil shale retorting, but thiosulfate was quantitatively degraded one year after the burn. Thiocyanate was found to be the best conservative tracer for retort water discharged into groundwater. Natural organic solutes, isolated from groundwater in contact with Green River Formation oil shale and from the White River near Rangely, Colorado, were readily distinguished from organic constituents in retort wastewaters by molecular weight and chemical characteristic differences. (USGS)

Professional Paper↗

USGS2011

Hydrogeochemical processes governing the origin, transport and fate of major and trace elements from mine wastes and mineralized rock to surface waters

The formation of acid mine drainage from metals extraction or natural acid rock drainage and its mixing with surface waters is a complex process that depends on petrology and mineralogy, structural geology, geomorphology, surface-water hydrology, hydrogeology, climatology, microbiology, chemistry, and mining and mineral processing history. The concentrations of metals, metalloids, acidity, alkalinity, Cl - , F - and SO 4 2- found in receiving streams, rivers, and lakes are affected by all of these factors and their interactions. Remediation of mine sites is an engineering concern but to design a remediation plan without understanding the hydrogeochemical processes of contaminant mobilization can lead to ineffective and excessively costly remediation. Furthermore, remediation needs a goal commensurate with natural background conditions rather than water-quality standards that might bear little relation to conditions of a highly mineralized terrain. This paper reviews hydrogeochemical generalizations, primarily from US Geological Survey research, that enhance our understanding of the origin, transport, and fate of contaminants released from mined and mineralized areas. Mobility of potential or actual contaminants from mining and mineral processing activities depends on (1) occurrence : is the mineral source of the contaminant actually present? (2) abundance : is the mineral present in sufficient quantity to make a difference? (3) reactivity : what are the energetics, rates, and mechanisms of sorption and mineral dissolution and precipitation relative to the flow rate of the water? and (4) hydrology : what are the main flow paths for contaminated water? Estimates of relative proportions of minerals dissolved and precipitated can be made with mass-balance calculations if minerals and water compositions along a flow path are known. Combined with discharge, these mass-balance estimates quantify the actual weathering rate of pyrite mineralization in the environment and compare reasonably well with laboratory rates of pyrite oxidation except when large quantities of soluble salts and evaporated mine waters have accumulated underground. Quantitative mineralogy with trace-element compositions can substantially improve the identification of source minerals for specific trace elements through mass balances. Post-dissolution sorption and precipitation (attenuation) reactions depend on the chemical behavior of each element, solution composition and pH, aqueous speciation, temperature, and contact-time with mineral surfaces. For example, little metal attenuation occurs in waters of low pH (<3.5) and metals tend to maintain element ratios indicative of the main mineral or group of minerals from which they dissolved, except Fe, SiO 2 , and redox-sensitive oxyanions (As, Sb, Se, Mo, Cr, V). Once dissolved, metal and metalloid concentrations are strongly affected by redox conditions and pH. Iron is the most reactive because it is rapidly oxidized by bacteria and archaea and Fe(III) hydrolyzes and precipitates at low pH (1–3) which is related directly to its first hydrolysis constant, pK 1 = 2.2. Several insoluble sulfate minerals precipitate at low pH including anglesite, barite, jarosite, alunite and basaluminite. Aluminum hydrolyzes near pH 5 (pK 1 = 5.0) and provides buffering and removal of Al by mineral precipitation from pH 4–5.5. Dissolved sulfate behaves conservatively because the amount removed from solution by precipitation is usually too small relative to the high concentrations in the water column and relative to the flow rate of the water.

Applied Geochemistry↗

USGS1985

A procedure for estimating Bacillus cereus spores in soil and stream-sediment samples — A potential exploration technique

The presence of bacterial spores of the Bacillus cereus group in soils and stream sediments appears to be a sensitive indicator of several types of concealed mineral deposits, including vein-type gold deposits. The B. cereus assay is rapid, inexpensive, and inherently reproducible. The test, currently under investigation for its potential in mineral exploration, is recommended for use on a research basis. Among the aerobic spore-forming bacilli, only B. cereus and closely related strains produce an opaque zone in egg-yolk emulsion agar. This characteristic, also known as the Nagler of lecitho-vitellin reaction, has long been used to rapidly indentify and estimate presumptive B. cereus . The test is here adapted to permit rapid estimation of B. cereus spores in soil and stream-sediment samples. Relative standard deviation was 10.3% on counts obtained from two 40-replicate pour-plate determinations. As many as 40 samples per day can be processed. Enough procedural detail is included to permit investigation of the test in conventional geochemical laboratories using standard microbiological safety precautions.

Journal of Geochemical Exploration↗

USGS2004

The microbial arsenic cycle in Mono Lake, California

Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO 2 into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less “extreme” environments, such as drinking water aquifers.

California↗

USGS2003

Foreshore sand as a source of Escherichia coli in nearshore water of a Lake Michigan beach

Swimming advisories due to excessive Escherichia coli concentrations are common at 63rd Street Beach, Chicago, Ill. An intensive study was undertaken to characterize the source and fate of E. coli in beach water and sand at the beach. From April through September 2000, water and sand samples were collected daily or twice daily at two depths on three consecutive days per week (water samples, n = 1,747; sand samples, n = 858); hydrometeorological conditions and bird and bather distributions were also recorded. E. coli concentrations in sand and water were significantly correlated, with the highest concentration being found in foreshore sand, followed by those in submerged sediment and water of increasing depth. Gull contributions to E. coli densities in sand and water were most apparent on the day following gull activity in a given area. E. coli recolonized newly placed foreshore sand within 2 weeks. Analysis of variance, correlation, cluster analyses, concentration gradients, temporal-spatial distribution, demographic patterns, and DNA fingerprinting suggest that E. coli may be able to sustain population density in temperate beach sand during summer months without external inputs. This research presents evidence that foreshore beach sand (i) plays a major role in bacterial lake water quality, (ii) is an important non-point source of E. coli to lake water rather than a net sink, (iii) may be environmentally, and perhaps hygienically, problematic, and (iv) is possibly capable of supporting an autochthonous, high density of indicator bacteria for sustained periods, independent of lake, human, or animal input.

Applied and Environmental Microbiology↗

USGS2020

Repetitive sampling and control threshold improve 16S rRNA results from produced waters associated with hydraulically fractured shales

Sequencing microbial DNA from deep subsurface environments is complicated by a number of issues ranging from contamination to non-reproducible results. Many samples obtained from these environments - which are of great interest due to the potential to stimulate microbial methane generation - contain low biomass. Therefore, samples from these environments are difficult to study as sequencing results can be easily impacted by contamination. In this case, the low amount of sample biomass may be effectively swamped by the contaminating DNA and generate misleading results. Additionally, performing field work in these environments can be difficult, as researchers generally have limited access to and time on site. Therefore, optimizing a sampling plan to produce the best results while collecting the greatest number of samples over a short period of time is ideal. This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to oil and gas-producing environments. Forty-nine different samples were collected by filtering specific volumes of produced water from a hydraulically fractured well producing from the Niobrara Shale. Water was collected in two different sampling events 24 hours apart. Four to five samples were collected from 11 specific volumes. These samples along with eight different blanks were submitted for analysis. DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. The qPCR results varied across sampled volumes, while no discernible trend correlated contamination to volume of water filtered. This suggests that collecting a larger volume of sample may not result in larger biomass concentrations or better representation of a sampled environment. Researchers could prioritize collecting many low volume samples over few high-volume samples. Our results suggest that there also may be variability in the concentration of microbial communities present in produced waters over short (i.e., hours) time scales, which warrants further investigation. Submission of multiple blanks is also vital to determining how contamination or low biomass effects may influence a sample set collected from an unknown environment.

Montana, Wyoming, Colorado, New Mexico, Texas, Okl↗

USGS2016

Microbial antimony biogeochemistry: Enzymes, regulation, and related metabolic pathways

Antimony (Sb) is a toxic metalloid that occurs widely at trace concentrations in soil, aquatic systems, and the atmosphere. Nowadays, with the development of its new industrial applications and the corresponding expansion of antimony mining activities, the phenomenon of antimony pollution has become an increasingly serious concern. In recent years, research interest in Sb has been growing and reflects a fundamental scientific concern regarding Sb in the environment. In this review, we summarize the recent research on bacterial antimony transformations, especially those regarding antimony uptake, efflux, antimonite oxidation, and antimonate reduction. We conclude that our current understanding of antimony biochemistry and biogeochemistry is roughly equivalent to where that of arsenic was some 20 years ago. This portends the possibility of future discoveries with regard to the ability of microorganisms to conserve energy for their growth from antimony redox reactions and the isolation of new species of “antimonotrophs.”

Applied and Environmental Microbiology↗

USGS2017

Human health screening and public health significance of contaminants of emerging concern detected in public water supplies

The source water and treated drinking water from twenty five drinking water treatment plants (DWTPs) across the United States were sampled in 2010–2012. Samples were analyzed for 247 contaminants using 15 chemical and microbiological methods. Most of these contaminants are not regulated currently either in drinking water or in discharges to ambient water by the U. S. Environmental Protection Agency (USEPA) or other U.S. regulatory agencies. This analysis shows that there is little public health concern for most of the contaminants detected in treated water from the 25 DWTPs participating in this study. For vanadium, the calculated Margin of Exposure (MOE) was less than the screening MOE in two DWTPs. For silicon, the calculated MOE was less than the screening MOE in one DWTP. Additional study, for example a national survey may be needed to determine the number of people ingesting vanadium and silicon above a level of concern. In addition, the concentrations of lithium found in treated water from several DWTPs are within the range previous research has suggested to have a human health effect. Additional investigation of this issue is necessary. Finally, new toxicological data suggest that exposure to manganese at levels in public water supplies may present a public health concern which will require a robust assessment of this information.

Science of Total Environment↗

USGS1973

Microbiological aspects of ground-water recharge injection of purified unchlorinated sewage effluent at Bay Park, Long Island, N. Y.

Unchlorinated, tertiary-treated sewage effluent was injected through a well at Bay Park, Long Island, N.Y., into a sand aquifer at a rate of 340 gpm for 10 days. Massive, biologically produced slime deposits formed in the filter pack immediately adjacent to the well screen. Observed head buildup in the recharge well was correlated with the formation of these deposits. Comparison of results from this test with results of earlier tests suggests that formation of these deposits may be avoided by addition of chlorine to the injectant.

New York↗

USGS2023

Antimony in mine wastes: Geochemistry, mineralogy, microbiology

Antimony (Sb) is a valuable mined commodity, used mostly in fire retardants, and considered a critical element. It is also a potential environment hazard classed as a carcinogen. Antimony is concentrated in tailings and waste rock from Sb mines as well as other locations, such as precious metal deposits, where Sb is present in the ore but not recovered. This review covers the aqueous geochemistry, isotope chemistry, mineralogy, and microbiology of Sb in the context of mine waste. The primary minerals stibnite and sulfosalts may release Sb in surface and groundwaters and result in contamination of soils, plants, and river sediments. In some cases, Sb mobility is limited by its adsorption and incorporation into Fe (oxyhydr)oxides. At higher Sb concentrations, precipitation of Sb secondary hosts such as tripuhyite (FeSbO 4 , relatively insoluble) and brandholzite (Mg[Sb(OH) 6 ] 2 · 6H 2 O, highly soluble) influence Sb concentrations in water associated with mine waste. Although Sb is nonessential to organisms, microorganisms are involved in oxidation, reduction, and methylation processes that can drive biogeochemical transformations. Limited toxicological information about Sb makes it challenging to establish regulations or guidelines limiting the concentration of Sb. Antimony is frequently associated with arsenic in mine waste, and remediation design is often based on the assumption that both metalloids behave in a similar way. However, new research suggests that in some environments, this is not the case, and Sb should be considered based on its unique biogeochemical behavior.

Economic Geology↗

USGS2024

A multi-marker assessment of sewage contamination in streams using human-associated indicator bacteria, human-specific viruses, and pharmaceuticals

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.

Wisconsin↗

USGS2009

Microbial disease and the coral holobiont

Tropical coral reefs harbour a reservoir of enormous biodiversity that is increasingly threatened by direct human activities and indirect global climate shifts. Emerging coral diseases are one serious threat implicated in extensive reef deterioration through disruption of the integrity of the coral holobiont – a complex symbiosis between the coral animal, endobiotic alga and an array of microorganisms. In this article, we review our current understanding of the role of microorganisms in coral health and disease, and highlight the pressing interdisciplinary research priorities required to elucidate the mechanisms of disease. We advocate an approach that applies knowledge gained from experiences in human and veterinary medicine, integrated into multidisciplinary studies that investigate the interactions between host, agent and environment of a given coral disease. These approaches include robust and precise disease diagnosis, standardised ecological methods and application of rapidly developing DNA, RNA and protein technologies, alongside established histological, microbial ecology and ecological expertise. Such approaches will allow a better understanding of the causes of coral mortality and coral reef declines and help assess potential management options to mitigate their effects in the longer term.

Trends in Microbiology↗

USGS2020

A new sampler for the collection and retrieval of dry dust deposition

Atmospheric dust can influence biogeochemical cycles, accelerate snowmelt, and affect air, water quality, and human health. Yet, the bulk of atmospherically transported material remains poorly quantified in terms of total mass fluxes and composition. This lack of information stems in part from the challenges associated with measuring dust deposition. Here we report on the design and efficacy of a new dry deposition sampler (Dry Deposition Sampling Unit (DSU)) and method that quantifies the gravitational flux of dust particles. The sampler can be used alone or within existing networks such as those employed by the National Atmospheric Deposition Program (NADP). Because the samplers are deployed sterile and the use of water to remove trapped dust is not required, this method allows for the recovery of unaltered dry material suitable for subsequent chemical and microbiological analyses. The samplers were tested in the laboratory and at 15 field sites in the western United States. With respect to material retention, sampler performance far exceeded commonly used methods. Retrieval efficiency was >97% in all trials and the sampler effectively preserved grain size distributions during wind exposure experiments. Field tests indicated favorable comparisons to dust-on-snow measurement across sites ( r 2 0.70, p < 0.05) and within sites to co-located aerosol data ( r 2 0.57–0.99, p < 0.05). The inclusion of dust deposition and composition monitoring into existing networks increases spatial and temporal understanding of the atmospheric transport on materials and substantively furthers knowledge of the effects of dust on terrestrial ecosystems and human exposure to dust and associated deleterious compounds.

Arizona, California, Colorado, Idaho, Nevada, Utah↗

USGS2026

Core microbiomes as a potential fingerprinting method of Western USA dust sources

Introduction: Changing frequency and intensity of dust emissions impacts ecosystems and human health. Dust carries microbes, nutrients, heavy metals, and other materials that may change environmental biogeochemistry at deposition sites. Identifying dust sources provides key information on where and when mitigation strategies should be employed. However, commonly used geochemical or isotopic tracers are often not capable of distinguishing between geographic regions. Methods: We explored whether soil bacterial communities may provide distinct fingerprints of dust sources in the western United States. We identified bacterial core communities of dust from ten locations monitored by the National Wind Erosion Research Network (NWERN) with varied land use (cropland, rangeland, and playa), and compared communities to location, soil, and regional characteristics. Samples were collected monthly from Modified Wilson and Cooke (MWAC) samplers, composited by season (spring, summer, and fall), and analyzed using 16S rRNA sequencing. Results: We found distinct bacterial core communities that reflected dust source characteristics. In order of importance, precipitation levels ( p = 0.0001), location ( p = 0.0001), soil texture ( p = 0.0001), seasonality ( p = 0.0001), and elevation (p = 0.0002) were correlated with bacterial community composition. Discussion: Distinct bacterial core communities were associated with site characteristics such as biocrusts, playas, and military base proximity. Our results suggest that the use of core microbiomes may offer a fingerprinting method to identify dust source regions.

Colorado, Nevada, New Mexico, North Dakota, Oklaho↗

USGS2012

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.

Microbiology and Molecular Biology Reviews↗

USGS2025

STREAMS guidelines: Standards for technical reporting in environmental and host-associated microbiome studies

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

Nature Microbiology↗

USGS2017

Multi-year microbial source tracking study characterizing fecal contamination in an urban watershed

Microbiological and hydrological data were used to rank tributary stream contributions of bacteria to the Little Blue River in Independence, Missouri. Concentrations, loadings and yields of E. coli and microbial source tracking (MST) markers, were characterized during base flow and storm events in five subbasins within Independence, as well as sources entering and leaving the city through the river. The E. coli water quality threshold was exceeded in 29% of base-flow and 89% of storm-event samples. The total contribution of E. coli and MST markers from tributaries within Independence to the Little Blue River, regardless of streamflow, did not significantly increase the median concentrations leaving the city. Daily loads and yields of E. coli and MST markers were used to rank the subbasins according to their contribution of each constituent to the river. The ranking methodology used in this study may prove useful in prioritizing remediation in the different subbasins.

Missouri↗

USGS2006

Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. Copyright ?? 2006, American Society for Microbiology. All Rights Reserved.

Applied and Environmental Microbiology↗