SEARCH · Search USGS

Results for “Applied Microbiology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

173 records · Page 10Linked to original sources

USGS2010

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

Ecosystems↗

USGS2005

Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt) sequences of the VHSV glycoprotein ( G ) gene, were used to predict restriction fragment length polymorphism (RFLP) patterns that were subsequently grouped and compared with a phylogenetic analysis of the G -gene sequences of the same set of isolates. Digestion of PCR amplicons from the full-length G -gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes. Experimental evaluation of the method consisted of three steps: (i) RT-PCR amplification of the G -gene of VHSV isolates using purified viral RNA as template, (ii) digestion of the PCR products with a panel of restriction endonucleases and (iii) interpretation of the resulting RFLP profiles. The RFLP analysis was shown to approximate the level of genetic discrimination obtained by other, more labour-intensive, molecular techniques such as the ribonuclease protection assay or sequence analysis. In addition, 37 previously uncharacterised isolates from diverse sources were assigned to specific genotypes. While the assay was able to distinguish between marine and continental isolates of VHSV, the differences did not correlate with the pathogenicity of the isolates.

Veterinary Microbiology↗

USGS2019

Predicting paleoclimate from compositional data using multivariate Gaussian process inverse prediction

Multivariate compositional count data arise in many applications including ecology, microbiology, genetics and paleoclimate. A frequent question in the analysis of multivariate compositional count data is what underlying values of a covariate(s) give rise to the observed composition. Learning the relationship between covariates and the compositional count allows for inverse prediction of unobserved covariates given compositional count observations. Gaussian processes provide a flexible framework for modeling functional responses with respect to a covariate without assuming a functional form. Many scientific disciplines use Gaussian process approximations to improve prediction and make inference on latent processes and parameters. When prediction is desired on unobserved covariates given realizations of the response variable, this is called inverse prediction. Because inverse prediction is often mathematically and computationally challenging, predicting unobserved covariates often requires fitting models that are different from the hypothesized generative model. We present a novel computational framework that allows for efficient inverse prediction using a Gaussian process approximation to generative models. Our framework enables scientific learning about how the latent processes co-vary with respect to covariates while simultaneously providing predictions of missing covariates. The proposed framework is capable of efficiently exploring the high dimensional, multi-modal latent spaces that arise in the inverse problem. To demonstrate flexibility, we apply our method in a generalized linear model framework to predict latent climate states given multivariate count data. Based on cross-validation, our model has predictive skill competitive with current methods while simultaneously providing formal, statistical inference on the underlying community dynamics of the biological system previously not available.

Annals of Applied Statistics↗

USGS2007

Ground water redox zonation near La Pine, Oregon: Relation to river position within the aquifer–riparian zone continuum

Increasing residential development since in the 1960s has lead to increases in nitrate concentrations in shallow ground water in parts of the 247 square mile study area near La Pine, Oregon. Denitrification is the dominant nitrate-removal process that occurs in suboxic ground water, and suboxic ground water serves as a barrier to transport of most nitrate in the aquifer. Oxic ground water, on the other hand, represents a potential pathway for nitrate transport from terrestrial recharge areas to the Deschutes and Little Deschutes Rivers. The effects of present and potential future discharge of ground-water nitrate into the nitrogen-limited Deschutes and Little Deschutes Rivers are not known. However, additions of nitrogen to nitrogen-limited rivers can lead to increases in primary productivity which, in turn, can increase the magnitudes of dissolved oxygen and pH swings in river water. An understanding of the distribution of oxic ground water in the near-river environment could facilitate understanding the vulnerability of these rivers and could be a useful tool for management of these rivers. In this study, transects of temporary wells were installed in sub-river sediments beneath the Deschutes and Little Deschutes Rivers near La Pine to characterize near-river reduction/oxidation (redox) conditions near the ends of ground-water flow paths. Samples from transects installed near the center of the riparian zone or flood plain were consistently suboxic. Where transects were near edges of riparian zones, most ground-water samples also were suboxic. Oxic ground water (other than hyporheic water) was uncommon, and was only detected near the outside edge of some meander bends. This pattern of occurrence likely reflects geochemical controls throughout the aquifer as well as geochemical processes in the microbiologically active riparian zone near the end of ground-water flow paths. Younger, typically less reduced ground water generally enters near-river environments through peripheral zones, whereas older, typically more reduced ground water tends to discharge closer to the center of the river corridor. Such distributions of redox state reflect ground-water movement and geochemical evolution at the aquifer-scale. Redox state of ground water undergoes additional modification as ground water nears discharge points in or adjacent to rivers, where riparian zone processes can be important. Lateral erosion of river systems away from the center of the flood plain can decrease or even eliminate interactions between ground water and reducing riparian zone sediments. Thus, ground water redox patterns in near-river sediments appear to reflect the position of a river within the riparian zone/aquifer continuum. Spatial heterogeneity of redox conditions near the river/aquifer boundary (that is, near the riverbed) makes it difficult to extrapolate transect-scale findings to a precise delineation of the oxic-suboxic boundary in the near-river environment of the entire study area. However, the understanding of relations between near-river redox state and proximity to riparian zone edges provides a basis for applying these results to the study-area scale, and could help guide management efforts such as nitrogen-reduction actions or establishment of Total Maximum Daily Load criteria. Coupling the ground-water redox-based understanding of river vulnerability with ground-water particle-tracking-based characterization of connections between upgradient recharge areas and receiving rivers demonstrates one means of linking effects of potential nitrate loads at the beginning of ground-water flow paths with river vulnerability.

Oregon↗

USGS2020

Mapping metabolic activity at single cell resolution in intact volcanic fumarole soil

Interactions among microorganisms and their mineralogical substrates govern the structure, function, and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset, and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu’s Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2, and SO2. With increasing distance from the soil-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, mineral exteriors accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities “as they really are” and explore determinants of metabolic activity across a range of microbiomes.

FEMS Microbiology Letters↗

USGS2000

Methodology for applying monitored natural attenuation to petroleum hydrocarbon-contaminated ground-water systems with examples from South Carolina

Natural attenuation processes such as dispersion, advection, and biogradation serve to decrease concentrations of disssolved contaminants as they are transported in all ground-water systems. However, the efficiency of these natural attenuation processes and the degree to which they help attain remediation goals, varies considerably from site to site. This report provides a methodology for quantifying various natural attenuation mechanisms. This methodology incorporates information on (1) concentrations of contaminants in space and/or time; (2) ambient reduction/oxidation (redox) conditions; (3) rates and directions of ground-water flow; (4) rates of contaminant biodegradation; and (5) demographic considerations, such as the presence of nearby receptor exposure points or property boundaries. This document outlines the hydrologic, geochemical, and biologic data needed to assess the efficiency of natural attenuation, provides a screening tool for making preliminary assessments, and provides examples of how to determine when natural attenuation can be a useful component of site remediation at leaking underground storage tank sites. At a site in the Piedmont Physiographic Province (Laurens, South Carolina), hydrologic and water-chemistry data indicate that the natural attenuation capacity for benzene is approximately 5 percent per foot of flowpath. As a result, benzene concentrations would decrease from about 28,000 micrograms per liter in ground water at the source area to less than 5 micrograms per liter 200 feet downgradient and prior to discharging to a stream. Because of this rapid attenuation, contaminants do not presently impact the stream downgradient of the site. In contrast, at a site in the coastal Plain Physiographic Province (Charleston, South Carolina), hydrologic and water-chemistry data indicate that, even thought the site has a substantial natural attenuation capacity, it may not be sufficient to fully protect a nearby point of ground-water discharge. These two sites illustrate how the efficiency of natural attenuation processes acting on petroleum hydrocarbons can be systematically evaluated using hydrologic, geochemical, and microbiologic methods. These methods, in turn, can be used to assess the role that the natural attenuation of petroleum hydrocarbons can play in achieving overall site remediation.

South Carolina↗

USGS2020

Formation and prevention of pipe scale from acid mine drainage at Iron Mountain and Leviathan Mines, California, USA

Pipelines carrying acid mine drainage (AMD) to treatment plants commonly form pipe scale, an Fe(III)-rich precipitate that forms inside the pipelines and requires periodic and costly cleanout and maintenance. Pipelines at Iron Mountain Mine (IMM) and Leviathan Mine (LM) in California carry acidic water from mine sources to a treatment plant and have developed pipe scale. Samples of scale and AMD were collected from both mine sites for mineralogical, microbiological, and chemical analysis. The scale mineralogy was primarily schwertmannite with minor amounts of poorly crystalline goethite. Although the bulk composition of the scale was similar along the length of the pipeline at IMM, the number of iron-oxidizing bacteria and concentrations of associated trace elements decreased along the flow-path inside the pipeline. Laboratory batch experiments with unfiltered AMD from IMM and LM showed that Fe(II) oxidation was driven by microbial activity when the pH was <5. A remediation strategy of decreasing the pH to <2.2 was tested through geochemical modeling and laboratory experiments. These experiments indicated that scale formation could be prevented by decreasing the pH, which could be achieved at IMM by mixing source waters. However, the presence of Fe(III)-rich scale in a pipeline buffers the pH to higher values that may affect the efficacy of this remedial approach.

California↗

USGS2015

Hydrogeochemistry and microbiology of mine drainage: An update

The extraction of mineral resources requires access through underground workings, or open pit operations, or through drillholes for solution mining. Additionally, mineral processing can generate large quantities of waste, including mill tailings, waste rock and refinery wastes, heap leach pads, and slag. Thus, through mining and mineral processing activities, large surface areas of sulfide minerals can be exposed to oxygen, water, and microbes, resulting in accelerated oxidation of sulfide and other minerals and the potential for the generation of low-quality drainage. The oxidation of sulfide minerals in mine wastes is accelerated by microbial catalysis of the oxidation of aqueous ferrous iron and sulfide. These reactions, particularly when combined with evaporation, can lead to extremely acidic drainage and very high concentrations of dissolved constituents. Although acid mine drainage is the most prevalent and damaging environmental concern associated with mining activities, generation of saline, basic and neutral drainage containing elevated concentrations of dissolved metals, non-metals, and metalloids has recently been recognized as a potential environmental concern. Acid neutralization reactions through the dissolution of carbonate, hydroxide, and silicate minerals and formation of secondary aluminum and ferric hydroxide phases can moderate the effects of acid generation and enhance the formation of secondary hydrated iron and aluminum minerals which may lessen the concentration of dissolved metals. Numerical models provide powerful tools for assessing impacts of these reactions on water quality.

Applied Geochemistry↗

USGS2015

Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells

Hydraulically fractured shales are becoming an increasingly important source of natural gas production in the United States. This process has been known to create up to 420 gallons of produced water (PW) per day, but the volume varies depending on the formation, and the characteristics of individual hydraulic fracture. PW from hydraulic fracturing of shales are comprised of injected fracturing fluids and natural formation waters in proportions that change over time. Across the state of Pennsylvania, shale gas production is booming; therefore, it is important to assess the variability in PW chemistry and microbiology across this geographical span. We quantified the inorganic and organic chemical composition and microbial communities in PW samples from 13 shale gas wells in north central Pennsylvania. Microbial abundance was generally low (66–9400 cells/mL). Non-volatile dissolved organic carbon (NVDOC) was high (7–31 mg/L) relative to typical shallow groundwater, and the presence of organic acid anions (e.g., acetate, formate, and pyruvate) indicated microbial activity. Volatile organic compounds (VOCs) were detected in four samples (&sim;1 to 11.7 μg/L): benzene and toluene in the Burket sample, toluene in two Marcellus samples, and tetrachloroethylene (PCE) in one Marcellus sample. VOCs can be either naturally occurring or from industrial activity, making the source of VOCs unclear. Despite the addition of biocides during hydraulic fracturing, H 2 S-producing, fermenting, and methanogenic bacteria were cultured from PW samples. The presence of culturable bacteria was not associated with salinity or location; although organic compound concentrations and time in production were correlated with microbial activity. Interestingly, we found that unlike the inorganic chemistry, PW organic chemistry and microbial viability were highly variable across the 13 wells sampled, which can have important implications for the reuse and handling of these fluids

Pennsylvania↗

USGS2022

Biosafety practices when working with bats: A guide to field research considerations

Introduction: Field work with bats is an important contribution to many areas of research in environmental biology and ecology, as well as microbiology. Work with bats poses hazards such as bites and scratches, and the potential for exposure to infectious pathogens such as rabies virus. It also exposes researchers to many other potential hazards inherent to field work, such as environmental conditions, delayed emergency responses, or challenging work conditions. Methods: This article discusses the considerations for a thorough risk assessment process around field work with bats, pre- and post-occupational health considerations, and delves into specific considerations for areas related to biosafety concerns—training, personal protective equipment, safety consideration in field methods, decontamination, and waste. It also touches on related legal and ethical issues that sit outside the realm of biosafety, but which must be addressed during the planning process. Discussion: Although the focal point of this article is bat field work located in northern and central America, the principles and practices discussed here are applicable to bat work elsewhere, as well as to field work with other animal species, and should promote careful considerations of how to safely conduct field work to protect both researchers and animals.

Applied Biosafety↗

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↗