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At least 55 records · Page 3Linked to original sources
USGS2024

Editorial: Subsurface microbiology within hydrocarbon resources or stored gases

A Research Topic on the microbiology of hydrocarbon and gas storage reservoirs has far reaching industrial applications. In recent decades, there has been a growing interest in understanding microbial communities in subsurface energy reservoirs, such as coal, oil, and shale beds. This area of research has broadened to include gas storage reservoirs for hydrogen and CO 2 . Scientists are beginning to unravel the unexpected impact microorganisms have on these systems, through changing the fluid geochemistry, the gas content, and even the permeability. By recognizing the influence of these tiny organisms on our engineered environments, we can develop better risk assessments, target mitigation strategies, expand energy production, and refine operational guidance, ultimately contributing to a more sustainable energy future.

Frontiers in Ecology and Evolution↗
USGS2019

SUSTAIN drilling at Surtsey volcano, Iceland, tracks hydrothermal and microbiological interactions in basalt 50 years after eruption

The 2017 Surtsey Underwater volcanic System for Thermophiles, Alteration processes and INnovative concretes (SUSTAIN) drilling project at Surtsey volcano, sponsored in part by the International Continental Scientific Drilling Program (ICDP), provides precise observations of the hydrothermal, geochemical, geomagnetic, and microbiological changes that have occurred in basaltic tephra and minor intrusions since explosive and effusive eruptions produced the oceanic island in 1963–1967. Two vertically cored boreholes, to 152 and 192 m below the surface, were drilled using filtered, UV-sterilized seawater circulating fluid to minimize microbial contamination. These cores parallel a 181 m core drilled in 1979. Introductory investigations indicate changes in material properties and whole-rock compositions over the past 38 years. A Surtsey subsurface observatory installed to 181 m in one vertical borehole holds incubation experiments that monitor in situ mineralogical and microbial alteration processes at 25–124 ∘C. A third cored borehole, inclined 55∘ in a 264∘ azimuthal direction to 354 m measured depth, provides further insights into eruption processes, including the presence of a diatreme that extends at least 100 m into the seafloor beneath the Surtur crater. The SUSTAIN project provides the first time-lapse drilling record into a very young oceanic basaltic volcano over a range of temperatures, 25–141 ∘C from 1979 to 2017, and subaerial and submarine hydrothermal fluid compositions. Rigorous procedures undertaken during the drilling operation protected the sensitive environment of the Surtsey Natural Preserve.

Scientific Drilling↗
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↗
USGS2007

Coral microbiology

In the last 30 years, there has been approximately a 30% loss of corals worldwide, largely due to emerging diseases (Harvell et al., 2002, 2007; Hughes et al., 2003). Coral microbiology is a new field, driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms and to use this knowledge to eventually prevent the spread of coral diseases.

Oceanography↗
USGS2017

Canyons microbiology studies

Off the eastern coast of the United States, several deep canyons cut through the continental shelf, acting like funnels to move sediment from the shelf out to the deep seafloor. Exposed rock outcrops and ledges along the walls of these canyons provide important habitat for deepsea corals and sponges. Although a few scientific expeditions have visited these canyons in the 1970s (Hecker and Blechschmidt 1979, Hecker et al. 1980), their purpose was mainly to map the contours and capture photographs of the bottom using manned submersibles and towed cameras. Our knowledge of the biodiversity in these complex ecosystems is limited; we know little about the macrofauna (e.g., fishes, crabs, sponges, and deepsea corals) and even less about the microbiota. The research described in this report was conducted from 2011 to 2015 as part of the Bureau of Ocean Energy Management (BOEM) study, entitled “Atlantic Deepwater Canyons” study. This work used molecular and microbiological techniques to examine the microbial ecology and diversity associated with Baltimore and Norfolk canyons. Specifically, this work focused on the microbial ecology of four species of octocorals (Acanthogorgia aspera, Anthothela grandiflora, Paramuricea placomus, and Primnoa resedaeformis), the microbial diversity in sediments within and outside the canyons, and a settling plate experiment designed to characterize microbial biofilm formation on a variety of hard substrates.

OCS Study↗
USGS2020

Nowcasting methods for determining microbiological water quality at recreational beaches and drinking-water source waters

Nowcasts are tools used to provide timely and accurate water-quality assessments of threats to drinking-water and recreational resources from fecal contamination or cyanobacterial harmful algal blooms. They use mathematical models and techniques to provide near-real-time estimates of fecal-indicator bacteria (FIB) and cyanotoxin concentrations. Techniques include logic-based thresholds, decision trees (built with machine learning), multiple linear and binary logistic regression, artificial neural networks, and process-based deterministic models. The type of site (freshwater, marine, or river) and dependent variable (FIB or cyanotoxin) dictate which explanatory variables are used in models. Nowcast systems notify the public of associated public-health risks and can also be used to manage data for FIB models; work is ongoing to incorporate cyanotoxin models into some nowcasts. The Great Lakes NowCast in the USA has been operational since 2010 and includes 25 lake beaches and one recreational river site. Examples of other operational FIB nowcasts are described for locations in the USA and around the world. In many cases, models predicted exceedances of FIB standards with accuracies as good as or better than using the previous measured FIB concentration (persistence method). Accuracy and timeliness are vital to beach management decisions that protect public health and support the local recreation-driven economy. Nowcasts benefit the public by providing estimates of water-quality conditions in near-real-time. Managers can use nowcasts at recreational and drinking-water treatment plant sites when FIB or cyanotoxins are projected to be elevated to target sample collection, to provide near-real-time recreational advisories to the public, or to preemptively optimize drinking-water treatments or change intake options to mitigate possible adverse effects on drinking-water quality.

Journal of Microbiological Methods↗
USGS2022

Spatially integrating microbiology and geochemistry to reveal complex environmental health issues: Anthrax in the contiguous United States

Maxent models were run using the B. anthracis presence data and/or the animal outbreak presence data. Models run using the animal outbreak data alone utilized two scales: the Outbreak State scale which included only states reporting animal anthrax outbreaks from 2001 to 2013 and the National scale which included all states in the contiguous United States. Three iterations of the environmental data were used and included the Sample Location dataset which utilized the environmental variable data with assigned latitude and longitude locations from the USGS NASGLP project; the Normalized dataset which scaled the environmental variables so that the values fell between 0 and 1; and the Interpolated dataset which provided an interpolation of the environmental variables averaged for each county and assigned to a point for that county at the centroid (rather than using the NASGLP latitude and longitude location). Two metrics were used to measure model performance including the widely used area under the curve (AUC) and an alternative method, the True Skill Statistic (TSS). The AUC gives the probability that a randomly chosen presence location has been correctly ranked higher than the absence/background site. AUC values at 0.5 or lower mean the ranking is no better than random, while the AUC values nearer to 1 mean the model is a better predictor. The TSS provides a comparison of how well the background predictions made by the model match the model results at the test dataset (presence) locations. TSS values near +1 means the model approaches perfect agreement, while values near −1 indicate the model is no better than random. Maxent models to determine the influence of environmental factors on the B. anthracis distribution using the PCR data yielded a low TSS, which suggested the model might be underfitting the data. This was not surprising due to the difficulty in recovering B. anthracis in soil samples as well as the samples themselves being discrete in nature and only capturing a snapshot in time. Therefore, the distribution of B. anthracis and its niche in the contiguous United States could not be determined in this study. However, efforts to investigate environmental factors that would have a higher potential of supporting an anthrax outbreak in wildlife and livestock yielded better results. Results showed that most of the Maxent models in this study performed best when using the Outbreak State scale. When the models were scaled up to the National scale, model performance declined, except for the Normalized variable dataset. At the Outbreak State scale, a large proportion of the area was predicted to be of higher probability for wildlife/livestock anthrax outbreaks, and the statistical measures assumed the model was underfitting the data. The model with the highest AUC and TSS scores for this study was the Outbreak State scale using Sample Location dataset (AUC = 0.918 and TSS = 0.82). Some of the variables found to be closely related to the occurrence of B. anthracis in this study included pH, drainage potential, and concentration of elements including Na, Ca, Sr, and Mg, which have also been found to be related to animal outbreaks or to the occurrence of B. anthracis in previous studies. The models in the current study indicated possible regions that have not had recent wildlife/livestock anthrax outbreaks but contained environmental conditions that could potentially support an outbreak if one were to occur (Michigan and Maine). This work provides an extension to the use of ecological niche modeling to outbreak potential in livestock/wildlife in the United States because it utilizes additional soil geochemistry data and has shown that further validation techniques, such as the TSS, should be considered in addition to AUC. Results from this study could be used by animal and public health officials to identify areas with a higher potential for anthrax outbreak in wildlife and livestock due to naturally occurring soil and environmental conditions.

Book chapter↗
USGS2009

Stratospheric microbiology at 20 km over the Pacific Ocean

An aerobiology sampling flight at 20 km was conducted on 28 April 2008 over the Pacific Ocean (36.5° N, 118–149° W), a period of time that coincided with the movement of Asian dust across the ocean. The aim of this study was to confirm the presence of viable bacteria and fungi within a transoceanic, atmospheric bridge and to improve the resolution of flight hardware processing techniques. Isolates of the microbial strains recovered were analyzed with ribosomal ribonucleic acid (rRNA) sequencing to identify bacterial species Bacillus sp., Bacillus subtilis, Bacillus endophyticus, and the fungal genus Penicillium. Satellite imagery and ground-based radiosonde observations were used to measure dust movement and characterize the high-altitude environment at the time of collection. Considering the atmospheric residency time (7–10 days), the extreme temperature regime of the environment (-75°C), and the absence of a mechanism that could sustain particulates at high altitude, it is unlikely that our samples indicate a permanent, stratospheric ecosystem. However, the presence of viable fungi and bacteria in transoceanic stratosphere remains relevant to understanding the distribution and extent of microbial life on Earth.

Aerobiologia↗
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↗
USGS2020

Evaluating the impacts of foreshore sand and birds on microbiological contamination at a freshwater beach

Beaches along the Great Lakes shorelines are important recreational and economic resources. However, contamination at the beaches can threaten their usage during the swimming season, potentially resulting in beach closures and/or advisories. Thus, understanding the dynamics that control nearshore water quality is integral to effective beach management. There have been significant improvements in this effort, including incorporating modeling (empirical, mechanistic) in recent years. Mechanistic modeling frameworks can contribute to this understanding of dynamics by determining sources and interactions that substantially impact fecal indicator bacteria concentrations, an index routinely used in water quality monitoring programs. To simulate E. coli concentrations at Jeorse Park beaches in southwest Lake Michigan, a coupled hydrodynamic and wave–current interaction model was developed that progressively added contaminant sources from river inputs, avian presence, bacteria–sediment interactions, and bacteria–sand–sediment interactions. Results indicated that riverine inputs affected E. coli concentrations at Jeorse Park beaches only marginally, while avian, shoreline sand, and sediment sources were much more substantial drivers of E. coli contamination at the beach. By including avian and riverine inputs, as well as bacteria–sand–sediment interactions at the beach, models can reasonably capture the variability in observed E. coli concentrations in nearshore water and bed sediments at Jeorse Park beaches. Consequently, it will be crucial to consider avian contamination sources and water-sand-sediment interactions in effective management of the beach for public health and as a recreational resource and to extend these findings to similar beaches affected by shoreline embayment.

Illlinois↗
USGS2018

Real-time nowcasting of microbiological water quality at recreational beaches: A wavelet and artificial neural network-based hybrid modeling approach

The number of beach closings caused by bacterial contamination has continued to rise in recent years, putting beachgoers at risk of exposure to contaminated water. Current approaches predict levels of indicator bacteria using regression models containing a number of explanatory variables. Data-based modeling approaches can supplement routine monitoring data and provide highly accurate short-term forecasts of beach water quality. In this paper, we apply the nonlinear autoregressive network with exogenous inputs (NARX) method with explanatory variables to predict Escherichia coli concentrations at four Lake Michigan beach sites. We also apply the nonlinear input–output network (NIO) and nonlinear autoregressive neural network (NAR) methods in addition to a hybrid wavelet-NAR (WA-NAR) model and demonstrate their application. All models were tested using 3 months of observed data. Results revealed that the NARX models provided the best performance and that the WA-NAR model, which requires no explanatory variables, outperformed the NIO and NAR models; therefore, the WA-NAR model is suitable for application to data scarce regions. The models proposed in this paper were evaluated using multiple performance metrics, including sensitivity and specificity measures, and produced results comparable or superior to those of previous mechanistic and statistical models developed for the same beach sites. The relatively high R 2 values between data and the NARX models ( R 2 values of ∼0.8 for the beach sites and ∼0.9 for the river site) indicate that the new class of models shows promise for beach management.

Environmental Science & Technology↗
USGS2013

Geographic setting influences Great Lakes beach microbiological water quality

Understanding of factors that influence Escherichia coli (EC) and enterococci (ENT) concentrations, pathogen occurrence, and microbial sources at Great Lakes beaches comes largely from individual beach studies. Using 12 representative beaches, we tested enrichment cultures from 273 beach water and 22 tributary samples for EC, ENT, and genes indicating the bacterial pathogens Shiga-toxin producing E. coli (STEC), Shigella spp., Salmonella spp, Campylobacter jejuni/coli, and methicillin-resistant Staphylococcus aureus, and 108–145 samples for Bacteroides human, ruminant, and gull source-marker genes. EC/ENT temporal patterns, general Bacteroides concentration, and pathogen types and occurrence were regionally consistent (up to 40 km), but beach catchment variables (drains/creeks, impervious surface, urban land cover) influenced exceedances of EC/ENT standards and detections of Salmonella and STEC. Pathogen detections were more numerous when the EC/ENT Beach Action Value (but not when the Geometric Mean and Statistical Threshold Value) was exceeded. EC, ENT, and pathogens were not necessarily influenced by the same variables. Multiple Bacteroides sources, varying by date, occurred at every beach. Study of multiple beaches in different geographic settings provided new insights on the contrasting influences of regional and local variables, and a broader-scale perspective, on significance of EC/ENT exceedances, bacterial sources, and pathogen occurrence.

Great Lakes↗
USGS1996

Hydrologic and microbiological factors affecting persistence and migration of petroleum hydrocarbons spilled in a continuous-permafrost region

Fuel spills, totaling about 1300 m3, occurred between 1976 and 1978 adjacent to Imikpuk Lake, a drinking water source near Barrow, AK. Substantial contamination of soils and groundwater near the lake persists. We examined the magnitude and direction of groundwater flux and the microbial activity at this site to understand the persistence of contamination and its effect on the lake. We found that groundwater flux is small due to shallow permafrost, which restricts the cross-sectional area available for flow, and to the short annual thaw season (ca. 90 days). The small flux and limited depth also constrain contaminant transport and dispersion, resulting in persistent, shallow contamination. The numbers of hydrocarbon-oxidizing microorganisms and their laboratory mineralization potentials for benzene (at 10 ??C) were higher in samples from contaminated areas than in reference samples. Benzene mineralization potentials in groundwater samples were comparable to more temperate systems (0.1-0.5 mg of benzene mineralized L-1 day-1) and were stimulated by nutrient additions. Field measurements of dissolved oxygen, nitrate, ferrous iron, and sulfide in groundwater provided evidence that biodegradation of petroleum hydrocarbons is occurring in situ. Despite evidence of an active microbial population, microbial processes, like contaminant transport, are likely limited at this site by the short annual thaw season.

Environmental Science & Technology↗
USGS2001

African desert dust in the Caribbean atmosphere: Microbiology and public health

Air samples collected on St. John in the U.S. Virgin Islands were screened for the presence of viable bacteria and fungi to determine if the number of cultivatable microbes in the atmosphere differed between "clear atmospheric conditions" and "African dust-events." Results indicate that during "African dust-events," the numbers of cultivatable airborne microorganisms can be 2 to 3 times that found during "clear atmospheric conditions." Direct microbial counts of air samples using an epifluorescent microscopy assay demonstrated that during an "African dust-event," bacteria-like and virus-like particle counts were approximately one log greater than during "clear atmospheric conditions." Bacteria-like particles exhibiting autofluoresence, a trait of phototrophs, were only detected during an "African dust-event.".

Aerobiologia↗
USGS2003

Atmospheric microbiology in the northern Caribbean during African dust events

Between July 2000 and August 2001 forty-three air samples were collected in the northern Caribbean: Twenty-six in the US Virgin Islands, and 17 samples aboard ship during two 1-week cruises. Samples were collected during African dust events and non-dust conditions and screened for the presence of culturable bacteria and fungi. A total of 3,652 liters of air were collected during non-dust conditions, with 19 bacteria and 28 fungi being recovered. During dust conditions a total of 2,369 liters of air were screened resulting in the recovery of 171 bacteria and 76 fungi. A statistically significant difference was found between the two data sets. These results support previous African dust research and further demonstrate that dust particles can serve as a vessel for the global dispersion of bacteria and fungi. Dustborne microorganisms may play a significant role in the ecology and health of downwind ecosystems.

Aerobiologia↗
USGS2007

Microbiological quality of Puget Sound Basin streams and identification of contaminant sources

Fecal coliforms, Escherichia coli , enterococci, and somatic coliphages were detected in samples from 31 sites on streams draining urban and agricultural regions of the Puget Sound Basin Lowlands. Densities of bacteria in 48 and 71 percent of the samples exceeded U.S. Environmental Protection Agency's freshwater recreation criteria for Escherichia coli and enterococci, respectively, and 81 percent exceeded Washington State fecal coliform standards. Male-specific coliphages were detected in samples from 15 sites. Male-specific F + RNA coliphages isolated from samples taken at South Fork Thornton and Longfellow Creeks were serotyped as Group II, implicating humans as potential contaminant sources. These two sites are located in residential, urban areas. F + RNA coliphages in samples from 10 other sites, mostly in agricultural or rural areas, were serotyped as Group I, implicating non-human animals as likely sources. Chemicals common to wastewater, including fecal sterols, were detected in samples from several urban streams, and also implicate humans, at least in part, as possible sources of fecal bacteria and viruses to the streams.

Journal of the American Water Resources Associatio↗
USGS2005

Microbiology: A microbial arsenic cycle in a salt-saturated, extreme environment

Searles Lake is a salt-saturated, alkaline brine unusually rich in the toxic element arsenic. Arsenic speciation changed from arsenate [As(V)] to arsenite [As(III)] with sediment depth. Incubated anoxic sediment slurries displayed dissimilatory As(V)-reductase activity that was markedly stimulated by H2 or sulfide, whereas aerobic slurries had rapid As(III)-oxidase activity. An anaerobic, extremely haloalkaliphilic bacterium was isolated from the sediment that grew via As(V) respiration, using either lactate or sulfide as its electron donor. Hence, a full biogeochemical cycle of arsenic occurs in Searles Lake, driven in part by inorganic electron donors.

Science↗