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At least 55 records · Page 3Linked to original sources
USGS2015

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.

Frontiers in Microbiology↗
USGS2014

Arsenic associated with historical gold mining in the Sierra Nevada foothills: Case study and field trip guide for Empire Mine State Historic Park, California

The Empire Mine, together with other mines in the Grass Valley mining district, produced at least 21.3 million troy ounces (663 tonnes) of gold (Au) during the 1850s through the 1950s, making it the most productive hardrock Au mining district in California history ( Clark 1970 ). The Empire Mine State Historic Park (Empire Mine SHP or EMSHP), established in 1975, provides the public with an opportunity to see many well-preserved features of the historic mining and mineral processing operations ( CDPR 2014a ). A legacy of Au mining at Empire Mine and elsewhere is contamination of mine wastes and associated soils, surface waters, and groundwaters with arsenic (As), mercury (Hg), lead (Pb), and other metals. At EMSHP, As has been the principal contaminant of concern and the focus of extensive remediation efforts over the past several years by the State of California, Department of Parks and Recreation (DPR) and Newmont USA, Ltd. In addition, the site is the main focus of a multidisciplinary research project on As bioavailability and bioaccessibility led by the California Department of Toxic Substances Control (DTSC) and funded by the U.S. Environmental Protection Agency’s (USEPA’s) Brownfields Program. This chapter was prepared as a guide for a field trip to EMSHP held on June 14, 2014, in conjunction with a short course on “Environmental Geochemistry, Mineralogy, and Microbiology of Arsenic” held in Nevada City, California on June 15–16, 2014. This guide contains background information on geological setting, mining history, and environmental history at EMSHP and other historical Au mining districts in the Sierra Nevada, followed by descriptions of the field trip stops.

Reviews in Mineralogy and Geochemistry↗
USGS2002

A rapid and efficient assay for extracting DNA from fungi

Aims: A method for the rapid extraction of fungal DNA from small quantities of tissue in a batch-processing format was investigated. Methods and Results: Tissue (< 3.0 mg) was scraped from freshly-grown fungal isolates. The tissue was suspended in buffer AP1 and subjected to seven rounds of freeze/thaw using a crushed dry ice/ethanol bath and a boiling water bath. After a 30 min boiling step, the tissue was quickly ground against the wall of the microfuge tube using a sterile pipette tip. The Qiagen DNeasy Plant Tissue Kit protocol was then used to purify the DNA for PCR/ sequencing applications. Conclusions: The method allowed batch DNA extraction from multiple fungal isolates using a simple yet rapid and reliable assay. Significance and Impact of the Study: Use of this assay will allow researchers to obtain DNA from fungi quickly for use in molecular assays that previously required specialized instrumentation, was time-consuming or was not conducive to batch processing.

Letters in Applied Microbiology↗
USGS2009

Gulf of Mexico Deep-Sea Coral Ecosystem Studies, 2008-2011

Most people are familiar with tropical coral reefs, located in warm, well-illuminated, shallow waters. However, corals also exist hundreds and even thousands of meters below the ocean surface, where it is cold and completely dark. These deep-sea corals, also known as cold-water corals, have become a topic of interest due to conservation concerns over the impacts of trawling, exploration for oil and gas, and climate change. Although the existence of these corals has been known since the 1800s, our understanding of their distribution, ecology, and biology is limited due to the technical difficulties of conducting deep-sea research. DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) is a new U.S. Geological Survey (USGS) program focused on deep-water coral ecosystems in the Gulf of Mexico. This integrated, multidisciplinary, international effort investigates a variety of topics related to unique and fragile deep-sea coral ecosystems from the microscopic level to the ecosystem level, including components of microbiology, population genetics, paleoecology, food webs, taxonomy, community ecology, physical oceanography, and mapping.

Fact Sheet↗
USGS2022

Microbially induced anaerobic oxidation of magnetite to maghemite in a hydrocarbon-contaminated aquifer

Iron mineral transformations occurring in hydrocarbon-contaminated sites are linked to the biodegradation of the hydrocarbons. At a hydrocarbon-contaminated site near Bemidji, Minnesota, USA, measurements of magnetic susceptibility (MS) are useful for monitoring the natural attenuation of hydrocarbons related to iron cycling. However, a transient MS, previously observed at the site, remains poorly understood and the iron mineral phases acting as reactants and products associated with this MS perturbation remain largely unknown. To address these unknowns, we acquired mineral magnetism measurements, including hysteresis loops, backfield curves, and isothermal remanent magnetizations on sediment core samples retrieved from the site and magnetite-filled mineral packets installed within the aquifer. Our data show that the core samples and magnetite packs display decreasing magnetization with time and that this loss in magnetization is accompanied by increasing bulk coercivity consistent with decreased average grain size and/or partial oxidation. Low-temperature magnetometry on all samples displayed behavior consistent with magnetite, but samples within the plume also show evidence of maghemitization. This interpretation is supported by the occurrence of shrinkage cracks on the surface of the grains imaged via scanning electron microscopy. Magnetite transformation to maghemite typically occurs under oxic conditions, here, we propose that maghemitization occurs within the anoxic portions of the plume via microbially mediated anaerobic oxidation. Mineral dissolution also occurs within the plume. Microorganisms capable of such anaerobic oxidation have been identified within other areas at the Bemidji site, but additional microbiological studies are needed to link specific anaerobic iron oxidizers with this loss of magnetization.

Minnesota↗
USGS2008

Understanding contaminants associated with mineral deposits

Interdisciplinary studies by the U.S. Geological Survey (USGS) have resulted in substantial progress in understanding the processes that control the release of metals and acidic water from inactive mines and mineralized areas, the transport of metals and acidic water to streams, and the fate and effect of metals and acidity on downstream ecosystems. The potential environmental effects associated with abandoned and inactive mines, resulting from the complex interaction of a variety of chemical and physical processes, is an area of study that is important to the USGS Mineral Resources Program. Understanding the processes contributing to the environmental effects of abandoned and inactive mines is also of interest to a wide range of stakeholders, including both those responsible for managing lands with historically mined areas and those responsible for anticipating environmental consequences of future mining operations. The recently completed (2007) USGS project entitled 'Process Studies of Contaminants Associated with Mineral Deposits' focused on abandoned and inactive mines and mineralized areas in the Rocky Mountains of Montana, Colorado, New Mexico, Utah, and Arizona, where there are thousands of abandoned mines. Results from these studies provide new information that advances our understanding of the physical and biogeochemical processes causing the mobilization, transport, reaction, and fate of potentially toxic elements (including aluminum, arsenic, cadmium, copper, iron, lead, and zinc) in mineralized near-surface systems and their effects on aquatic and riparian habitat. These interdisciplinary studies provide the basis for scientific decisionmaking and remedial action by local, State, and Federal agencies charged with minimizing the effects of potentially toxic elements on the environment. Current (2007) USGS research highlights the need to understand (1) the geologic sources of metals and acidity and the geochemical reactions that release them from their sources, (2) the pathways that facilitate transport from those sources, and (3) the processes that control the fate of the elements once released from the sources. Experts in the fields of economic geology, structural geology, mineralogy, geophysics, geochemistry, hydrology, ground-water modeling, microbiology, and toxicology came together for a series of studies that address these relationships on scales ranging from the microscopic to the watershed. This Circular presents results and highlights from the detailed, interdisciplinary studies that include investigations in both mining-affected areas and mineralized but unmined areas. The first section of the Circular describes laboratory and site-scale field investigations that primarily focus on mineralogic and biologic controls on the source and release of metals and acidity from mine-waste rock and hydrothermally altered areas. The second section describes a set of basin- to watershed-scale studies that not only investigate the source and release of metals and acidity but also the transport of these constituents away from the source areas. The third section is a summary of results from postremediation ecosystem monitoring. For more information on these and other project-related studies, please visit the project Web site at http://minerals.cr.usgs.gov/projects/contaminants/index.html. The Web site includes a complete bibliography and detailed descriptions of each interdisciplinary study.

Circular↗
USGS2011

Microbial ecology of deep-water mid-Atlantic canyons

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

Fact Sheet↗
USGS2023

Comparing sediment microbial communities of Arctic beaver ponds to tundra lakes and streams

In recent decades the habitat of North American beaver ( Castor canadensis ) has expanded from boreal forests into Arctic tundra ecosystems. Beaver ponds in Arctic watersheds are known to alter stream biogeochemistry, which is likely coupled with changes in the activity and composition of microbial communities inhabiting beaver pond sediments. We investigated bacterial, archaeal, and fungal communities in beaver pond sediments along tundra streams in northwestern Alaska (AK), USA and compared them to those of tundra lakes and streams in north-central Alaska that are unimpacted by beavers. β -glucosidase activity assays indicated higher cellulose degradation potential in beaver ponds than in unimpacted streams and lakes within a watershed absent of beavers. Beta diversity analyses showed that dominant lineages of bacteria and archaea in beaver ponds differed from those in tundra lakes and streams, but dominant fungal lineages did not differ between these sample types. Beaver pond sediments displayed lower relative abundances of Crenarchaeota and Euryarchaeota archaea and of bacteria from typically anaerobic taxonomic groups, suggesting differences in rates of fermentative organic matter (OM) breakdown, syntrophy, and methane generation. Beaver ponds also displayed low relative abundances of Chytridiomycota (putative non-symbiotic) fungi and high relative abundances of ectomycorrhizal (plant symbionts) Basidiomycota fungi, suggesting differences in the occurrence of plant and fungi mutualistic interactions. Beaver ponds also featured microbes with taxonomic identities typically associated with the cycling of nitrogen and sulfur compounds in higher relative abundances than tundra lakes and streams. These findings help clarify the microbiological implications of beavers expanding into high latitude regions.

Alaska↗
USGS2024

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology

Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and ’omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.

mSphere↗
USGS2016

Antemortem detection of chronic wasting disease prions in nasal brush collections and rectal biopsies from white-tailed deer by real time quaking-induced conversion

Chronic wasting disease (CWD), a transmissible spongiform encephalopathy of cervids, was first documented nearly 50 years ago in Colorado and Wyoming and has since spread to cervids in 23 states, two Canadian provinces, and the Republic of Korea. The expansion of this disease makes the development of sensitive diagnostic assays and antemortem sampling techniques crucial for the mitigation of its spread; this is especially true in cases of relocation/reintroduction of farmed or free-ranging deer and elk or surveillance studies of private or protected herds, where depopulation is contraindicated. This study sought to evaluate the sensitivity of the real-time quaking-induced conversion (RT-QuIC) assay by using recto-anal mucosa-associated lymphoid tissue (RAMALT) biopsy specimens and nasal brush samples collected antemortem from farmed white-tailed deer ( n = 409). Antemortem findings were then compared to results from ante- and postmortem samples (RAMALT, brainstem, and medial retropharyngeal lymph nodes) evaluated by using the current gold standard in vitro assay, immunohistochemistry (IHC) analysis. We hypothesized that the sensitivity of RT-QuIC would be comparable to IHC analysis in antemortem tissues and would correlate with both the genotype and the stage of clinical disease. Our results showed that RAMALT testing by RT-QuIC assay had the highest sensitivity (69.8%) compared to that of postmortem testing, with a specificity of >93.9%. These data suggest that RT-QuIC, like IHC analysis, is an effective assay for detection of PrP CWD in rectal biopsy specimens and other antemortem samples and, with further research to identify more sensitive tissues, bodily fluids, or experimental conditions, has potential for large-scale and rapid automated testing for CWD diagnosis.

Journal of Clinical Microbiology↗
USGS2006

Wildlife tuberculosis in South African conservation areas: Implications and challenges

Tuberculosis, caused by Mycobacterium bovis, was first diagnosed in African buffalo in South Africa's Kruger National Park in 1990. Over the past 15 years the disease has spread northwards leaving only the most northern buffalo herds unaffected. Evidence suggests that 10 other small and large mammalian species, including large predators, are spillover hosts. Wildlife tuberculosis has also been diagnosed in several adjacent private game reserves and in the Hluhluwe-iMfolozi Park, the third largest game reserve in South Africa. The tuberculosis epidemic has a number of implications, for which the full effect of some might only be seen in the long-term. Potential negative long-term effects on the population dynamics of certain social animal species and the direct threat for the survival of endangered species pose particular problems for wildlife conservationists. On the other hand, the risk of spillover infection to neighboring communal cattle raises concerns about human health at the wildlife-livestock-human interface, not only along the western boundary of Kruger National Park, but also with regards to the joint development of the Greater Limpopo Transfrontier Conservation Area with Zimbabwe and Mozambique. From an economic point of view, wildlife tuberculosis has resulted in national and international trade restrictions for affected species. The lack of diagnostic tools for most species and the absence of an effective vaccine make it currently impossible to contain and control this disease within an infected free-ranging ecosystem. Veterinary researchers and policy-makers have recognized the need to intensify research on this disease and the need to develop tools for control, initially targeting buffalo and lion. ?? 2005 Elsevier B.V. All rights reserved.

Kruger National Park↗
USGS2020

Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA

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.

Minnesota↗
USGS2011

Vulnerability of high-latitude soil organic carbon in North America to disturbance

This synthesis addresses the vulnerability of the North American high-latitude soil organic carbon (SOC) pool to climate change. Disturbances caused by climate warming in arctic, subarctic, and boreal environments can result in significant redistribution of C among major reservoirs with potential global impacts. We divide the current northern high-latitude SOC pools into (1) near-surface soils where SOC is affected by seasonal freeze-thaw processes and changes in moisture status, and (2) deeper permafrost and peatland strata down to several tens of meters depth where SOC is usually not affected by short-term changes. We address key factors (permafrost, vegetation, hydrology, paleoenvironmental history) and processes (C input, storage, decomposition, and output) responsible for the formation of the large high-latitude SOC pool in North America and highlight how climate-related disturbances could alter this pool's character and size. Press disturbances of relatively slow but persistent nature such as top-down thawing of permafrost, and changes in hydrology, microbiological communities, pedological processes, and vegetation types, as well as pulse disturbances of relatively rapid and local nature such as wildfires and thermokarst, could substantially impact SOC stocks. Ongoing climate warming in the North American high-latitude region could result in crossing environmental thresholds, thereby accelerating press disturbances and increasingly triggering pulse disturbances and eventually affecting the C source/sink net character of northern high-latitude soils. Finally, we assess postdisturbance feedbacks, models, and predictions for the northern high-latitude SOC pool, and discuss data and research gaps to be addressed by future research.

Journal of Geophysical Research G: Biogeosciences↗
USGS2025

Microbial ecology of permafrost soils: Populations, processes, and perspectives

Permafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost-affected systems.

Permafrost and Periglacial Processes↗
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↗
USGS2015

Biological and geochemical data along Indian Point, Vermilion Bay, Louisiana

Scientists from the U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center collected shallow sediment cores and surface samples from a coastal salt marsh environment next to Vermilion Bay in southwest Louisiana in January 2013. The sampling was part of a larger USGS study to gather data for assessing environmental changes over the past 150 years. The objective of the study was to expand upon the historical context of sea level and storms affecting coastal systems and how these systems might change under persistent or varying conditions. The data from this report add to a regional environmental change database that aids with the continuing effort to understand the evolution of coastal systems. This report serves as an archive for sedimentological, radiochemical, and microbiological data derived from the sediment cores. Data are available for January 2013. Downloadable data are available as Excel spreadsheets and as JPEG files. Additional files include ArcGIS shapefiles of the sampling sites, detailed results of sediment analyses, and formal Federal Geographic Data Committee metadata. Acknowledgments The authors thank Nancy DeWitt, B.J. Reynolds, Christopher Reich (USGS, St. Petersburg Coastal and Marine Science Center), for help with sample collection and processing; Michael Ball, Sarai Piazza, and Gregory Steyer (USGS, Coastal Restoration Assessment Branch) for assistance accessing CRMS Site 541; and Darrell Anders and Phillip Turnipseed (USGS National Wetlands Research Center) for technical support while in the field. We would also like to thank Caitlyn Reynolds and Nicholas Zaremba for their pre-release commentary and peer review. Information Statement This publication was prepared by an agency of the United States Government. Although these data were processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data on any other system, or for general or scientific purposes, nor shall the act of distribution imply any such warranty. The U.S. Geological Survey shall not be held liable for improper or incorrect use of the data described and (or) contained herein. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency

Louisiana↗
USGS2013

Reply to “Ranking filter methods for concentrating pathogens in lake water”

Accurately comparing filtration methods is indeed difficult. Our method ( 1 ) and the method described by Borchardt et al. for determining recoveries are both acceptable approaches; however, each is designed to achieve a different research goal. Our study was designed to compare recoveries of multiple microorganisms in surface-water samples. Because, in practice, water-matrix effects come into play throughout filtration, concentration, and detection processes, we felt it important to incorporate those effects into the recovery results.

Applied and Environmental Microbiology↗
USGS2018

Understanding how microbiomes influence the systems they inhabit

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Nature Microbiology↗