Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Environmental Technology”

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

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

At least 1,171 records · Page 65Linked to original sources
USGS2020

The effects of tissue fixation on sequencing and transcript abundance of nucleic acids from microdissected liver samples of smallmouth bass (Micropterus dolomieu)

There is an increasing emphasis on effects-based monitoring to document responses associated with exposure to complex mixtures of chemicals, climate change, pathogens, parasites and other environmental stressors in fish populations. For decades aquatic monitoring programs have included the collection of tissues preserved for microscopic pathology. Consequently, formalin-fixed, paraffin-embedded (FFPE) tissue can be an important reservoir of nucleic acids as technologies emerge that utilize molecular endpoints. Despite the cross-linking effects of formalin, its impact on nucleic acid quality and concentration, amplification, and sequencing are not well described. While fresh-frozen tissue is optimal for working with nucleic acids, FFPE samples have been shown to be conducive for molecular studies. Laser capture microdissection (LCM) is one technology which allows for collection of specific regions or cell populations from fresh or preserved specimens with pathological alterations, pathogens, or parasites. In this study, smallmouth bass (Micropterus dolomieu) liver was preserved in three different fixatives, including 10% neutral buffered formalin (NBF), Z-Fix® (ZF), and PAXgene® (PG) for four time periods (24 hr, 48 hr, seven days, and 14 days). Controls consisted of pieces of liver preserved in RNALater® or 95% ethanol. Smallmouth bass were chosen as they are an economically important sportfish and have been utilized as indicators of exposure to endocrine disruptors and other environmental stressors. Small liver sections were cut out with laser microdissection and DNA and RNA were purified and analyzed for nucleic acid concentration and quality. Sanger sequencing and the NanoString nCounter® technology were used to assess the suitability of these samples in downstream molecular techniques. The results revealed that of the formalin fixatives, NBF samples fixed for 24 and 48 hr were superior to ZF samples for both Sanger sequencing and the Nanostring nCounter®. The non-formalin PAXgene® samples were equally successful and they showed greater stability in nucleic acid quality and concentration over longer fixation times. This study demonstrated that small quantities of preserved tissue from smallmouth bass can be utilized in downstream molecular techniques; however, future studies will need to optimize the methods presented here for different tissue types, fish species, and pathological conditions.

PLoS ONE↗
USGS2015

National Unmanned Aircraft Systems Project Office

The U.S. Geological Survey (USGS) National Unmanned Aircraft Systems (UAS) Project Office leads the implementation of UAS technology in the Department of the Interior (DOI). Our mission is to support the transition of UAS into DOI as a new cost-effective tool for collecting remote-sensing data to monitor environmental conditions, respond to natural hazards, recognize the consequences and benefits of land and climate change and conduct wildlife inventories. The USGS is teaming with all DOI agencies and academia as well as local, State, and Tribal governments with guidance from the Federal Aviation Administration and the DOI Office of Aviation Services (OAS) to lead the safe, efficient, costeffective and leading-edge adoption of UAS technology into the scientific research and operational activities of the DOI.

Fact Sheet↗
USGS2016

Can you hear me now? Range-testing a submerged passive acoustic receiver array in a Caribbean coral reef habitat

Submerged passive acoustic technology allows researchers to investigate spatial and temporal movement patterns of many marine and freshwater species. The technology uses receivers to detect and record acoustic transmissions emitted from tags attached to an individual. Acoustic signal strength naturally attenuates over distance, but numerous environmental variables also affect the probability a tag is detected. Knowledge of receiver range is crucial for designing acoustic arrays and analyzing telemetry data. Here, we present a method for testing a relatively large-scale receiver array in a dynamic Caribbean coastal environment intended for long-term monitoring of multiple species. The U.S. Geological Survey and several academic institutions in collaboration with resource management at Buck Island Reef National Monument (BIRNM), off the coast of St. Croix, recently deployed a 52 passive acoustic receiver array. We targeted 19 array-representative receivers for range-testing by submersing fixed delay interval range-testing tags at various distance intervals in each cardinal direction from a receiver for a minimum of an hour. Using a generalized linear mixed model (GLMM), we estimated the probability of detection across the array and assessed the effect of water depth, habitat, wind, temperature, and time of day on the probability of detection. The predicted probability of detection across the entire array at 100 m distance from a receiver was 58.2% (95% CI: 44.0–73.0%) and dropped to 26.0% (95% CI: 11.4–39.3%) 200 m from a receiver indicating a somewhat constrained effective detection range. Detection probability varied across habitat classes with the greatest effective detection range occurring in homogenous sand substrate and the smallest in high rugosity reef. Predicted probability of detection across BIRNM highlights potential gaps in coverage using the current array as well as limitations of passive acoustic technology within a complex coral reef environment.

Ecology and Evolution↗
USGS2011

A study of topics for distance education-A survey of U.S. Fish and Wildlife Service employees

The purpose of this study was to identify training topics and distance education technologies preferred by U.S. Fish and Wildlife Service employees. This study was conducted on behalf of the National Conservation Training Center to support their distance education strategy planning and implementation. When selecting survey recipients, we focused on employees in positions involving conservation and environmental education and outreach programming. We conducted the study in two phases. First, we surveyed 72 employees to identify useful training topics. The response rate was 61 percent; respondents were from all regions and included supervisors and nonsupervisors. Five topics for training were identified: creating and maintaining partnerships (partnerships), technology, program planning and development (program planning), outreach methods to engage the community (outreach methods), and evaluation methods. In the second phase, we surveyed 1,488 employees to assess preferences for training among the five topics identified in the first survey and preferences among six distance education technologies: satellite television, video conferencing, audio conferencing, computer mediated training, written resources, and audio resources. Two types of instructor-led training were included on the survey to compare to the technology options. Respondents were asked what types of information, such as basic facts or problem solving skills, were needed for each of the five topics. The adjusted response rate was 64 percent; respondents were from all regions and included supervisors and nonsupervisors. The results indicated clear preferences among respondents for certain training topics and technologies. All five training topics were valued, but the topics of partnerships and technology were given equal value and were valued more than the other three topics. Respondents indicated a desire for training on the topics of partnerships, technology, program planning, and outreach methods. For the six distance education technologies, respondents indicated different levels of usability and access. Audio conferencing and written resources were reported to be most usable and accessible. The ratings of technology usability/access differed according to region; respondents in region 9 rated most technologies higher on usability/access. Respondents indicated they would take courses through either onsite or distance education approaches, but they prefer onsite training for most topics and most types of information.

Open-File Report↗
USGS2010

Guidelines for the use of the semipermeable membrane device (SPMD) and the polar organic chemical integrative sampler (POCIS) in environmental monitoring studies

The success of an environmental monitoring study using passive samplers, or any sampling method, begins in the office or laboratory. Regardless of the specific methods used, the general steps include the formulation of a sampling plan, training of personnel, performing the field (sampling) work, processing the collected samples to recover chemicals of interest, analysis of the enriched extracts, and interpretation of the data. Each of these areas will be discussed in the following sections with emphasis on specific considerations with the use of passive samplers. Water is an extremely heterogeneous matrix both spatially and temporally (Keith, 1991). The mixing and distribution of dissolved organic chemicals in a water body are controlled by the hydrodynamics of the water, the sorption partition coefficients of the chemicals, and the amount of organic matter (suspended sediments, colloids, and dissolved organic carbon) present. In lakes and oceans, stratification because of changes in temperature, water movement, and water composition can occur resulting in dramatic changes in chemical concentrations with depth (Keith, 1991). Additional complications related to episodic events, such as surface runoff, spills, and other point source contamination, can result in isolated or short-lived pulses of contaminants in the water. The application of passive sampling technologies for the monitoring of legacy and emerging organic chemicals in the environment is becoming widely accepted worldwide. The primary use of passive sampling methods for environmental studies is in the area of surface-water monitoring; however, these techniques have been applied to air and groundwater monitoring studies. Although these samplers have no mechanical or moving parts, electrical or fuel needs which require regular monitoring, there are still considerations that need to be understood in order to have a successful study. Two of the most commonly used passive samplers for organic contaminants are the semipermeable membrane device (SPMD) and the polar organic chemical integrative sampler (POCIS). The tips given in this document focus on these two samplers but are applicable to most types of passive sampling devices. The information in this guide is heavily weighted towards the sampling of water; however, information specific to the use of SPMDs for air sampling will also be covered.

Techniques and Methods↗
USGS2018

Weather-centric rangeland revegetation planning

Invasive annual weeds negatively impact ecosystem services and pose a major conservation threat on semiarid rangelands throughout the western United States. Rehabilitation of these rangelands is challenging due to interannual climate and subseasonal weather variability that impacts seed germination, seedling survival and establishment, annual weed dynamics, wildfire frequency, and soil stability. Rehabilitation and restoration outcomes could be improved by adopting a weather-centric approach that uses the full spectrum of available site-specific weather information from historical observations, seasonal climate forecasts, and climate-change projections. Climate data can be used retrospectively to interpret success or failure of past seedings by describing seasonal and longer-term patterns of environmental variability subsequent to planting. A more detailed evaluation of weather impacts on site conditions may yield more flexible adaptive-management strategies for rangeland restoration and rehabilitation, as well as provide estimates of transition probabilities between desirable and undesirable vegetation states. Skillful seasonal climate forecasts could greatly improve the cost efficiency of management treatments by limiting revegetation activities to time periods where forecasts suggest higher probabilities of successful seedling establishment. Climate-change projections are key to the application of current environmental models for development of mitigation and adaptation strategies and for management practices that require a multidecadal planning horizon. Adoption of new weather technology will require collaboration between land managers and revegetation specialists and modifications to the way we currently plan and conduct rangeland rehabilitation and restoration in the Intermountain West.

Rangeland Ecology and Management↗
USGS2023

A recruitment niche framework for improving seed-based restoration

As larger tracts of land experience degradation, seed-based restoration (SBR) will be a primary tool to reestablish vegetation and ecosystem function. SBR has advanced in terms of technical and technological approaches, yet plant recruitment remains a major barrier in some systems, notably drylands. There is an unmet opportunity to test science-based approaches to seed mix design and application, based not only on diversity or local provenance, but on the unique recruitment strategies of species. We lay out a framework that uses a quantitative representation of species' recruitment niches to match them to targeted goals (e.g. drought or invasion resistance) and methods (e.g. precision tools and technologies) in SBR. We first describe how to quantify the recruitment niche with seed and seedling traits tied to observed recruitment responses to environmental factors. We then show how a quantified recruitment niche framework can serve as the foundation to address three major restoration challenges: (1) designing forward-looking seed mixes that increase resilience to future climate and disturbance, (2) accounting for natural recovery in SBR planning, and (3) applying precision seeding practices to maximize restoration success. Finally, we demonstrate these ideas with existing data and discuss key challenges to adoption in SBR practice. While the ideas in this framework are based in ecological theory, they will require substantial testing and refinement by scientists engaged in SBR efforts. If this framework is integrated into research agendas, we believe it has the potential to unify and advance diverse elements of seed-based restoration ecology and improve restoration outcomes.

Restoration Ecology↗
USGS1971

Status of engineering geologic and environmental geologic mapping in the United States

1. Engineering geologic maps in the United States may be one map prepared as part of a larger study of environmental geology, individual areal geologic maps containing additional engineering geologic data, or engineering geologic maps of single construction sites. 2. No systematic methodology for engineering geologic or environmental geologic maps has been developed. 3. Environmental geology studies combine the efforts of workers in a number of geologic fields to produce many maps of basic data, as well as various interpretative maps, only one of which may be an engineering geologic or foundation conditions map. Maps of many scales may be prepared for a single study, depending upon the geologic conditions, the main problems of the area, and the principal needs. 4. New technology, including computers and various types of aerial photography, is constantly being developed, and its use is being encouraged to increase the speed and efficiency of map preparation. 5. The use of engineering geologic and environmental geologic maps in the United States is constantly growing; such maps will continue to be made in increasing numbers.

Bulletin of the International Association of Engin↗
USGS2010

Evolution of Ore Deposits and Technology Transfer Project: Isotope and Chemical Methods in Support of the U.S. Geological Survey Science Strategy, 2003-2008

Principal functions of the U.S. Geological Survey (USGS) Mineral Resources Program are providing assessments of the location, quantity, and quality of undiscovered mineral deposits, and predicting the environmental impacts of exploration and mine development. The mineral and environmental assessments of domestic deposits are used by planners and decisionmakers to improve the stewardship of public lands and public resources. Assessments of undiscovered mineral deposits on a global scale reveal the potential availability of minerals to the United States and other countries that manufacture goods imported to the United States. These resources are of fundamental relevance to national and international economic and security policy in our globalized world economy. Performing mineral and environmental assessments requires that predictions be made of the likelihood of undiscovered deposits. The predictions are based on geologic and geoenvironmental models that are constructed for the diverse types of mineral deposits from detailed descriptions of actual deposits and detailed understanding of the processes that formed them. Over the past three decades the understanding of ore-forming processes has benefited greatly from the integration of laboratory-based geochemical tools with field observations and other data sources. Under the aegis of the Evolution of Ore Deposits and Technology Transfer Project (referred to hereinafter as the Project), a 5-year effort that terminated in 2008, the Mineral Resources Program provided state-of-the-art analytical capabilities to support applications of several related geochemical tools to ore-deposit-related studies. The analytical capabilities and scientific approaches developed within the Project have wide applicability within Earth-system science. For this reason the Project Laboratories represent a valuable catalyst for interdisciplinary collaborations of the type that should be formed in the coming years for the United States to meet its natural-resources and natural-science needs. This circular presents an overview of the Project. Descriptions of the Project laboratories are given first including descriptions of the types of chemical or isotopic analyses that are made and the utility of the measurements. This is followed by summaries of select measurements that were carried out by the Project scientists. The studies are grouped by science direction. Virtually all of them were collaborations with USGS colleagues or with scientists from other governmental agencies, academia, or the private sector.

Circular↗
USGS2021

The Robinson Forest environmental monitoring network: Long‐term evaluation of streamflow and precipitation quantity and stream‐water and bulk deposition chemistry in eastern Kentucky watersheds

The University of Kentucky (U KY) has owned Robinson Forest (37.460723° N, 83.158598° W) since 1923, conducting experiments crucial to understanding the environmental effects of land management in the region. Part of the management of Robinson Forest has been collection of environmental data, including precipitation quantity, bulk‐deposition chemistry, streamflow, stream‐water chemistry, and air and stream temperature. Over the years, these data have been collected and archived using various technologies and have been mostly inaccessible for research use – unedited and uncompiled, scattered across several spreadsheets and paper records. Through a partnership between the U.S. Geological Survey (USGS) and U KY, daily precipitation data for six stations and stream data from four watersheds in Robinson Forest have been compiled for 1971–2018, checked for transcription errors, and annotated for changes in methodologies. These data are available as a USGS data release at https://doi.org/10.5066/P9FPLG1O . Improved accessibility of this data set provides an important research resource for understanding water quality in minimally effected forests in the region. Preliminary results indicate that these data present a valuable opportunity to evaluate linkages among atmospheric deposition and stream chemistry, the effects of environmental policy, such as the Clean Air Act, and effects from nearby land disturbance in the form of surface mining. Furthermore, these data fill a geographic and physiographic gap in what is available to examine deposition and streamflow patterns over the last 45 years, supplementing those long‐term records of research sites in northern (e.g., Hubbard Brook Experimental Forest), central (e.g., Fernow Experimental Forest) and southern Appalachia (e.g., Coweeta Hydrologic Laboratory). As an oasis in the midst of significant surface mining activity, Robinson Forest presents a unique opportunity to understand environmental conditions characteristic of minimally disturbed forests similar to pre‐mining conditions in the Central Appalachian region.

Kentucky↗
USGS2018

Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing (NGS) have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal (GI) tracts. All GI tracts were obtained from the Museum of Southwestern Biology (MSB), USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at -80°C). Our proof of concept demonstrates the feasibility of applying NGS techniques to authoritatively identify the parasite/pathogen communities within whole GI tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole GI tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.

International Journal for Parasitology↗
USGS2020

Reduction in drinking water arsenic exposure and health risk through arsenic treatment among private well households in Maine and New Jersey, USA

Over 2 million people in the United States (U.S.) drink water from private wells that contain arsenic (As) exceeding the U.S. Environmental Protection Agency (USEPA) Maximum Contaminant Level (MCL) of 10 micrograms per liter (μg/L). While there are a number of commercially available treatment technologies for removing As from drinking water, it is up to the private well households to decide whether to treat for As or not. However, how well existing treatment technologies perform in real world situations, and to what extent they reduce health risks, are not well understood. This study evaluates the effectiveness of household As treatment systems in southern-central Maine (ME, n=156) and northern New Jersey (NJ, n=94) and ascertains how untreated well water chemistry and other factors influence As removal. Untreated and treated water samples, as well as a treatment questionnaire, were collected. Most ME households in this study had point-of-use reverse-osmosis systems (POU RO), while in NJ, dual-tank point-of-entry (POE) whole house systems were popular. Arsenic treatment systems reduced well water arsenic concentrations ([As]) by up to two orders of magnitude, i.e. from a median of 71.7 to 0.8 μg/L and from a mean of 105 to 14.3 μg/L in ME, and from a median of 8.6 to 0.2 μg/L and a mean of 15.8 to 2.1 μg/L in NJ. More than half (53%) of the systems in ME reduced water [As] to below 1 µg/L, compared to 69% in NJ. The treatment system failure rates were 19% in ME (> USEPA MCL 10 µg/L) and 16% in NJ (> NJ standard 5 μg/L). In both states, the higher the untreated well water [As] and the As(III)/As ratio, the higher the rate of treatment failure. POE systems failed less than POU systems, as did the treatment systems installed and maintained by vendors than those by homeowners. The 7-fold reduction of [As] in the treated water reduced skin cancer risk alone from 3,765 to 514 in 1 million in ME, and from 568 to 75 in 1 million in NJ.

Maine, New Jersey↗
USGS2002

Environmentalism and natural aggregate mining

Sustaining a developed economy and expanding a developing one require the use of large volumes of natural aggregate. Almost all human activity (commercial, recreational, or leisure) is transacted in or on facilities constructed from natural aggregate. In our urban and suburban worlds, we are almost totally dependent on supplies of water collected behind dams and transported through aqueducts made from concrete. Natural aggregate is essential to the facilities that produce energy—hydroelectric dams and coal-fired powerplants. Ironically, the utility created for mankind by the use of natural aggregate is rarely compared favorably with the environmental impacts of mining it. Instead, the empty quarries and pits are seen as large negative environmental consequences. At the root of this disassociation is the philosophy of environmentalism, which flavors our perceptions of the excavation, processing, and distribution of natural aggregate. The two end-member ideas in this philosophy are ecocentrism and anthropocentrism. Ecocentrism takes the position that the natural world is a organism whose arteries are the rivers—their flow must not be altered. The soil is another vital organ and must not be covered with concrete and asphalt. The motto of the ecocentrist is “man must live more lightly on the land.” The anthropocentrist wants clean water and air and an uncluttered landscape for human use. Mining is allowed and even encouraged, but dust and noise from quarry and pit operations must be minimized. The large volume of truck traffic is viewed as a real menace to human life and should be regulated and isolated. The environmental problems that the producers of natural aggregate (crushed stone and sand and gravel) face today are mostly difficult social and political concerns associated with the large holes dug in the ground and the large volume of heavy truck traffic associated with quarry and pit operations. These concerns have increased in recent years as society's demand for living space has encroached on the sites of production; in other words, the act of production has engendered condemnation. Many other environmental problems that are associated with dust and noise and blasting from quarry and pit operations have been reduced through the efficient use of technology. Recycling concrete in buildings, bridges, and roads and asphaltic pavements will ultimately reduce the demand for virgin natural aggregate. The impact created by the large holes in the ground required for the mining of natural aggregate can be greatly reduced by planning their reclamation before mining begins.

Natural Resources Research↗
USGS2012

Chapter A6. Section 6.8. Use of multiparameter instruments for routine field measurements

The miniaturization of sensors and other technological advances in electronics have resulted in water-quality instruments that house multiple sensors capable of simultaneous readings for various field measurements in environmental waters. With the use of these multiparameter instruments, field measurements can be determined with considerable reduction in the field work that generally is required when using multiple single-parameter instruments. This section addresses the short-term or discrete-measurement use of portable multiparameter instruments. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.'

Techniques of Water-Resources Investigations↗
USGS2020

Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)

Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental, etc.). Relatively little work, however, has explored the feasibility of utilizing historical samples (e.g., museum archived samples) of varying age, quality, and preservation type. Because natural history collections span multiple decades, these biorepositories have the potential to provide fundamental historical baselines to measure and better understand biodiversity on a changing planet. Utilizing even a small proportion of museum specimens could provide a means of sampling past microbial communities, allowing for direct comparison to contemporary communities and more complete understanding of dynamic shifts through time. We examined the feasibility of obtaining 16S rRNA amplicon microbiome data from whole gastrointestinal tracts (GIs) of shrews of varying age and preservation method, including 5 freshly collected shrew GIs immediately fixed in liquid nitrogen (LN2), 10 ten-year old shrew GIs frozen at −20°C (whole animal), and 10 shrews of varying ages (4 from 1968, 1 from 1980, 1 from 2001, 1 from 2004, 1 from 2007, 1 from 2011 and 2 from 2013) fixed and stored whole in 70% ethanol. Not surprisingly, results of 16S rDNA amplicon sequencing reveal significantly different bacterial communities between different preservation techniques and age of samples. Ten-year old frozen samples had bacterial communities most similar to freshly collected (LN2) samples, while the bacterial communities of both were significantly different from the 70% ethanol preserved samples of various ages. Amongst those preserved in 70% ethanol, age of samples also influenced bacterial community composition. Additionally, we compare results of OTU based and ASV based analyses. Looking ahead, field collectors and museums should develop and adopt best practices related to frozen preservation to ensure adequate material for future microbiome investigations.

Frontiers in Ecology and Evolution↗
USGS2007

Invasive species management and research using GIS

Geographical Information Systems (GIS) are powerful tools in the field of invasive species management. GIS can be used to create potential distribution maps for all manner of taxa, including plants, animals, and diseases. GIS also performs well in the early detection and rapid assessment of invasive species. Here, we used GIS applications to investigate species richness and invasion patterns in fish in the United States (US) at the 6-digit Hydrologic Unit Code (HUC) level. We also created maps of potential spread of the cane toad (Bufo marinus) in the southeastern US at the 8-digit HUC level using regression and environmental envelope techniques. Equipped with this potential map, resource managers can target their field surveys to areas most vulnerable to invasion. Advances in GIS technology, maps, data, and many of these techniques can be found on websites such as the National Institute of Invasive Species Science (www.NIISS.org). Such websites provide a forum for data sharing and analysis that is an invaluable service to the invasive species community.

Conference Paper↗
USGS2005

A method adapting microarray technology for signature tagged mutagenesis of Dusulfovibrio dusulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments

Signature-tagged mutagenesis (STM) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. To date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. We used a mini-Tn 10 transposon-bearing plasmid, pBSL180, that efficiently and randomly mutagenized Desulfovibrio desulfuricans G20 in addition to Shewanella oneidensis MR-1. Using these organisms as model sediment-dwelling anaerobic bacteria, we developed a new screening system, modified from former STM procedures, to identify genes that are critical for sediment survival. The screening system uses microarray technology to visualize tags from input and output pools, allowing us to identify those lost during sediment incubations. While the majority of data on survival genes identified will be presented in future papers, we report here on chemotaxis-related genes identified by our STM method in both bacteria in order to validate our method. This system may be applicable to the study of numerous environmental bacteria, allowing us to identify functions and roles of survival genes in various habitats.

Applied and Environmental Microbiology↗
USGS2025

Scaling from microsite to landscape to resolve litter decomposition dynamics in globally extensive drylands

1. Decomposition controls the release of carbon and nutrients from decaying plant litter into soils or the atmosphere. In most biomes decomposition rates can be accurately predicted with simple mathematical models, but these models have long under-predicted decomposition in globally- extensive drylands. 2. We posit that the exposed surface conditions characteristic of drylands makes litter decomposition uniquely subject to microsite-specific environmental controls and spatially-variable microbial communities. As such, decomposition in dryland ecosystems – which are characterized by extremes in temporal heterogeneity of climate conditions and spatial heterogeneity of vegetation cover with corresponding microclimate variability – is a prime example of a macrosystems process that can be addressed by merging field data with new predictive models operating across a hierarchical continuum of spatial scales and process resolutions. 3. A macrosystems approach offers promise to reconcile model-measurement discrepancies by integrating observations and experiments across multiple scales, from microsites (e.g., shrub sub-canopy or intercanopy) to regions (e.g., across a 100s of km2 study site with complex topography, precipitation, and temperature) and ultimately to a continental perspective (e.g., North American drylands). 4. Recent developments in technology and data availability position the scientific community to integrate lab, field, modeling, and remote sensing approaches across a hierarchical range of scales to capture the spatiotemporal distribution of litter and environmental conditions needed to predict decay dynamics at the micro-to-macroscale. This multi-scale approach promises a path forward to resolving a longstanding disconnect between measured and modeled data in dryland litter decomposition. 5. Dryland litter decomposition presents an excellent case study for resolving spatially and temporally complex biogeochemical dynamics through a hierarchical, multidisciplinary macrosystems approach. 6. We focus on dryland litter decomposition, but the hierarchical, multidisciplinary macrosystems approach we outline shows great potential for resolving other spatially and temporally complex biogeochemical processes across a wide range of ecosystems.

Functional Ecology↗