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At least 19 recordsLinked to original sources
USGS2022

Combining tangential flow filtration and size fractionation of mesocosm water as a method for the investigation of waterborne coral diseases

The causative agents of most coral diseases today remain unknown, complicating disease response and restoration efforts. Pathogen identifications can be hampered by complex microbial communities naturally associated with corals and seawater, which create complicating “background noise” that can potentially obscure a pathogen’s signal. Here, we outline an approach to investigate waterborne coral diseases that use a combination of coral mesocosms, tangential flow filtration, and size fractionation to reduce the impact of this background microbial diversity, compensate for unknown infectious dose, and further narrow the suspect pool of potential pathogens. As proof of concept, we use this method to compare the bacterial communities shed into six Montastraea cavernosa coral mesocosms and demonstrate this method effectively detects differences between diseased and healthy coral colonies. We found several amplicon sequence variants (ASVs) in the diseased mesocosms that represented 100% matches with ASVs identified in prior studies of diseased coral tissue, further illustrating the effectiveness of our approach. Our described method is an effective alternative to using coral tissue or mucus to investigate waterborne coral diseases of unknown etiology and can help more quickly narrow the pool of possible pathogens to better aid in disease response efforts. Additionally, this versatile method can be easily adapted to characterize either the entire microbial community associated with a coral or target-specific microbial groups, making it a beneficial approach regardless of whether a causative agent is suspected or is completely unknown.

Florida↗
USGS1998

Geospatial Technology Applications and Infrastructure in the Biological Resources Division

Executive Summary -- Automated spatial processing technology such as geographic information systems (GIS), telemetry, and satellite-based remote sensing are some of the more recent developments in the long history of geographic inquiry. For millennia, humankind has endeavored to map the Earth's surface and identify spatial relationships. But the precision with which we can locate geographic features has increased exponentially with satellite positioning systems. Remote sensing, GIS, thematic mapping, telemetry, and satellite positioning systems such as the Global Positioning System (GPS) are tools that greatly enhance the quality and rapidity of analysis of biological resources. These technologies allow researchers, planners, and managers to more quickly and accurately determine appropriate strategies and actions. Researchers and managers can view information from new and varying perspectives using GIS and remote sensing, and GPS receivers allow the researcher or manager to identify the exact location of interest. These geospatial technologies support the mission of the U.S. Geological Survey (USGS) Biological Resources Division (BRD) and the Strategic Science Plan (BRD 1996) by providing a cost-effective and efficient method for collection, analysis, and display of information. The BRD mission is 'to work with others to provide the scientific understanding and technologies needed to support the sound management and conservation of our Nation's biological resources.' A major responsibility of the BRD is to develop and employ advanced technologies needed to synthesize, analyze, and disseminate biological and ecological information. As the Strategic Science Plan (BRD 1996) states, 'fulfilling this mission depends on effectively balancing the immediate need for information to guide management of biological resources with the need for technical assistance and long-range, strategic information to understand and predict emerging patterns and trends in ecological systems.' Information sharing plays a key role in nearly everything BRD does. The Strategic Science Plan discusses the need to (1) develop tools and standards for information transfer, (2) disseminate information, and (3) facilitate effective use of information. This effort centers around the National Biological Information Infrastructure (NBII) and the National Spatial Data Infrastructure (NSDI), components of the National Information Infrastructure. The NBII and NSDI are distributed electronic networks of biological and geographical data and information, as well as tools to help users around the world easily find and retrieve the biological and geographical data and information they need. The BRD is responsible for developing scientifically and statistically reliable methods and protocols to assess the status and trends of the Nation's biological resources. Scientists also conduct important inventory and monitoring studies to maintain baseline information on these same resources. Research on those species for which the Department of the Interior (DOI) has trust responsibilities (including endangered species and migratory species) involves laboratory and field studies of individual animals and the environments in which they live. Researchboth tactical and strategicis conducted at the BRD's 17 science centers and 81 field stations, 54 Cooperative Fish and Wildlife Research Units in 40 states, and at 11 former Cooperative Park Study Units. Studies encompass fish, birds, mammals, and plants, as well as their ecosystems and the surrounding landscape. Biological Resources Division researchers use a variety of scientific tools in their endeavors to understand the causes of biological and ecological trends. Research results are used by managers to predict environmental changes and to help them take appropriate measures to manage resources effectively. The BRD Geospatial Technology Program facilitates the collection, analysis, and dissemination of data and informat

Information and Technology Report↗
USGS2018

General introduction for the “National Field Manual for the Collection of Water-Quality Data”

Background As part of its mission, the U.S. Geological Survey (USGS) collects data to assess the quality of our Nation’s water resources. A high degree of reliability and standardization of these data are paramount to fulfilling this mission. Documentation of nationally accepted methods used by USGS personnel serves to maintain consistency and technical quality in data-collection activities. “The National Field Manual for the Collection of Water-Quality Data” (NFM) provides documented guidelines and protocols for USGS field personnel who collect water-quality data. The NFM provides detailed, comprehensive, and citable procedures for monitoring the quality of surface water and groundwater. Topics in the NFM include (1) methods and protocols for sampling water resources, (2) methods for processing samples for analysis of water quality, (3) methods for measuring field parameters, and (4) specialized procedures, such as sampling water for low levels of mercury and organic wastewater chemicals, measuring biological indicators, and sampling bottom sediment for chemistry. Personnel who collect water-quality data for national USGS programs and projects, including projects supported by USGS cooperative programs, are mandated to use protocols provided in the NFM per USGS Office of Water Quality Technical Memorandum 2002.13. Formal training, for example, as provided in the USGS class, “Field Water-Quality Methods for Groundwater and Surface Water,” and field apprenticeships supplement the guidance provided in the NFM and ensure that the data collected are high quality, accurate, and scientifically defensible.

Techniques and Methods↗
USGS2015

Standard operating procedures for collection of soil and sediment samples for the Sediment-bound Contaminant Resiliency and Response (SCoRR) strategy pilot study

An understanding of the effects on human and ecological health brought by major coastal storms or flooding events is typically limited because of a lack of regionally consistent baseline and trends data in locations proximal to potential contaminant sources and mitigation activities, sensitive ecosystems, and recreational facilities where exposures are probable. In an attempt to close this gap, the U.S. Geological Survey (USGS) has implemented the Sediment-bound Contaminant Resiliency and Response (SCoRR) strategy pilot study to collect regional sediment-quality data prior to and in response to future coastal storms. The standard operating procedure (SOP) detailed in this document serves as the sample-collection protocol for the SCoRR strategy by providing step-by-step instructions for site preparation, sample collection and processing, and shipping of soil and surficial sediment (for example, bed sediment, marsh sediment, or beach material). The objectives of the SCoRR strategy pilot study are (1) to create a baseline of soil-, sand-, marsh sediment-, and bed-sediment-quality data from sites located in the coastal counties from Maine to Virginia based on their potential risk of being contaminated in the event of a major coastal storm or flooding (defined as Resiliency mode); and (2) respond to major coastal storms and flooding by reoccupying select baseline sites and sampling within days of the event (defined as Response mode). For both modes, samples are collected in a consistent manner to minimize bias and maximize quality control by ensuring that all sampling personnel across the region collect, document, and process soil and sediment samples following the procedures outlined in this SOP. Samples are analyzed using four USGS-developed screening methods—inorganic geochemistry, organic geochemistry, pathogens, and biological assays—which are also outlined in this SOP. Because the SCoRR strategy employs a multi-metric approach for sample analyses, this protocol expands upon and reconciles differences in the sample collection protocols outlined in the USGS “National Field Manual for the Collection of Water-Quality Data,” which should be used in conjunction with this SOP. A new data entry and sample tracking system also is presented to ensure all relevant data and metadata are gathered at the sample locations and in the laboratories.

Open-File Report↗
USGS2006

Effects of streambank fencing of pasture land on benthic macroinvertebrates and the quality of surface water and shallow ground water in the Big Spring Run basin of Mill Creek watershed, Lancaster County, Pennsylvania, 1993-2001

Streambank fencing along stream channels in pastured areas and the exclusion of pasture animals from the channel are best-management practices designed to reduce nutrient and suspended-sediment yields from drainage basins. Establishment of vegetation in the fenced area helps to stabilize streambanks and provides better habitat for wildlife in and near the stream. This study documented the effectiveness of a 5- to 12-foot-wide buffer strip on the quality of surface water and near-stream ground water in a 1.42-mi2 treatment basin in Lancaster County, Pa. Two miles of stream were fenced in the basin in 1997 following a 3- to 4-year pre-treatment period of monitoring surface- and ground-water variables in the treatment and control basins. Changes in surface- and ground-water quality were monitored for about 4 years after fence installation. To alleviate problems in result interpretation associated with climatic and hydrologic variation over the study period, a nested experimental design including paired-basin and upstream/downstream components was used to study the effects of fencing on surface-water quality and benthic-macroinvertebrate communities. Five surface-water sites, one at the outlet of a 1.77-mi2 control basin (C-1), two sites in the treatment basin (T-3 and T-4) that were above any fence installation, and two sites (one at an upstream tributary site (T-2) and one at the outlet (T-1)) that were treated, were sampled intensively. Low-flow samples were collected at each site (approximately 25-30 per year at each site), and stormflow was sampled with automatic samplers at all sites except T-3. For each site where stormflow was sampled, from 35 to 60 percent of the storm events were sampled over the entire study period. Surface-water sites were sampled for analyses of nutrients, suspended sediment, and fecal streptococcus (only low-flow samples), with field parameters (only low-flow samples) measured during sample collection. Benthic-macroinvertebrate samples were collected in May and September of each year; samples were collected at the outlet of the control and treatment basins and at three upstream sites, two in the treatment basin and one in the control basin. For each benthic-macroinvertebrate sample: Stream riffles and pools were sampled using the kick-net method; habitat was characterized using Rapid Bioassessment Protocols (RBP); water-quality samples were collected for nutrients and suspended sediment; stream field parameters were measured; and multiple biological metrics were calculated. The experimental design to study the effects of fencing on the quality of near-stream shallow ground water involved a nested well approach. Two well nests were in the treatment basin, one each at surface-water sites T-1 and T-2. Within each well nest, the data from one deep well and three shallow wells (no greater than 12 ft deep) were used for regional characterization of ground-water quality. At each site, two of the shallow wells were inside the eventual fence (treated wells); the other shallow well was outside the eventual fence (control well). The wells were sampled monthly, primarily during periods with little to no recharge, for laboratory analysis of nutrients and fecal streptococcus; field parameters of water quality also were measured.

Pennsylvania↗
USGS1998

Revised Methods for Characterizing Stream Habitat in the National Water-Quality Assessment Program

Stream habitat is characterized in the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. The goal of stream habitat characterization is to relate habitat to other physical, chemical, and biological factors that describe water-quality conditions. To accomplish this goal, environmental settings are described at sites selected for water-quality assessment. In addition, spatial and temporal patterns in habitat are examined at local, regional, and national scales. This habitat protocol contains updated methods for evaluating habitat in NAWQA Study Units. Revisions are based on lessons learned after 6 years of applying the original NAWQA habitat protocol to NAWQA Study Unit ecological surveys. Similar to the original protocol, these revised methods for evaluating stream habitat are based on a spatially hierarchical framework that incorporates habitat data at basin, segment, reach, and microhabitat scales. This framework provides a basis for national consistency in collection techniques while allowing flexibility in habitat assessment within individual Study Units. Procedures are described for collecting habitat data at basin and segment scales; these procedures include use of geographic information system data bases, topographic maps, and aerial photographs. Data collected at the reach scale include channel, bank, and riparian characteristics.

Water-Resources Investigations Report↗
USGS2024

Thinking beyond the closure assumption: Designing surveys for estimating biological truth with occupancy models

Occupancy models estimate distributions of imperfectly detected species, but violations of the closure assumption can bias results. However, researchers working with mobile animals may find it impossible to eliminate such violations. Here, we tested the hypothesis that occupancy models fit to realistic sampling data can generate unbiased occupancy estimates for an itinerant Wood Thrush ( Hylocichla mustelina ) population. In 2013 and 2014, we tracked movements of 41 breeding Wood Thrush males. We modelled territory shift probabilities using logistic exposure models and within-territory movements using continuous-time stochastic process models. We then constructed an individual-based model, simulated (1000 iterations) spatiotemporal locations for individuals and simulated sampling these populations using 162 different point count protocols with variable spatial (sampling radius and point placement method), and temporal (survey length, between-survey intervals and number of surveys) characteristics. We compared occupancy estimates with true values of instantaneous, daily and seasonal occupancy from the simulations. We parameterized continuous time stochastic process models based on movements within 34 unique territories and estimated a daily territory shift probability of 0.0099 (95% CI: 0.0060, 0.0152). Simulated data indicated that estimates of occupancy ranged from 0.18 (0.06, 1.00) to 0.80 (0.71, 0.89) depending on protocol characteristics. Occupancy estimates increased with increasing survey radius, survey length and between-survey interval. Protocols using shorter surveys and between-survey intervals were good estimators for instantaneous occupancy (low bias and mean-squared error) but poor estimators for daily and seasonal occupancy; longer surveys and intervals generated unbiased estimators of daily occupancy but underestimated seasonal occupancy. Logistic regression models that ignored imperfect detection outperformed occupancy models for estimating instantaneous occupancy but not daily or seasonal occupancy. For mobile animals, occupancy of sampling sites changes in space and time. Consequently, the spatial and temporal aspects of a sampling protocol have strong, but predictable, effects on occupancy model parameter estimates. Our results demonstrate that how these factors interact is critical for designing surveys that produce occupancy estimates representative of the biological process of interest to a researcher.

Methods in Ecology and Evolution↗
USGS2015

A reply to Iversen et al.'s comment “Monitoring of animal abundance by environmental DNA - An increasingly obscure perspective”

We appreciate the conversation put forward by Iversen et al. (2015) in their response to our article “Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix ” in the 2015 environmental DNA special issue of Biological Conservation. We agree with Iversen et al.'s concern about overly optimistic conclusions that could be drawn from the current eDNA literature. One hope for eDNA technology is that it can be used in estimating abundance or population density. Evidence suggests that eDNA measurements correlate with total biomass (Takahara et al., 2012) rather than abundance. We demonstrate a similar relationship between biomass and eDNA shedding rates. Nevertheless, without field testing of these methods and specific survey protocols, we cannot make strong conclusions regarding the technique's field applicability. In our manuscript, we attempted to point out areas in which more research is needed.

Biological Conservation↗
USGS2002

Water-quality, biological, and habitat assessment of the Boeuf River Basin, southeastern Arkansas, 1994-96

Water-quality and biological samples were collected at several sites in the Boeuf River Basin between November 1994 and December 1996. Water-quality and benthic macroinvertebrate community samples were collected and habitat was measured once at 25 ambient monitoring sites during periods of seasonal low flow. Water-quality storm-runoff samples were collected during 11 storm events at two sites (one draining a cotton field and one draining a forested area). Water-quality samples were collected at one site during the draining of a catfish pond. Water-quality samples from the 25 ambient sites indicate that streams in the Boeuf River Basin typically are turbid and nutrient enriched in late fall during periods of relatively low flow. Most suspended solids concentrations ranged from about 50 to 200 milligrams per liter (mg/L), most total nitrogen concentrations ranged from about 1.1 to 1.8 mg/L, and most total phosphorus concentrations ranged from about 0.25 to 0.40 mg/L. Suspended solids, total nitrogen, total ammonia plus organic nitrogen, total phosphorus, and dissolved orthophosphorus concentrations from samples collected during storm events were typically higher at the cotton field site than at the forested site. Estimated annual yields of suspended solids, nitrogen, and phosphorus were substantially higher from the cotton field than from the forested area. Dissolved chloride concentrations typically were higher at the forested site than from the cotton field site. Typically, the suspended solids and nutrient concentrations from the 25 ambient sites were lower than concentrations in runoff from the cotton field but higher than concentrations in runoff from the forest area. Concentrations of sulfate, chloride, suspended solids, and some nutrients in samples from the catfish pond generally were greater than concentrations in samples from other sites. Total phosphorus, orthophosphorus, and fecal coliform bacteria concentrations from the catfish pond generally were lower than concentrations in samples from other sites. Biological condition scores calculated using macroinvertebrate samples and U.S. Environmental Protection Agency Rapid Bioassessment Protocol II indicated that most of the 25 ambient sites would be in the 'moderately impaired' category. However, substantial uncertainty exists in this rating because bioassessment data were compared with data from a reference site outside of the Boeuf River Basin sampled using different methods. Several metrics indicated that communities at most of the ambient sites are composed of more tolerant macroinvertebrates than the community at the reference site. Habitat assessments (using Rapid Bioassessment Protocol II) indicated the reference site outside the Boeuf River Basin had better habitat than the ambient sites. Physical habitat scores for the 25 ambient sites indicated that most ambient sites had poor bottom substrate cover, embeddedness values, and flow and had poor to fair habitat related to most other factors. Most habitat factors at the reference site were considered good to excellent. Part of the variation in biological condition scores was explained by physical habitat scores and concentrations of suspended solids and dissolved oxygen. However, a considerable amount of variability in biological condition scores is not explained by these factors.

Water-Resources Investigations Report↗
USGS2000

Evaluation of biological data, Guanella Pass Area, Clear Creek and Park Counties, Colorado, water years 1995-97

Macroinvertebrate and algal community samples were collected during a 3-year period at sites located near Guanella Pass, Colorado, to provide baseline characterization data. Water-quality sampling and habitat evaluations were used to aid in the interpretation of the biological data. The study was part of an environmental investigation for a proposed roadway reconstruction project on Guanella Pass. Discharge was strongly affected by snowmelt during May–July. Habitat scores were optimal (147–199), as determined by U.S. Environmental Protection Agency Rapid Bioassessment Protocol methods. Generally, low median concentrations of nitrogen and phosphorus (less than 0.02 milligram per liter) were detected at all sites. The water temperatures ranged from 0.4 to 11.2 degrees Celsius. The average pH for all sites was neutral, and specific conductivities were dilute (less than 160 microsiemens per centimeter at 25 degrees Celsius). The median suspended-sediment concentration was less than 20 milligrams per liter at all sites. During the study, 100 macroinvertebrate taxa were identified. The dominant taxonomic groups of macroinvertebrates were Diptera (true flies), Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies). Macroinvertebrate density ranged from 6.6 to 4,300 organisms per square meter at sampled sites. Shannon-Weaver diversity values for the macroinvertebrate samples ranged from 1.6 to 4.5. Collector-gatherers dominated the functional feeding groups at most sites. Average abundance of Ephemeroptera, Plecoptera, and Trichoptera (EPT) was 56.7 percent; EPT:Chironomidae ratios were greater than 2:1 for every site except during water years 1996 and 1997. Chironomids were greater than EPT at four sites in water year 1996 and at one site in water year 1997. The percentage of macroinvertebrate community similarity between site pairs varied from 0 to 80 percent. The number of algal taxa identified was 280. The dominant algal divisions, in terms of density, were Cyanophyta (blue-green algae), Chrysophyta (diatoms), Chlorophyta (green algae), Rhodophyta (red algae), and Euglenophyta (euglenoids). In general, diatom biovolumes dominated the algal assemblage, followed by blue-green algae, green algae, red algae, and euglenoids. Algal densities ranged from 3.1 X 10 2 to more than 4.7 X 10 6 cells per square centimeter, and algal biovolume ranged from 2.3 X 10 4 to 4.6 X 10 9 cells per cubic centimeter. Diversity values for diatoms ranged from 1.5 to 4.9. The pollution tolerance index (PTI) for diatoms ranged from 1.8 to 3.0. Sensitive diatoms were present at each site and ranged from 21 to 97 percent. The percentage of motile diatoms ranged from 0 to 13 percent. The presence of acid-tolerant diatoms ranged from less than 0.5 to greater than 20 percent. The percentage of community similarity between site pairs ranged from 1 to 97 percent. Overall, the biotic metrics that were evaluated during this study indicate that the macroinvertebrate and algal communities in the streams on Guanella Pass are not degraded by the existing road. Erosion may cause some localized effects but may not affect the overall health of the whole stream system. The degraded condition of Geneva Creek probably is due to natural effects as opposed to road effects. Although upper South Clear Creek, upstream from Naylor Creek, is located downstream from several sources of road runoff, the biological community at this site does not seem to be negatively affected.

Colorado↗
USGS2020

Testing environmental DNA from wolf snow tracks for species, sex, and individual identification

Monitoring elusive, relatively low-density, large predators, such as the grey wolf (Canis lupus), has often been accomplished by live-capture and radiocollaring. Increasingly, non-invasive methods are considered best practice whenever it is possible to use them. Recently, environmental DNA (eDNA) deposited in snow tracks was demonstrated as useful for identifying lynx (Lynx canadensis), fisher (Pekania pennanti), wolverine (Gulo gulo), sika deer (Cervus nippon), red fox (Vulpes vulpes), and the Japanese marten (Martes melampus) to species level using mitochondrial DNA (mtDNA) markers. We tested whether eDNA from fresh wolf snow tracks collected in the Superior National Forest, Minnesota, USA during winter 2019 could be used to identify species, sex, and individual. Seven of the 8 snow track samples were successfully identified to “wolf-dog” species using mtDNA, with alleles amplifying in 5 of the samples at 1 or both of loci u250 and FH2096 in the allele range for wolves for this population. None yielded enough high-quality DNA to obtain genotypes to determine individual or sex. We recommend additional field trials to determine the minimum number of tracks required per individual to obtain sufficient, high-quality eDNA, as well as collecting associated urine or blood (from estrus) when possible. If individual wolves could be identified and sexed by the eDNA in their snow tracks, researchers should be able to determine population and family or group metrics with greater precision and less effort than typically required when conducting winter scat or hair-based genetic field studies of low density, elusive carnivores. Furthermore, this method would have applications to other areas of research and management, such as hunting quota determinations, validation of field methods and, in particular regards to wolves and other predators, livestock depredation issues. Overall, this technique holds significant future promise as field and laboratory methods are further refined for greater precision and optimized regarding the varying collection, filtration, and extraction protocols for different species in various environments.

Minnesota↗
USGS2012

Protocols for collection of streamflow, water-quality, streambed-sediment, periphyton, macroinvertebrate, fish, and habitat data to describe stream quality for the Hydrobiological Monitoring Program, Equus Beds Aquifer Storage and Recovery Program, city of Wichita, Kansas

The city of Wichita, Kansas uses the Equus Beds aquifer, one of two sources, for municipal water supply. To meet future water needs, plans for artificial recharge of the aquifer have been implemented in several phases. Phase I of the Equus Beds Aquifer Storage and Recovery (ASR) Program began with injection of water from the Little Arkansas River into the aquifer for storage and subsequent recovery in 2006. Construction of a river intake structure and surface-water treatment plant began as implementation of Phase II of the Equus Beds ASR Program in 2010. An important aspect of the ASR Program is the monitoring of water quality and the effects of recharge activities on stream conditions. Physical, chemical, and biological data provide the basis for an integrated assessment of stream quality. This report describes protocols for collecting streamflow, water-quality, streambed-sediment, periphyton, macroinvertebrate, fish, and habitat data as part of the city of Wichita's hydrobiological monitoring program (HBMP). Following consistent and reliable methods for data collection and processing is imperative for the long-term success of the monitoring program.

Kansas↗
USGS2004

Rehabilitation of a lignite mine-disturbed area in the Indian Desert

Extensive lignite mining in the Indian (Thar) Desert commenced within the past decade. Accompanying extraction of this valuable resource there have been visible, important environmental impacts. The resultant land degradation has prompted concern from both public and regulatory bodies. This research assesses the success of rehabilitation plans implemented to revegetate a lignite mine-disturbed area, near the village of Giral in western Rajasthan State. Rehabilitation success was achieved within the environmental constraints of this northwest Indian hot-desert ecosystem using a combination of: (1) backfilling (abandoned pits) with minespoil and of covering the backfilled-surfaces with fresh topsoil to a thickness of about 0??30 m; (2) use of micro-catchment rainwater harvesting (MCWH) technique; (3) soil profile modification approaches; (4) plant establishment methodologies; and (5) the selection of appropriate germplasm material (trees, shrubs and grasses). Preliminary results indicate that the resulting vegetative cover will be capable of self-perpetuation under natural conditions while at the same time meeting the land-use requirements of the local people. The minespoil is alkaline in nature and has high electrical conductance. The average content of organic carbon, N, P and K is lower than in the regional topsoil. However, the concentration of Ca, Mg, Na and total S in the minespoil is much higher than in the topsoil. Further, the spoil material has no biological activity. Enhanced plant growth was achieved in MCWH plots, compared to control plots, where minespoil moisture storage was improved by 18-43 per cent. The rehabilitation protocol used at the site appears to have been successful because, in addition to the planted species, desirable native invasive species have become established. This study developed methods for the rehabilitation of lignite mine-disturbed areas and has also resulted in an understanding of rehabilitation processes in arid regions with an emphasis on the long-term monitoring of rehabilitation success. ?? 2004 John Wiley and Sons, Ltd.

Land Degradation and Development↗
USGS2007

Biological uptake of polychlorinated biphenyls by Macoma balthica from sediment amended with activated carbon

This work characterizes the efficacy of activated carbon amendment in reducing polychlorinated biphenyl (PCB) bioavailability to clams ( Macoma balthica ) from field-contaminated sediment (Hunters Point Naval Shipyard, San Francisco Bay, CA, USA). Test methods were developed for the use of clams to investigate the effects of sediment amendment on biological uptake. Sediment was mixed with activated carbon for one month. Bioaccumulation tests (28 d) were employed to assess the relationships between carbon dose and carbon particle size on observed reductions in clam biological uptake of PCBs. Extraction and cleanup protocols were developed for the clam tissue. Efficacy of activated carbon treatment was found to increase with both increasing carbon dose and decreasing carbon particle size. Average reductions in bioaccumulation of 22, 64, and 84% relative to untreated Hunters Point sediment were observed for carbon amendments of 0.34, 1.7, and 3.4%, respectively. Average bioaccumulation reductions of 41, 73, and 89% were observed for amendments (dose = 1.7% dry wt) with carbon particles of 180 to 250, 75 to 180, and 25 to 75 μm, respectively, in diameter, indicating kinetic phenomena in these tests. Additionally, a biodynamic model quantifying clam PCB uptake from water and sediment as well as loss through elimination provided a good fit of experimental data. Model predictions suggest that the sediment ingestion route contributed 80 to 95% of the PCB burdens in the clams.

Environmental Toxicology and Chemistry↗
USGS2022

Understanding the Avian-Impact Offset Method—A tutorial

Biodiversity offsetting, or compensatory mitigation, is increasingly being used in temperate grassland and wetland ecosystems to compensate for unavoidable environmental damage from anthropogenic disturbances such as energy development and road construction. Energy-extraction and -generation facilities continue to proliferate across the natural landscapes of the United States, yet mitigation tools to ameliorate the negative behavioral effects on wildlife from these types of facilities are rarely implemented. Scientists from the U.S. Geological Survey conducted a 10-year before-after-control-impact (commonly referred to as BACI) study that evaluated the displacement effects of wind facilities on breeding grassland birds. The study determined behavioral avoidance for 7 of 9 species. This research is notable because of its design, geographical scope, and duration, which allowed for the determination of immediate, short-term effects; delayed or sustained effects; and discrete distances at which effects occurred. In addition, the U.S. Fish and Wildlife Service and Ducks Unlimited conducted a 3-year concurrent-year paired-reference study to determine behavioral avoidance for five species of dabbling ducks. By quantifying displacement rate from these two studies, U.S. Geological Survey and U.S. Fish and Wildlife Service scientists developed the Avian-Impact Offset Method (AIOM) to quantify and compensate for loss in value of breeding habitat. The AIOM converts the biological value (that is, number of bird pairs) lost by way of avoidance and estimates the site-specific number of hectares of grasslands and number of wetlands needed to compensate for displaced pairs of grassland birds and waterfowl. By converting biological value to traditional units of measure in which land is described and purchased or sold, the AIOM lends itself readily to the delivery of offsetting measures such as easement protections and restoration projects. The AIOM tool is applicable to wind, solar, oil, gas, and transportation infrastructure. This tutorial was designed to increase awareness of the AIOM and to promote its proper application. The tutorial is divided into four sections, each of which explains a discrete topic concerning aspects of behavioral displacement. The first section provides geographical and biological context, and the second section describes the field and statistical methods and results. The third section provides step-by-step instructions for applying the AIOM to several scenarios involving grassland birds or waterfowl at wind or oil facilities. The fourth section describes decision-support tools created to implement the AIOM. The appendices provide the actual field protocols constituting the methods for the research, provide detailed results by species and wind facility for that research, and provide detailed instructions for downloading and applying the decision-support tools.

Open-File Report↗
USGS2019

The status of mussel health assessment and a path forward

Declines of freshwater mussel (order Unionida) populations worldwide are attributed to habitat degradation, pollution, and invasive species, among other factors. However, these purported causes do not fully explain the enigmatic decline and large-scale die-offs of mussels that have occurred in assumedly “healthy” streams across a wide geographic region. The roles of the microbiota and pathogens in mussel health has been understudied, and, as a result, few references exist to compare the microbiota of healthy mussels to that of stressed or dying mussels. Captive propagation and stocking programs have expanded across the globe without standard diagnostic protocols to assess health or potential diseases in hatchery-reared or wild stocks. Introduction of nonindigenous species, contaminants of emerging concern and anthropogenic climate change could adversely alter underlying variables that support mussel health such as nutrient and microbial composition, in addition to increased risk for outbreaks of opportunistic disease and emergent diseases in freshwater mussel populations. We suggest a coordinated, collaborative, and multidisciplinary effort to advance methods for assessing freshwater mussel health. We identify research and resources needed to answer central questions surrounding mussel health including identifying potential agents of disease, defining clinical signs of declining condition, refining stress-specific biomarkers for health assessment, and developing protocols specific for mussels.

Freshwater Mollusk Biology and Conservation↗
USGS1994

Measuring and monitoring biological diversity: Standard methods for amphibians

Measuring and Monitoring Biological Diversity is the first book to provide comprehensive coverage of standard methods for biodiversity sampling of amphibians, with information on analyzing and using data that will interest biologists in general. In this manual, nearly fifty herpetologists recommend ten standard sampling procedures for measuring and monitoring amphibian and many other populations. The contributors discuss each procedure, along with the circumstances for its appropriate use. In addition, they provide a detailed protocol for each procedure's implementation, a list of necessary equipment and personnel, and suggestions for analyzing the data. The data obtained using these standard methods are comparable across sites and through time and, as a result, are extremely useful for making decisions about habitat protection, sustained use, and restoration—decisions that are particularly relevant for threatened amphibian populations.

Book↗
USGS2020

Reduction of taxonomic bias in diatom species data

Inconsistency in taxonomic identification and analyst bias impede the effective use of diatom data in regional and national stream and lake surveys. In this study, we evaluated the effect of existing protocols and a revised protocol on the precision of diatom species counts. The revised protocol adjusts four elements of sample preparation, taxon identification and enumeration, and quality control (QC). We used six independent datasets to assess the effect of the adjustments on analytical outcomes. The first dataset was produced by three laboratories with a total of five analysts following established protocols (Charles et al. 2002), or their slight variations. The remaining datasets were produced by 1-3 laboratories with a total of 2-3 analysts following a revised protocol. The revised protocol included the following modifications: 1) development of coordinated pre-count voucher floras based on morphological operational taxonomic units (mOTUs), 2) random assignment of samples to analysts, 3) post-count identification and documentation of taxa (as opposed to an approach in which analysts assign names while they enumerate), and 4) increased use of QC samples. The revised protocol reduced taxonomic bias, as measured by reduction in analyst signal, and improved similarity among QC samples. Reduced taxonomic bias improves the performance of biological assessments, facilitates transparency across studies, and refines estimates of diatom species distributions.

Limnology and Oceanography: Methods↗