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USGS2003

Anaerobic degradation of 1,1,2,2-tetrachloroethane and association with microbial communities in a freshwater tidal wetland, Aberdeen Proving Ground, Maryland: Laboratory experiments and comparisons to field data

Defining biodegradation rates and processes is a critical part of assessing the feasibility of monitored natural attenuation as a remediation method for ground water containing organic contaminants. During 1998–2001, the U.S. Geological Survey conducted a microbial study at a freshwater tidal wetland along the West Branch Canal Creek, Aberdeen Proving Ground, Maryland, as part of an investigation of natural attenuation of chlorinated volatile organic compounds (VOCs) in the wetland sediments. Geochemical analyses and molecular biology techniques were used to investigate factors controlling anaerobic degradation of 1,1,2,2-tetrachloroethane (TeCA), and to characterize the microbial communities that potentially are important in its degradation. Rapid TeCA and daughter product degradation observed in laboratory experiments and estimated with field data confirm that natural attenuation is a feasible remediation method at this site. The diverse microbial community that seems to be involved in TeCA degradation in the wetland sediments varies with changing spatial and seasonal conditions, allowing continued effective natural attenuation throughout the year. Rates of TeCA degradation in anaerobic microcosm experiments conducted with wetland sediment collected from two different sites (WB23 and WB30) and during three different seasons (March–April 1999, July–August 1999, and October–November 2000) showed little spatial variability but high seasonal variability. Initial first-order degradation rate constants for TeCA ranged from 0.10±0.01 to 0.16±0.05 per day (halflives of 4.3 to 6.9 days) for March–April 1999 and October–November 2000 microcosms incubated at 19 degrees Celsius, whereas lower rate constants of 0±0.03 and 0.06±0.03 per day were obtained in July–August 1999 microcosms incubated at 19 degrees Celsius. Microbial community profiles showed that low microbial biomass and microbial diversity in the summer, possibly due to competition for nutrients by the wetland vegetation, could account for these unexpectedly low degradation rates. In microcosms incubated at 5 degrees Celsius, about 50 percent of the initial TeCA in solution was converted to daughter products within a 35-day incubation period, indicating that biodegradation in the wetland sediments can continue during cold winter temperatures. Initial pathways of TeCA degradation were the same in the wetland sediment microcosms regardless of the season or sediment collection site, the reduction-oxidation conditions, and the previous exposure of the sediment to contamination. Immediate and simultaneous dichloroelimination and hydrogenolysis, producing 1,2-dichloroethene (12DCE) and 1,1,2-trichloroethane (112TCA), respectively, were the initial TeCA degradation pathways in all live microcosm experiments. The production and degradation of vinyl chloride (VC), which is the most toxic of the TeCA daughter compounds, was affected by spatial and seasonal variability, reduction-oxidation condition, and pre-exposure of the wetland sediment. TeCA-amended microcosms constructed with WB30 sediment showed approximately twice as much VC production as those constructed with WB23 sediment. Results of 112TCA-amended microcosms indicated that the greater production of VC in the WB30 sediment resulted from a greater predominance of the 112TCA dichloro elimination pathway in these sediments. VC degradation also was substantially higher in microcosms constructed with WB30 sediment than those constructed with WB23 sediment, resulting in lower VC concentrations at the end of WB30 microcosms. Enrichment experiments in which microcosm slurry was amended with high initial VC concentrations showed that the spatial difference in VC degradation was negligible after prolonged incubation under methanogenic conditions. Inhibition of methanogenic activity in microcosms by addition of sulfate or of 2-bromoethanesulfonic acid inhibited production and degradation of VC. Inhibition of methanogenesis by addition of ferric iron or of 2-bromoethanesulfonic acid also completely inhibited VC degradation in VC-amended enrichment experiments. Pre-exposure to VC substantially increased degradation in VC-amended enrichment experiments. A microbial consortium, rather than one microbial species or group, likely is involved in the degradation of TeCA, as indicated by the occurrence of multiple degradation pathways and the variability in VC production and degradation. A bacterial peak at 90 base pair (bp) fragment length in terminal- restriction fragment length polymorphism (TRFLP) profiles was associated with TeCA hydrogenolysis to 112TCA, and bacterial species represented by 198 and 170 bp fragment lengths were associated with TeCA dichloroelimination to 12DCE. Dichloroelimination of 112TCA to VC was associated with increasing dominance of the 198 bp bacterial peak in March–April 1999 and October–November 2000 microcosms, whereas an 86 bp or the 170 bp bacterial peak was associated with 112TCA dichloroelimination in the summer experiment. Hydrogenolysis of 12DCE to VC was associated with a carbon dioxide-utilizing methanogen at 307 bp in the March–April 1999 and October–November 2000 microcosm experiments, whereas production of VC occurred despite low methanogen biomass and methane production in the July–August 1999 experiments. Production of VC in the absence of methane production also occurred in 12DCE-amended enrichment cultures. The exponential production of VC in the 12DCE-amended enrichment cultures after an initial lag indicated growth of a microbial species or group, possibly one of the known dehalorespiring bacteria. Molecular analyses using specific primers targeting dehalorespiring bacteria of the Dehalococcoides group (Dehalococcoides ethenogenes and Dehalococcoides sp. strain FL2) and of the acetate-oxidizing Desulfuromonas group (Desulfuromonas sp. strain BB1 and Desulfuromonas chloroethenica) showed the presence of these bacteria in microcosm slurry from site WB30 but not from site WB23. Addition of hydrogen, which is the favored substrate of Dehalococcoides, tripled VC production in 12DCE-amended enrichment cultures. VC degradation showed a marked association with an increase in the relative proportion of Methanosarcinaceae, a family of methanogens that includes all those capable of utilizing acetate as a substrate, in the total methanogen community. Half-lives for TeCA and TCE estimated from field data were in the range of 60 to 100 days, which agrees well with laboratory estimates of degradation rates considering the inherent differences in the laboratory and field systems. Both laboratory microcosm experiments and field data showed that 12DCE and VC are the predominant, persistent daughter compounds from TeCA degradation. In addition, porewater chemistry showed higher accumulation of VC in the wetland sediment at site WB30 than at site WB23, as was observed in the microcosm experiments. Molecular analyses of grab samples of surficial wetland sediment showed that all the microbial species or groups linked to TeCA degradation in the microcosm experiments were present in all sediment samples. Microbial biomass and diversity were lowest in an area of the wetland (transect C-C') where porewater VOC concentrations are highest, indicating that the higher VOC concentrations could result from lower degradation rates. The lower microbial biomass and diversity in this area could be caused by toxic effects of the contaminants, or possibly from differences in frequency and duration of tidal inundation.

Maryland↗

USGS1987

Determination of benthic-invertebrate indices and water-quality trends of selected streams in Chester County, Pennsylvania, 1969-80

The trends of biological and chemical data collected for 12 years (1969-80) from 46 sites in Chester County were evaluated by using the sea- sonal Kendall test. Brillouin's diversity index was calculated and plotted against time for each site. The diversity index at 7 sites had upward trends significant at the 99-percent confidence level, the index at 9 sites had upward trends significant at the 95 to 98 percent confidence level, and the index at 11 sites had upward trends significant at the 90 to 94 percent con- fidence level. Although the trends were not statistically significant, 17 of the remaining sites had upward trends and 2 had downward trends. The seasonal Kendall test was used to test the chemical data for temporal trends at eight sites having stream discharge data. Significant trends were found at one or more sites for flow-adjusted values of specific conductance, pH, total nitrate, total phosphorus, dissolved chloride, and dissolved sulfate. The chemical data for 11 sites, which were not flow adjusted, were tested for trends by plotting against time and determining a correlation coefficient. Significant trends were found at one or more sites in nitrate and chloride. Selected chemical constituents were tested by regression analysis for correlation with the diversity index. Only total dissolved solids correlated significantly with diversity index. Several suggestions are made to improve the monitoring program.

Water-Resources Investigations Report↗

USGS1984

Water quality in the New River from Calexico to the Salton Sea, Imperial County, California

The New River enters the United States at Calexico, Calif., after it crosses the international boundary. Water-quality data from routine collection indicated that the New River was degraded by high organic and bacterial content. Intensive sampling for chemical and physical constituents and properties of the river was done May 9-13, 1977, to quantify the chemical composition of the water and to identify water-quality problems. Concentrations of total organic carbon in the New River at Calexico ranged from 80 to 161 milligrams per liter and dissolved organic carbon ranged from 34 to 42 milligrams per liter; the maximum chemical oxygen demand was 510 milligrams per liter. Intensive sampling for chemical and biological characteristics was done in the New River from May 1977 to June 1978 to determine the occurrence of the organic material and its effects on downstream water quality. Dissolved-oxygen concentration was measured along longitudinal profiles of the river from Calexico to the Salton Sea. A dissolved-oxygen sag downstream from the Calexico gage varied seasonally. The sag extended farther downstream and had lower concentrations of dissolved oxygen during the summer months than during the winter months. The sag of zero dissolved-oxygen concentration extended 26 miles in July 1977. In December 1976, the sag extended 20 miles but the minimum dissolved-oxygen concentration was 2.5 milligrams per liter. The greatest diel (24-hour) variation in dissolved-oxygen concentration occurred in the reach from the Calexico gage to Lyons Crossing, 8.8 miles downstream. High concentrations of organic material were detected as far as Highway 80, 19.5 miles downstream from the international boundary. Biological samples analyzed for benthic invertebrates showed that water at the Calexico and Lyons Crossing sites, nearest the international boundary, was of such poor quality that very few bottom-dwelling organisms could survive. Although the water was of poor quality at Keystone Road, 36 miles downstream, it was able to support a benthic community. The April sample had more than 9,150 organisms on a multiplate sampler, 8,770 of which were of one species. Farther downstream at the Westmorland gage, the water quality, as indicated by the number and diversity of organisms, had improved over that at the Keystone site. The Alamo River at its outlet to the Salton Sea--the control site--had the greatest diversity of all the study sites. This diversity, when compared with the diversity at the Westmorland gage, indicated that the effects of the degraded water quality observed at the New River at Calexico are detected as far as 62 miles downstream. Standard bacteria indicator tests indicate that fecal contamination exists in the New River. Counts of fecal coliform bacteria ranged from 180,000 to 2,800,000 colonies per 100 milliliters for the 20-mile reach from Calexico to Highway 80, and fecal streptococcal bacteria ranged from 5,000 to 240,000 colonies per 100 milliliters.

California↗

USGS2025

A practical framework for identifying genetic subpopulations and ESUs: Insights for IUCN assessments and broader management

The International Union for Conservation of Nature (IUCN) sets global conservation standards, including the Red List of Threatened Species and the Green Status of Species. Recent analyses showed that genetic diversity has not been effectively considered by IUCN species assessments, despite being fundamental to species’ fitness and adaptive potential. Incorporation of genetic diversity into IUCN assessments can support its successful long-term conservation. To enhance the preservation of genetic diversity, assessments should include genetically meaningful within-species units. Subpopulations are recognized units by the IUCN for protecting natural connectivity, however infrequently evaluated. Evolutionarily Significant Units (ESUs) are currently not recognized as a formal unit by the IUCN. However, incorporating ESUs into conservation frameworks could significantly enhance our capacity to identify and protect adaptive genetic diversity. To facilitate inclusion of these units in IUCN assessments, we outline a widely applicable framework for their identification that uses non-molecular and molecular data for global accessibility.

EcoEvoRxiv↗

USGS2003

Two distinct phylogenetic clades of infectious hematopoietic necrosis virus overlap within the Columbia River basin

Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus, causes a highly lethal disease of salmonid fish in North America. To evaluate the genetic diversity of IHNV from throughout the Columbia River basin, excluding the Hagerman Valley, Idaho, the sequences of a 303 nt region of the glycoprotein gene (mid-G) of 120 virus isolates were determined. Sequence comparisons revealed 30 different sequence types, with a maximum nucleotide diversity of 7.3% (22 mismatches) and an intrapopulational nucleotide diversity of 0.018. This indicates that the genetic diversity of IHNV within the Columbia River basin is 3-fold higher than in Alaska, but 2-fold lower than in the Hagerman Valley, Idaho. Phylogenetic analyses separated the Columbia River basin IHNV isolates into 2 major clades, designated U and M. The 2 clades geographically overlapped within the lower Columbia River basin and in the lower Snake River and tributaries, while the upper Columbia River basin had only U clade and the upper Snake River basin had only M clade virus types. These results suggest that there are co-circulating lineages of IHNV present within specific areas of the Columbia River basin. The epidemiological significance of these findings provided insight into viral traffic patterns exhibited by IHNV in the Columbia River basin, with specific relevance to how the Columbia River basin IHNV types were related to those in the Hagerman Valley. These analyses indicate that there have likely been 2 historical events in which Hagerman Valley IHNV types were introduced and became established in the lower Columbia River basin. However, the data also clearly indicates that the Hagerman Valley is not a continuous source of waterborne virus infecting salmonid stocks downstream.

Diseases of Aquatic Organisms↗

USGS2005

Oceanographic conditions structure forage fishes into lipid-rich and lipid-poor communities in lower Cook Inlet, Alaska, USA

Forage fishes were sampled with a mid-water trawl in lower Cook Inlet, Alaska, USA, from late July to early August 1996 to 1999. We sampled 3 oceanographically distinct areas of lower Cook Inlet: waters adjacent to Chisik Island, in Kachemak Bay, and near the Barren Islands. In 163 tows using a mid-water trawl, 229437 fishes with fork length <200 mm were captured. More than 39 species were captured in lower Cook Inlet, but Pacific sand lance Ammodytes hexapterus, juvenile Pacific herring Clupea pallasi, and juvenile walleye pollock Theragra chalcogramma comprised 97.5% of the total individuals. Both species richness and species diversity were highest in warm, low-salinity, weakly stratified waters near Chisik Island. Kachemak Bay, which had thermohaline values between those found near Chisik Island and the Barren Islands, had an intermediate value of species richness. Species richness was lowest at the Barren Islands, an exposed region that regularly receives oceanic, upwelled water from the Gulf of Alaska. Non-metric multidimensional scaling (NMDS) was used to compute axes of species composition based on an ordination of pairwise site dissimilarities. Each axis was strongly rank-correlated with unique groups of species and examined separately as a function of environmental parameters (temperature, salinity, depth), area, and year. Oceanographic parameters accounted for 41 and 12% of the variability among forage fishes indicated by Axis 1 and Axis 2, respectively. Axis 1 also captured the spatial variability in the upwelled area of lower Cook Inlet and essentially contrasted the distribution of species among shallow, nearshore (sand lance, herring) and deep, offshore (walleye pollock) habitats. Axis 2 captured the spatial variability in forage fish communities from the north (Chisik Island) to the south (Barren Islands) of lower Cook Inlet and essentially contrasted a highly diverse community dominated by salmonids and osmerids (warmer, less saline) with a fish community dominated by Pacific sand lance (colder, more saline). Axis 3 reflected the negative spatial association of capelin Mallotus villosus and Pacific cod Gadus macrocephalus. Correlations of year with Axes 1 and 3 indicate that from 1996 to 1999 the forage fish community significantly decreased in lipid-poor gadids (walleye pollock and Pacific cod), and significantly increased in lipid-rich species such as Pacific sand lance, Pacific herring, and capelin.

Alaska↗

USGS2020

Genetic and environmental indicators of climate change vulnerability for desert bighorn sheep

Assessments of organisms’ vulnerability to potential climatic shifts are increasingly common. Such assessments are often conducted at the species level and focused primarily on the magnitude of anticipated climate change (i.e., climate exposure). However, wildlife management would benefit from population-level assessments that also incorporate measures of local or regional potential for organismal adaptation to change. Estimates of genetic diversity, gene flow, and landscape connectivity can address this need and complement climate exposure estimates to establish management priorities at broad to local scales. We provide an example of this holistic approach for desert bighorn sheep ( Ovis canadensis nelsoni ) within and surrounding lands administered by the U.S. National Park Service. We used genetic and environmental data from 62 populations across the southwestern U.S. to delineate genetic structure, evaluate relationships between genetic diversity and isolation, and estimate relative climate vulnerability for populations as a function of five variables associated with species’ responses to climate change: genetic diversity, genetic isolation, geographic isolation, forward climate velocity within a population’s habitat patch (a measure of geographic movement rate required for an organism to maintain constant climate conditions), and maximum elevation within the habitat patch (a measure of current climate stress, as lower maximum elevation is associated with higher temperature, lower precipitation, and lower population persistence). Genetic structure analyses revealed a high-level division between populations in southeastern Utah and populations in the remainder of the study area, which were further differentiated into four lower-level genetic clusters. Genetic diversity decreased with population isolation, whereas genetic differentiation increased, but these patterns were stronger for native populations than for translocated populations. Populations exhibited large variation in predicted vulnerability across the study area with respect to all variables, but native populations occupying relatively intact landscapes, such as Death Valley and Grand Canyon national parks, had the lowest overall vulnerability. These results provide local and regional context for conservation and management decisions regarding bighorn populations in a changing climate. Our study further demonstrates how assessments combining multiple factors could allow a more integrated response, such as increasing efforts to maintain connectivity and thus potential for adaptation in areas experiencing rapid climate change.

Arizona, California, Nevada, Utah↗

USGS2023

DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico

With viruses often having devastating effects on wildlife population fitness and wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat ( Lynx rufus , n = 9) and puma ( Puma concolor , n = 13) scat samples non-invasively collected from Sonora, Mexico, to characterize fecal DNA viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research including samples from additional sources (e.g., prey items, tissues) may help to clarify host associations and determine the pathogenicity of detected viruses.

Sonora↗

USGS2024

Benthic macroinvertebrate response to estuarine emergent marsh restoration across a delta-wide environmental gradient

Benthic invertebrates play vital roles in estuarine ecosystems, but like other taxa they have been excluded from former marshlands by diking and land use conversion. Dike removal is one way of restoring marsh, but the response of benthic invertebrates has been little studied. Also understudied is variation in benthic invertebrate communities across entire deltas, particularly in the Pacific Northwest of North America where deltas receive high flows and sediment loads for their size. Our goals were to evaluate invertebrate response to large-scale dike removal on the Nisqually River Delta in Puget Sound, Washington, U.S.A., characterize delta-wide invertebrate community variation, and relate invertebrate response and spatial variation to environmental conditions. We sampled invertebrates annually from one year before to three years after dike removal in restoring marsh, previously restored marsh, undisturbed reference marsh, and adjacent tidal flats. Marine taxa immediately colonized the area recently restored to tidal inundation and population size grew exponentially thereafter for several of them. Community composition and diversity recovered completely, and density and biomass were approaching recovery three years later. Invertebrate communities converged between restoring and pre-existing marsh (previously restored and reference), suggesting an influence of reestablished connectivity. Just offshore from the dike line, invertebrates declined one year after dike removal but then rebounded indicating resilience to short-term disturbance. Dike removal effects were not detected farther offshore. Near the offshore edge of the delta, invertebrate biomass and body size were greater than elsewhere and a diverse assemblage of crustaceans, polychaetes, and bivalves was present. Farther inshore, tidal flats were dominated by a few species of small-bodied polychaetes and had higher density but lower biomass and diversity. Facultative detritivores, which can also filter feed, were the dominant feeding guild everywhere on the tidal flats. Density, biomass, diversity, and community composition on the marsh were more similar to the inner than outer tidal flats. Environmental variables most associated with invertebrate community variation were elevation, salinity, and sediment grain size and organic content. Our results are relevant to assessing performance and setting expectations for future restorations and have broad implications for the role of benthic invertebrates in estuarine ecosystems.

Washington↗

USGS2021

Novel insights into the genetic population connectivity of transient whale sharks (Rhincodon typus) in Pacific Panama provide crucial data for conservation efforts

The whale shark ( Rhincodon typus ) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity ( H d = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2 , were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3 , PTY4 , and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

Gulf of Chiriqu↗

USGS2025

Metal fingerprints of Eocene rhyolite magmas coincident with Carlin-type gold deposition in Nevada USA

Eocene magmatic systems contemporaneous with world-class Carlin-type Au deposits in Nevada (USA) have been proposed by some researchers as a key ingredient for Au mineralization, though evidence conclusively demonstrating their genetic relationship remains tenuous. This study provides the first direct evidence of the pre-eruptive metal budget of volatile- and metal-charged silicic magmas coincident in time (~41 to 34 Ma) and space (within 5 km) with Carlin-type Au deposits. We characterize the pre-eruptive metal fingerprints of these diverse magmatic systems to assess their potential as sources of metals for Carlin-type Au mineralization. Metal abundances from quartz-hosted melt inclusions (Au, Te, Ag, Sb, Tl, Mo, W, Sn, As, Pb, Co, Cu, Ni, and Zn) characterized in situ by SHRIMP-RG and LA-ICP-MS represent our best (and only) estimates for the pre-eruptive metal budget in these systems. Median metal concentrations are generally within one order of magnitude of average upper crust and average continental rhyolite values. But there are two notable exceptions, with median Au contents extending >1 order of magnitude higher than average upper crust and median Cu contents ranging >1 order of magnitude lower than upper crust. Despite this, melts contain lower Au/Cu (<0.1), Au/Ag (<5), and Au/Tl (<0.3) than most ore-grade Carlin-type rock samples and quartz-hosted fluid inclusions, regardless of their age and timing relative to nearby Carlin-type Au mineralization. The metal fingerprints of these magmatic systems, de-fined both by traditional and multivariate compositional data analysis techniques, are distinct from one another. Yet none are particularly specialized, e.g., high Au/Cu, in terms of being ideal ingredients as postulated by magmatic models for Carlin-type Au mineralization. Magmatic Au contents do not appear to be correlated with rhyolite “flavors” in the way that Cu, Sn, and Nb contents are. Fluid/melt partitioning modeling and magma volume estimates support the idea that a diverse array of non-specialized silicic magmas could feasibly contribute some or potentially all of the Au, Ag, and Cu in Carlin-type systems. The compositional diversity among contemporaneous magmatic systems could possibly contribute to some of the diversity observed across Carlin-type Au districts in Nevada.

Nevada↗

USGS2012

Associations of benthic macroinvertebrate assemblages with environmental variables in the upper Clear Creek watershed, California

Benthic macroinvertebrates are integral components of stream ecosystems and are often used to assess the ecological integrity of streams. We sampled streams in the upper Clear Creek drainage in the Klamath—Siskiyou Ecoregion of northwestern California in fall 2004 (17 sites) and 2005 (original 17 plus 4 new sites) with the objectives of documenting the benthic macroinvertebrate assemblages supported by the streams in the area, determining how those assemblages respond to environmental variables, assessing the biological condition of the streams using a benthic index of biotic integrity (IBI), and understanding the assemblages in the context of biodiversity of the ecoregion. We collected both reach-wide (RW) and targeted-riffle (TR) macroinvertebrate samples at each site. The macroinvertebrate assemblages were diverse, with over 150 genera collected for each sampling protocol. The macroinvertebrate assemblages appeared to be most responsive to a general habitat gradient based on stream size, gradient, flow, and dominance of riffles. A second important habitat gradient was based on elevation and dominance of riffles. A gradient in water quality based on concentrations of dissolved ions and metals was also important. Models based on these 3 gradients had Spearman's rank correlations with macroinvertebrate taxonomic composition of 0.60 and 0.50 for the TR and RW samples, respectively. The majority (>50%) of the sites were in good or very good biological condition based on IBI scores. The diversity of macroinvertebrate assemblages is associated with the diversity of habitats available in the Klamath—Siskiyou Ecoregion. Maintaining the aquatic habitats in good condition is important in itself but is also vital to maintaining biodiversity in this diverse and unique ecoregion.

California↗

USGS2017

Conservation genetics of American crocodile, Crocodylus acutus , populations in Pacific Costa Rica

Maintaining genetic diversity is crucial for the survival and management of threatened and endangered species. In this study, we analyzed genetic diversity and population genetic structure at neutral loci in American crocodiles, Crocodylus acutus, from several areas (Parque Nacional Marino Las Baulas, Parque Nacional Santa Rosa, Parque Nacional Palo Verde, Rio Tarcoles, and Osa Conservation Area) in Pacific Costa Rica. We genotyped 184 individuals at nine microsatellite loci to describe the genetic diversity and conservation genetics between and among populations. No population was at Hardy-Weinberg Equilibrium (HWE) over all loci tested and a small to moderate amount of inbreeding was present. Populations along the Pacific coast had an average heterozygosity of 0.572 across all loci. All populations were significantly differentiated from each other with both FST and RST measures of population differentiation with a greater degree of molecular variance (81%) found within populations. Our results suggest C. acutus populations in Pacific Costa Rica were not panmictic with moderate levels of genetic diversity. An effective management plan that maintains the connectivity between clusters is critical to the success of C. acutus in Pacific Costa Rica.

Nature Conservation↗

USGS2025

The Grouse & Grazing Project: Effects of cattle grazing on demographic traits of greater sage-grouse

Greater sage-grouse (Centrocercus urophasianus) were once widespread within sagebrush -grassland ecosystems of western North America, but populations have declined since the mid-1960s. Though sage-grouse were not listed as threatened or endangered under the Endangered Species Act (ESA), when examined in 2015, they remain a species of interest and concern. Roughly half of the sage-grouse’s remaining habitat is on federal land, most of it managed by the Bureau of Land Management (BLM) and the U.S. Forest Service (USFS). Livestock grazing is the most extensive land use within sage-grouse habitat and the effects of livestock grazing on sage-grouse are often debated. The extensive decade-long research project summarized in this report was initiated to provide rigorous experimental research to inform the debate regarding the relationship between livestock grazing and sage-grouse. In 2012, the Idaho Grouse & Grazing Project was started with several partners including the University of Idaho, BLM, Idaho Department of Fish and Game (IDFG), and other partners to evaluate the effects of cattle grazing on sage-grouse vital rates. Many additional supporters have provided resources to this research effort including the Public Lands Council, Idaho Cattle Association, Idaho Governor’s Office of Species Conservation, Western Association of Fish & Wildlife Agencies, U.S. Fish and Wildlife Service, USFS, and numerous grazing associations and ranchers in Idaho. This 10-year research project was a scientifically rigorous and replicated experiment, occurring across five study sites in Idaho. This document is intended to provide a summary of the findings of this unprecedented study. Annual reports are available on the project’s website: https://idahogrousegrazing.org and scientific papers are being prepared and submitted to journals. The project focused on the influence of spring cattle grazing on sage-grouse vital rates across five study sites in Idaho including 21 BLM grazing pastures. From 2014-2023, we captured 1,343 grouse, documented the fate of 1,285 nests, and tracked 399 broods. Vegetation was characterized at 4,777 plots and grazing utilization levels were recorded at >30,000 locations. Because insects are an important food source for sage-grouse hens and their chicks, insect biomass and diversity were also examined in this study. We collected arthropods in 12,151 pitfall samples and 6,217 sweep-net samples across 786 plots within our five study sites. At each study site, three or four grazing treatments were implemented after two years of pre-treatment field investigations. These controlled cattle grazing treatments included spring-grazing in even years, spring-grazing in odd years, spring-and-fall grazing in alternating years, and a no grazing (or rested) control. Once grazing treatments were implemented at a study site, we measured sage-grouse demographic traits for 4-8 years post-treatment. Stocking rate (grazing intensity) was assessed across pastures each year and was influenced by vegetation communities, topography, and water sources. Grazed pastures exhibited lower grass cover and height compared to the no grazing pastures, and the extent of this difference varied based on annual precipitation levels. Rested pastures maintained higher grass cover and grass height, but the differences in habitat structure did not consistently translate to differences in sage-grouse demographic traits. Apparent nesting success varied annually and by site, ranging from 24% to 44% over the study period. Like some other studies, results from this research show that successful (i.e., hatched) sage-grouse nests have taller grass heights than failed nests. The average grass height surrounding successful nests in grazed pastures was shorter than that surrounding successful nests in non-grazed (i.e., rested) pastures. It is well documented that grazing reduces grass height, and these observations have led to widely held assumptions that livestock grazing reduces grass height which negatively affects sage-grouse nesting habitat. At the pasture scale, this study has found that sage-grouse nesting success is no greater in pastures that were rested for 4-8 years than those currently or recently grazed. This study gives no indication that removing cattle from pastures affected nesting success. We found some evidence that nest density varied among the grazing treatments, but we did not see compelling evidence of increases in density of nesting hens following cessation of grazing in the no grazing treatments. Brood survival varied by site and year but showed no strong effect of grazing treatment. Climatic conditions, particularly drought in 2021, had a greater effect on brood survival than grazing metrics. We also found no differences in hen survival among the grazing treatments. Results of this study suggest that hens nesting in spring and fall grazed pastures had similar or even slightly higher brood survival than hens in the rested pastures or the spring grazed pastures. Arthropod biomass and species diversity varied among our study sites and the differences between grazed and rested pastures also varied among study sites. Average biomass and diversity of arthropods was higher in the spring grazed pastures on two of three sites examined but higher in the rested pastures on the other site examined. Some taxa of arthropods were more abundant in grazed pastures while other taxa were more abundant in rested pastures. For example, Carabidae (Ground Beetles) and Formicidae (Ants) had higher biomass in grazed pastures, while Tenebrionidae (Darkling Beetles) and Acrididae (Grasshoppers) had higher biomass in non-grazed pastures. Results indicate that grazing effects on arthropod biomass and arthropod diversity are study site-dependent, suggesting a need to better quantify the most important prey taxa for sage-grouse chicks and to better control for other factors that influence arthropod abundance. Based on results of this research, livestock grazing, when properly managed, does not appear to negatively impact sage-grouse nest survival or brood success. This study provides critical insights for land managers balancing livestock production with sage-grouse conservation, supporting adaptive grazing strategies that maintain both economic and ecological objectives.

Idaho↗

USGS2026

Genomic structural variation rescues a classic biological invader from a population bottleneck

Invasion genetics presents a classic paradox: how do species successfully spread despite severe population bottlenecks? The brown treesnake ( Boiga irregularis ) in Guam represents a striking example of this phenomenon, having been introduced with only a handful of individuals. We show that the population endured an extreme bottleneck, with roughly half of the genome exhibiting runs of homozygosity, comparable to species of conservation concern. Despite this, we uncovered extensive diversity in the form of nearly 19,000 genomic structural variants, which affect almost eight times more of the genome than single-nucleotide variants and provide material for ‘rescuing’ the population from inbreeding-driven declines. Structural variant density was highest in gene promoters, where recombination and DNA repair often occur, providing a mechanism for rapid evolution of gene-linked diversity. This diversity is enriched in genes vital for adaptive immunity and olfaction, suggesting genomic diversity in key chromosomal regions can rescue populations from inbreeding. This work has critical implications for invasion biology and conservation genetics practitioners.

BioRxiv↗

USGS2024

Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland

Mineral-rich hardgrounds, such as ferromanganese (FeMn) crusts and phosphorites, occur on seamounts and continental margins, gaining attention for their resource potential due to their enrichment in valuable metals in some regions. This study focuses on the Southern California Borderland (SCB), an area characterized by uneven and heterogeneous topography featuring FeMn crusts, phosphorites, basalt, and sedimentary rocks that occur at varying depths and are exposed to a range of oxygen concentrations. Due to its heterogeneity, this region serves as an optimal setting for investigating the relationship between mineral-rich hardgrounds and benthic fauna. This study characterizes the density, diversity, and community composition of macrofauna (>300 μm) on hardgrounds as a function of substrate type and environment (depth and oxygen ranges). Rocks and their macrofauna were sampled quantitatively using remotely operated vehicles (ROVs) during expeditions in 2020 and 2021 at depths above, within, and below the oxygen minimum zone (OMZ). A total of 3,555 macrofauna individuals were counted and 416 different morphospecies (excluding encrusting bryozoans and hydrozoans) were identified from 82 rocks at depths between 231 and 2,688 m. Average density for SCB macrofauna was 11.08 ± 0.87 ind. 200 cm −2 and mean Shannon-Wiener diversity per rock (H′ [loge] ) was 2.22 ± 0.07. A relationship was found between substrate type and macrofaunal communities. Phosphorite rocks had the highest H′ of the four substrates compared on a per-rock basis. However, when samples were pooled by substrate, FeMn crusts had the highest H′ and rarefaction diversity. Of all the environmental variables examined, water depth explained the largest variance in macrofaunal community composition. Macrofaunal density and diversity values were similar at sites within and outside the OMZ. This study is the first to analyze the macrofaunal communities of mineral-rich hardgrounds in the SCB, which support deep-ocean biodiversity by acting as specialized substrates for macrofaunal communities. Understanding the intricate relationships between macrofaunal assemblages and mineral-rich substrates may inform effects from environmental disruptions associated with deep-seabed mining or climate change. The findings contribute baseline information useful for effective conservation and management of the SCB and will support scientists in monitoring changes in these communities due to environmental disturbance or human impact in the future.

California↗

USGS2018

The influence of different deep-sea coral habitats on sediment macrofaunal community structure and function

Deep-sea corals can create a highly complex, three-dimensional structure that facilitates sediment accumulation and influences adjacent sediment environments through altered hydrodynamic regimes. Infaunal communities adjacent to different coral types, including reef-building scleractinian corals and individual colonies of octocorals, are known to exhibit higher macrofaunal densities and distinct community structure when compared to non-coral soft-sediment communities. However, the coral types have different morphologies, which may modify the adjacent sediment communities in discrete ways. Here we address: (1) how infaunal communities and their associated sediment geochemistry compare among deep-sea coral types ( Lophelia pertusa, Madrepora oculata, and octocorals) and (2) do infaunal communities adjacent to coral habitats exhibit typical regional and depth-related patterns observed in the Gulf of Mexico (GOM). Sediment push cores were collected to assess diversity, composition, numerical abundance, and functional traits of macrofauna (>300 µm) across 450 kilometers in the GOM at depths ranging from 263–1,095 m. Macrofaunal density was highest in L. pertusa habitats, but similar between M. oculata and octocorals habitats. Density overall exhibited a unimodal relationship with depth, with maximum densities between 600 and 800 m. Diversity and evenness were highest in octocoral habitats; however, there was no relationship between diversity and depth. Infaunal assemblages and functional traits differed among coral habitats, with L. pertusa habitats the most distinct from both M. oculata and octocorals. These patterns could relate to differences in sediment geochemistry as L. pertusa habitats contained high organic carbon content but low proportions of mud compared to both M. oculata and octocoral habitats. Distance-based linear modeling revealed depth, mud content, and organic carbon as the primary factors in driving coral infaunal community structure, while geographic location (longitude) was the primary factor in functional trait composition, highlighting both the location and ecological differences of L. pertusa habitats from other coral habitats. Enhanced habitat structural complexity associated with L. pertusa and differences in localized hydrodynamic flow may contribute to the dissimilarities in the communities found among the coral types. Our results suggest a decoupling for infaunal coral communities from the typical depth-related density and diversity patterns present throughout soft-sediment habitats in the GOM, highlighting the importance of deep-sea corals in structuring unique communities in the nearby benthos.

PeerJ↗

USGS2002

Management and conservation of San Francisco Bay salt ponds: effects of pond salinity, area, tide, and season on Pacific Flyway waterbirds

Throughout the world, coastal salt ponds provide habitat for large numbers and diversities of water- birds. San Francisco Bay contains the most important coastal salt pond complexes for waterbirds in the United States, supporting more than a million waterbirds through the year. As an initial step in attempting to understand how the anticipated conversion of salt ponds to tidal marsh might affect the Bay's bird populations, the number of birds using salt ponds on high and low tides was counted during the winter months of 1999/00 and 2000/01. Be- havior and habitat use of birds in these ponds were assessed, and the effects of tide cycle, pond salinity, and pond area on bird use were examined. We recorded 75 species ofwaterbirds in surveys of salt ponds in the South Bay from September 1999 to February 2001, totaling over a million bird use days on high tide. Shorebirds and dabbling ducks were the most abundant groups of birds using the salt ponds. Waterbird numbers and diversity were significantly affected by the salinity of ponds in a non-linear fashion with lower numbers and diversity on the highest salinity ponds. With the exception of ducks and Eared Grebe (Podiceps nigricollis), tide height at the Bay significantly affect- ed bird numbers in the salt ponds with ponds at high tides having higher numbers of birds than the same ponds on low tides. Considerable numbers of birds fed in the salt ponds on high and low tides, although this varied greatly by species. Habitat use varied by tide. Management recommendations include maintaining ponds of varying salini- ties and depths. Restoring salt ponds to tidal marsh should proceed with caution to avoid loss of waterbird diversity and numbers in San Francisco Bay.

Waterbirds↗