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At least 811 records · Page 45Linked to original sources

USGS2012

A comparison of artificial incubation and natural incubation hatching success of gopher tortoise (Gopherus polyphemus) eggs in southern Mississippi

Recent studies have found that Gopher Tortoise, Gopherus polyphemus, populations in southern Mississippi exhibit low recruitment, due in part to very low hatching success of their eggs. We sought to determine if the cause(s) of this low hatching success was related to egg quality (intrinsic factors), unsuitability of the nest environment (extrinsic factors), or a combination of the two. In 2003, hatching success was monitored simultaneously for eggs from the same clutches that were incubated in the laboratory and left to incubate in nests. A subset of randomly chosen eggs from each clutch was incubated in the laboratory under physical conditions that were known to be conducive to successful hatching to estimate the proportion of eggs that were capable of hatching in a controlled setting. Hatching success in the laboratory was compared with that of eggs incubated in natural nests to estimate the proportion of eggs that failed to hatch presumably from extrinsic factors. Laboratory hatching success was 58.8%, suggesting that roughly 40% of the eggs were intrinsically incapable of hatching even when incubated under controlled conditions. Hatching success in natural nests, 16.7%, was significantly lower than hatching success in the laboratory, suggesting that approximately 42.1% of eggs were capable of hatching but failed to hatch due to some extrinsic aspect(s) of the nest environment. Thus, the low hatching success of Gopher Tortoise eggs in southern Mississippi appears to be attributable to a combination of intrinsic (egg quality) and extrinsic (nest environment) factors.

Mississippi↗

USGS2013

Challenge theme 7: Information support for management of border security and environmental protection: Chapter 9 in United States-Mexican Borderlands: Facing tomorrow's challenges through USGS science

Historically, international borders were located far from the major political and economic capitals of their countries and rarely received adequate planning or infrastructure development. Today, as a result of global economics and increased movement of goods between nations, border regions play a much greater role in commerce, tourism, and transportation. For example, Mexico is the second largest destination for United States exports (Woodrow Wilson Center Mexico Institute, 2009). The rapid population and economic growth along the United States–Mexican border, undocumented human border crossings, and the unique natural diversity of resources in the Borderlands present challenges for border security and environmental protection. Assessing risks and implementing sustainable growth policies to protect the environment and quality of life greatly increase in complexity when the issues cross an international border, where social services, environmental regulations, lifestyles, and cultural beliefs are unique for each country. Shared airsheds, water and biological resources, national security issues, and disaster management needs require an integrated binational approach to assess risks and develop binational management strategies.

United States-Mexico Borderlands↗

USGS2001

Natural hazards on alluvial fans: the debris flow and flash flood disaster of December 1999, Vargas state, Venezuela

Large populations live on or near alluvial fans in locations such as Los Angeles, California, Salt Lake City, Utah, Denver, Colorado, and lesser known areas such as Sarno, Italy, and Vargas, Venezuela. Debris flows and flash floods occur episodically in these alluvial fan environments, and place many communities at high risk during intense and prolonged rainfall. In December 1999, rainstorms induced thousands of landslides along the Cordillera de la Costa, Vargas, Venezuela. Rainfall accumulation of 293 mm during the first 2 weeks of December was followed by an additional 911 mm of rainfall on December 14 through 16. Debris flows and floods inundated coastal communities resulting in a catastrophic death toll of as many as 30,000 people. Flash floods and debris flows caused severe property destruction on alluvial fans at the mouths of the coastal mountain drainage network. In time scales spanning thousands of years, the alluvial fans along this Caribbean coastline are dynamic zones of high geomorphic activity. Because most of the coastal zone in Vargas consists of steep mountain fronts that rise abruptly from the Caribbean Sea, the alluvial fans provide practically the only flat areas upon which to build. Rebuilding and reoccupation of these areas requires careful determination of hazard zones to avoid future loss of life and property. KEY TERMS: Debris flows, flash floods, alluvial fans, natural hazards, landslides, Venezuela

Conference Paper↗

USGS2009

Salinity tolerance of non-native Asian swamp eels (Teleostei: Synbranchidae) in Florida, USA: Comparison of three populations and implications for dispersal

Three populations of non-native Asian swamp eels are established in peninsular Florida (USA), and comprise two different genetic lineages. To assess potential for these fish to penetrate estuarine habitats or use coastal waters as dispersal routes, we determined their salinity tolerances. Swamp eels from the three Florida populations were tested by gradual (chronic) salinity increases; additionally, individuals from the Miami population were tested by abrupt (acute) salinity increases. Results showed significant tolerance by all populations to mesohaline waters: Mean survival time at 14 ppt was 63 days. The Homestead population, a genetically distinct lineage, exhibited greater tolerance to higher salinity than Tampa and Miami populations. Acute experiments indicated that swamp eels were capable of tolerating abrupt shifts from 0 to 16 ppt, with little mortality over 10 days. The broad salinity tolerance demonstrated by these experiments provides evidence that swamp eels are physiologically capable of infiltrating estuarine environments and using coastal waters to invade new freshwater systems. ?? 2009 US Government.

Environmental Biology of Fishes↗

USGS2023

Decadal shifts in the population growth, regeneration, and health of Taxodium distichum in swamps of the Cache River Watershed, Illinois

Population projection models based on long-term trends in regeneration and tree survival can be used to predict the future stability of swamp forest species using water management. Population growth and regeneration of a foundational tree species in North American cypress swamps ( Taxodium distichum ) were compared in the Cache River watershed of southern Illinois USA over several decades. This study examined T. distichum population growth in several regional swamps within the Cache River watershed along a moisture gradient to model growth, stability, or decline based on data of life history stage transitions, using data from the following time periods: the 1990s, 2002–2011, and 2012–2022. Using data from the 1990s, T. distichum populations in Crawford Tract in Buttonland Swamp were projected to increase over time because of the high frequency of juvenile stages at elevations with growing season drawdown and winter flooding. The situation in Crawford Tract had changed by 2019–2021 because T. distichum seedlings had not transitioned (i.e., saplings and young trees were absent) although no old-growth trees had died during or after the 1990s. In other regional swamps, projection models were constructed over two decades (2006–2021) along a dry-to-wet flood gradient including Section 8 Woods, Deer Pond, Wildcat Bluff, Snake Hole, and Heron Pond. Populations in swamps on the drier end of the gradient had more support from juvenile stages. In a tree health survey in 2022 within the impounded interior of Buttonland Swamp (not Crawford Tract), seventy percent of the old-growth T. distichum trees were stressed or declining. Coupled with the fact that no seedlings or saplings were observed, the populations in the interior of the swamp were not stable. Many factors could further stress these ancient T. distichum including interactions of impoundment with chemicals, disease, and changes in air temperature and precipitation. Overall, the seedling abundance in these swamps increased in these environments from 2012 to 2021, except in the most flooded swamps. From a management perspective, drier conditions were more conducive to the success of the earlier life history stages of T. distichum in these old-growth forests.

Illinois↗

USGS2023

Environmental transmission of Pseudogymnoascus destructans to hibernating little brown bats

Pathogens with persistent environmental stages can have devastating effects on wildlife communities. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused widespread declines in bat populations of North America. In 2009, during the early stages of the WNS investigation and before molecular techniques had been developed to readily detect P. destructans in environmental samples, we initiated this study to assess whether P. destructans can persist in the hibernaculum environment in the absence of its conclusive bat host and cause infections in naive bats. We transferred little brown bats ( Myotis lucifugus ) from an unaffected winter colony in northwest Wisconsin to two P. destructans contaminated hibernacula in Vermont where native bats had been excluded . Infection with P. destructans was apparent on some bats within 8 weeks following the introduction of unexposed bats to these environments, and mortality from WNS was confirmed by histopathology at both sites 14 weeks following introduction. These results indicate that environmental exposure to P. destructans is sufficient to cause the infection and mortality associated with WNS in naive bats, which increases the probability of winter colony extirpation and complicates conservation efforts.

Nature↗

USGS2013

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Environmental Microbiology Reports↗

USGS1994

Black Hills hydrology study

The Black Hills area of western South Dakota is a valuable resource center. The area has attracted numerous residents and industries because of the availability of mineral, timber, agricultural, recreational, and water resources. The water resources of the area have been stressed locally by increasing population, periodic drought, and development of other resources. In response to residents' concerns about these stresses on the water resources, the Black Hills Hydrology Study was initiated in 1990 as a cooperative effort among the U.S. Geological Survey, the South Dakota Department of Environment and Natural Resources, and the West Dakota Water Development District. West Dakota represents the various local and county cooperators. This report describes the purpose, scope, approach, and status of the study and presents highlights from the first project data report produced for the study.

Open-File Report↗

USGS2000

Ecotoxicology of Amphibians and Reptiles

For many years, ecological research on amphibians and reptiles has lagged behind that of other vertebrates such as fishes, birds, and mammals, despite the known importance of these animals in their environments. The lack of study has been particularly acute in the he area of ecotoxicology where the number of published scientific papers is a fraction of that found for the other vertebrate classes. Recently, scientists have become aware of severe crises among amphibian populations, including unexplained and sudden extinctions, worldwide declines, and hideous malformations. In many of these instances, contaminants have been listed as probable contributors. Data on the effects of contaminants on reptiles are so depauperate that even the most elementary interpretations are difficult. This state-of-the-science review and synthesis of amphibian and reptile ecotoxicology demonstrates the inter-relationships among distribution, ecology, physiology, and contaminant exposure, and interprets these topics as they pertain to comparative toxicity, population declines, malformations, and risk assessment . In this way, the book identifies and serves as a basis for the most pressing research needs in the coming years. The editors have invited 27 other internationally respected experts to examine the state of existing data in specific areas, interpret it in light of current problems, and identify research gaps and needs. Through its emphasis on recent research, extensive reviews and synthesis, Ecotoxicology of Amphibians and Reptiles will remain a definitive reference work well into the new century.

SETAC Technical Publications Series.↗

USGS2003

Ecosystem history of southern and central Biscayne Bay: Summary report on sediment core analyses

During the last century, the environs of Biscayne Bay have been greatly affected by anthropogenic alteration through urbanization of the Miami/Dade County area. The sources, timing, delivery, and quality of freshwater flow into the Bay have been changed by construction of a complex canal system that controls movement of water throughout south Florida. Changes in shoreline and sub-aquatic vegetation and marine organisms have been observed and changes in water delivery are believed to be the cause. Current restoration goals are attempting to restore natural flow of fresh water into Biscayne and Florida Bays and to restore the natural fauna and flora, but first we need to determine pre-alteration baseline conditions in order to establish targets and performance measures for restoration. This research is part of an ongoing study designed to address the needs of the Biscayne Bay Coastal Wetlands Project (BBCW) of the Comprehensive Everglades Restoration Plan (CERP). By establishing the natural patterns of temporal change in salinity, water quality, vegetation, and benthic fauna in Biscayne Bay and the nearby wetlands over the last 100- 500 years the USGS, in collaboration with our partners, will provide the data necessary to set realistic targets to achieve the BBCW Project goals. Six cores from three sites in Biscayne Bay were collected in April 2002 for multidisciplinary multi-proxy analyses. This report details the results of these analyses and compares the 2002 cores to cores collected in 1997. The following are our significant findings to date: The salinity of central Biscayne Bay has become increasingly marine and increasingly stable over the last 100 years. At No Name Bank, prior to approximately 1915, the inter-decadal and decadal salinity fluctuations appear to have been greater than after 1915 when salinities stabilized at that site. Continental shelf/open marine influence on the sites has increased during the 20th century. There is no indication of inter-decadal salinity extremes or periods of hypersalinity. Freshwater and mesohaline salinities have had a minor influence on No Name bank throughout the time of deposition. At Featherbed Bank, the influence is reduced to mesohaline salinities. Card Bank has experienced relatively large swings in salinity over multi-decadal and centennial timescales, compared to central Biscayne Bay, but marine influence at the site has increased over the last century. Indications of regional scale patterns have been found, especially in the shell chemistry data and the pollen assemblages. These regional patterns indicate that the changes are not site specific and may not be limited to Biscayne Bay. Sub-aquatic vegetation has undergone bay-wide patterns of change over the last 200-500 years, which includes expansion prior to 1900 and declines during the last century in central Biscayne Bay. Thalassia appears to have increased at all three core sites sometime between 1550 and 1750 AD. A decline in Thalassia appears to have occurred after 1950 at No Name Bank and slightly earlier in the 20th century at Featherbed Bank. Card Bank does not appear to have experienced any declines in vegetation on an inter-decadal scale during the 20th century. Molluscan faunal abundance and diversity have undergone significant changes in central Biscayne Bay. Indicators of increased organic-rich sediments at No Name occur between 1869 to 1888 and between the 1930’s to 1975. These changes may correlate to human activities (settlement, population growth). These findings represent a first step towards the project’s goal to reconstruct the history of Biscayne Bay and they provide us with a working model to be tested at other sites. It is clear from our findings that Biscayne Bay has been a dynamic environment over the last 500 years, with natural changes occurring in salinity and benthic habitats. However, several significant changes have occurred in the 20th century: 1) increased stabilization of marine salinities; 2) declines in seagrass in central Biscayne Bay; 3) dramatic changes in molluscan abundance and diversity in central Biscayne Bay. The question remains - how do we better differentiate natural cycles of change from anthropogenic change within these observed trends? The preliminary implications from our research are that changes in salinity and benthic habitats have occurred naturally in Biscayne Bay on inter-decadal to centennial scales, perhaps due to climatic changes, changes in sea level, bank migrations, or a combination of factors. However, further work needs to be done to determine which components of change in the 20th century are human-induced and which are natural. By examining the historical records preserved in the sediments of Biscayne Bay, we can provide restoration trust agencies with the information necessary to set realistic targets and performance measures for Biscayne Bay.

Florida↗

USGS1980

High duck nesting success in a predator-reduced environment

Duck nesting and production were studied during 1969-74 on a 51-ha field of undisturbed grass-legume cover and a surrounding 8.13-km 2 area in north-central South Dakota. The principal mammalian predators of ducks were reduced within a 259-km 2 zone from May 1969 through August 1971. Dabbling duck nest densities, hatching success, and breeding populations attained high levels. Seven duck species produced 1,062 nests on the 51-ha field during 6 years, 864 (81%) hatched, 146 (14%) were destroyed, and 52 (5%) had other fates. During 1970-72, when predator reduction was most effective, the hatching success for 756 nests was 94%. The number of mallard ( Anas platyrhynchos ) nests increased from 37 (0.7/ha) in 1969 to 181 (3.5/ha) in 1972. Mallard pairs increased from 2.8/km 2 to 16.8/km 2 on the 8.13-km 2 area during the same period. A minimum of 7,250 ducklings hatched on the 51-ha field during the 6 years, including 2,342 ducklings in 1972. Exceptionally high duck nesting densities and hatching rates occurred when predators were controlled.

South Dakota↗

USGS2025

Public, bottled, and private drinking water: Shared contaminant-mixture exposures and effects challenge

BACKGROUND: Humans are primary drivers of environmental contaminant exposures worldwide, including in drinking-water (DW). In the United States (US), point-of-use DW (POU DW) is supplied via private tapwater (TW, predominantly private wells), public-supply TW, and bottled water (BW). Differences in management, monitoring, and messaging and lack of directly intercomparable exposure data influence the actual and perceived quality and safety of different DW supplies and directly impact consumer decision making. OBJECTIVES: The purpose of this paper is to provide a meta-analysis (quantitative synthesis) of POU DW contaminant mixture exposures and corresponding potential human health effects of private-TW, public-TW, and BW by aggregating exposure results and harmonizing apical health benchmark weighted and bioactivity weighted effects predictions across previous studies by this research group. DISCUSSION: Simultaneous exposures to multiple inorganic and organic contaminants of known or suspected human-health concern are common across all three DW supplies, with substantial variability observed in each and no systematic difference in predicted cumulative risk between supply chains. Differences in contaminant or contaminant class exposures (e.g., trace metals, disinfection byproducts), with important implications for DW quality improvements, were observed and attributed to corresponding differences in regulation and compliance monitoring. CONCLUSION: The results indicate that human-health risks from contaminant exposures are common to and comparable in all three DW supplies, including BW. Importantly, this study’s target analytical coverage, which exceeds that currently feasible for water purveyors or homeowners, nevertheless is a substantial underestimation of the full breadth of contaminant mixtures in the environment and potentially present in DW. Thus, the results emphasize the need for improved understanding of the adverse human-health implications of long-term exposures to low level inorganic /organic contaminant mixtures across all three distribution pipelines and do not support commercial messaging of BW as a systematically safer alternative to public-TW. Regardless of the supply, increased engagement in source-water protection and drinking-water treatment, including consumer point of use treatment, is necessary to reduce risks associated with long-term DW contaminant exposures, especially in vulnerable populations, and to reduce environmental waste and plastics contamination.

Environment International↗

USGS2021

Identification of seasonal streamflow regimes and streamflow drivers for daily and peak flows in Alaska

Alaska is among northern high‐latitude regions where accelerated climate change is expected to impact streamflow properties, including seasonality and primary flow drivers. Evaluating changes to streamflow, including flood characteristics, across this large and diverse environment can be improved by identifying the distribution and influence of flow drivers. Using metrics of mean monthly streamflow data from 253 streamgages, seasonal flow regimes were clustered to guide identification of seasonal‐flow drivers and form hydrologic groups for identification of peak‐flow populations. Nine seasonally distinct subclasses described variability within three classes dominated by (mostly fall) rainfall, (spring) snowmelt, and (summer) high‐elevation melt. The most glacierized basins exclusively grouped into high‐elevation melt subclasses, and less glacierized basins sometimes exhibited seasonal patterns aligned with rainfall‐ and snowmelt‐dominated regimes. Peak‐flow populations varied by subclass from dominant rainfall or dominant snowmelt to mixed rainfall‐snowmelt or mixed rainfall, snowmelt, and high‐elevation melt. Within subclasses, rainfall generated higher mean peak flows (relative to mean annual flow) than snowmelt or high‐elevation melt. Seasonal flow regimes showed clear but complex associations with basin characteristics, primarily elevation and winter temperature, and with geographic location. These dependencies provided elevation‐based analogies for changes associated with warming and insights for seasonal flow regime prediction and hydrologic region delineation. These results provide a spatially comprehensive perspective on seasonal streamflow drivers across Alaska from historical data and serve as an important historical basis for analysis.

Alaska↗

USGS2006

Integration of coral reef ecosystem process studies and remote sensing

Worldwide, local-scale anthropogenic stress combined with global climate change is driving shifts in the state of reef benthic communities from coral-rich to micro- or macroalgal-dominated (Knowlton, 1992; Done, 1999). Such phase shifts in reef benthic communities may be either abrupt or gradual, and case studies from diverse ocean basins demonstrate that recovery, while uncertain (Hughes, 1994), typically involves progression through successional stages (Done, 1992). These transitions in benthic community structure involve changes in community metabolism, and accordingly, the holistic evaluation of associated biogeochemical variables is of great intrinsic value (Done, 1992). Effective reef management requires advance prediction of coral reef alteration in the face of anthropogenic stress and change in the global environment (Hatcher, 1997a). In practice, this goal requires techniques that can rapidly discern, at an early stage, sublethal effects that may cause long-term increases in mortality (brown, 1988; Grigg and Dollar, 1990). Such methods would improve our understanding of the differences in the population, community, and ecosystem structure, as well as function, between pristine and degraded reefs. This knowledge base could then support scientifically based management strategies (Done, 1992). Brown (1988) noted the general lack of rigor in the assessment of stress on coral reefs and suggested that more quantitative approaches than currently exist are needed to allow objective understanding of coral reef dynamics. Sensitive techniques for the timely appraisal of pollution effects or generalized endemic stress in coral reefs are sorely lacking (Grigg and Dollar, 1990; Wilkinsin, 1992). Moreover, monitoring methods based on population inventories, sclerochronology, or reproductive biology tend to myopic and may give inconsistent results. Ideally, an improved means of evaluating reef stress would discriminate mortality due to natural causes from morality to anthropogenic causes (Brown, 1988). Models of coral reef ecosystems, parameterized by process measurements and scaled in time-space using remote sensing, have the potential to address pressing research questions that are central to devising valid management strategies (Grigg el al., 1984; Hatcher, 1997b). To attain this goal, ecosystem-level models that integrate studies of physical and chemical forcing with observed biological and geological responses are required. This interdisciplinary approach to understanding reef biogeochemical dynamics can allow investigations that integrate the scales of time and space (Hatcher, 1997a), thereby enabling prediction of coral reef change (Andréfouët and Payri, 2001). In turn, prediction of holistic ecosystem function within various environmental focusing scenarios has substantial promise in mitigating future disturbance. Indeed, management of coral reefs at the ecosystem level has been suggested as the only meaningful approach to preserving coral reefs (Bohnsack and Ault, 1996; Christensen et al., 1996).

Florida↗

USGS2023

Latency and geofence testing of wireless emergency alerts intended for the ShakeAlert® earthquake early warning system for the West Coast of the United States of America

ShakeAlert, the earthquake early warning (EEW) system for the West Coast of the United States, attempts to provides crucial warnings before strong shaking occurs. However, because the alerts are triggered only when an earthquake is already in progress, and the alert latencies and delivery times are platform dependent, the time between these warnings and the arrival of shaking is variable. The ShakeAlert system uses, among other public alerting platforms like a mobile phone operating system, smartphone apps, and the Federal Emergency Management Agency Integrated Public Alert & Warning System (IPAWS). IPAWS sends Wireless Emergency Alerts (WEAs) informing people via their smartphones and other mobile devices about various events, such as natural hazards, child abductions, or public health information about COVID-19. However, little is known about the IPAWS delivery latencies. Given that people may have only a few seconds of notice after they receive an alert to take a protective action before they feel earthquake shaking, quantifying latencies is critical to understanding whether the IPAWS system is useful for EEW. In this study, we developed new methods to test the IPAWS distribution system's performance, both with devices in a controlled environment and as well as with a 2019 community-based feedback form, in Oakland and San Diego County, California, respectively. The controlled environment test used mobile phones (including smart and non-smart phones) and associated devices to determine alert receipt times; the community research form had participants self-report their receipt times. By triangulating the data between the controlled test environment and the community research, we determined the latency statistics as well as whether the geofence (the geographic area where the alert was intended to be sent) held broadly. We found that the latencies were similar between the two tests despite the large differences in population sizes. WEA messages were received within a median time frame of 6–12 s, and the geofence held with only a few exceptions. We use this latency to assess how the system would have performed in two large earthquakes, the 1989 M6.9 Loma Prieta and 2019 M7.1 Ridgecrest earthquakes, which both occurred near our WEA test locations. Our analysis revealed that had IPAWS been available during those earthquakes, particularly Loma Prieta, it would have provided crucial seconds of notice that damaging shaking was imminent in some locations relatively far from the epicenter. Further, we find affordable non-smart phones can receive WEAs as fast as smartphones. Finally, our new method can be used for latency and geospatial testing going forward for IPAWS and other similar alerting systems.

California↗

USGS2000

Cadmium toxicity among wildlife in the Colorado Rocky Mountains

Cadmium is known to be both extremely toxic and ubiquitous in natural environments. It occurs in almost all soils, surface waters and plants, and it is readily mobilized by human activities such as mining. As a result, cadmium has been named as a potential health threat to wildlife species; however, because it exists most commonly in the environment as a trace constituent, reported incidences of cadmium toxicity are rare. Here we have measured trace metals in the food web and tissues of white-tailed ptarmigan (Lagopus leucurus) in Colorado. Our results suggest that cadmium toxicity may be more common among natural populations of vertebrates than has been appreciated to date and that cadmium toxicity may often go undetected or unrecognized. In addition, our research shows that ingestion of even trace quantities of cadmium can influence not only the physiology and health of individual organisms, but also the demographics and the distribution of species.

Nature↗

USGS2017

Effects of host species and environment on the skin microbiome of Plethodontid salamanders

The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus , 17 Plethodon glutinosus , 10 Plethodon cylindraceus ) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient ( n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% ( SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

Journal of Animal Ecology↗

USGS2016

Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans , from swab and environmental samples

The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans , in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid from P. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer–based qPCR test for P. destructans to refine quantification capabilities of this assay.

Journal of Veterinary Diagnostic Investigation↗