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At least 361 records · Page 20Linked to original sources
USGS1984

Bioavailability of Pb and Zn from mine tailings as indicated by erythrocyte aminolevulinic acid dehydratase (ALA-D) activity in suckers (Pisces: catostomidae)

The activity of the erythrocyte enzyme δ-aminolevulinic acid dehydratase (ALA-D) was measured in 35 catostomids (black redhorse, Moxostoma duquesnei ; golden redhorse, M . erythrurum ; northern hogsucker, Hypentelium nigricans ) collected from three sites on a stream contaminated with Pb-, Cd-, and Zn-rich mine tailings and from an uncontaminated site upstream. Enzyme activity was expressed in terms of hemoglobin (Hb), DNA, and protein concentrations; these variables can be determined in the laboratory on once-frozen blood samples. Concentrations of Pb and Zn in blood and of Pb in edible tissues were significantly higher, and ALA-D activity was significantly lower, at all three contaminated sites than upstream. At the most contaminated site, ALA-D activity was 62–67% lower than upstream. Lead concentrations in the edible tissues and in blood were positively correlated ( r = 0.80), whereas ALA-D activity was negatively correlated with Pb in blood ( r = −0.70) and in edible tissues ( r = −0.59). Five statistically significant relations between Pb and Zn in blood and ALA-D activity were determined. The two models that explained the highest percentage (> 74%) of the total variance also included factors related to Hb concentration. All five significant models included negative coefficients for variables that represented Pb in blood and positive coefficients for Zn in blood. The ALA-D assay with results standardized to Hb concentration represents an expedient alternative to the more traditional hematocrit standardization, and the measurement of ALA-D activity by this method can be used to document exposure of fish to environmental Pb.

Missouri↗
USGS2012

Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

Pacific walruses ( Odobenus rosmarus divergens ) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (Φ ST =0.051), and between the eastern Chukchi and other nonbreeding aggregations (Φ ST =0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite F ST =0.019; mtDNA Φ ST =0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite F ST =0.019–0.035; mtDNA Φ ST =0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

Journal of Mammalogy↗
USGS2021

The demographic and ecological factors shaping diversification among rare Astragalus species

Aim Evolutionary radiations are central to the origin and maintenance of biodiversity, yet we rarely understand how they are jointly shaped by demography and ecological opportunity. Astragalus is the largest plant genus in the world and is disproportionately comprised of rare species restricted to narrow geographic and ecological regions. Here, we explored the demographic and ecological mechanisms underlying patterns of diversification in a threatened Astragalus species complex endemic to a small desert region in the western United States. Location Southeast Utah, USA. Methods We used high‐throughput DNA sequencing to infer genetic structure, genetic diversity, and demographic history (i.e., the timing of population divergence, effective population sizes and gene flow) among Astragalus taxa. We performed landscape genetic analyses to quantify the relationships between genetic differentiation, geographic distance, and ecological distance based on bioclimatic and soil variables. Finally, we identified putative adaptive loci that show higher genetic differentiation between taxa than expected based on our inferred neutral demographic model. Results We found evidence of low gene flow between three highly differentiated taxa (currently delineated as A . iselyi , A . sabulosus var. sabulosus and A. sabulosus var. vehiculus ) that rapidly diverged from a small ancestral population near the beginning of the last glacial period. Genomic signatures revealed long‐term effective population sizes are 2–10× larger than recent census sizes, perhaps due to the maintenance of standing genetic variation through seed banks. Consistent with limited dispersal and local adaptation, genome‐wide patterns of differentiation are shaped by geographic distance (isolation‐by‐distance) and climate and soil variation (isolation‐by‐environment). Taxon‐specific adaptation is further supported by uncovering putative adaptive loci. Main Conclusions Our findings suggest that interactions between demography (i.e., dispersal limitations and seeds banks) and ecological opportunity (i.e., spatial and temporal environmental heterogeneity) may promote diversification, endemism, and rarity among closely related Astragalus species and similar plant clades distributed across complex landscapes.

Utah↗
USGS2018

Deciphering the link between doubly uniparental inheritance of mtDNA and sex determination in bivalves: Clues from comparative transcriptomics

Bivalves exhibit an astonishing diversity of sexual systems and sex-determining mechanisms. They can be gonochoric, hermaphroditic or androgenetic, with both genetic and environmental factors known to determine or influence sex. One unique sex-determining system involving the mitochondrial genome has also been hypothesized to exist in bivalves with doubly uniparental inheritance (DUI) of mtDNA. However, the link between DUI and sex determination remains obscure. In this study, we performed a comparative gonad transcriptomics analysis for two DUI-possessing freshwater mussel species to better understand the mechanisms underlying sex determination and DUI in these bivalves. We used a BLAST reciprocal analysis to identify orthologs between Venustaconcha ellipsiformis and Utterbackia peninsularis and compared our results with previously published sex-specific bivalve transcriptomes to identify conserved sex-determining genes. We also compared our data with other DUI species to identify candidate genes possibly involved in the regulation of DUI. A total of ∼12,000 orthologous relationships were found, with 2,583 genes differentially expressed in both species. Among these genes, key sex-determining factors previously reported in vertebrates and in bivalves (e.g., Sry, Dmrt1, Foxl2 ) were identified, suggesting that some steps of the sex-determination pathway may be deeply conserved in metazoans. Our results also support the hypothesis that a modified ubiquitination mechanism could be responsible for the retention of the paternal mtDNA in male bivalves, and revealed that DNA methylation could also be involved in the regulation of DUI. Globally, our results suggest that sets of genes associated with sex determination and DUI are similar in distantly-related DUI species.

Genome Biology and Evolution↗
USGS2020

Low O2 level enhances CH4-derived carbon flow into microbial communities in landfill cover soils

CH 4 oxidation in landfill cover soils plays a significant role in mitigating CH 4 release to the atmosphere. Oxygen availability and the presence of co-contaminants are potentially important factors affecting CH 4 oxidation rate and the fate of CH 4 -derived carbon. In this study, microbial populations that oxidize CH 4 and the subsequent conversion of CH 4 -derived carbon into CO 2 , soil organic C and biomass C were investigated in landfill cover soils at two O 2 tensions, i.e., O 2 concentrations of 21% (“sufficient”) and 2.5% (“limited”) with and without toluene. CH 4 -derived carbon was primarily converted into CO 2 and soil organic C in the landfill cover soils, accounting for more than 80% of CH 4 oxidized. Under the O 2 -sufficient condition, 52.9%–59.6% of CH 4 -derived carbon was converted into CO 2 (CE CO2-C ), and 29.1%–39.3% was converted into soil organic C (CE organic-C ). A higher CE organic-C and lower CE CO2-C occurred in the O 2 -limited environment, relative to the O 2 -sufficient condition. With the addition of toluene, the carbon conversion efficiency of CH 4 into biomass C and organic C increased slightly, especially in the O 2 -limited environment. A more complex microbial network was involved in CH 4 assimilation in the O 2 -limited environment than under the O 2 -sufficient condition. DNA-based stable isotope probing of the community with 13 CH 4 revealed that Methylocaldum and Methylosarcina had a higher relative growth rate than other type I methanotrophs in the landfill cover soils, especially at the low O 2 concentration, while Methylosinus was more abundant in the treatment with both the high O 2 concentration and toluene. These results indicated that O 2 -limited environments could prompt more CH 4 -derived carbon to be deposited into soils in the form of biomass C and organic C, thereby enhancing the contribution of CH 4 -derived carbon to soil community biomass and functionality of landfill cover soils (i.e. reduction of CO 2 emission).

Environmental Pollution↗
USGS2025

Assessing diet and genotyping success of goat pellet surveys from 2019 in Glacier National Park

Fecal pellets contain genetic information and can be used to identify individuals, their diet, and more. Individual identification can be useful in understanding movements of individuals, developing population estimates, assessing vital rates, genetic diversity and structure, and evaluating trends over time (e.g., Epps et al 2024). Successful genotyping depends on the quality of the sample, which can be influenced by many things including the initial state of the sample, environmental conditions that the pellets were exposed to, and the method of storage. The diet of mountain goats ( Oreamnos americanus ) is hard to study as they are habitat specialists in some of the most remote and rugged alpine environments (Festa-Bianchet & Côté 2012). These iconic ungulates epitomize the renowned wilderness character of Glacier National Park (GNP), yet the population has declined by 45% since 2008 likely due at least in part to changing climate (Graves et al. 2025). This is well above the International Union for the Conservation of Nature’s population decline criterion used to designate a species as vulnerable (IUCN 2012). Mountain goats are known as dietary generalists employing highly variable diets across systems, but diets have not been identified for GNP. Identifying goat diet composition in GNP can provide the information needed to determine whether this population decline could be related to climate-change induced shifts in forage phenology, diversity, productivity, and plant community structure. Other anthropogenic changes in GNP, such as increases in exotic and invasive plant species, will continue to affect plant community composition (Lesica et al. 1993). These alterations may reduce optimal forage availability and quality, which could have a deleterious effect on mountain goat survival. To examine these possibilities, we must first ask- What precisely are the mountain goats of Glacier National Park eating? DNA metabarcoding of fecal pellets provides a cutting-edge, non-invasive method for assessing herbivore diet. Previous studies of mountain goat diet have used methods such as fecal crude protein analysis (Festa-Bianchet & Côté 2012), rumen analysis (Saunders 1955), fecal microhistology (Cobb et al. 2012), and bite-for-bite feeding observations (Daily et al. 1984). Many of these studies have only been able to identify diet components to functional plant type and the methods used are biased towards less digestible diet components such as grasses (McInnis et al. 1983). Metabarcoding of fecal pellets can provide a higher taxonomic resolution than previous methods (Scasta et al. 2019, Stapleton et al. 2022) and open the field for increased participation of volunteers, also called community or citizen scientists. Here, we use mountain goat fecal pellets to conduct 1) an evaluation of which conditions might influence genotyping success and 2) a preliminary assessment of diet using metabarcoding. This pilot study allowed us to evaluate which pellets to focus on collecting, identify the best storage methods, explore approaches for analyzing metabarcoding data, examine the utility of metabarcoding for acquiring taxonomically specific diet information, and to identify genetic sequences that could not be resolved to genus or species levels using these methods. We examined the frequency of occurrence and relative diet composition of identified forbs, shrubs, graminoids, mosses, and trees in mountain goat diets.

Montana↗
USGS2019

Assessment of the presence of sewage in the Mill River under low-flow conditions, Springfield, Massachusetts, 2010–11

The U.S. Geological Survey, in cooperation with the Pioneer Valley Planning Commission, the U.S. Environmental Protection Agency, and the Massachusetts Department of Environmental Protection Senator William X. Wall Experiment Station, assessed the presence of 14 commonly used human-health pharmaceutical compounds, fecal indicator bacteria, and other man-made compounds indicative of the presence of human sewage in the lower reach of the Mill River near its confluence with the Connecticut River in Springfield, Massachusetts. The study was part of the Tri-State Connecticut River Targeted Watershed Initiative and involved the collection and analysis of raw river water at three sites along the reach, extending from Watershops Pond to the mouth, over the course of a low-flow period, July through November 2010. Previous studies in the region indicated that nonpoint or undocumented sources of wastewater contributed a variety of organic contaminants and potentially harmful bacteria to rivers under both high- and low-flow conditions. Additional samples, including a raw sewage sample collected near a Mill River combined sewer overflow during a non-overflow period, were collected in March 2011. The study was designed to determine if city sewage or other domestic sources of wastewater were entering the river within this reach during low-flow conditions. No definitive evidence of sewage was measured in Mill River water samples collected during the study period. Fecal indicator bacteria, including Escherichia coli ( E. coli ) and enterococci bacteria, were detected in all Mill River water samples. In the DNA analysis of enterococci cultures from the Mill River, samples generally tested negative for the Enterococcus faecium ( esp ) human-specific genetic marker, whereas the raw sewage sample tested positive. Samples also generally tested negative in the human-specific rDNA marker assay for the anaerobic bacterium Bacteroidetes . Samples tested negative in 2010 for two Bacteroidetes human-specific genetic markers, HF134 and HF183, except samples from near the mouth of the Mill River, which tested positive. Samples collected in March 2011 from all three measurement sites tested positive for both markers. The results of bacterial analyses suggest that the fecal bacteria in summer and fall months are most likely of animal origin rather than human. Despite the urban setting, long history of development, and many potential sources of man-made contamination in the Mill River, none of the 12 water samples collected during the study contained targeted pharmaceutical compounds at concentrations greater than the analytical reporting levels. Other man-made compounds, like fluorescent whitening agents, were measured and detected in samples at low concentrations 4 out of 5 times the samples were collected; however, the other lines of evidence do not support a sewer source but rather other nonpoint sources upstream in the watershed. The results of this study do not support the hypothesis that aging sewer lines or combined sewer overflow infrastructure leak into the Mill River as tested during the low-flow conditions during sampling for this study. None of the results from Mill River samples offer conclusive evidence of the presence of sewage. Some low-level detections of pharmaceutical compounds, other man-made chemicals, and bacteria suggest an upstream, nonpoint source. A single raw sewage sample was collected, diluted, and examined for comparison with Mill River water samples and to ensure that the analytical methods could detect typical wastewater constituents. High levels of bacteria were measured, and low levels of three anthropogenic pharmaceutical compounds were detected, confirming the effectiveness of the sub-part-per-million method. The concentration of fluorescent whitening agent-1 in the sewage sample was 90,000 times greater than the median concentration in the Mill River samples.

Massachusetts↗
USGS2009

Metal exposure and effects in voles and small birds near a mining haul road in Cape Krusenstern National Monument, Alaska

Voles and small passerine birds were live-captured near the Delong Mountain Regional Transportation System (DMTS) haul road in Cape Krusenstern National Monument in northwest Alaska to assess metals exposure and sub-lethal biological effects. Similar numbers of animals were captured from a reference site in southern Cape Krusenstern National Monument for comparison. Histopathological examination of selected organs, and analysis of cadmium, lead, and zinc concentrations in liver and blood samples were performed. Voles and small birds captured from near the haul road had about 20 times greater blood and liver lead concentrations and about three times greater cadmium concentrations when compared to those from the reference site, but there were no differences in zinc tissue concentrations. One vole had moderate metastatic mineralization of kidney tissue, otherwise we observed no abnormalities in internal organs or DNA damage in the blood of any of the animals. The affected vole also had the greatest liver and blood Cd concentration, indicating that the lesion might have been caused by Cd exposure. Blood and liver lead concentrations in animals captured near the haul road were below concentrations that have been associated with adverse biological effects in other studies; however, subtle effects resulting from lead exposure, such as the suppression of the activity of certain enzymes, cannot be ruled out for some individual animals. Results from our 2006 reconnaissance-level study indicate that overall, voles and small birds obtained from near the DMTS road in Cape Krusenstern National Monument were not adversely affected by metals exposure; however, because of the small sample size and other uncertainties, continued monitoring of lead and cadmium in terrestrial habitats near the DMTS road is advised.

Alaska↗
USGS2006

Dissimilatory arsenate and sulfate reduction in sediments of two hypersaline, arsenic-rich soda lakes: Mono and Searles Lakes, California

A radioisotope method was devised to study bacterial respiratory reduction of arsenate in sediments. The following two arsenic-rich soda lakes in California were chosen for comparison on the basis of their different salinities: Mono Lake (∼90 g/liter) and Searles Lake (∼340 g/liter). Profiles of arsenate reduction and sulfate reduction were constructed for both lakes. Reduction of [ 73 As]arsenate occurred at all depth intervals in the cores from Mono Lake (rate constant [ k ] = 0.103 to 0.04 h −1 ) and Searles Lake ( k = 0.012 to 0.002 h −1 ), and the highest activities occurred in the top sections of each core. In contrast, [ 35 S]sulfate reduction was measurable in Mono Lake ( k = 7.6 ×10 4 to 3.2 × 10 −6 h −1 ) but not in Searles Lake. Sediment DNA was extracted, PCR amplified, and separated by denaturing gradient gel electrophoresis (DGGE) to obtain phylogenetic markers (i.e., 16S rRNA genes) and a partial functional gene for dissimilatory arsenate reduction ( arrA ). The amplified arrA gene product showed a similar trend in both lakes; the signal was strongest in surface sediments and decreased to undetectable levels deeper in the sediments. More arrA gene signal was observed in Mono Lake and was detectable at a greater depth, despite the higher arsenate reduction activity observed in Searles Lake. A partial sequence (about 900 bp) was obtained for a clone (SLAS-3) that matched the dominant DGGE band found in deeper parts of the Searles Lake sample (below 3 cm), and this clone was found to be closely related to SLAS-1, a novel extremophilic arsenate respirer previously cultivated from Searles Lake.

Applied and Environmental Microbiology↗
USGS1993

Biomarkers of contaminant exposure in common terns and black-crowned night herons in the Great Lakes

Morphological and biochemical indexes of contaminant exposure were examined in hatching common terns ( Sterna hirundo ) and black-crowned night herons ( Nycticorax nycticorax ) from industrialized and nonindustrialized locations in the Great Lakes. In 1984, naturally incubated, pipping common tern and black-crowned night heron embryos collected from industrialized locations exhibited smaller femur-length-to-body-weight ratios, elevated hepatic microsomal aryl hydrocarbon hydroxylase (AHH) activities, and lower hepatic DNA concentrations ( P < 0.05). In addition, a high incidence of subcutaneous edema was noted in pipping herons ( P < 0.01). In 1985, reduced hatching success was observed for laboratory-incubated common tern eggs collected from the industrialized sites, compared to nonindustrialized sites ( P < 0.01). Day-old hatchlings exhibited reduced femur-length-to-body-weight ratio, developmental anomalies, and elevated hepatic AHH activity ( P < 0.05). For hatching common terns studied in 1984 and 1985, femur-length-to-body-weight ratio was inversely related to AHH activity ( r = −0.67, P < 0.05) and inversely related to log-transformed PCB concentrations ( r = −0.70, P ≤ 0.05) of unincubated eggs from the same colony. The activity of AHH in hatching terns was also directly related ( r = 0.71, P ≤ 0.05) to log-transformed PCB concentrations in unincubated eggs. Other examined contaminants, including DDE, other organochlorine pesticides, and mercury, were not directly related to these effects.

Environmental Toxicology and Chemistry↗
USGS2007

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Applied and Environmental Microbiology↗
USGS2018

Biomarker responses of Peromyscus leucopus exposed to lead and cadmium in the Southeast Missouri Lead Mining District

Biomarker responses and histopathological lesions have been documented in laboratory mammals exposed to elevated concentrations of lead and cadmium. The exposure of white-footed mice ( Peromyscus leucopus ) to these metals and the potential associated toxic effects were examined at three contaminated sites in the Southeast Missouri Lead Mining District and at a reference site in MO, USA. Mice from the contaminated sites showed evidence of oxidative stress and reduced activity of red blood cell δ-aminolevulinic acid dehydratase (ALAD). Histological examinations of the liver and kidney, cytologic examination of blood smears, and biomarkers of lipid peroxidation and DNA damage failed to show indications of toxic effects from lead. The biomagnification factor of cadmium (hepatic concentration/soil concentration) at a site with a strongly acid soil was 44 times the average of the biomagnification factors at two sites with slightly alkaline soils. The elevated concentrations of cadmium in the mice did not cause observable toxicity, but were associated with about a 50% decrease in expected tissue lead concentrations and greater ALAD activity compared to the activity at the reference site. Lead was associated with a decrease in concentrations of hepatic glutathione and thiols, whereas cadmium was associated with an increase. In addition, to support risk assessment efforts, we developed linear regression models relating both tissue lead dosages (based on a previously published a laboratory study) and tissue lead concentrations in Peromyscus to soil lead concentrations.

Missouri↗
USGS2025

From subsidies to stressors: Shifting ecological baselines alter biological responses to nutrients in highly modified agricultural streams

Subsidy–stress gradients offer a useful framework for understanding ecological responses to perturbation and may help inform ecological metrics in highly modified systems. Historic, region-wide shifts from bottomland hardwood forest to row crop agriculture can cause positively skewed impact gradients in alluvial plain ecoregions, resulting in tolerant organisms that typically exhibit a subsidy response (increased abundance in response to environmental stressors) shifting to a stress response (declining abundance at higher concentrations). As a result, observed biological tolerance in modified ecosystems may differ from less modified regions, creating significant challenges for detecting biological responses to restoration efforts. Using the agriculturally dominated Mississippi Alluvial Plain (MAP) ecoregion in Mississippi, USA, as a case study, we tested the hypothesis that macroinvertebrate taxa that typically display a subsidy response to nutrient enrichment in less modified ecoregions (i.e., nutrient-tolerance) shift to a stress response to increasing nutrients in highly modified watersheds with elevated baseline nutrient conditions (i.e., nutrient intolerance). The abundance and diversity of MAP-specific intolerant taxa identified with threshold indicator taxa analysis were either unresponsive or exhibited a subsidy response to increasing nutrients in less modified ecoregions in Mississippi with less land alteration and lower nutrient concentrations, but declined at higher concentrations, providing evidence for a stress response to elevated nutrients in the MAP. Additionally, MAP-specific tolerant and intolerant taxa richness responded to increased nutrients predictably and consistently across space and time within the MAP. However, in MAP streams, elevated specific conductance was predicted to dampen the response of tolerant and intolerant taxa richness to increasing nutrient concentrations, highlighting the importance of considering multistressor interactions when interpreting biological data. Lastly, we demonstrate the efficacy of this approach with sediment bacterial communities characterized with amplicon sequencing, which lack sufficient life history characteristics necessary for the development of multimetric indices. Both macroinvertebrate and bacterial communities responded similarly to increasing nutrient concentrations, suggesting DNA-based approaches may provide an efficient biological assessment tool for monitoring water quality improvements in highly modified watersheds.

Mississippi↗
USGS2001

Integration of genotoxicity and population genetic analyses in kangaroo rats ( Dipodomys merriami ) exposed to radionuclide contamination at the Nevada Test Site, USA

We examined effects of radionuclide exposure at two atomic blast sites on kangaroo rats (Dipodomys merriami) at the Nevada Test Site, Nevada, USA, using genotoxicity and population genetic analyses. We assessed chromosome damage by micronucleus and flow cytometric assays and genetic variation by randomly amplified polymorphic DNA (RAPD) and mitochondrial DNA (mtDNA) analyses. The RAPD analysis showed no population structure, but mtDNA exhibited differentiation among and within populations. Genotoxicity effects were not observed when all individuals were analyzed. However, individuals with mtDNA haplotypes unique to the contaminated sites had greater chromosomal damage than contaminated-site individuals with haplotypes shared with reference sites. When interpopulation comparisons used individuals with unique haplotypes, one contaminated site had greater levels of chromosome damage than one or both of the reference sites. We hypothesize that shared-haplotype individuals are potential migrants and that unique-haplotype individuals are potential long-term residents. A parsimony approach was used to estimate the minimum number of migration events necessary to explain the haplotype distributions on a phylogenetic tree. The observed predominance of migration events into the contaminated sites supported our migration hypothesis. We conclude the atomic blast sites are ecological sinks and that immigration masks the genotoxic effects of radiation on the resident populations.

Nevada↗
USGS2011

Diversity and distribution of white-tailed deer mtDNA lineages in chronic wasting disease (CWD) outbreak areas in southern Wisconsin, USA

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy affecting North American cervids. Because it is uniformly fatal, the disease is a major concern in the management of white-tailed deer populations. Management programs to control CWD require improved knowledge of deer interaction, movement, and population connectivity that could influence disease transmission and spread. Genetic methods were employed to evaluate connectivity among populations in the CWD management zone of southern Wisconsin. A 576-base-pair region of the mitochondrial DNA of 359 white-tailed deer from 12 sample populations was analyzed. Fifty-eight variable sites were detected within the sequence, defining 43 haplotypes. While most sample populations displayed similar levels of haplotype diversity, individual haplotypes were clustered on the landscape. Spatial clusters of different haplotypes were apparent in distinct ecoregions surrounding CWD outbreak areas. The spatial distribution of mtDNA haplotypes suggests that clustering of the deer matrilineal groups and population connectivity are associated with broad-scale geographic landscape features. These landscape characteristics may also influence the contact rates between groups and therefore the potential spread of CWD; this may be especially true of local disease spread between female social groups. Our results suggest that optimal CWD management needs to be tailored to fit gender-specific dispersal behaviors and regional differences in deer population connectivity. This information will help wildlife managers design surveillance and monitoring efforts based on population interactions and potential deer movement among CWD-affected and unaffected areas.

Wisconsin↗
USGS2020

Legacy and contaminants of emerging concern (CECs) in tree swallows along an agricultural to industrial gradient: Maumee River, OH

Exposure to multiple classes of contaminants, both legacy and contaminants of emerging concern (CECs), were assessed in tree swallow ( Tachycineta bicolor ) tissue and diet samples from 6 sites along the Maumee River, Ohio, USA, to understand both exposure and possible effects of exposure to those CECs for which there are little avian data. The 6 sites represented a gradient from intensive agriculture upstream to highly urbanized and industrial landscapes downstream; 1 or 2 remote Wisconsin lakes were assessed for comparative purposes. Cytochrome P450 induction, DNA damage, and thyroid function were also assessed relative to contaminant exposure. Bioaccumulative CECs, such as polybrominated diphenyl ethers (PBDEs) and perfluorinated substances, did not follow any upstream to downstream gradient; but both had significantly greater concentrations along the Maumee River than at the remote lake sites. Greater exposure to PBDEs was apparent in swallows at or near wastewater‐treatment facilities than at other sites. Total polychlorinated biphenyl and total polycyclic aromatic hydrocarbon concentrations were greater in swallows at downstream locations compared to upstream sites and were associated with higher ethoxyresorufin‐ O ‐dealkylase activity. Few herbicides or nonorganochlorine insecticides were detected in swallow tissues or their food, except for atrazine and its metabolite desethylatrazine. Few pharmaceuticals and personal care products were detected except for DEET and iopamidol. Both were detected in most liver samples but not in eggs, as well as detected at the remote lake sites. This is one of the most comprehensive assessments to date of exposure and effects of a wide variety of CECs in birds.

Ohio↗
USGS2007

Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period

To monitor the dissemination of resistance genes into the environment, we determined the occurrence of tetracycline resistance (Tcr) genes in groundwater underlying two swine confinement operations. Monitoring well networks (16 wells at site A and 6 wells at site C) were established around the lagoons at each facility. Groundwater (n = 124) and lagoon (n = 12) samples were collected from the two sites at six sampling times from 2000 through 2003. Total DNA was extracted, and PCR was used to detect seven Tcr genes [tet(M), tet(O), tet(Q), tet(W), tet(C), tet(H), and tet(Z)]. The concentration of Tcr genes was quantified by real-time quantitative PCR. To confirm the Tcr gene source in groundwater, comparative analysis of tet(W) gene sequences was performed on groundwater and lagoon samples. All seven Tcr genes were continually detected in groundwater during the 3-year monitoring period at both sites. At site A, elevated detection frequency and concentration of Tcr genes were observed in the wells located down-gradient of the lagoon. Comparative analysis of tet(W) sequences revealed that the impacted groundwater contained gene sequences almost identical (99.8% identity) to those in the lagoon, but these genes were not found in background libraries. Novel sequence clusters and unique indigenous resistance gene pools were also found in the groundwater. Thus, antibiotic resistance genes in groundwater are affected by swine manure, but they are also part of the indigenous gene pool. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Applied and Environmental Microbiology↗
USGS2004

Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer

In a contaminated water‐table aquifer, we related microbial community structure on aquifer sediments to gradients in 24 geochemical and contaminant variables at five depths, under three recharge conditions. Community amplified ribsosomal DNA restriction analysis (ARDRA) using universal 16S rDNA primers and denaturing gradient gel electrophoresis (DGGE) using bacterial 16S rDNA primers indicated: (i) communities in the anoxic, contaminated central zone were similar regardless of recharge; (ii) after recharge, communities at greatest depth were similar to those in uncontaminated zones; and (iii) after extended lack of recharge, communities at upper and lower aquifer margins differed from communities at the same depths on other dates. General aquifer geochemistry was as important as contaminant or terminal electron accepting process (TEAP) chemistry in discriminant analysis of community groups. The Shannon index of diversity ( H ) and the evenness index ( E ), based on DGGE operational taxonomic units (OTUs), were statistically different across community groups and aquifer depths. Archaea or sulphate‐reducing bacteria 16S rRNA abundance was not clearly correlated with TEAP chemistry indicative of methanogenesis or sulphate reduction. Eukarya rRNA abundance varied by depth and date from 0 to 13% of the microbial community. This contaminated aquifer is a dynamic ecosystem, with complex interactions between physical, chemical and biotic components, which should be considered in the interpretation of aquifer geochemistry and in the development of conceptual or predictive models for natural attenuation or remediation.

Environmental Microbiology↗