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At least 451 records · Page 25Linked to original sources

Genetic structure among greater white-fronted goose populations of the Pacific Flyway

An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose ( Anser albifrons ), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.

Ecology and Evolution↗

Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival

In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel ( Urocitellus brunneus ) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL ) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.

Idaho↗

Hybridization and asymmetrical introgression between the vulnerable Gray‐Headed Chickadee and a more abundant congener, the Boreal Chickadee: Implications for conservation

Hybridization is a common process among bird species that can precipitate a mix of positive or negative species outcomes. Particularly for rare populations, detrimental effects of hybridization on demographic growth rates and genetic integrity are of serious concern. In Alaska and a small region of northwestern Canada, the endemic subspecies of Gray-headed Chickadee ( Poecile cinctus lathami ) has declined in recent decades from being locally common to being extremely rare. The more widespread Boreal Chickadee ( P. hudsonicus ) has become increasingly abundant in areas of sympatry. These changes in abundance may have led to hybridization between Gray-headed Chickadees and Boreal Chickadees. We used a series of analyses to test for signatures of introgression at mitochondrial DNA and nuclear DNA using historical museum samples of both species collected between 1875 and 1979 as well as contemporary Boreal Chickadee samples. In addition, we modeled Gray-headed Chickadee and Boreal Chickadee demographic histories to better understand patterns of effective population size changes and gene flow over time. Introgression of Gray-headed Chickadee nuclear DNA was detected in contemporary and historical Boreal Chickadee populations, and two first-generation hybrid backcrosses were observed in the historical Boreal Chickadee samples. Lack of mitochondrial DNA introgression or backcrossing into the Gray-headed Chickadee historical samples may be an artifact of mate scarcity during the period before local abundances of Boreal Chickadee exceeded Gray-headed Chickadees. Demographic modeling with nuclear loci estimated a low level of symmetric gene flow between Gray-headed Chickadees and Boreal Chickadees since the time of divergence. Our study suggests that hybridization may be linked to Gray-headed Chickadee declines and represents a case study of how museum collections can be used to infer introgression in a population too scarce to directly investigate.

Ecology and Evolution↗

Development of PCR blocking primers enabling DNA metabarcoding analysis of dietary composition in hematophagous sea lamprey

Conventional dietary assessments are challenging in hematophagous species, particularly in sea lamprey ( Petromyzon marinus ). However, recent technological developments and molecular approaches have provided an attractive alternative through the use of DNA metabarcoding. While DNA metabarcoding has been used for dietary analyses in numerous species, including lampreys, applications of universal primers that detect a diverse set of prey items can be limited by the amplification of predator DNA. In this study, we designed and tested eight blocking primers designed to suppress the amplification of sea lamprey DNA with vertebrate-universal primers targeting the mitochondrial 12S rRNA gene. This approach allowed for the use of a single marker to amplify a taxonomically diverse suite of host species, in contrast to previous studies that used multiple taxon-specific primer pairs (e.g., Salmonidae, Cyprinidae, and Catostomidae). Candidate blocking primers evaluated in this study differed in base pair length, end sequence modification, and purification method. Samples with different sea lamprey-to-host DNA ratios were subjected to multiple detection methods including gel electrophoresis, quantitative PCR, and DNA metabarcoding to assess the ability of each blocking primer to selectively suppress amplification of the sea lamprey 12S gene region. All blocking primers tested performed well and demonstrated high effectiveness, suppressing sea lamprey reads by > 99.9% in mock communities and improving host DNA sequence recovery across various sample types, including wild-caught lamprey. Results show that the blocking primers evaluated can facilitate molecular diet analysis in sea lamprey, allowing the amplification of a taxonomically diverse range of host fish species with universal primers.

Great Lakes↗

Genetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning

The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.

Indiana, Kentucky, Ohio, Pennsylvania, Tennessee, ↗

Spatially-structured statistical network models for landscape genetics

A basic understanding of how the landscape impedes, or creates resistance to, the dispersal of organisms and hence gene flow is paramount for successful conservation science and management. Spatially structured ecological networks are often used to represent spatial landscape‐genetic relationships, where nodes represent individuals or populations and resistance to movement is represented using non‐binary edge weights. Weights are typically assigned or estimated by the user, rather than observed, and validating such weights is challenging. We provide a synthesis of current methods used to estimate edge weights and an overview of common model types, stressing the advantages and disadvantages of each approach and their ability to model landscape‐genetic data. We further explore a set of spatial‐statistical methods that provide ecologists with alternative approaches for modeling spatially explicit processes that may affect genetic structure. This includes an overview of spatial autoregressive models, with a particular focus on how correlation and partial correlation are used to represent neighborhood structure with the inverse of the covariance matrix (i.e., precision matrix). We then demonstrate how to model resistance by specifying an appropriate statistical model on the nodes, conditioned on the edge weights, through the precision matrix. This integration of network ecology and spatial statistics provides a practical analytical framework for landscape‐genetic studies. The results can be used to make statistical inferences about the relative importance of individual landscape characteristics, such as the vegetative cover, hillslope, or the presence of roads or rivers, on gene flow. In addition, the R code we include allows readers to explore landscape‐genetic structure in their own datasets, which will potentially provide new insights into the evolutionary processes that generated ecological networks, as well as valuable information about the optimal characteristics of conservation corridors.

Ecological Monographs↗

Pathway-based approaches for assessment of real-time exposure to an estrogenic wastewater treatment plant effluent on fathead minnow reproduction

Wastewater treatment plant (WWTP) effluents are known contributors of chemical mixtures into the environment. Of particular concern are endocrine-disrupting compounds, such as estrogens, which can affect the hypothalamic-pituitary-gonadal axis function in exposed organisms. The present study examined reproductive effects in fathead minnows exposed for 21 d to a historically estrogenic WWTP effluent. Fathead minnow breeding pairs were held in control water or 1 of 3 effluent concentrations (5%, 20%, and 100%) in a novel onsite, flow-through system providing real-time exposure. The authors examined molecular and biochemical endpoints representing key events along adverse outcome pathways linking estrogen receptor activation and other molecular initiating events to reproductive impairment. In addition, the authors used chemical analysis of the effluent to construct a chemical-gene interaction network to aid in targeted gene expression analyses and identifying potentially impacted biological pathways. Cumulative fecundity was significantly reduced in fish exposed to 100% effluent but increased in those exposed to 20% effluent, the approximate dilution factor in the receiving waters. Plasma vitellogenin concentrations in males increased in a dose-dependent manner with effluent concentration; however, male fertility was not impacted. Although in vitro analyses, analytical chemistry, and biomarker responses confirmed the effluent was estrogenic, estrogen receptor agonists were unlikely the primary driver of impaired reproduction. The results provide insights into the significance of pathway-based effects with regard to predicting adverse reproductive outcomes.

Environmental Toxicology and Chemistry↗

RNA sequencing analysis of transcriptional change in the freshwater mussel Elliptio complanata after environmentally relevant sodium chloride exposure

To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled sodium chloride (NaCl) exposures. Ribonucleic acid sequencing (RNA-Seq) of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for 7 d, of which 290 had nonoverlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism. The rate-limiting enzyme for synthesis of taurine, an amino acid frequently linked to osmotic stress in aquatic species, was upregulated, as was the transmembrane ion pump sodium/potassium adenosine 5′-triphosphatase. These patterns confirm a primary transcriptional response to the experimental dose, albeit likely overlapping with nonspecific secondary stress responses. Substantial involvement of the heat shock protein 70 chaperone family and the water-transporting aquaporin family was not detected, however, in contrast to some studies in other bivalves. A subset of the most significantly regulated genes was confirmed by quantitative polymerase chain reaction in an independent sample. Cluster analysis showed separation of mussels exposed to 2 ppt NaCl from control mussels in multivariate space, but mussels exposed to 1 ppt NaCl were largely indistinguishable from controls. Transcriptome-scale analysis of salt exposure under laboratory conditions efficiently identified candidate biomarkers for further functional analysis and field validation

Environmental Toxicology and Chemistry↗

Identifying chemicals and mixtures of potential biological concern detected in passive samplers from Great Lakes tributaries using high-throughput data and biological pathways

Waterborne contaminants were monitored in 69 tributaries of the Laurentian Great Lakes in 2010 and 2014 using semipermeable membrane devices (SPMDs) and polar organic chemical integrative samplers (POCIS). A risk-based screening approach was used to prioritize chemicals and chemical mixtures, identify sites at greatest risk for biological impacts, and identify potential hazards to monitor at those sites. Analyses included 185 chemicals (143 detected) including polycyclic aromatic hydrocarbons (PAHs), legacy and current-use pesticides, fire retardants, pharmaceuticals, and fragrances. Hazard quotients were calculated by dividing detected concentrations by biological effect concentrations reported in the ECOTOX Knowledgebase (toxicity quotients) or ToxCast database (exposure–activity ratios [EARs]). Mixture effects were estimated by summation of EAR values for chemicals that influence ToxCast assays with common gene targets. Nineteen chemicals—atrazine, N,N -diethyltoluamide, di(2-ethylhexyl)phthalate, dl-menthol, galaxolide, p-tert-octylphenol, 3 organochlorine pesticides, 3 PAHs, 4 pharmaceuticals, and 3 phosphate flame retardants—had toxicity quotients >0.1 or EARs for individual chemicals >10 –3 at 10% or more of the sites monitored. An additional 4 chemicals (tributyl phosphate, triethyl citrate, benz[ a ]anthracene, and benzo[ b ]fluoranthene) were present in mixtures with EARs >10 –3 . To evaluate potential apical effects and biological endpoints to monitor in exposed wildlife, in vitro bioactivity data were compared to adverse outcome pathway gene ontology information. Endpoints and effects associated with endocrine disruption, alterations in xenobiotic metabolism, and potentially neuronal development would be relevant to monitor at the priority sites. The EAR threshold exceedance for many chemical classes was correlated with urban land cover and wastewater effluent influence, whereas herbicides and fire retardants were also correlated to agricultural land cover. Environ Toxicol Chem 2021;40:2165–2182. Published 2021. This article is a U.S. Government work and is in the public domain in the USA. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Great Lakes↗

Prioritizing pesticides of potential concern and identifying potential mixture effects in Great Lakes tributaries using passive samplers

To help meet the objectives of the Great Lakes Restoration Initiative with regard to increasing knowledge about toxic substances, 223 pesticides and pesticide transformation products were monitored in 15 Great Lakes tributaries using polar organic chemical integrative samplers. A screening-level assessment of their potential for biological effects was conducted by computing toxicity quotients (TQs) for chemicals with available US Environmental Protection Agency (USEPA) Aquatic Life Benchmark values. In addition, exposure activity ratios (EAR) were calculated using information from the USEPA ToxCast database. Between 16 and 81 chemicals were detected per site, with 97 unique compounds detected overall, for which 64 could be assessed using TQs or EARs. Ten chemicals exceeded TQ or EAR levels of concern at two or more sites. Chemicals exceeding thresholds included seven herbicides (2,4-dichlorophenoxyacetic acid, diuron, metolachlor, acetochlor, atrazine, simazine, and sulfentrazone), a transformation product (deisopropylatrazine), and two insecticides (fipronil and imidacloprid). Watersheds draining agricultural and urban areas had more detections and higher concentrations of pesticides compared with other land uses. Chemical mixtures analysis for ToxCast assays associated with common modes of action defined by gene targets and adverse outcome pathways (AOP) indicated potential activity on biological pathways related to a range of cellular processes, including xenobiotic metabolism, extracellular signaling, endocrine function, and protection against oxidative stress. Use of gene ontology databases and the AOP knowledgebase within the R-package ToxMixtures highlighted the utility of ToxCast data for identifying and evaluating potential biological effects and adverse outcomes of chemicals and mixtures. Results have provided a list of high-priority chemicals for future monitoring and potential biological effects warranting further evaluation in laboratory and field environments. Environ Toxicol Chem 2023;42:340–366. Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Great Lakes tributaries↗

Inconsistent transcriptomic responses to hexabromocyclododecane in Japanese quail: A comparative analysis of results from four different study designs

Efforts to use transcriptomics for toxicity testing have classically relied on the assumption that chemicals consistently produce characteristic transcriptomic signatures that are reflective of their mechanism of action. However, the degree to which transcriptomic responses are conserved across different test methodologies has seldom been explored. With increasing regulatory demand for New Approach Methods (NAMs) that use alternatives to animal models and high‐content approaches such as transcriptomics, this type of comparative analysis is needed. We examined whether common genes are dysregulated in Japanese quail ( Coturnix japonica ) liver following sublethal exposure to the flame retardant hexabromocyclododecane (HBCD), when life stage and test methodologies differ. The four exposure scenarios included one NAM: Study 1—early‐life stage (ELS) exposure via a single egg injection, and three more traditional approaches; Study 2—adult exposure using a single oral gavage; Study 3—ELS exposure via maternal deposition after adults were exposed through their diet for 7 weeks; and Study 4—ELS exposure via maternal deposition and re‐exposure of nestlings through their diet for 17 weeks. The total number of differentially expressed genes (DEGs) detected in each study was variable (Study 1, 550; Study 2, 192; Study 3, 1; Study 4, 3) with only 19 DEGs shared between Studies 1 and 2. Factors contributing to this lack of concordance are discussed and include differences in dose, but also quail strain, exposure route, sampling time, and HBCD stereoisomer composition. The results provide a detailed overview of the transcriptomic responses to HBCD at different life stages and routes of exposure in a model avian species and highlight certain challenges and limits of comparing transcriptomics across different test methodologies.

Environmental Toxicology and Chemistry↗

Population fragmentation and inter-ecosystem movements of grizzly bears in Western Canada and the Northern United States

Population fragmentation compromises population viability, reduces a species ability to respond to climate change, and ultimately may reduce biodiversity. We studied the current state and potential causes of fragmentation in grizzly bears over approximately 1,000,000 km 2 of western Canada, the northern United States (US), and southeast Alaska. We compiled much of our data from projects undertaken with a variety of research objectives including population estimation and trend, landscape fragmentation, habitat selection, vital rates, and response to human development. Our primary analytical techniques stemmed from genetic analysis of 3,134 bears, supplemented with radiotelemetry data from 792 bears. We used 15 locus microsatellite data coupled withmeasures of genetic distance, isolation-by-distance (IBD) analysis, analysis of covariance (ANCOVA), linear multiple regression, multi-factorial correspondence analysis (to identify population divisions or fractures with no a priori assumption of group membership), and population-assignment methods to detect individual migrants between immediately adjacent areas. These data corroborated observations of inter-area movements from our telemetry database. In northern areas, we found a spatial genetic pattern of IBD, although there was evidence of natural fragmentation from the rugged heavily glaciated coast mountains of British Columbia (BC) and the Yukon. These results contrasted with the spatial pattern of fragmentation in more southern parts of their distribution. Near the Canada-US border area, we found extensive fragmentation that corresponded to settled mountain valleys andmajor highways. Genetic distances across developed valleys were elevated relative to those across undeveloped valleys in central and northern BC. In disturbed areas, most inter-area movements detected were made by male bears, with few female migrants identified. North-south movements within mountain ranges (Mts) and across BC Highway 3 were more common than east-west movements across settled mountain valleys separating Mts. Our results suggest that relatively distinct subpopulations exist in this region, including the Cabinet, Selkirk South, and the decadesisolated Yellowstone populations. Current movement rates do not appear sufficient to consider the subpopulations we identify along the Canada-US border as 1 inter-breeding unit. Although we detected enough male movement to mediate gene flow, the current low rate of female movement detected among areas is insufficient to provide a demographic rescue effect between areas in the immediate future (0-15 yr). In Alberta, we found fragmentation corresponded to major east-west highways (Highways 3, 11, 16, and 43) and most inter-area movements were made by males. Gene flow and movement rates between Alberta and BC were highest across the Continental Divide south of Highway 1 and north of Highway 16. In the central region between Highways 1 and 11, we found evidence of natural fragmentation associated with the extensive glaciers and icefields along the Continental Divide. The discontinuities that we identified would form appropriate boundaries formanagement units. We related sex-specific movement rates between adjacent areas to several metrics of human use (highway traffic, settlement, and humancaused mortality) to understand the causes of fragmentation. This analysis used data from 1,508 bears sampled over a 161,500-km 2 area in southeastern BC, western Alberta, northern Idaho, and northern Montana during 1979-2007. This area was bisected by numerous human transportation and settlement corridors of varying intensity and complexity. We used multiple linear regression and ANCOVA to document the responses of female and male bears to disturbance. Males and females both demonstrated reduced movement rates with increasing settlement and traffic. However, females reduced their movement rates dramatically when settlement increased to >20% of the fracture zone. At this same

Wildlife Monographs↗

Mercury biogeochemistry in the Idrija River, Slovenia, from above the mine into the Gulf of Trieste

The Idrija Mine is the second largest Hg mine in the world which operated for 500 years. Mercury (Hg)-laden tailings still line the banks, and the system is a threat to the Idrija River and water bodies downstream including the Soca/Isonzo River and the Gulf of Trieste in the northern Adriatic Sea. A multidisciplinary study was conducted in June 1998 on water samples collected throughout the Idrija and Soca River systems and waters and sediments in the Gulf. Total Hg in the Idrija River increased >20-fold downstream of the mine from <3 to >60 ng liter-1 with methyl mercury (MeHg) accounting for ~0.5%. Concentrations increased again downstream and into the estuary with MeHg accounting for nearly 1.5% of the total. While bacteria upstream of the mine did not contain mercury detoxification genes (mer), such genes were detected in bacteria collected downstream. Benthic macroinvertebrate diversity decreased downstream of the mine. Gulf waters near the river mouth contained up to 65 ng liter-1 total Hg with ~0.05 ng liter-1 MeHg. Gulf sediments near the river mouth contained 40 ??g g-1 total Hg with MeHg concentrations of about 3 ng g-1. Hg in sediment pore waters varied between 1 and 8 ng liter-1, with MeHg accounting for up to 85%. Hg methylation and MeHg demethylation were active in Gulf sediments with highest activities near the surface. MeHg was degraded by an oxidative pathway with >97% C released from MeHg as CO2. Hg methylation depth profiles resembled profiles of dissolved MeHg. Hg-laden waters still strongly impact the riverine, estuarine, and marine systems. Macroinvertebrates and bacteria in the Idrija River responded to Hg stress, and high Hg levels persist into the Gulf. Increases in total Hg and MeHg in the estuary demonstrate the remobilization of Hg, presumably as HgS dissolution and recycling. Gulf sediments actively produce MeHg, which enters bottom waters and presumably the marine food chain. (C) 2000 Academic Press.

Conference Paper↗

The transformative impact of genomics on sage-grouse conservation and management

For over two decades, genetic studies have been used to assist in the conservation and management of both Greater Sage-grouse ( Centrocercus urophasianus ) and Gunnison Sage-grouse ( C. minimus ), addressing a wide variety of topics including taxonomy, parentage, population connectivity, and demography. The field of conservation genetics has been transformed by dramatic improvements in sequencing technology, facilitating genomic studies in many wildlife species. The quality and amount of data generated by genomic methods vastly exceed that of traditional genetic studies, allowing for increased precision in estimating genetic parameters of interest. Perhaps more importantly, genomic methods can provide insight into non-neutral evolution such as adaptive divergence. Here we recount the shift from genetic to genomic methods using two wildlife species of substantial conservation interest, focusing on the improved capabilities and advantages of genomic methods. For instance, reassessment of divergence in sage-grouse using genomic methods confirmed strong differentiation between the two species and revealed that a small population in the state of Washington was more genetically distinct than previously recognized. Further, new genomic resources and approaches have been used to identify a family of genes linked to local dietary adaptation suggesting that sage-grouse may possess digestive and metabolic adaptations that mitigate the effects of consuming plant secondary metabolites like those found in sagebrush. Genetic variation among populations in these gene regions is thought to be involved with local dietary adaptations, and therefore maintaining the tie between sage-grouse and the chemistry of local sagebrush may be an important management consideration. We posit that the integration of newly developed genomic resources combined with the vast wealth of ecological and behavioral data for sage-grouse has the potential to shed light on mechanistic relationships that ultimately are vital to the conservation and management of these species.

Book chapter↗

Bacteria versus selenium: A view from the inside out

Bacteria and selenium (Se) are closely interlinked as the element serves both essential nutrient requirements and energy generation functions. However, Se can also behave as a powerful toxicant for bacterial homeostasis. Conversely, bacteria play a tremendous role in the cycling of Se between different environmental compartments, and bacterial metabolism has been shown to participate to all valence state transformations undergone by Se in nature. Bacteria possess an extensive molecular repertoire for Se metabolism. At the end of the 1980s, a novel mode of anaerobic respiration based on Se oxyanions was experimentally documented for the first time. Following this discovery, specific enzymes capable of reducing Se oxyanions and harvesting energy were found in a number of anaerobic bacteria. The genes involved in the expression of these enzymes have later been identified and cloned. This iterative approach undertaken outside-in led to the understanding of the molecular mechanisms of Se transformations in bacteria. Based on the extensive knowledge accumulated over the years, we now have a full(er) view from the inside out , from DNA-encoding genes to enzymes and thermodynamics. Bacterial transformations of Se for assimilatory purposes have been the object of numerous studies predating the investigation of Se respiration. Remarkable contributions related to the understating of the molecular picture underlying seleno-amino acid biosynthesis are reviewed herein. Under certain circumstances, Se is a toxicant for bacterial metabolism and bacteria have evolved strategies to counteract this toxicity, most notably by the formation of elemental Se (nano)particles. Several biotechnological applications, such as the production of functional materials and the biofortification of crop species using Se-utilizing bacteria, are presented in this chapter.

Book chapter↗

Identifying non-point sources of endocrine active compounds and their biological impacts in freshwater lakes

Contaminants of emerging concern, particularly endocrine active compounds (EACs), have been identified as a threat to aquatic wildlife. However, little is known about the impact of EACs on lakes through groundwater from onsite wastewater treatment systems (OWTS). This study aims to identify specific contributions of OWTS to Sullivan Lake, Minnesota, USA. Lake hydrology, water chemistry, caged bluegill sunfish ( Lepomis macrochirus ), and larval fathead minnow ( Pimephales promelas ) exposures were used to assess whether EACs entered the lake through OWTS inflow and the resultant biological impact on fish. Study areas included two OWTS-influenced near-shore sites with native bluegill spawning habitats and two in-lake control sites without nearby EAC sources. Caged bluegill sunfish were analyzed for plasma vitellogenin concentrations, organosomatic indices, and histological pathologies. Surface and porewater was collected from each site and analyzed for EACs. Porewater was also collected for laboratory exposure of larval fathead minnow, before analysis of predator escape performance and gene expression profiles. Chemical analysis showed EACs present at low concentrations at each study site, whereas discrete variations were reported between sites and between summer and fall samplings. Body condition index and liver vacuolization of sunfish were found to differ among study sites as did gene expression in exposed larval fathead minnows. Interestingly, biological exposure data and water chemistry did not match. Therefore, although results highlight the potential impacts of seepage from OWTS, further investigation of mixture effects and life history factor as well as chemical fate is warranted.

Minnesota↗

Insights into biodegradation through depth-resolved microbial community functional and structural profiling of a crude-oil contaminant plume

Small-scale geochemical gradients are a key feature of aquifer contaminant plumes, highlighting the need for functional and structural profiling of corresponding microbial communities on a similar scale. The purpose of this study was to characterize the microbial functional and structural diversity with depth across representative redox zones of a hydrocarbon plume and an adjacent wetland, at the Bemidji Oil Spill site. A combination of quantitative PCR, denaturing gradient gel electrophoresis, and pyrosequencing were applied to vertically sampled sediment cores. Levels of the methanogenic marker gene, methyl coenzyme-M reductase A (mcrA), increased with depth near the oil body center, but were variable with depth further downgradient. Benzoate degradation N (bzdN) hydrocarbon-degradation gene, common to facultatively anaerobic Azoarcus spp., was found at all locations, but was highest near the oil body center. Microbial community structural differences were observed across sediment cores, and bacterial classes containing known hydrocarbon degraders were found to be low in relative abundance. Depth-resolved functional and structural profiling revealed the strongest gradients in the iron-reducing zone, displaying the greatest variability with depth. This study provides important insight into biogeochemical characteristics in different regions of contaminant plumes, which will aid in improving models of contaminant fate and natural attenuation rates.

Minnesota↗

The presence of denitrifiers in bacterial communities of urban stormwater best management practices (BMPs)

Stormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK , and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.

Maryland↗