The effects of tissue fixation on sequencing and transcript abundance of nucleic acids from microdissected liver samples of smallmouth bass (Micropterus dolomieu).

There is an increasing emphasis on effects-based monitoring to document responses associated with exposure to complex mixtures of chemicals, climate change, pathogens, parasites and other environmental stressors in fish populations. For decades aquatic monitoring programs have included the collection of tissues preserved for microscopic pathology. Consequently, formalin-fixed, paraffin-embedded (FFPE) tissue can be an important reservoir of nucleic acids as technologies emerge that utilize molecular endpoints.

An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications.

Background: Lake Sinai Viruses (LSV) are common RNA viruses of honey bees () that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in are not understood. Even less is known about their distribution in other species.

11-Deoxycortisol controls hydromineral balance in the most basal osmoregulating vertebrate, sea lamprey (Petromyzon marinus).

It is unknown whether and how osmoregulation is controlled by corticosteroid signaling in the phylogenetically basal vertebrate group Agnatha, including lampreys and hagfishes. It is known that a truncated steroid biosynthetic pathway in lampreys produces two predominant circulating corticosteroids, 11-deoxycortisol (S) and 11-deoxycorticosterone (DOC). Furthermore, lampreys express only a single, ancestral corticosteroid receptor (CR).

Capture of Environmental DNA (eDNA) from Water Samples by Flocculation.

The analysis of environmental DNA (eDNA) has become a widely used approach to problem solving in species management. The detection of cryptic species including invasive and (or) species at risk is the goal, typically accomplished by testing water and sediment for the presence of characteristic DNA signatures. Reliable and efficient procedures for the capture of eDNA are required, especially those that can be performed easily in the field by personnel with limited training and citizen scientists.

Hyperpigmented melanistic skin lesions of smallmouth bass Micropterus dolomieu from the Chesapeake Bay watershed.

Hyperpigmented melanistic skin lesions (HPMLs) of smallmouth bass Micropterus dolomieu are observed in the Potomac and Susquehanna rivers, Chesapeake Bay watershed, USA. Routine, nonlethal population surveys were conducted at 8 sites on the mainstem Susquehanna River and 9 on the Juniata River, a tributary of the Susquehanna River, between 2012 and 2018, and the prevalence of HPMLs was documented. A total of 4078 smallmouth bass were collected from the mainstem Susquehanna River and 6478 from the Juniata River.

Poultry litter as potential source of pathogens and other contaminants in groundwater and surface water proximal to large-scale confined poultry feeding operations.

Manure from livestock production has been associated with the contamination of water resources. To date, research has primarily focused on runoff of these contaminants from animal operations into surface water, and the introduction of poultry-derived pathogenic zoonoses and other contaminants into groundwater is under-investigated. We characterized pathogens and other microbial and chemical contaminants in poultry litter, groundwater, and surface water near confined poultry feeding operations (chicken layer, turkey) at 9 locations in Iowa and one in Wisconsin from May and June 2016.

How repeatable is CT within individual brook trout over short- and long-time intervals?

As stream temperatures increase due to factors such as heated runoff from impervious surfaces, deforestation, and climate change, fish species adapted to cold water streams are forced to move to more suitable habitat, acclimate or adapt to increased thermal regimes, or die. To estimate the potential for adaptation, a (within individual) repeatable metric of thermal tolerance is imperative. Critical thermal maximum (CT) is a dynamic test that is widely used to measure thermal tolerance across many taxa and has been used in fishes for decades, but its repeatability in most species is unknown.

Spatiotemporal variation in occurrence and co-occurrence of pesticides, hormones, and other organic contaminants in rivers in the Chesapeake Bay Watershed, United States.

Investigating the spatiotemporal dynamics of contaminants in surface water is crucial to better understand how introduced chemicals are interacting with and potentially influencing aquatic organisms and environments. Within the Chesapeake Bay Watershed, United States, there are concerns about the potential role of contaminant exposure on fish health. Evidence suggests that exposure to contaminants in surface water is causing immunosuppression and intersex in freshwater fish species.

Development of microsatellite markers for three at risk tiger beetles Cicindela dorsalis dorsalis, C. d. media, and C. puritana.

Objective: Tiger beetles inhabiting sandy beaches and cliffs along the east coast of the United States are facing increasing habitat loss due to erosion, urbanization, and sea level rise. The northeastern beach tiger beetle Cicindela dorsalis dorsalis and Puritan tiger beetle Cicindela puritana are both listed as threatened under the Endangered Species Act of 1973, while the white beach tiger beetle Cicindela dorsalis media is not listed but has been declining. Extirpation of these beetles, in some cases from entire states, has isolated many populations reducing gene flow and elevating the risk for the loss of genetic variation.

Monitoring chemical contaminants in the Gulf of Maine, using sediments and mussels (Mytilus edulis): An evaluation.

The objective of this paper is to determine whether contaminant data on mussels and sediments can be used interchangeably, or not, when assessing the degree of anthropogenic contamination of a water body. To obtain adequate coverage of the entire Gulf of Maine, Bay of Fundy sediment samples were collected, analyzed and combined with similar data from four coastal monitoring programs. This required careful interpretation but provided robust results consistent with published literature.

Draft Genome Sequence of an Adomavirus Associated with Raised Mucoid Skin Lesions on Smallmouth Bass (Micropterus dolomieu).

Raised mucoid skin lesions have been observed on smallmouth bass () for years. Here, we report the draft genome of a novel adomavirus ( adomavirus 2) associated with this disease. The circular genome is 17,561 bp and most similar to that of alpha-adomaviruses.

Mercury bioaccumulation in freshwater fishes of the Chesapeake Bay watershed.

Chemical contaminants are a threat to the Chesapeake Bay watershed, with mercury (Hg) among the most prevalent causes of impairment. Despite this, large-scale patterns of Hg concentrations, and the potential risks to fish, wildlife, and humans across the watershed, are poorly understood. We compiled fish Hg data from state monitoring programs and recent research efforts to address this knowledge gap and provide a comprehensive assessment of fish Hg concentrations in the watershed's freshwater habitats.

Reconnaissance of Surface Water Estrogenicity and the Prevalence of Intersex in Smallmouth Bass () Inhabiting New Jersey.

The observation of testicular oocytes in male fishes has been utilized as a biomarker of estrogenic endocrine disruption. A reconnaissance project led in the Northeastern United States (US) during the period of 2008-2010 identified a high prevalence of intersex smallmouth bass on or near US Fish & Wildlife Service National Wildlife Refuges that included the observation of 100% prevalence in smallmouth bass males collected from the Wallkill River, NJ, USA. To better assess the prevalence of intersex smallmouth bass across the state of New Jersey, a tiered reconnaissance approach was initiated during the fall of 2016.

Tissue Distribution and Immunomodulation in Channel Catfish () Following Dietary Exposure to Polychlorinated Biphenyl Aroclors and Food Deprivation.

Although most countries banned manufacturing of polychlorinated biphenyls (PCBs) over 40 years ago, PCBs remain a global concern for wildlife and human health due to high bioaccumulation and biopersistance. PCB uptake mechanisms have been well studied in many taxa; however, less is known about depuration rates and how post-exposure diet can influence PCB concentrations and immune response in fish and wildlife populations. In a controlled laboratory environment, we investigated the influence of subchronic dietary exposure to two PCB Aroclors and food deprivation on tissue-specific concentrations of total PCBs and PCB homologs and innate immune function in channel catfish ().

American eels produce and release bile acid profiles that vary across life stage.

The American eel (Anguilla rostrata) is an imperilled fish hypothesized to use conspecific cues, in part, to coordinate long-distance migration during their multistage life history. Here, holding water and tissue from multiple American eel life stages was collected and analysed for the presence, profile and concentration of bile acids. Distinct bile acid profiles were identified in glass, elver, yellow eel and silver eel holding waters using ultraperformance liquid chromatography high-resolution mass spectrometry and principal component analysis.

Divergent genes encoding the putative receptors for growth hormone and prolactin in sea lamprey display distinct patterns of expression.

Growth hormone receptor (GHR) and prolactin receptor (PRLR) in jawed vertebrates were thought to arise after the divergence of gnathostomes from a basal vertebrate. In this study we have identified two genes encoding putative GHR and PRLR in sea lamprey (Petromyzon marinus) and Arctic lamprey (Lethenteron camtschaticum), extant members of one of the oldest vertebrate groups, agnathans. Phylogenetic analysis revealed that lamprey GHR and PRLR cluster at the base of gnathostome GHR and PRLR clades, respectively.

Shale gas development has limited effects on stream biology and geochemistry in a gradient-based, multiparameter study in Pennsylvania.

The number of horizontally drilled shale oil and gas wells in the United States has increased from nearly 28,000 in 2007 to nearly 127,000 in 2017, and research has suggested the potential for the development of shale resources to affect nearby stream ecosystems. However, the ability to generalize current studies is limited by the small geographic scope as well as limited breadth and integration of measured chemical and biological indicators parameters. This study tested the hypothesis that a quantifiable, significant relationship exists between the density of oil and gas (OG) development, increasing stream water concentrations of known geochemical tracers of OG extraction, and the composition of benthic macroinvertebrate and microbial communities.

Disentangling the potential effects of land-use and climate change on stream conditions.

Land-use and climate change are significantly affecting stream ecosystems, yet understanding of their long-term impacts is hindered by the few studies that have simultaneously investigated their interaction and high variability among future projections. We modeled possible effects of a suite of 2030, 2060, and 2090 land-use and climate scenarios on the condition of 70,772 small streams in the Chesapeake Bay watershed, United States. The Chesapeake Basin-wide Index of Biotic Integrity, a benthic macroinvertebrate multimetric index, was used to represent stream condition.

Influence of demographics, exposure, and habitat use in an urban, coastal river on tumor prevalence in a demersal fish.

Neoplasia and associated tissue biomarkers in benthic fishes are commonly used to characterize effects of contaminated sediments in aquatic ecosystems. However, these fish are often migratory or partially-migratory, and thus assessing the effect of location-specific contamination is challenging because the fish will have a complex exposure history. We determined liver and skin neoplasia prevalence for a benthic, partially-migratory fish, white sucker (Catostomus commersonii), and used carbon and nitrogen stable isotope ratios to determine the diet contribution associated with areas of contaminated sediments within the urbanized portion of the St.

Exposure and potential effects of pesticides and pharmaceuticals in protected streams of the US National park Service southeast region.

Globally, protected areas offer refugia for a broad range of taxa including threatened and endangered species. In the United States (US), the National Park Service (NPS) manages public lands to preserve biodiversity, but increasing park visitation and development of surrounding landscapes increase exposure to and effects from bioactive contaminants. The risk (exposure and hazard) to NPS protected-stream ecosystems within the highly urbanized southeast region (SER) from bioactive contaminants was assessed in five systems based on 334 pesticide and pharmaceutical analytes in water and 119 pesticides in sediment.

A Random Forest Approach for Bounded Outcome Variables.

Random forests have become an established tool for classification and regression, in particular in high-dimensional settings and in the presence of non-additive predictor-response relationships. For bounded outcome variables restricted to the unit interval, however, classical modeling approaches based on mean squared error loss may severely suffer as they do not account for heteroscedasticity in the data. To address this issue, we propose a random forest approach for relating a beta dis-tributed outcome to a set of explanatory variables.

Author Correction: The evolutionary consequences for seawater performance and its hormonal control when anadromous Atlantic salmon become landlocked.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Osmoregulatory role of the intestine in the sea lamprey ().

Lampreys are the most basal vertebrates with an osmoregulatory strategy. Previous research has established that the salinity tolerance of sea lamprey increases dramatically during metamorphosis, but underlying changes in the gut have not been examined. In the present work, we examined changes in intestinal function during metamorphosis and seawater exposure of sea lamprey ().

Malignant melanoma of brown bullhead (Ameiurus nebulosus) in Lake Memphremagog, Vermont/Quebec.

In 2012, brown bullhead (Ameiurus nebulosus) with large, raised, black growths were first reported from multiple areas within the Vermont portion of Lake Memphremagog. Subsequent surveys conducted from 2014 to 2017 at two sites within the lake indicated a prevalence of 30% in adult brown bullhead 200 mm and above total length. These lesions ranged from slightly raised smooth black areas to large nodular areas on the body surface and fins and within the oral cavity.

Functional characterization and osmoregulatory role of the Na-K-2Cl cotransporter in the gill of sea lamprey (), a basal vertebrate.

The present study provides molecular and functional characterization of Na-K-2Cl cotransporter (NKCC1/Slc12a2) in the gills of sea lamprey (), the most basal extant vertebrate with an osmoregulatory strategy. We report the full-length peptide sequence for the lamprey Na-K-Cl cotransporter 1 (NKCC1), which we show groups strongly with and occupies a basal position among other vertebrate NKCC1 sequences. In postmetamorphic juvenile lamprey, mRNA was present in many tissues but was fivefold higher in the gill than any other examined tissue, and NKCC1 protein was only detected in the gill.