Health of white sucker within the St. Louis River area of concern associated with habitat usage as assessed using stable isotopes

Discovery and Genomic Characterization of a Novel Hepadnavirus from Asymptomatic Anadromous Alewife (Alosa pseudoharengus)

The alewife (Alosa pseudoharengus) is an anadromous herring that inhabits waters of northeastern North America. This prey species is a critical forage for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify potentially emerging pathogens of this species, we obtained the full genome of a novel hepadnavirus (ApHBV) from clinically normal alewives collected from the Maurice River, Great Egg Harbor River, and Delaware River in New Jersey, USA during 2015-2018. This previously undescribed hepadnavirus contained a circular DNA genome of 3146 nucleotides. Phylogenetic analysis of the polymerase protein placed this virus in the clade of metahepadnaviruses (family: Hepadnaviridae; genus: Metahepadnavirus). There was no evidence of pathology in the internal organs of infected fish and virions were not observed in liver tissues by electron microscopy. We developed a Taqman-based quantitative (qPCR) assay and screened 182 individuals collected between 2015 and 2018 and detected additional qPCR positives (n = 6). An additional complete genome was obtained in 2018 and it has 99.4% genome nucleotide identity to the first virus. Single-nucleotide polymorphisms were observed between the two genomes, including 7/9 and 12/8 synonymous vs nonsynonymous mutations across the polymerase and surface proteins, respectively. While there was no evidence that this virus was associated with disease in this species, alewives are migratory interjurisdictional fishes of management concern. Identification of microbial agents using de novo sequencing and other advanced technologies is a critical aspect of understanding disease ecology for informed population management.

Integration of environmental signatures and omics-based approaches on the European flounder to assist with health assessment of estuarine ecosystems in Brittany, France

This study aimed to develop a multidisciplinary approach to assess the ecological status of six moderate-sized French estuaries. For each estuary, we gathered geographical information, hydrobiological data, chemistry of pollutants and fish biology, including integration of proteomics and transcriptomics data. This integrative study covered the entire hydrological system studied, from the watershed to the estuary, and considered all the anthropogenic factors that can impact this environment. To reach this goal, European flounder (Platichthys flesus) were collected from six estuaries in September, which ensures a minimum residence time of five months within an estuary. Geographical metrics are used to characterize land use in each watershed. The concentrations of nitrite, nitrate, organic pollutants, and trace elements were measured in water, sediments and biota. All of these environmental parameters allowed to set up a typology of estuaries. Classical fish biomarkers, coupled with molecular data from transcriptomics and shotgun proteomics, highlighted the flounder's responses to stressors in its environment. We analysed the protein abundances and gene expression levels in the liver of fish from the different estuaries. We showed clear positive deregulation of proteins associated with xenobiotic detoxification in a system characterized by a large population density and industrial activity, as well as in a predominantly agricultural catchment area (mostly cultures of vegetables and pig breeding) mainly impacted by pesticides. Fish from the latter estuary also displayed strong deregulation of the urea cycle, most probably related to high nitrogen load. Proteomic and transcriptomic data also revealed a deregulation of proteins and genes related to the response to hypoxia, and a probable endocrine disruption in some estuaries. Coupling these data allowed the precise identification of the main stressors interacting within each hydrosystem.

Genome Sequences of 26 White Sucker Hepatitis B Virus Isolates from White Sucker, Catostomus commersonii, Inhabiting Transboundary Waters from Alberta, Canada, to the Great Lakes, USA

We report 26 genome sequences of the white sucker hepatitis B virus (WSHBV) from the white sucker, Catostomus commersonii The genome length ranged from 3,541 to 3,543 bp, and nucleotide identity was 96.7% or greater across genomes. This work suggests a geographical range of this virus that minimally extends from the Athabasca River, Alberta, Canada, to the Great Lakes, USA.

Phylogeographic Genetic Diversity in the White Sucker Hepatitis B Virus across the Great Lakes Region and Alberta, Canada

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.

High prevalence of biliary neoplasia in white perch Morone americana: potential roles of bile duct parasites and environmental contaminants

Recent surveys of white perch Morone americana from Chesapeake Bay, USA, revealed a high prevalence of hepatic and biliary lesions, including neoplasia, and bile duct parasites. Here, we describe lesions in the liver and gallbladder and evaluate for statistical associations among lesions, parasites, and biomarkers of chemical exposure in fish from 2 tributaries of Chesapeake Bay. Fish were collected from an estuarine site in the Choptank River (n = 122, ages 3-11), a tributary with extensive agriculture within the watershed, and the Severn River (n = 131, ages 2-16), a tributary with extensive urban development. Passive integrative samplers were deployed at the fish collection site and an upstream, non-tidal site in each river for 30 d. Intrahepatic biliary lesions observed in fish from both rivers included neoplasia (23.3%), dysplasia (16.2%), hyperplasia (46.6%), cholangitis (24.9%), and dilated ducts containing plasmodia of Myxidium sp. (24.9%). Hepatocellular lesions included foci of hepatocellular alteration (FHA, 15.8%) and neoplasia in 4 Severn River fish (2.3%). Age of fish and Myxidium sp. infections were significant risk factors for proliferative and neoplastic biliary lesions, age alone was a risk factor for FHA, and Goussia bayae infections were associated with cholangitis and cholecystitis. Lesion prevalence was higher in fish from the Severn River, which contained higher concentrations of PAHs, organochlorine pesticides, and brominated diphenyl ethers. Metabolite biomarkers indicated higher PAH exposures in Severn River fish. This study suggests Myxidium sp. as a promoter of bile duct tumors, but more data are needed to evaluate the biological effects of environmental contaminants in this species.

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. Louis River. We then tested which factors were significantly related to neoplasia prevalence, including age, sex, and the percent diet obtained from contaminated areas within the St. Louis River relative to Lake Superior, the reference area. Overall, the prevalence of contaminant-related internal and external tumors was low, <5%. For skin neoplasia prevalence, both sex and age were significant factors, whereas location-specific diet contribution based on stable isotope analysis was not a significant factor. For liver neoplasia prevalence, only age was a significant factor. Nevertheless, for all contaminants measured (polychlorinated biphenyls [PCBs], polychlorinated dibenzodioxins [PCDDs], and polychlorinated dibenzofurans [PCDFs]), there was a significant, negative correlation between liver tissue concentration and Lake Superior diet contribution, confirming that the St. Louis River is the primary source of contaminant exposure. The research highlights the complexity of exposure to location-specific contaminants and potentially infectious agents associated with neoplasia at urban, contaminated sites in the Great Lakes, and elsewhere. It also demonstrates the need to determine the full set of risk factors across life-stages, habitats, and biological endpoints.

Seasonal development of the coccidian parasite Goussia bayae and hepatobiliary histopathology in white perch Morone americana from Chesapeake Bay

The coccidium Goussia bayae infects the gallbladder and bile ducts of white perch Morone americana from Chesapeake Bay, USA. Seasonal changes in coccidian infections were analyzed from bile specimens of 1588 fish from the Choptank River during 2016-2018 using wet mount preparations with a Sedgwick-Rafter counting chamber. Histopathology of the gallbladder and liver was analyzed from a subset (n = 480) of these fish. Maximum parasite prevalence (100%) and intensities in the gallbladder occurred during the fish spawning season in March and April. Asynchronous coccidian development and prevalence of infections in fish increased gradually during autumn and winter, but coccidian intensity increased sharply 2-4 wk prior to the onset of fish spawning activity and decreased after spawning activity concluded. Sporulation was internal, and the gallbladder was the primary reservoir for oocysts. Two previously undescribed species of coccidia were observed in the intestine. Lesions in the gallbladder were rare and included cholecystitis and epithelial necrosis. Intrahepatic bile duct lesions were more common and included distension, cholangitis, epithelial erosion and necrosis, cholestasis, hyperplasia, and neoplasia. Cholangitis and necrosis of intrahepatic bile ducts were significantly associated with coccidial infections, while plasmodia of a myxosporean (spore morphology consistent with the genera Myxidium and Zschokella) were significantly associated with bile duct hyperplasia. Biliary neoplasia included cholangiomas (5% prevalence) and cholangiocarcinomas (1% prevalence). No association was detected between G. bayae and biliary neoplasms, but an association may exist between these lesions and the myxosporean plasmodia.

Indicators of exposure to estrogenic compounds at Great Lakes Areas of Concern: species and site comparisons

Adverse effects resulting from potential exposure of wild fishes to estrogenic endocrine disruptors were assessed at seven United States Great Lakes Areas of Concern using biomarkers ranging from organismal (gonadosomatic indices) to tissue/plasma (histology, plasma vitellogenin) and molecular (hepatic gene transcripts) levels. Biomonitoring was conducted on pelagic, top predator species, largemouth Micropterus salmoides and smallmouth M. dolomieu bass and benthic, omnivorous white sucker Catostomus commersonii. Seasonal (spring and fall) comparisons were conducted at select sites. Intersex (testicular oocytes), plasma vitellogenin, and hepatic vitellogenin transcripts were commonly observed in bass species. Testicular oocyte severity was positively, although weakly, correlated with plasma vitellogenin, hepatic transcripts of vitellogenin, estrogen receptor α, and estrogen receptor β2, while negatively correlated with androgen receptor β and phosphoenolpyruvate carboxykinase. No testicular oocytes were observed in white sucker; however, plasma vitellogenin and hepatic vitellogenin transcripts were commonly detected in the males. The results demonstrate the importance of utilizing multiple endpoints to assess exposure to estrogenic compounds as well as the importance of choosing sensitive species.

Ratio of Mercury Concentration to PCB Concentration Varies with Sex of White Sucker (Catostomus commersonii)

The whole-fish total mercury (Hg) concentrations were determined in 25 mature female and 26 mature male white suckers (Catostomus commersonii) caught during their spawning run in the Kewaunee River, a tributary to Lake Michigan. The age of each fish was estimated using thin-sectioned otoliths, and total length (TL) and weight were determined for each fish. When adjusted for the effect of age, males were found to be 7% higher in Hg concentration than females. Nearly all (about 98%) of the Hg found in the white suckers was determined to be methylmercury. In an earlier study on the same 51 white suckers from the Kewaunee River spawning run, males were found to be 18% higher than females in polychlorinated biphenyl (PCB) concentration. We determined that the ratio of Hg concentration to PCB concentration in females was significantly higher than that in males. Thus, sex significantly interacted with contaminant type (Hg or PCBs) in determining contaminant concentrations. The most plausible explanation for this interaction was that males eliminated Hg at a faster rate than females, most likely due to the boosting of the Hg-elimination rate by certain androgens such as testosterone and 11-ketotestosterone. Hg concentrations in the white suckers were well below federal guidelines for fish consumption.

Micronuclei and other erythrocyte nuclear abnormalities in fishes from the Great Lakes Basin, USA

Biological markers (biomarkers) sensitive to genotoxic and mutagenic contamination in fishes are widely used to identify exposure effects in aquatic environments. The micronucleus assay was incorporated into a suite of indicators to assess exposure to genotoxic and mutagenic contamination at five Great Lakes Areas of Concern (AOCs), as well as one non-AOC (reference) site. The assay allowed enumeration of micronuclei as well as other nuclear abnormalities for both site and species comparisons. Erythrocyte abnormality data was also compared to skin and liver tumor prevalence and hepatic transcript abundance. Erythrocyte abnormalities were observed at all sites with variable occurrence and severity among sites and species. Benthic-oriented brown bullhead (Ameiurus nebulosus) and white sucker (Catostomus commersonii) expressed lower rates of erythrocyte abnormalities, but higher rates of skin and liver neoplasms, when compared to pelagic-oriented largemouth bass (Micropterus salmoides) or smallmouth bass (Micropterus dolomieu) at the same site. The reduced erythrocyte abnormalities, increased transcript abundance associated with Phase I and II toxicant responsive pathways, and increased neoplastic lesions among benthic-oriented taxa may indicate the development of contaminant resistance of these species to more acute effects. Environ. Mol. Mutagen. 58:570-581, 2017. © 2017 This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.

Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays

Environmental studies increasingly identify the presence of both contaminants of emerging concern (CECs) and legacy contaminants in aquatic environments; however, the biological effects of these compounds on resident fishes remain largely unknown. High throughput methodologies were employed to establish partial transcriptomes for three wild-caught, non-model fish species; smallmouth bass (Micropterus dolomieu), white sucker (Catostomus commersonii) and brown bullhead (Ameiurus nebulosus). Sequences from these transcriptome databases were utilized in the development of a custom nCounter CodeSet that allowed for direct multiplexed measurement of 50 transcript abundance endpoints in liver tissue. Sequence information was also utilized in the development of quantitative real-time PCR (qPCR) primers. Cross-species hybridization allowed the smallmouth bass nCounter CodeSet to be used for quantitative transcript abundance analysis of an additional non-model species, largemouth bass (Micropterus salmoides). We validated the nCounter analysis data system with qPCR for a subset of genes and confirmed concordant results. Changes in transcript abundance biomarkers between sexes and seasons were evaluated to provide baseline data on transcript modulation for each species of interest.

Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the United States

The white sucker Catostomus commersonii is a freshwater teleost often utilized as a resident sentinel. Here, we sequenced the full genome of a hepatitis B-like virus that infects white suckers from the Great Lakes Region of the United States. Dideoxy sequencing confirmed that the white sucker hepatitis B virus (WSHBV) has a circular genome (3,542 bp) with the prototypical codon organization of hepadnaviruses. Electron microscopy demonstrated that complete virions of approximately 40 nm were present in the plasma of infected fish. Compared to avi- and orthohepadnaviruses, sequence conservation of the core, polymerase, and surface proteins was low and ranged from 16 to 27% at the amino acid level. An X protein homologue common to the orthohepadnaviruses was not present. The WSHBV genome included an atypical, presumptively noncoding region absent in previously described hepadnaviruses. Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses. The level of divergence in protein sequences between WSHBV and other hepadnaviruses and the identification of an HBV-like sequence in an African cichlid provide evidence that a novel genus of the family Hepadnaviridae may need to be established that includes these hepatitis B-like viruses in fishes. Viral transcription was observed in 9.5% (16 of 169) of white suckers evaluated. The prevalence of hepatic tumors in these fish was 4.9%, and only 2.4% of fish were positive for both virus and hepatic tumors. These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.

IMPORTANCE We report the first full-length genome of a hepadnavirus from fishes. Phylogenetic analysis of this genome indicates divergence from genomes of previously described hepadnaviruses from mammalian and avian hosts and supports the creation of a novel genus. The discovery of this novel virus may better our understanding of the evolutionary history of hepatitis B-like viruses of other hosts. In fishes, knowledge of this virus may provide insight regarding possible risk factors associated with hepatic neoplasia in the white sucker. This may also offer another model system for mechanistic research.