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Deborah D. Iwanowicz

Publications and source records attributed to Deborah D. Iwanowicz.

At least 37 records · Page 2Linked to original sources
USGS2019

Establishing molecular methods to quantitatively profile gastric diet items of fish—Application to the invasive blue catfish (ictalurus furcatus)

Understanding the diet of invasive species helps researchers to more accurately assess the health, survivorship, growth, and stability of an invasive fish species, as well as their effects on native populations. Techniques capable of identifying multiple prey species from fish stomach contents have been developed. In this study, a multi-locus metabarcoding approach was used to identify fish and invertebrate prey in stomach samples of Ictalurus furcatus (blue catfish), which were collected from two sites on the Mattawomen Creek and Nanjemoy Creek in Maryland. The mitochondrial 12S (mt12S) and mitochondrial 16S (mt16S) gene regions were sequenced and compared. First, a mock sample for each gene region was created with the pooled polymerase chain reaction product of known fish species, and quantities of the sample were used to determine efficacy of the amplicon. Results varied between gene regions analyzed. Then, when using the mt12S primers, next-generation sequencing determined that nine fish species were found at levels greater than 1 percent of the diet of blue catfish. The most common species were Perca flavescens (yellow perch) and Cyprinus carpio (common carp). The mt16S gene region analyses found 10 fish species at greater than 1 percent of the diet, which primarily included Orconectes limosus (spinycheek crayfish), Alosa pseudoharengus (alewife), and yellow perch. Partially digested eggs were identified using next-generation sequencing of yellow perch in two of the stomach samples, and a TaqMan® quantitative polymerase chain reaction (qPCR) assay was developed to more economically identify egg species in the future. The yellow-perch-specific TaqMan® qPCR assay was tested using primers that were developed to detect a 154-base-pair amplicon in the mitochondrial control region. Consumption of yellow perch eggs indicates that blue catfish could potentially negatively affect young-of-year recruitment of this native sportfish. Analyses of two gene regions helped confirm the major prey of the fish sampled and allowed identification of fish species as prey that were not included in a database for the two gene regions. We concluded that the mitochondrial ribosomal-marker-based next-generation sequencing method is useful in determining the prey of fish species.

Potomac River↗
USGS2019

Isolation, characterization and molecular identification of a novel aquareovirus that infects the endangered fountain darter, Etheostoma fonticola

The fountain darter Etheostoma fonticola (FOD) is a federally endangered fish listed under the US Endangered Species Act. Here, we identified and characterized a novel aquareovirus isolated from wild fountain darters inhabiting the San Marcos River. This virus was propagated in Chinook salmon embryo (CHSE)-214, rainbow trout gonad-2 and fathead minnow cells at 15°C. The epithelioma papulosum cyprini cell line was refractory at all temperatures evaluated. High throughput sequencing technologies facilitated the complete genome sequencing of this virus utilizing ribosomal RNA-depleted RNA extracted from infected CHSE-214 cells. Conventional PCR primer sets were developed for the detection and confirmation of this virus to assist diagnostic screening methods. Phylogenetic analysis suggests this virus belongs to the Aquareovirus A genus. This research provides requisite initial data critical to support hatchery and refugia biosecurity measures for this endangered species.

Diseases of Aquatic Organisms↗
USGS2018

A method for determining avian influenza virus hemagglutinin and neuraminidase subtype association

Methods for grouping specific avian influenza virus (AIV) hemagglutinin (HA) and neuraminidase (NA) subtype reverse-transcription polymerase chain reaction (RT-PCR) products into HA:NA subtypes when egg incubation is technically not feasible were evaluated. These approaches were adopted for use as post hoc methods after melt curve analysis. The methods are based on ratios obtained from amplicon copy count and amplicon molarity and were founded on the premise that infectious particles contain an equal copy count of single-stranded ribonucleic acid segments that encode HA or NA, and thus subtype-specific amplicons from a single AIV isolate should yield a theoretical HA:NA ratio of 1. Single and mixed HA:NA AIV subtype samples were evaluated to determine whether the calculated HA:NA ratios would approach the theoretical value. With these samples, preference was given to the molarity methods to better define and correct for the effects of multiple potential amplicons in the amplification mix. Further, the molarity method was used to evaluate pond sediment spiked with intact virus of known HA:NA subtype to determine whether the method is sufficiently robust to be used with complex samples, such as those acquired from waterfowl habitat. This was a proof-of-concept study intended to guide future methods development. The methods here are not meant to be applied in any other context. From the analysis of fully characterized isolates of North American AIV, the HA:NA molarity-based ratios were found to be 1.63 ± 0.75 (mean ± standard deviation) when corrected for the difference in amplification strength and the production of multiple amplicons in some reactions using equations developed in this study. Copy count HA:NA ratios, obtained from HA and NA subtype (RT-qPCR), were 1.146 ± 0.124 (mean ± standard deviation) when corrected for amplification efficiency. Correct associations of HA:NA subtype sample composition were made with mixed samples containing 1 HA and 2 NA, and 2 HA and 2 NA. When spiked pond sediment was evaluated, the molar ratio obtained for the H4 and N6 identified in the sample was 1.28 with correction and 1.14 without correction.

Open-File Report↗
USGS2018

Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis

Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.

Florida, Hawaii↗
USGS2018

Exposure to synthetic hydraulic fracturing waste influences the mucosal bacterial community structure of the brook trout (Salvelinus fontinalis) epidermis

Production of natural gas using unconventional technologies has risen as demand for alternative fuels has increased. Impacts on the environment from waste generated from these processes are largely unexplored. In particular, the outcomes of organismal exposure to hydraulic fracturing waste have not been rigorously evaluated. We evaluated the effects of exposure to surrogate hydraulic fracturing waste (HF waste) on mucosal bacterial community structure of the brook trout ( Salvelinus fontinalis ) epidermis. Brook trout are fish native to streams at risk to HF waste exposure. Here, fish were exposed to four treatments (control, 0.00%; low, 0.01%; medium, 0.10%; and high, 1.0% concentrations) of surrogate HF waste synthesized to mimic concentrations documented in the field. Epidermal mucus samples were collected and assessed 15 days post-exposure to determine if the associated bacterial community varied among treatments. We observed differences in epidermal mucosal bacterial community composition at multiple taxonomic scales among treatments. These community changes reflected compositional differences in taxa dominance and community similarity rather than losses or gains in taxonomic richness. The dominant bacterial genus that explained the greatest variation in community structure between exposed and unexposed fish was Flavobacterium . Two genera associated with salmonid diseases, Flavobacterium and Pseudomonas , were statistically more abundant in high treatments than controls. These results suggest that exposure to low levels of HF waste influences bacterial colonization and may lead to a disruption that favors bacterial populations associated with fish disease.

Pennsylvania↗
USGS2017

Using colony monitoring devices to evaluate the impacts of land use and nutritional value of forage on honey bee health

Colony monitoring devices used to track and assess the health status of honey bees are becoming more widely available and used by both beekeepers and researchers. These devices monitor parameters relevant to colony health at frequent intervals, often approximating real time. The fine-scale record of hive condition can be further related to static or dynamic features of the landscape, such as weather, climate, colony density, land use, pesticide use, vegetation class, and forage quality. In this study, we fit commercial honey bee colonies in two apiaries with pollen traps and digital scales to monitor floral resource use, pollen quality, and honey production. One apiary was situated in low-intensity agriculture; the other in high-intensity agriculture. Pollen traps were open for 72 h every two weeks while scales recorded weight every 15 min throughout the growing season. From collected pollen, we determined forage quantity per day, species identity using DNA sequencing, pesticide residues, amino acid content, and total protein content. From scales, we determined the accumulated hive weight change over the growing season, relating to honey production and final colony weight going into winter. Hive scales may also be used to identify the occurrence of environmental pollen and nectar dearth, and track phenological changes in plant communities. We provide comparisons of device-derived data between two apiaries over the growing season and discuss the potential for employing apiary monitoring devices to infer colony health in the context of divergent agricultural land use conditions.

Agriculture↗
USGS2017

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↗
USGS2017

A comparison of honey bee-collected pollen from working agricultural lands using light microscopy and ITS metabarcoding

Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying bee-collected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010–2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa. We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts.

Environmental Entomology↗
USGS2017

Low pathogenic avian influenza viruses in wild migratory waterfowl in a region of high poultry production, Delmarva, Maryland

Migratory waterfowl are natural reservoirs for low pathogenic avian influenza viruses (AIVs) and may contribute to the long-distance dispersal of these pathogens as well as spillover into domestic bird populations. Surveillance for AIVs is critical to assessing risks for potential spread of these viruses among wild and domestic bird populations. The Delmarva Peninsula on the east coast of the United States is both a key convergence point for migratory Atlantic waterfowl populations and a region with high poultry production (>4,700 poultry meat facilities). Sampling of key migratory waterfowl species occurred at 20 locations throughout the Delmarva Peninsula in fall and winter of 2013–14. Samples were collected from 400 hunter-harvested or live-caught birds via cloacal and oropharyngeal swabs. Fourteen of the 400 (3.5%) birds sampled tested positive for the AIV matrix gene using real-time reverse transcriptase PCR, all from five dabbling duck species. Further characterization of the 14 viral isolates identified two hemagglutinin (H3 and H4) and four neuraminidase (N2, N6, N8, and N9) subtypes, which were consistent with isolates reported in the Influenza Research Database for this region. Three of 14 isolates contained multiple HA or NA subtypes. This study adds to the limited baseline information available for AIVs in migratory waterfowl populations on the Delmarva Peninsula, particularly prior to the highly pathogenic AIV A(H5N8) and A(H5N2) introductions to the United States in late 2014.

Delaware, Maryland↗
USGS2017

Molecular detection of avian influenza virus from sediment samples in waterfowl habitats on the Delmarva Peninsula, United States

Avian influenza viruses (AIV) affect many species of birds including waterfowl and may persist in sediment in aquatic habitats. Sediment samples were collected from two areas representative of prime migration and overwintering waterfowl habitat in Dorchester County, Maryland in the fall and winter of 2013–2014. Samples were screened for the presence of AIV via reverse transcriptase–quantitative PCR targeting the matrix gene. Although 13.6% of sediment samples were positive for the AIV matrix gene across all collection dates and locations, differences in detection were noted with location and collection season. Percentage of AIV-positive sediment samples recovered corresponded to trends in waterfowl abundance at collection sites both temporally and spatially. These findings provide further support for the assertion that the presence of AIV in the aquatic environment is likely affected by the total number, site-specific density, and array of waterfowl species.

Delmarva Peninsula↗
USGS2017

Endozoicomonas dominates the gill and intestinal content microbiomes of Mytilus edulis from Barnegat Bay, New Jersey

Blue mussels, Mytilus edulis, Linnaeus 1758 from southern Barnegat Bay, New Jersey were examined to determine the make-up of the normal blue mussel microbiome. Sequencing of 16S ribosomal DNA amplicons from gill and intestinal content microbiomes using the Illumina® MiSeq platform yielded 1,276,161 paired end sequence reads from the gill libraries and 1,092,333 paired end sequence reads from the intestinal content libraries. General bioinformatic analyses were conducted with the open-source packages Qiime and Mothur. Phylotype assignments to the genus level were made using the commercial One Codex platform. This resulted in 1,697,852 gill and 988,436 intestinal content sequences being classified to genus. A majority of these (67.6% and 37.2% respectively) were assigned to a single operational taxonomic unit (Mytilus edulis Symbiont, MeS) that has homologies with other recently described Endozoicomonas pathogens and symbionts of marine invertebrates. MeS shares 98% identity with an uncultured bacterium from the gill tissue of an invasive indo-Pacific oyster and with HQE1 and HQE2 isolated from the sea squirt, Styela clava. Other than MeS, most of the detected bacterial species are known from marine sediments and seawater.

New Jersey↗
USGS2017

Potential concerns with analytical Methods Used for the detection of Batrachochytrium salamandrivorans from archived DNA of amphibian swab samples, Oregon, USA

Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying bee-collected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010–2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa. We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts.

Oregon↗
USGS2016

Metabarcoding of fecal samples to determine herbivore diets: A case study of the endangered Pacific pocket mouse

Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus ). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

California↗
USGS2016

Effects of urban land-use on largescale stonerollers in the Mobile River Basin, Birmingham, AL

During the spring and fall of 2001 and the spring of 2002 a study was conducted to evaluate the health of the largescale stoneroller ( Campostoma oligolepis) populations in streams along an urban land-use gradient. Sites were selected from a pool of naturally similar sub-basins (eco-region, basin size, and geology) of the Mobile River basin (MRB), using an index of urban intensity derived from infrastructure, socioeconomic, and land-use data. This urban land-use gradient (ULUG) is a multimetric indicator of urban intensity, ranging from 0 (background) to 100 (intense urbanization). Campostoma sp. have been used previously as indicators of stream health and are common species found in all sites within the MRB. Endpoints used to determine the effects of urban land-use on the largescale stoneroller included total glutathione, histology, hepatic apoptosis, condition factor and external lesions. Liver glutathione levels were positively associated with increasing urban land-use (r 2 = 0.94). Histopathological examination determined that some abnormalities and lesions were correlated with the ULUG and generally increased in prevalence or severity with increasing urbanization. Liver macrophage aggregates were positively correlated to the ULUG. The occurrence of nucleosomal ladders (indicating apoptotic cell death) did not correspond with urban intensity in a linear fashion. Apoptosis, as well as prevalence and severity of a myxozoan parasite, appeared to have a hormetic dose–response relationship. The majority of the biomarkers suggested fish health was compromised in areas where the ULUG ≥ 36.

Alabama↗
USGS2016

Evidence of estrogenic endocrine disruption in smallmouth and largemouth bass inhabiting Northeast U.S. National Wildlife Refuge waters: A reconnaissance study

Intersex as the manifestation of testicular oocytes (TO) in male gonochoristic fishes has been used as an indicator of estrogenic exposure. Here we evaluated largemouth bass ( Micropterus salmoides ) or smallmouth bass ( Micropterus dolomieu ) form 19 National Wildlife Refuges (NWRs) in the Northeast U.S. inhabiting waters on or near NWR lands for evidence of estrogenic endocrine disruption. Waterbodies sampled included rivers, lakes, impoundments, ponds, and reservoirs. Here we focus on evidence of endocrine disruption in male bass evidenced by gonad histopathology including intersex or abnormal plasma vitellogenin (Vtg) concentrations. During the fall seasons of 2008–2010, we collected male smallmouth bass ( n =118) from 12 sites and largemouth bass ( n =173) from 27 sites. Intersex in male smallmouth bass was observed at all sites and ranged from 60% to 100%; in male largemouth bass the range was 0–100%. Estrogenicity, as measured using a bioluminescent yeast reporter, was detected above the probable no effects concentration (0.73 ng/L) in ambient water samples from 79% of the NWR sites. Additionally, the presence of androgen receptor and glucocorticoid receptor ligands were noted as measured via novel nuclear receptor translocation assays. Mean plasma Vtg was elevated (>0.2 mg/ml) in male smallmouth bass at four sites and in male largemouth bass at one site. This is the first reconnaissance survey of this scope conducted on US National Wildlife Refuges. The baseline data collected here provide a necessary benchmark for future monitoring and justify more comprehensive NWR-specific studies.

Maine, Maryland, Massachusetts, New Hampshire, New↗
USGS2016

Transforming growth factor-β1 expression in endangered age-0 shortnose suckers ( Chasmistes brevirostris ) from Upper Klamath Lake, OR relative to histopathology, meristic, spatial, and temporal data

During July – September of 2008, 2009, and 2010 endangered age-0 juvenile shortnose suckers were sampled from Upper Klamath Lake, OR in a health evaluation that included the measurement of transforming growth factor – beta (TGF-β) expression in spleen in combination with a histopathology assessment. This analysis was performed to determine if the expression of this immuno-regulator could be used as a component of a larger health evaluation intended to identify potential risk-factors that may help to explain why very few of these fish survive to age-1. Potential associations between TGF-β1 expression, histopathological findings, meristic data as well as temporal and spatial data were evaluated using analysis-of-variance. In this analysis, the absence or presence of opercula deformity and hepatic cell necrosis were identified as significant factors in accounting for the variance in TGF-β1 expression observed in age-0 shortnose suckers (n = 122, squared multiple R = 0.989). Location of sample collection and the absence or presence of anchor worms ( Lernaea spp.) were identified as significant cofactors. The actual mechanisms involved with these relationships have yet to be determined. The strength, however, of our findings support the concept of using TGF-β1 expression as part of a broader fish health assessment and suggests the potential for using additional immunologic measures in future studies. Specifically, our results indicate that the measure of TGF-β1 expression in age-0 shortnose sucker health assessments can facilitate the process of identifying disease risks that are associated with the documented lack of recruitment into the adult population.

Oregon↗