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Cynthia R. Adams

Publications and source records attributed to Cynthia R. Adams.

12 recordsLinked to original sources
USGS2021

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 genomes of the white sucker hepatitis B virus (WSHBV) from the white sucker, Catostomus commersonii. Genome length ranged from 3541 to 3543 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.

Microbiology Resource Announcements↗
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

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

Dermocystidium sp. infection in Blue Ridge Sculpin captured in Maryland

Raised pale cysts were observed on Blue Ridge Sculpin Cottus caeruleomentum during stream fish community surveys in Catoctin Mountain Park, Maryland. When examined histologically, preserved sculpin exhibited multiple cysts containing spherical endospores with a refractile central body characteristic of Dermocystidium spp. Cysts were not observed on the gills or internally. The portion of the watershed in which affected sculpin were observed contained lower than expected numbers of sculpin, raising concerns about the population effects of this infection. A nearby stream lacked sculpin even though they are common in this region, further suggesting the possibility of regional effects. This is the first report of a Dermocystidium infecting any fish species in the eastern United States.

Maryland↗
USGS1986

Determination of the components of stormflow using water chemistry and environmental isotopes, Mattole River basin, California

The chemical and isotopic composition of rainfall and stream water was monitored during a storm in the Mattole River basin of northwestern California. About 250 mm of rain fell during 6 days (∼80% within a 42 h period) in late January, 1972, following 24 days of little or no precipitation. River discharge near Petrolia increased from 22 m 3 s −1 to a maximum of 1300 m 3 s −1 while chloride and silica concentrations decreased only from 3.2 to 2.1 and 11.5 to 8.6 mgl −1 , respectively. Meanwhile, the isotopic composition of the river changed from δD = -42%, δ 18 O = -6.8% and 40 tritium units (T.U.) to extreme values at highest flow of δD = -35%, δ 18 O = -5.9% and 25 T.U. in response to volume-weighted rainfall averaging δD = -19.5%, δ 18 O = -3.1% and 18 T.U. Despite much rainfall of a composition quite different from that of the prestorm river water, “buffering” processes in the watershed greatly restricted changes in the chemical and isotopic content of the river during storm runoff. Because of the physical and hydrologic characteristics of the watershed, major contributions of groundwater to stormflow are very unlikely. The large increase in dissolved chemical load observed at maximum river discharge required that extensive interaction with, and presumably penetration of, soils occurred within a few hours time. Such a large increase in chemical load also required subsurface stormflow throughout a high proportion of the watershed. Chemical and isotopic stabilization of stormflow is believed to be due mainly to displacement of prestorm soil water, with some effects on river chemistry due to rapid rain-soil interactions. The isotopic and chemical composition of prestorm soil moisture cannot readily be predicted a priori because of possible variability in rainfall composition, evaporation, and exchange with atmospheric moisture, nor can it be assumed that baseflow has a predictable relation to the chemical or isotopic composition of water displaced from soils during storms. Therefore, it seems inappropriate to draw conclusions as to the relative proportions of groundwater and rainfall in runoff from a particular storm based only on the average compositions of rainfall, stormflow, and prestorm river water, as has been done in most previous isotope hydrograph studies. Given the great variation in hydrology, topography, soil characteristics, rainfall intensity and quantity, etc. from place to place, the relative amount of overland flow, subsurface flow from the unsaturated zone and of groundwater in stormflow can vary greatly in time and space.

California↗