Geology topics

William B. Schill

Publications and source records attributed to William B. Schill.

9 recordsLinked to original sources

USGS2021

Novel microbiome dominated by Arcobacter during anoxic excurrent flow from an ocean blue hole in Andros Island, The Bahamas

Andros Island, The Bahamas, composed of porous carbonate rock, has about 175 inland blue holes and over 50 known submerged ocean caves along its eastern barrier reef. These ocean blue holes can have both vertical and horizontal zones that penetrate under the island. Tidal forces drive water flow in and out of these caves. King Kong Cavern has a vertical collapse zone and a deep penetration under Andros Island that emits sulfidic, anoxic water and masses of thin, mucoid filaments ranging to meters in length and off-white turbid water during ebb flow. Our objective was to determine the microbial composition of this mucoid material and the unconsolidated water column turbidity based on the concept that they represent unique lithoautotrophic microbial material swept from the cave into the surrounding ocean. Bacterial DNA extracted from these filaments and surrounding turbid water was characterized using PCR that targeted a portion of the 16S rRNA gene. The genus Arcobacter dominated both the filaments and the water column above the cave entrance. Arcobacter nitrofigilis and Arcobacter sp. UDC415 in the mucoid filaments accounted for as much as 80% of mapped DNA reads. In the water column Arcobacter comprised from 65% to over 85% of the reads in the depth region from about 18 m to 34 m. Bacterial species diversity was much higher in surface water and in water deeper than 36 m than in the intermediate zone. Community composition indicates that ebb flow from the cavern influences the entire water column at least to within 6 m of the surface and perhaps the near surface as well.

Andros Island, King Kong Cavern↗

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↗

USGS2015

Strategy to evaluate persistent contaminant hazards resulting from sea-level rise and storm-derived disturbances—Study design and methodology for station prioritization

Coastal communities are uniquely vulnerable to sea-level rise (SLR) and severe storms such as hurricanes. These events enhance the dispersion and concentration of natural and anthropogenic chemicals and pathogenic microorganisms that could adversely affect the health and resilience of coastal communities and ecosystems in coming years. The U.S. Geological Survey has developed a strategy to define baseline and post-event sediment-bound environmental health (EH) stressors (hereafter referred to as the Sediment-Bound Contaminant Resiliency and Response [SCoRR] strategy). A tiered, multimetric approach will be used to (1) identify and map contaminant sources and potential exposure pathways for human and ecological receptors, (2) define the baseline mixtures of EH stressors present in sediments and correlations of relevance, (3) document post-event changes in EH stressors present in sediments, and (4) establish and apply metrics to quantify changes in coastal resilience associated with sediment-bound contaminants. Integration of this information provides a means to improve assessment of the baseline status of a complex system and the significance of changes in contaminant hazards due to storm-induced (episodic) and SLR (incremental) disturbances. This report describes the purpose and design of the SCoRR strategy and the methods used to construct a decision support tool to identify candidate sampling stations vulnerable to contaminants that may be mobilized by coastal storms.

Connecticut, Delaware, District of Columbia, Maine↗

USGS2015

An investigation of the bactericidal activity of selected essential oils to Aeromonas spp.

Diseases of fishes caused by Aeromonas spp. are common, have broad host ranges and may cause high mortality. Treatments of captive-reared populations using antimicrobials are limited with concerns for bacterial resistance development and environmental dissemination. This study was done to determine whether selected plant-derived essential oils were bactericidal to Aeromonas spp. Initially, twelve essential oils were evaluated using a disk diffusion assay to an isolate of A . salmonicida subsp. salmonicida , cause of fish furunculosis. The greatest zones of inhibition were obtained with oils of cinnamon Cinnamomum cassia , oregano Origanum vulgare , lemongrass Cymbopogon citratus and thyme Thymus vulgaris . Minimum bactericidal concentrations (MBC’s) were determined for these four oils, Allimed® (garlic extract, Allium sativum ) and colloidal silver to sixty-nine isolates representing nine Aeromonas spp. The lowest mean MBCs (0.02–0.04%) were obtained with three different sources of cinnamon oil. MBCs for three sources of oregano and lemongrass oils ranged from 0.14% to 0.30% and 0.10% to 0.65%, respectively, and for two thyme oils were 2.11% and 2.22%. The highest concentration (5%) of Allimed® tested resulted in MBCs to twelve isolates. A concentration of silver greater than 15 mg/L would be required to determine MBCs for all but one isolate.

Journal of Advanced Research↗

USGS2012

Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

West Virginia↗

USGS2008

Ecology of coral reefs in the US Virgin Islands

The US Virgin Islands (USVI ) in the northeastern Caribbean, consist of St. Croix (207 km 2 ), St. Thomas (83 km 2 ), St. John (52 km 2 ) and numerous smaller islands (Dammann and Nellis 1992). They are part of the Lesser Antilles and Leeward Islands on the eastern boundary of the Caribbean plate (Fig. 8.1). An extensive platform underlies St. Thomas and St. John and connects these islands to Puerto Rico and the British Virgin Islands. This platform extends about 32 km north of the islands and then slopes gradually to depths of over 300 m and eventually descends into the 8,000 m deep Puerto Rican Trench. South of the islands, the platform extends about 13 km and then abruptly drops off to over 4,000 m. St. Croix, about 60 km to the south, is on a separate platform which is much shallower than the northern Virgin Islands’ platform and extends less than 5 km from shore except on the east end of the island. The deepest part of the Virgin Islands Trough that separates St. Thomas and St. John from St. Croix is 4,200 m.

Virgin Islands↗

USGS2007

Presumptive Sources of Fecal Contamination in Four Tributaries to the New River Gorge National River, West Virginia, 2004

Several methods were used to determine the sources of fecal contamination in water samples collected during September and October 2004 from four tributaries to the New River Gorge National River -- Arbuckle Creek, Dunloup Creek, Keeney Creek, and Wolf Creek. All four tributaries historically have had elevated levels of fecal coliform bacteria. The source-tracking methods used yielded various results, possibly because one or more methods failed. Sourcing methods used in this study included the detection of several human-specific and animal-specific biological or molecular markers, and library-dependent pulsed-field gel electrophoresis analysis that attempted to associate Escherichia coli bacteria obtained from water samples with animal sources by matching DNA-fragment banding patterns. Evaluation of the results of quality-control analysis indicated that pulsed-field gel electrophoresis analysis was unable to identify known-source bacteria isolates. Increasing the size of the known-source library did not improve the results for quality-control samples. A number of emerging methods, using markers in Enterococcus, human urine, Bacteroidetes, and host mitochondrial DNA, demonstrated some potential in associating fecal contamination with human or animal sources in a limited analysis of quality-control samples. All four of the human-specific markers were detected in water samples from Keeney Creek, a watershed with no centralized municipal wastewater-treatment facilities, thus indicating human sources of fecal contamination. The human-specific Bacteroidetes and host mitochondrial DNA markers were detected in water samples from Dunloup Creek, Wolf Creek, and to a lesser degree Arbuckle Creek. Results of analysis for wastewater compounds indicate that the September 27 sample from Arbuckle Creek contained numerous human tracer compounds likely from sewage. Dog, horse, chicken, and pig host mitochondrial DNA were detected in some of the water samples with the exception of the October 5 sample from Dunloup Creek. Cow, white-tailed deer, and Canada goose DNA were not detected in any of the samples collected from the four tributaries, despite the presence of these animals in the watersheds. Future studies with more rigorous quality-control analyses are needed to investigate the potential applicability and use of these emerging methods. Because many of the detections for the various methods could vary over time and with flow conditions, repeated sampling during both base flow and storm events would be necessary to more definitively determine the sources of fecal contamination for each watershed.

Open-File Report↗

USGS2002

IL-2 and IL-12 alter NK cell responsiveness to IFN-γ-inducible protein 10 by down-regulating CXCR3 expression

Cytokine treatment of NK cells results in alterations in multiple cellular responses that include cytotoxicity, cytokine production, proliferation, and chemotaxis. To understand the molecular mechanisms underlying these responses, microarray analysis was performed and the resulting gene expression patterns were compared between unstimulated, IL-2, IL-2 plus IL-12, and IL-2 plus IL-18-stimulated NK92 cells. RNase protection assays and RT-PCR confirmed microarray predictions for changes in mRNA expression for nine genes involved in cell cycle progression, signal transduction, transcriptional activation, and chemotaxis. Multiprobe RNase protection assay also detected changes in the expression of CCR2 mRNA, a gene that was not imprinted on the microarray. We subsequently expanded our search for other chemokine receptor genes absent from the microarray and found an IL-2- and IL-12-dependent decrease in CXCR3 receptor mRNA expression in NK92 cells. A detailed analysis of CXCR3 expression in primary NK cells revealed that an IL-2 and an IL-12 together significantly decreased the CXCR3 receptor mRNA and receptor surface expression by 6 and 24 h of treatment, respectively. This decrease in receptor expression was associated with a significant reduction in chemotaxis in the presence of IFN-γ-inducible protein-10. The decline in CXCR3 mRNA was due to transcriptional and posttranscriptional mechanisms as the addition of actinomycin D to IL-2- and IL-12-treated NK92 slightly altered the half-life of the CXCR3 mRNA. Collectively, these data suggest that IL-2 and IL-12 directly affect NK cell migratory ability by rapid and direct down-regulation of chemokine receptor mRNA expression. Natural killer (NK) cells are large granular lymphocytes that play an important role in the defense against virally infected or malignant cells (1). Their activity can be characterized as nonadaptive and independent of MHC restriction (1, 2). A variety of NK cell functions including cytotoxicity, proliferation, chemotaxis, and cytokine production are modulated by regulatory cytokines including IFN-αβ, IL-2, IL-12, IL-18, IL-10, and TNF (reviewed in Refs. 3 and 4). Because cytokines induce such a broad range of effects in NK cells, the potential for alterations in gene expression in stimulated cells is very great. To determine which genes are regulated in response to cytokine stimulation, our laboratory has used cDNA microarray technology to examine gene expression in NK cells. Microarray technology is very useful because it allows for large-scale examination of gene expression. Additionally, this technology has proved useful in identifying physiologically relevant gene expression patterns in eukaryotic systems such as yeast (5) and fibroblasts (6) as well as predicting patterns of gene expression in tumor cells (7, 8). To examine gene expression in response to cytokine stimulation, a human NK cell line, NK92, was stimulated with IL-2 alone or in combination with IL-12 or IL-18. These cytokines were chosen because of their ability to induce NK cell responses; however, little is known about the repertoire of genes that are activated by these cytokines. Microarray analysis of gene expression in NK92 cells identified a variety of genes whose mRNA expression patterns change in response to cytokine stimulation. The genes encoding the mRNAs are not specific to any one pathway; however, changes in cytokine, chemokine, and chemokine receptor gene mRNAs were prevalent. Our mRNA studies on chemokine receptor gene expression were extended to cell surface analysis of receptor densities in cytokine-treated primary NK cells. Using FACS analysis, we observed a significant decrease in CXCR3 receptor expression in NK cells treated for 24 h with IL-2 and IL-12 alone or in combination. Recently, alterations in chemokine receptor expression were reported in IL-2-stimulated NK cells (9); however, the cells were cultured in IL-2 for 8–10 days. In contrast, our data demonstrate that cytokines can modify chemokine receptor function within hours, thus supporting a model whereby cytokines, in particular IL-2 and IL-12, regulate chemokine receptor expression in a direct, rapid, and novel manner.

Journal of Immunology↗