Geology topics

Bonnie L. Brown

Publications and source records attributed to Bonnie L. Brown.

9 recordsLinked to original sources

USGS2025

Flow cytometric detection of waterborne bacteria metabolic response to anthropogenic chemical inputs to aquatic ecosystems

Typical investigations into the biological consequences of suspected xenobiotics or nutrients introduced in watersheds include analytical chemistry screens of environmental samples—such as periphyton responses or studies of fish condition—which are all costly in terms of equipment, reagents, time, and human resources. An alternative is to assess pollutant effects on waterborne bacteria. A flow cytometric method was developed to yield rapid, same-day results that could be used to proactively screen for suspected chemical inputs into watersheds using water sampling methods that are identical to those in standard use. The analytical methods are microbe cultivation-independent, for use with waterborne bacteria that are typically viable but not culturable. The procedure is quick and inexpensive, generating measures of bacterial esterase that reflect metabolic activity and are sensitive and statistically robust. After phosphate-EDTA incubation to increase cell wall permeability, staining was performed with 5(6) carboxyfluorescein diacetate (enzyme activity) and propidium iodide (cell viability) with three bacterial species in exponential phase growth having been incubated with organic wastewater compounds (atrazine, pharmaceuticals [17α-ethynylestradiol and trenbolone], and antimicrobials [tylosin and butylparaben]). This method successfully detected metabolic changes in all bacterial species, with atrazine inducing the greatest change. Additional fluorescent stains can target specific microbial structures or functions of interest in a particular watershed. This biotechnology can inform analytical chemistry and study of biota at sites of interest and has the potential to be automated.

Cells↗

USGS2024

Flow cytometric assessments of metabolic activity in bacterial assemblages provide insight into ecosystem condition along the Buffalo National River, Arkansas

The Buffalo National River (BNR), on karst terrain in Arkansas, is considered an extraordinary water resource. Water collected in Spring 2017 along BNR was metagenomically analyzed using 16S rDNA, and for 17 months (5/2017–11/2018), bacterial responses were measured in relation to nutrients sampled along a stretch of BNR near a concentrated animal feed operation (CAFO) on Big Creek. Because cell count and esterase activity can increase proportionally with organic enrichment, they were hypothesized to be elevated near the CAFO. Counts (colony forming units; CFUs) were different among sites for 73 % of the months; Big Creek generated highest CFUs 27 % of the time, with the closest downstream site at 13.3 %. Esterase activity was different among sites 94 % of the time, with Big Creek exhibiting lowest activity 71 % of the time. Over the months, activity was similar across sites at ~70 % active, except at Big Creek (56 %). The α-diversity of BNR microbial consortia near a wastewater treatment plant (WWTP) and the CAFO was related to distance from the WWTP and CAFO. The inverse relationship between high CFUs and low esterase activity at Big Creek ( r = −0.71) actuated in vitro exposures of bacteria to organic wastewater contaminants (OWC) previously identified in the watershed. Exponential-phase Escherichia coli (stock strain), Streptococcus suis (avirulent, from swine), and S. dysgalactiae (virulent, from silver carp, Hypophthalmichthys molitrix ) were incubated with atrazine, pharmaceuticals (17 α-ethynylestradiol and trenbolone), and antimicrobials (tylosin and butylparaben). Bacteria were differentially responsive. Activity varied with exposure time and OWC type, but not concentration; atrazine decreased it most. Taken together - the metagenomic taxonomic similarities along BNR, slightly higher bacterial growth and lower bacterial esterase at the CAFO, and the lab exposures of bacterial strains showing that OWC altered metabolism - the results indicated that bioactive OWC entering the watershed can strongly influence microbial processes in the aquatic ecosystem.

Science of the Total Environment↗

USGS2023

Amino acid variation at the mitochondrial binding site of Antimycin A is proposed to reflect sensitivity and toxicity differences among fish species

To better understand differential sensitivities among fish species to the piscicidal compound Antimycin-A (ANT-A), we hypothesized that variations in amino acids at the ANT-A binding site may reflect toxicity differences. Protein sequences for six motifs comprising the ANT-A binding site were obtained and compared for invasive carp species ( N = 515) and seven non-target species ( N = 277); a consensus was delineated from each species. The carp species, Common Carp ( Cyprinus carpio ), Silver Carp ( Hypophthalmichthys molitrix ), Bighead Carp ( Hypophthalmichthys nobilis ), Grass Carp ( Ctenopharyngodon idella ), and Black Carp ( Mylopharyngodon piceus ) , showed the same amino acids at the site; thus, it was termed the carp consensus motif sequence (CCM). Channel Catfish ( Ictalurus punctatus ) showed the most amino acid polymorphisms, with three motifs 96–100% different from CCM. Within a species, Bluegill ( Lepomis macrochirus ) and Fathead Minnow ( Pimephales promelas ) variation per motif was most dissimilar (46.7% and 21.6%, respectively). Organismal mortality data from the literature indicated Yellow Perch ( Perca flavescens ) , Walleye ( Sander vitreus ) , and American Gizzard Shad ( Dorosoma cepedianum ) to be most sensitive to the piscicide, Catfish least sensitive, and all others intermediate. The protein sequence variations of the binding site appeared to be in accord with organismal sensitivity categories when they differed from the CCM; the motifs in Gizzard Shad and Walleye were the same as in CCM. The physical/chemical nature of ANT-A is important to consider in organismal response comparisons. This cellular approach of studying ANT-A binding at its target enzyme is a non-destructive way to predict piscicidal efficacy of ANT-A against fishes of interest, informs management decisions in control efforts for invasives, and can be used to forecast effects on sympatric species.

Fishes↗

USGS2021

Juvenile African clawed frogs (Xenopus laevis) express growth, metamorphosis, mortality, gene expression, and metabolic changes when exposed to thiamethoxam and clothianidin

Neonicotinoids (NEO) represent the main class of insecticides currently in use, with thiamethoxam (THX) and clothianidin (CLO) primarily applied agriculturally. With few comprehensive studies having been performed with non-target amphibians, the aim was to investigate potential biomarker responses along an adverse outcome pathway of NEO exposure, whereby data were collected on multiple biological hierarchies. Juvenile African clawed frogs, Xenopus laevis , were exposed to commercial formulations of THX and CLO at high (100 ppm) and low (20 ppm) concentrations of the active ingredient. Mortality, growth, development, liver metabolic enzyme activity, and gene expression endpoints were quantified. Tadpoles ( n > 1000) from NF 47 through tail resorption stage (NF 66) were exposed to NEO or to NEO-free media treatments. Liver cell reductase activity and cytotoxicity were quantified by flow cytometry. Compared to control reference gene expressions, levels of expression for NEO receptor subunits, cell structure, function, and decontamination processes were measured by RT-qPCR by using liver and brain. Mortality in THX high was 21.5% compared to the control (9.1%); the metabolic conversion of THX to CLO may explain these results. The NF 57 control tadpoles were heavier, longer, and more developed than the others. The progression of development from NF 57–66 was reduced by THX low, and weight gain was impaired. Liver reductases were highest in the control (84.1%), with low NEO exhibiting the greatest reductions; the greatest cytotoxicity was seen with THX high. More transcriptional activity was noted in brains than in livers. Results affirm the utility of a study approach that considers multiple complexities in ecotoxicological studies with non-target amphibians, underscoring the need for simultaneously considering NEO concentration-response relationships with both whole-organism and biomarker endpoints.

International Journal of Molecular Sciences↗

USGS2019

Defensible standardized ploidy assessments for Grass Carp (Ctenopharyngodon idella, Cyprinidae) intercepted from the commercial supply chain

Although methods are in place through the U.S. Fish and Wildlife (USFWS) program for ploidy testing of feral caught Grass Carp ( Ctenopharyngodon idella ) and black carp ( Mylopharyngodon piceus ), no guidelines exist for carp hauled across state lines. Using 1200 Grass Carp purchased by undercover Ohio law enforcement during 2015–2016, we developed a standardized protocol for discriminating ploidy by using two parameters, nuclear size and DNA content. Bead standards at 2 μm or 4 μm were used to establish nuclear size from Nile Tilapia ( Oreochromis niloticus ), known diploid ( n = 20) and triploid (n = 20) Grass Carp blood, and cells derived from eyeballs of purchased field carp. The control for establishing DNA content was cryopreserved or fresh tilapia blood (2.40 pg). Time postmortem indicated nuclear size was similar over 4 days, but DNA quality from triploids was best at 24 h. Occasionally, only size or DNA content was measurable. Tilapia mean nuclear size ( n = 501 samples) was 4.61 μm (SE 0.05) (R 2 = 0.94). Known diploid and triploid blood nuclear sizes, compared with tilapia size, were 3.62 μm (SE 0.13) (R 2 = 0.96) and 7.58 μm (SE 0.27) (R 2 = 0.96), respectively. Mean field carp eye nuclear size was 5.83 μm (SE 0.13). Mean DNA content of cells from field carp eyes ( n = 698 fish) was 3.51 pg (SE 0.06). No diploid Grass Carp were detected in the USFWS certified triploid Grass Carp transports. This standard protocol reliably discriminates ploidy and can be used for enforcement of regulations that differ among state jurisdictions.

Journal of Great Lakes Research↗

USGS2017

An accurate method for measuring triploidy of larval fish spawns

A standard flow cytometric protocol was developed for estimating triploid induction in batches of larval fish. Polyploid induction treatments are not guaranteed to be 100% efficient, thus the ability to quantify the proportion of triploid larvae generated by a particular treatment helps managers to stock high-percentage spawns and researchers to select treatments for efficient triploid induction. At 3 d posthatch, individual Grass Carp Ctenopharyngodon idella were mechanically dissociated into single-cell suspensions; nuclear DNA was stained with propidium iodide then analyzed by flow cytometry. Following ploidy identification of individuals, aliquots of diploid and triploid cell suspensions were mixed to generate 15 levels (0–100%) of known triploidy ( n = 10). Using either 20 or 50 larvae per level, the observed triploid percentages were lower than the known, actual values. Using nonlinear regression analyses, quadratic equations solved for triploid proportions in mixed samples and corresponding estimation reference plots allowed for predicting triploidy. Thus, an accurate prediction of the proportion of triploids in a spawn can be made by following a standard larval processing and analysis protocol with either 20 or 50 larvae from a single spawn, coupled with applying the quadratic equations or reference plots to observed flow cytometry results. Due to the universality of triploid DNA content being 1.5 times the diploid level and because triploid fish consist of fewer cells than diploids, this method should be applicable to other produced triploid fish species, and it may be adapted for use with bivalves or other species where batch analysis is appropriate.

North American Journal of Aquaculture↗

USGS2015

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10 6 reads revealed >3 × 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria , predominantly Comamonadaceae . The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae , pathogenic Pseudomonadaceae , and ‘ Vibrionales' ) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

Virginia↗

USGS2014

A nuclear DNA perspective on delineating evolutionarily significant lineages in polyploids: the case of the endangered shortnose sturgeon ( Acipenser brevirostrum )

The shortnose sturgeon, Acipenser brevirostrum , oft considered a phylogenetic relic, is listed as an “endangered species threatened with extinction” in the US and “Vulnerable” on the IUCN Red List. Effective conservation of A. brevirostrum depends on understanding its diversity and evolutionary processes, yet challenges associated with the polyploid nature of its nuclear genome have heretofore limited population genetic analysis to maternally inherited haploid characters. We developed a suite of polysomic microsatellite DNA markers and characterized a sample of 561 shortnose sturgeon collected from major extant populations along the North American Atlantic coast. The 181 alleles observed at 11 loci were scored as binary loci and the data were subjected to multivariate ordination, Bayesian clustering, hierarchical partitioning of variance, and among-population distance metric tests. The methods uncovered moderately high levels of gene diversity suggesting population structuring across and within three metapopulations (Northeast, Mid-Atlantic, and Southeast) that encompass seven demographically discrete and evolutionarily distinct lineages. The predicted groups are consistent with previously described behavioral patterns, especially dispersal and migration, supporting the interpretation that A. brevirostrum exhibit adaptive differences based on watershed. Combined with results of prior genetic (mitochondrial DNA) and behavioral studies, the current work suggests that dispersal is an important factor in maintaining genetic diversity in A. brevirostrum and that the basic unit for conservation management is arguably the local population.

PLoS ONE↗

USGS2014

Beta-thymosin gene polymorphism associated with freshwater invasiveness of alewife ( Alosa pseudoharengus )

Predicting the success of a species’ colonization into a novel environment is routinely considered to be predicated on niche-space similarity and vacancy, as well as propagule pressure. The role genomic variation plays in colonization success (and the interaction with environment) may be suggested, but has not rigorously been documented. To test an hypothesis that previously observed ecotype-specific polymorphisms between anadromous and landlocked alewife (Alosa pseudoharengus) populations are an adaptive response to osmoregulatory challenges rather than a result of allele sampling at founding, we examined multiple anadromous and landlocked (colonized) populations for their allelic profiles at a conserved region (3’-UTR end) of a β-thymosin gene whose protein product plays a central role in the organization of cytoskeleton. The putatively ancestral β-thymosin allele was prevalent in anadromous populations, whereas a newly derived allele was overrepresented in landlocked populations; a third allele was exclusive to the anadromous populations. We also conducted a complementary set of salinity exposure experiments to test osmoregulatory performance of the alewife ecotypes in contrasting saline environments. The pattern of variation and results from these challenges indicate a strong association of β-thymosin with colonization success and a transition for species with an anadromous life-history to one with only a freshwater component.

Journal of Experimental Zoology↗