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At least 55 records · Page 3Linked to original sources
USGS2015

Integrating gene transcription-based biomarkers to understand desert tortoise and ecosystem health

Tortoises are susceptible to a wide variety of environmental stressors, and the influence of human disturbances on health and survival of tortoises is difficult to detect. As an addition to current diagnostic methods for desert tortoises, we have developed the first leukocyte gene transcription biomarker panel for the desert tortoise ( Gopherus agassizii ), enhancing the ability to identify specific environmental conditions potentially linked to declining animal health. Blood leukocyte transcript profiles have the potential to identify physiologically stressed animals in lieu of clinical signs. For desert tortoises, the gene transcript profile included a combination of immune or detoxification response genes with the potential to be modified by biological or physical injury and consequently provide information on the type and magnitude of stressors present in the animal’s habitat. Blood from 64 wild adult tortoises at three sites in Clark County, NV, and San Bernardino, CA, and from 19 captive tortoises in Clark County, NV, was collected and evaluated for genes indicative of physiological status. Statistical analysis using a priori groupings indicated significant differences among groups for several genes, while multidimensional scaling and cluster analyses of transcription C T values indicated strong differentiation of a large cluster and multiple outlying individual tortoises or small clusters in multidimensional space. These analyses highlight the effectiveness of the gene panel at detecting environmental perturbations as well as providing guidance in determining the health of the desert tortoise.

California, Nevada↗
USGS2024

Gene flow prevents genetic diversity loss despite small effective population size in fragmented grizzly bear (Ursus arctos) populations

Genetic monitoring is important in small, fragmented populations that rely on gene flow to maintain genetic diversity. The Selkirk, Yaak, and Cabinet grizzly bear ( Ursus arctos ) populations are among the smallest in North America and are near the southernmost extent of the species’ range. These populations received little to no effective migration for generations but have recently experienced increased gene flow through natural migration and a population augmentation program. A long-term dataset of grizzly bear microsatellite genotypes from 1973 to 2021 presented a unique opportunity to examine genetic trends in these populations over time. We used this dataset of 464 bears to evaluate if gene flow affected observed heterozygosity ( H O ), expected heterozygosity ( H E ), allelic richness ( A R ), and average pairwise relatedness ( r ) in each of these populations. We also estimated effective population size ( N e ) using the temporal and linkage disequilibrium (LD) methods. Post gene flow, A R increased in the Selkirk and Cabinet populations and r decreased in all three populations. We did not observe any significant changes in H E or H O , but H E values in our populations were significantly higher than those estimated using a model without gene flow. Our N e estimates were consistent between the temporal and LD methods and ranged from 15.2 to 15.8, 15.4–17.5, and 5.6–8.9 for the Selkirk, Yaak, and Cabinet populations, respectively. Overall, our findings indicate that gene flow is increasing or maintaining genetic diversity in these populations. However, N e remains low and additional connectivity or augmentation may be needed, particularly in the Cabinet population.

Idaho, Montana, Washington↗
USGS2019

Bisphenol A and 17 alpha-ethinylestradiol-induced transgenerational differences in expression of osmoregulatory genes in the gill of medaka (Oryzias latipes)

Embryonic bisphenol A (BPA) and 17α-ethinylestradiol (EE2) exposure can have far reaching health effects in fish, including adult onset transgenerational reproductive abnormalities, anxiety, and cardiac disorders. It is unknown whether these two environmental estrogens can induce transgenerational abnormalities in the gill. The present study examined transgenerational effects of BPA or EE2 exposure on genes that are critical for osmoregulation in fish. Medaka ( Oryzias latipes ) embryos were exposed to either BPA (100 μg/L) or EE2 (0.05 μg/L) for the first 7 days of embryonic development and never thereafter for the remainder of that generation (F0) and in subsequent generations of this study (F1, F2, and F3). Expression of osmoregulatory genes ( NKAα1a , NKAα1b , NKAα1c , NKAα3a , NKAα3b , NKCC1a, and CFTR ) were examined in gills of the first-generation (F0) adults which were directly exposed as embryo and in the fourth-generation adults (F3), which were never exposed to either of these environmental estrogens. Significant alterations in expression of osmoregulatory genes were observed in both F0 and F3 generations. Within the F0 generation, a sex-specific expression pattern was observed with a downregulation of osmoregulatory genes in males and an upregulation of osmoregulatory genes in females. At the F3 generation, this pattern reversed with the majority of the osmoregulatory genes upregulated in males and downregulated in females, suggesting that exposure to BPA and EE2 during embryonic development induced transgenerational impairment in molecular events associated with osmoregulatory functions in subsequent generations. These adverse outcomes may have impacts on physiological functions related to osmoregulation of fish inhabiting contaminated aquatic environments.

Aquatic Toxicology↗
USGS2007

Gene expression in the liver of rainbow trout, Oncorhynchus mykiss , during the stress response

To better appreciate the mechanisms underlying the physiology of the stress response, an oligonucleotide microarray and real-time RT-PCR (QRT-PCR) were used to study gene expression in the livers of rainbow trout ( Oncorhynchus mykiss ). For increased confidence in the discovery of candidate genes responding to stress, we conducted two separate experiments using fish from different year classes. In both experiments, fish exposed to a 3 h stressor were compared to control (unstressed) fish. In the second experiment some additional fish were exposed to only 0.5 h of stress and others were sampled 21 h after experiencing a 3 h stressor. This 21 h post-stress treatment was a means to study gene expression during recovery from stress. The genes we report as differentially expressed are those that responded similarly in both experiments, suggesting that they are robust indicators of stress. Those genes are a major histocompatibility complex class 1 molecule ( MHC1 ), JunB , glucose 6-phosphatase ( G6Pase ), and nuclear protein 1 ( Nupr1 ). Interestingly, Nupr1 gene expression was still elevated 21 h after stress, which indicates that recovery was incomplete at that time.

Comparative Biochemistry and Physiology, Part D: G↗
USGS2016

SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep ( Ovis canadensis ) exon capture data and directly from the domestic sheep genome ( Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep ( Ovis dalli dalli ) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches ( lositan and bayescan ), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.

Molecular Ecology Resources↗
USGS2017

Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife

Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife ( Alosa pseudoharengus ) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked populations, which exhibit reduced tolerance of saltwater and enhanced tolerance of fresh water. Using RNA-seq, we compared transcriptional responses of an anadromous Alewife population to two landlocked populations after acclimation to fresh (0 ppt) and saltwater (35 ppt). Our results suggest that the gill transcriptome has evolved in primarily discordant ways between independent landlocked populations and their anadromous ancestor. By contrast, evolved shifts in the transcription of a small suite of well-characterized osmoregulatory genes exhibited a strong degree of parallelism. In particular, transcription of genes that regulate gill ion exchange has diverged in accordance with functional predictions: freshwater ion-uptake genes (most notably, the ‘freshwater paralog’ of Na + /K + -ATPase α-subunit) were more highly expressed in landlocked forms, whereas genes that regulate saltwater ion secretion (e.g. the ‘saltwater paralog’ of NKAα) exhibited a blunted response to saltwater. Parallel divergence of ion transport gene expression is associated with shifts in salinity tolerance limits among landlocked forms, suggesting that changes to the gill's transcriptional response to salinity facilitate freshwater adaptation.

Molecular Ecology↗
USGS2013

Dynamics of fecal indicator bacteria, bacterial pathogen genes, and organic wastewater contaminants in the Little Calumet River: Portage Burns Waterway, Indiana

Little information exists on the co-occurrence of fecal indicator bacteria (FIB), bacterial pathogens, and organic wastewater-associated chemicals (OWCs) within Great Lakes tributaries. Fifteen watershed sites and one beach site adjacent to the Little Calumet River–Portage Burns Waterway (LCRPBW) on Lake Michigan were tested on four dates for pH, dissolved oxygen, specific conductance, chloride, color, ammonia- and nitrate-nitrogen, soluble phosphorus, sulfate, turbidity, and atrazine; for concentrations of FIB; and for genes indicating the presence of human-pathogenic enterococci (ENT) and of Shiga-toxin producing Escherichia coli (EC) from various animal sources. Nineteen samples were also tested for 60 OWCs. Half of the watershed samples met EC recreational water quality standards; none met ENT standards. Human-wastewater-associated OWC detections were correlated with human-influence indicators such as population/km 2 , chloride concentrations, and the presence of WWTP effluents, but EC and ENT concentrations were not. Bacterial pathogen genes indicated rural human and several potential animal sources. OWCs of human or ecosystem health concern (musk fragrances AHTN and HHCB, alkylphenols, carbamazepine) and 3 bacterial pathogen genes were detected at the mouth of the LCRPBW, but no such OWCs and only 1 pathogen gene were detected at the beach. The LCRPBW has significant potential to deliver FIB, potential bacterial pathogens, and OWCs of human or ecosystem health concern to the nearshore of Lake Michigan, under conditions enhancing nearshore transport of the river plume. Nearshore mixing of lake and river water, and the lack of relationship between OWCs and FIB or pathogen genes, pose numerous challenges for watershed and nearshore assessment and remediation.

Indiana↗
USGS2008

Transcriptional profiling of MHC class I genes in rainbow trout infected with infectious hematopoietic necrosis virus

Major histocompatibility complex (MHC) molecules are important mediators of cell-mediated immunity in vertebrates. MHC class IA molecules are important for host anti-viral immunity as they present intracellular antigens and regulate natural killer cell (NK) activity. MHC class Ib molecules on the other hand are less understood and have demonstrated diverse immune and non-immune functions in mammals. Rainbow trout possess a single classical MHC IA locus ( Onmy -UBA) that is believed to function similar to that of mammalian MHC class Ia. Numerous MHC class Ib genes with undetermined functions have also been described in trout. Here we utilize quantitative reverse transcriptase PCR (qRT-PCR) techniques to survey the levels of basal and inducible transcription for selected trout MHC class Ib genes, sIgM and sentinels of IFN induction in response to viral infection. Basal transcription of all the class Ib genes examined in this study was lower than Onmy -UBA in naïve fish. UBA, along with all of the non-classical genes were induced in fish infected with virus but not in control fish. Our results support a non-classical designation for the majority of the class IB genes surveyed in this study based upon expression levels while also indicating that they may play an important role in anti-viral immunity in trout.

Molecular Immunology↗
USGS2014

Methylmercury-induced changes in gene transcription associated with neuroendocrine disruption in largemouth bass (Micropterus salmoides)

Methyl-mercury (MeHg) is a potent neuroendocrine disruptor that impairs reproductive processes in fish. The objectives of this study were to (1) characterize transcriptomic changes induced by MeHg exposure in the female largemouth bass (LMB) hypothalamus under controlled laboratory conditions, (2) investigate the health and reproductive impacts of MeHg exposure on male and female largemouth bass (LMB) in the natural environment, and (3) identify MeHg-associated gene expression patterns in whole brain of female LMB from MeHg-contaminated habitats. The laboratory experiment was a single injection of 2.5 μg MeHg/g body weight for 96 h exposure. The field survey compared river systems in Florida, USA with comparably lower concentrations of MeHg (Wekiva, Santa Fe, and St. Johns Rivers) in fish and one river system with LMB that contained elevated concentrations of MeHg (St. Marys River). Microarray analysis was used to quantify transcriptomic responses to MeHg exposure. Although fish at the high-MeHg site did not show overt health or reproductive impairment, there were MeHg-responsive genes and pathways identified in the laboratory study that were also altered in fish from the high-MeHg site relative to fish at the low-MeHg sites. Gene network analysis suggested that MeHg regulated the expression targets of neuropeptide receptor and steroid signaling, as well as structural components of the cell. Disease-associated gene networks related to MeHg exposure, based upon expression data, included cerebellum ataxia, movement disorders, and hypercalcemia. Gene responses in the CNS are consistent with the documented neurotoxicological and neuroendocrine disrupting effects of MeHg in vertebrates.

General and Comparative Endocrinology↗
USGS2025

Comparative genomics of Bacillus anthracis A and B-clades reveals genetic variation in genes responsible for spore germination

Bacillus anthracis , the causative agent of anthrax, is composed of three genetic clades (A, B, and C). Clade-A is the most common and distributed worldwide, B-clade has a narrow geographic distribution, and C-clade is rare. South Africa's Kruger National Park (KNP) has high diversity of B. anthracis , with strains from A and B clades described from its northernmost region, Pafuri. We employed whole genome sequencing to investigate the genomic diversity of B. anthracis strains isolated from animal carcasses ( n = 34) during the 2012–2015 outbreaks. Whole-genome single-nucleotide polymorphism (wgSNP) analysis assigned the 2012–2015 B. anthracis genomes to the A-clade branch, distributed across the branch's two minor sub-clades A.Br.005/006. Additionally, pan-genomic analysis distinguished the A- and B-clade genomes, identifying unique accessory genes. Notable genetic differences include the biosynthetic spore cell wall genes; long-chain fatty acid CoA ligases ( FaD13 ), Bacillus collagen-like protein of anthracis (BclA) involved in the exosporium germination, as well as a truncated murein DD-endopeptidase ( mepH ) found in the pXO2 plasmid of the B-clade strains. The tryptophan synthase subunit alpha gene ( trpA ), which results in a pseudogene in B-clade genomes separates the A- and B-clade genomes. These differences in biosynthetic cell wall genes suggest variation in adaptability or cell growth of the B-clade strains in the environment, further influenced by the truncation of the trpA gene involved in spore germination. The A.Br.005/006-clade strains in KNP exhibit higher genetic diversity, which may enhance their resilience to environmental stressors. In contrast, the KNP B-clade (B.Br.001/002) strains show limited genetic variation, potentially reducing their adaptability. This pattern is evident through whole-genome SNP analysis and pan-genomics investigating the evolution of B. anthracis .

Kruger National Park↗
USGS2007

Incidence of the enterococcal surface protein ( esp ) gene in human and animal fecal sources

The occurrence of the enterococcal surface protein ( esp ) gene in the opportunistic pathogens Enterococcus faecalis and E. faecium is well-documented in clinical research. Recently, the esp gene has been proposed as a marker of human pollution in environmental waters; however, information on its relative incidence in various human and animal fecal sources is limited. We have determined the occurrence of the esp gene in enterococci from human ( n = 64) and animal ( n = 233) fecal samples by polymerase chain reaction using two primer sets: one presumably specific for E. faecium ( esp fm ) and the other for both E. faecalis and E. faecium ( esp fs/fm ). We believe that this research is the first to explore the use of esp fs/fm for the detection of human waste in natural environmental settings. The incidence in human sources was 93.1% esp fm and 100% esp fs/fm in raw sewage influent; 30% for both esp fm and esp fs/fm in septic waste; and 0% esp fm and 80% esp fs/fm in active pit toilets. The overall occurrence of the gene in animal feces was 7.7% ( esp fs/fm ) and 4.7% ( esp fm ); animal types with positive results included dogs (9/43, all esp fm ), gulls (10/34, esp fs/fm ; 2/34, esp fm ), mice (3/22, all esp fs/fm ), and songbirds (5/55, all esp fs/fm ). The esp gene was not detected in cat (0/34), deer (0/4), goose (0/18), or raccoon (0/23) feces. The inconsistent occurrence, especially in septic and pit toilet sewage, suggests a low statistical power of discrimination between animal and human sources, which means a large number of replicates should be collected. Both esp fm and esp fs/fm were common in raw sewage, but neither one efficiently differentiated between animal and other human sources.

Environmental Science & Technology↗
USGS2008

Environmental occurrence of the enterococcal surface protein ( esp ) gene is an unreliable indicator of human fecal contamination

The enterococcal surface protein ( esp ) gene found in Enterococcus faecalis and E. faecium has recently been explored as a marker of sewage pollution in recreational waters but its occurrence and distribution in environmental enterococci has not been well-documented. If the esp gene is found in environmental samples, there are potential implications for microbial source tracking applications. In the current study, a total of 452 samples (lake water, 100; stream water, 129; nearshore sand, 96; and backshore sand, 71; Cladophora sp. (Chlorophyta), 41; and periphyton (mostly Bacillariophyceae ), 15) collected from the coastal watersheds of southern Lake Michigan were selectively cultured for enterococci and then analyzed for the esp gene by PCR, targeting E. faecalis/ E. faecium ( esp fs/fm ) and E. faecium ( esp fm ). Overall relative frequencies for esp fs/fm and esp fm were 27.4 and 5.1%. Respective percent frequency for the esp fs/fm and esp fm was 36 and 14% in lake water; 38.8 and 2.3% in stream water; 24 and 6.3% in nearshore sand; 0% in backshore sand; 24.4 and 0% in Cladophora sp.; and 33.3 and 0% in periphyton. The overall occurrence of both esp fs/fm and esp fm was significantly related ( χ 2 = 49, P < 0.0001). Post-rain incidence of esp fs/fm increased in lake and stream water and nearshore sand. Further, E. coli and enterococci cell densities were significant predictors for esp fs/fm occurrence in post-rain lake water, but esp fm was not. F + coliphage densities were not significant predictors for esp fm or esp fs/fm gene incidence. In summary, the differential occurrence of the esp gene in the environment suggests that it is not limited to human fecal sources and thus may weaken its use as a reliable tool in discriminating contaminant sources (i.e., human vs nonhuman).

Environmental Science & Technology↗
USGS2005

Interaction of rearing environment and reproductive tactic on gene expression profiles in Atlantic salmon

Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment. ?? 2005 The American Genetic Association.

Conference Paper↗
USGS2020

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Yellow perch, Perca flavescens , is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene ( amhr2by ) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males ( amhr2by + ) from XX genetic females ( amhr2by − ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

Molecular Ecology Resources↗
USGS2017

Divergence and gene flow in the globally distributed blue-winged ducks

The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence-with-gene-flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue-winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub-lineages, the globally-distributed shoveler group and the New World blue-winged/cinnamon teal group. The blue-winged/cinnamon sub-lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler (A. clypeata) and the more sedentary, African Cape shoveler (A. smithii) into the Australasian shoveler (A. rhynchotis), although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue-winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.

Journal of Avian Biology↗
USGS2024

Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression

Genomes are heterogeneous during the early stages of speciation, with small ‘islands’ of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA (‘rivers’) to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad ( Anaxyrus canorus ) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.

Molecular Ecology↗
USGS2024

Quantitative microbial risk assessment for ingestion of antibiotic resistance genes from private wells contaminated by human and livestock fecal sources

We used quantitative microbial risk assessment to estimate ingestion risk for intI1 , erm (B), sul1 , tet (A), tet (W), and tet (X) in private wells contaminated by human and/or livestock feces. Genes were quantified with five human-specific and six bovine-specific microbial source-tracking (MST) markers in 138 well-water samples from a rural Wisconsin county. Daily ingestion risk (probability of swallowing ≥1 gene) was based on daily water consumption and a Poisson exposure model. Calculations were stratified by MST source and soil depth over the aquifer where wells were drilled. Relative ingestion risk was estimated using wells with no MST detections and >6.1 m soil depth as a referent category. Daily ingestion risk varied from 0 to 8.8 × 10 −1 by gene and fecal source (i.e., human or bovine). The estimated number of residents ingesting target genes from private wells varied from 910 ( tet (A)) to 1,500 ( intI1 and tet (X)) per day out of 12,000 total. Relative risk of tet (A) ingestion was significantly higher in wells with MST markers detected, including wells with ≤6.1 m soil depth contaminated by bovine markers (2.2 [90% CI: 1.1–4.7]), wells with >6.1 m soil depth contaminated by bovine markers (1.8 [1.002–3.9]), and wells with ≤6.1 m soil depth contaminated by bovine and human markers simultaneously (3.1 [1.7–6.5]). Antibiotic resistance genes (ARGs) were not necessarily present in viable microorganisms, and ingestion is not directly associated with infection. However, results illustrate relative contributions of human and livestock fecal sources to ARG exposure and highlight rural groundwater as a significant point of exposure.

Wisconsin↗
USGS2015

Genes indicative of zoonotic and swine pathogens are persistent in stream water and sediment following a swine manure spill

Manure spills to streams are relatively frequent, but no studies have characterized stream contamination with zoonotic and veterinary pathogens, or fecal chemicals, following a spill. We tested stream water and sediment over 25 days and downstream for 7.6 km for: fecal indicator bacteria (FIB); the fecal indicator chemicals cholesterol and coprostanol; 20 genes for zoonotic and swine-specific bacterial pathogens by presence/absence polymerase chain reaction (PCR) for viable cells; one swine-specific Escherichia coli toxin gene ( STII ) by quantitative PCR (qPCR); and nine human and animal viruses by qPCR, or reverse-transcriptase qPCR. Twelve days post-spill, and 4.2 km downstream, water concentrations of FIB, cholesterol, and coprostanol were 1-2 orders of magnitude greater than those detected before, or above, the spill, and genes indicating viable zoonotic or swine-infectious Escherichia coli , were detected in water or sediment. STII increased from undetectable before, or above the spill, to 10 5 copies/100 mL water 12 days post-spill. Thirteen of 14 water (8/9 sediment) samples had viable STII -carrying cells post-spill. Eighteen days post-spill porcine adenovirus and teschovirus were detected 5.6 km downstream. Sediment FIB concentrations (per gram wet weight) were greater than in water, and sediment was a continuous reservoir of genes and chemicals post-spill. Constituent concentrations were much lower, and detections less frequent, in a runoff event (200 days post-spill) following manure application, although the swine-associated STII and stx 2e genes were detected. Manure spills are an underappreciated pathway for livestock-derived contaminants to enter streams, with persistent environmental outcomes, and the potential for human and veterinary health consequences.

Iowa↗