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At least 451 records · Page 25Linked to original sources
USGS2024

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.

Nature Microbiology↗
USGS2019

Functional divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis

Smoltification is a metamorphic event in salmon life history, which initiates downstream migration and pre-adapts juvenile salmon for seawater entry. While a number of reports concern thyroid hormones and smoltification, few and inconclusive studies have addressed the potential role of thyrotropin (TSH). TSH is composed of a α-subunit common to gonadotropins, and a β-subunit conferring hormone specificity. We report the presence and functional divergence of duplicated TSH β-subunit paralogs (tshβa and tshβb) in Atlantic salmon. Phylogeny and synteny analyses allowed us to infer that they originated from teleost-specific whole genome duplication. Expression profiles of both paralogs in the pituitary were measured by qPCR throughout smoltification in Atlantic salmon from the endangered Loire-Allier population raised at the Conservatoire National du Saumon Sauvage. This revealed a striking peak of tshβb expression in April, concomitant with downstream migration initiation, while tshβa expression remained relatively constant. In situ hybridization showed two distinct pituitary cell populations, tshβa cells in the anterior adenohypophysis, and tshβb cells near to the pituitary stalk, a location comparable to the pars tuberalis TSH cells involved in seasonal physiology and behaviour in birds and mammals. Functional divergence of tshβ paralogs in Atlantic salmon supports a specific role of tshβb in smoltification.

Scientific Reports↗
USGS2019

Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques

To inform management and conservation decisions, environmental DNA (eDNA) methods are used to detect genetic material shed into the water by imperiled and invasive species. Methodological enhancements are needed to reduce filter clogging, PCR inhibition, and false-negative detections when eDNA is at low concentrations. In the first of three simple experiments, we sought to ameliorate filter clogging from particulates and organic material through a scaled-up, multi-filter protocol. We combined four filters in a 5 mL Phenol-Chloroform-Isoamyl (PCI) procedure to allow for larger volumes of water (~1 L) to be filtered rapidly. Increasing the filtered water volume by four times resulted in 4.4X the yield of target DNA. Next, inhibition from organic material can reduce or block eDNA detections in PCR-based assays. To remove inhibitory compounds retained during eDNA isolation, we tested three methods to chemically strip inhibitors from eDNA molecules. The use of CTAB as a short-term (5–8 day) storage buffer, followed by a PCI isolation, resulted in the highest eDNA yields. Finally, as opposed to a linear relationship among increasing concentrations of filtered genomic eDNA, we observed a sharp change between the lower (70–280 ng) and higher (420–560 ng) amounts. This may be important for effectively precipitating eDNA during protocol testing.

Scientific Reports↗
USGS2021

Tissue and salinity specific Na+/Cl− cotransporter (NCC) orthologues involved in the adaptive osmoregulation of sea lamprey (Petromyzon marinus)

Two orthologues of the gene encoding the Na + -Cl − cotransporter (NCC), termed ncca and nccb , were found in the sea lamprey genome. No gene encoding the Na + -K + -2Cl − cotransporter 2 ( nkcc2 ) was identified. In a phylogenetic comparison among other vertebrate NCC and NKCC sequences, the sea lamprey NCCs occupied basal positions within the NCC clades. In freshwater, ncca mRNA was found only in the gill and nccb only in the intestine, whereas both were found in the kidney. Intestinal nccb mRNA levels increased during late metamorphosis coincident with salinity tolerance. Acclimation to seawater increased nccb mRNA levels in the intestine and kidney. Electrophysiological analysis of intestinal tissue ex vivo showed this tissue was anion absorptive. After seawater acclimation, the proximal intestine became less anion absorptive, whereas the distal intestine remained unchanged. Luminal application of indapamide (an NCC inhibitor) resulted in 73% and 30% inhibition of short-circuit current (I sc ) in the proximal and distal intestine, respectively. Luminal application of bumetanide (an NKCC inhibitor) did not affect intestinal I sc . Indapamide also inhibited intestinal water absorption. Our results indicate that NCCb is likely the key ion cotransport protein for ion uptake by the lamprey intestine that facilitates water absorption in seawater. As such, the preparatory increases in intestinal nccb mRNA levels during metamorphosis of sea lamprey are likely critical to development of whole animal salinity tolerance.

Scientific Reports↗
USGS2021

Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.

Scientific Reports↗
USGS2026

Validation and application of a standardized quantitative PCR assay for the assessment of antimicrobial resistance genes in surface water

Antimicrobial resistance can be an indicator of anthropogenic contamination in surface waters and is a potential public health threat. Methodological standardization for characterization of antimicrobial resistance in the environment is lacking. Quantitative PCR (qPCR) is used for rapid assessment of antibiotic resistance genes (ARGs) from environmental sources, including surface water. Here we describe the validation and application of a qPCR assay for 47 bacterial gene targets intended for surface water samples. The qPCR assay displayed excellent sensitivity (97.66%) and specificity (98.71%) for detecting ARGs when compared to whole genome sequencing of bacterial isolates. The qPCR assay was able to detect up to 6/8 (75.0%) of ARGs spiked into sterile water at varying concentrations and four sample ultrafiltration volumes. Nineteen different ARGs were detected across six samples sites at three national parks in Alaska using ultrafiltered surface water samples. The number of unique ARGs detected was higher at sites within parks with greater visitation. The relative abundance of ARGs/16S from Exit Creek in Kenai Fjords National Park, downstream from a visitor center was greater than all other sampled sites. We have demonstrated a robust qPCR assay for monitoring ARGs in surface waters, including those that are minimally human impacted.

Alaska↗
USGS2025

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well

The expansion of natural gas production and utilization worldwide has led to the decline of many once-productive wells, eventually resulting in costly well-plugging and unused infrastructure. However, in areas like the Michigan basin, MI, where the majority of natural gas is biogenically produced, microbial communities could potentially be stimulated to generate additional methane, increasing gas supply and reducing the need to drill new wells. In this study, we performed metaproteomic, metagenomic, and geochemical analyses of Antrim Shale formation water from a marginally producing natural gas well to evaluate resident microbial community functions in the context of potential bioenergy production. Functional proteins involved in methanogenesis, degradation/catabolism (including organic matter degradation), biosynthesis, energy utilization, transmembrane transport, and stress response were among the most commonly identified groups. Three metagenome-assembled genomes (MAGs) were characterized, including Methanomicrobiaceae, Methanothrix , and Smithella . For each, the identified proteins involved in methanogenesis and the degradation of diverse organic compounds, strongly suggest their role in utilizing shale-derived organic matter. These findings provide an increased understanding of the microorganisms and their metabolisms generating natural gas in the Antrim Shale and establish a foundation for future stimulation efforts aimed at enhancing biogenic methane production in marginal gas wells.

Michigan↗
USGS2003

Abundance and characteristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces

Aims: To evaluate the numbers and selected phenotypic and genotypic characteristics of the faecal indicator bacteria Escherichia coli and enterococci in gull faeces at representative Great Lakes swimming beaches in the United States. Methods and Results: E. coli and enterococci were enumerated in gull faeces by membrane filtration. E. coli genotypes (rep‐PCR genomic profiles) and E. coli (Vitek ® GNI+) and enterococci (API ® rapid ID 32 Strep and resistance to streptomycin, gentamicin, vancomycin, tetracycline and ampicillin) phenotypes were determined for isolates obtained from gull faeces both early and late in the swimming season. Identical E. coli genotypes were obtained only from single gull faecal samples but most faecal samples yielded more than one genotype (median of eight genotypes for samples with 10 isolates). E. coli isolates from the same site that clustered at ≥85% similarity were from the same sampling date and shared phenotypic characteristics, and at this similarity level there was population overlap between the two geographically isolated beach sites. Enterococcus API ® profiles varied with sampling date. Gull enterococci displayed wide variation in antibiotic resistance patterns, and high‐level resistance to some antibiotics. Conclusions: Gull faeces could be a major contributor of E. coli (10 5 –10 9 CFU g −1 ) and enterococci (10 4 –10 8 CFU g −1 ) to Great Lakes recreational waters. E. coli and enterococci in gull faeces are highly variable with respect to their genotypic and phenotypic characteristics and may exhibit temporal or geographic trends in these features. Significance and Impact of the Study: The high degree of variation in genotypic or phenotypic characteristics of E. coli or enterococci populations within gull hosts will require extensive sampling for adequate characterization, and will influence methods that use these characteristics to determine faecal contamination sources for recreational waters.

Journal of Applied Microbiology↗
USGS2002

Genetic diversity in a morphologically conservative invasive taxon: Multiple introductions of swamp eels to the southeastern United States

Genetic analysis of introduced populations, especially in morphologically conservative taxa, can clarify introduction histories, identify management units and source populations, provide a more realistic estimate of the frequency of successful invasion, and suggest strategies for preventing further introductions. In the last 7 years, populations of swamp eels, referred to the Asian genus Monopterus (Family Synbranchidae) on the basis of external morphology, have been discovered in aquatic habitats near Atlanta, Georgia; Tampa, Florida; North Miami, Florida; and most recently in close proximity to Everglades National Park in Homestead, Florida. Swamp eels are large predators capable of dispersal over land and have the potential to disrupt already threatened ecosystems. We analyzed mitochondrial DNA sequences from four known populations in the continental United States and samples from Malaysia, Indonesia, Vietnam, and two locations in China to determine introduction histories, source populations, genetic diversity, and relationships among populations. Our results indicate that there have been at least three independent introductions of genetically distinct forms. Introduced populations in close proximity (separated by <40 km) are genetically distinct. The level of sequence difference among introduced populations reaches levels seen among sister families of teleost fishes for the same region of the mitochondrial genome. These genetically distinct introduced populations in all likelihood represent at least two and possibly three species. Regardless of species status, these genetically distinct lineages may be expected to vary in ecological or life-history traits, representing different potential threats to the ecosystems where they have been introduced. Given the success of swamp eels in invading many habitats around the world, further study of these eels is warranted to elucidate the characteristics of successful invaders and invasions.

Conservation Biology↗
USGS1998

How organisms do the right thing: The attractor hypothesis

Neo-Darwinian theory is highly successful at explaining the emergence of adaptive traits over successive generations. However, there are reasons to doubt its efficacy in explaining the observed, impressively detailed adaptive responses of organisms to day-to-day changes in their surroundings. Also, the theory lacks a clear mechanism to account for both plasticity and canalization. In effect, there is a growing sentiment that the neo-Darwinian paradigm is incomplete, that something more than genetic structure, mutation, genetic drift, and the action of natural selection is required to explain organismal behavior. In this paper we extend the view of organisms as complex self-organizing entities by arguing that basic physical laws, coupled with the acquisitive nature of organisms, makes adaptation all but tautological. That is, much adaptation is an unavoidable emergent property of organisms' complexity and, to some a significant degree, occurs quite independently of genomic changes wrought by natural selection. For reasons that will become obvious, we refer to this assertion as the attractor hypothesis. The arguments also clarify the concept of "adaptation." Adaptation across generations, by natural selection, equates to the (game theoretic) maximization of fitness (the success with which one individual produces more individuals), while self-organizing based adaptation, within generations, equates to energetic efficiency and the matching of intake and biosynthesis to need. Finally, we discuss implications of the attractor hypothesis for a wide variety of genetical and physiological phenomena, including genetic architecture, directed mutation, genetic imprinting, paramutation, hormesis, plasticity, optimality theory, genotype-phenotype linkage and puncuated equilibrium, and present suggestions for tests of the hypothesis. ?? 1998 American Institute of Physics.

Chaos↗
USGS2008

An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species

The genetic impacts of hybridization between native and introduced species are of considerable conservation concern, while the possibility of reticulate evolution affects our basic understanding of how species arise and shapes how we use genetic data to understand evolutionary diversification. By using mitochondrial NADH dehydrogenase subunit 2 (ND2) sequences and 467 amplified fragment-length polymorphism nuclear DNA markers, we show that the introduced white sucker (Catostomus commersoni) has hybridized with two species native to the Colorado River Basin - the flannelmouth sucker (Catostomus latipinnis) and the bluehead sucker (Catostomus discobolus). Hybrids between the flannelmouth sucker and white sucker have facilitated introgression between the two native species, previously isolated by reproductive barriers, such that individuals exist with contributions from all three genomes. Most hybrids had the mitochondrial haplotype of the introduced white sucker, emphasizing its pivotal role in this three-way hybridization. Our findings highlight how introduced species can threaten the genetic integrity of not only one species but also multiple previously reproductively isolated species. Furthermore, this complex three-way reticulate (as opposed to strictly bifurcating) evolution suggests that seeking examples in other vertebrate systems might be productive. Although the present study involved an introduced species, similar patterns of hybridization could result from natural processes, including stream capture or geological formations (e.g., the Bering land bridge). ?? 2008 by The National Academy of Sciences of the USA.

Proceedings of the National Academy of Sciences of↗
USGS2017

Opinion: Why we need a centralized repository for isotopic data

Stable isotopes encode and integrate the origin of matter; thus, their analysis offers tremendous potential to address questions across diverse scientific disciplines ( 1 , 2 ). Indeed, the broad applicability of stable isotopes, coupled with advancements in high-throughput analysis, have created a scientific field that is growing exponentially, and generating data at a rate paralleling the explosive rise of DNA sequencing and genomics ( 3 ). Centralized data repositories, such as GenBank, have become increasingly important as a means for archiving information, and “Big Data” analytics of these resources are revolutionizing science and everyday life.

Proceedings of the National Academy of Sciences of↗
USGS2025

Iguanas rafted more than 8,000 km from North America to Fiji

Founder-event speciation can occur when one or more organisms colonize a distant, unoccupied area via long-distance dispersal, leading to the evolution of a new species lineage. Species radiations established by long-distance, and especially transoceanic, dispersal can cause substantial shifts in regional biodiversity. Here, we investigate the occurrence and timing of the greatest known long-distance oceanic dispersal event in the history of terrestrial vertebrates—the rafting of iguanas from North America to Fiji. Iguanas are large-bodied herbivores that are well-known overwater dispersers, including species that colonized the Caribbean and the Galápagos islands. However, the origin of Fijian iguanas had not been comprehensively tested. We estimated the phylogenetic relationships and evolutionary timescale of the iguanid lizard radiation using genome-wide exons and ultraconserved elements (UCEs). Those data indicate that the closest living relative of extant Fijian iguanas is the North American desert iguana and that the two taxa likely diverged during the late Paleogene near or after the onset of volcanism that produced the Fijian archipelago. Biogeographic models estimate North America as the most probable ancestral range of Fijian iguanas. Our analyses support the hypothesis that iguanas reached Fiji via an extraordinary oceanic dispersal event from western North America, and which spanned a fifth of the earth’s circumference (>8,000 km). Overwater rafting of iguanas from North America to Fiji strengthens the importance of founder-event speciation in the diversification of iguanids and elucidates the scope of long-distance dispersal across terrestrial vertebrates.

Proceedings of the National Academy of Sciences↗
USGS2025

Eradication efforts catalyze rapid evolution in an invasive predatory fish

pecies invasions spur costly and labor-intensive control efforts, yet even local eradication is seldom achieved. When control measures are initially effective, they may drive evolutionary adaptation that prevents full eradication, as has been documented for some chemical and biocontrol approaches. Although the intensity, directionality, and persistence of selection required to increase the frequency of resistant genotypes in complex natural ecosystems remains an open question, theory predicts that high mortality can cause life-history evolution even in the absence of a strong selective agent. Here, we use annually collected ecological and genetic data to show that rapid evolution of introduced smallmouth bass has undermined a 20-y manual suppression effort in a mid-sized lake. Despite nearly doubling annual mortality, our intensive control program produced a larger bass population dominated by young and early-maturing fish. These shifts were accompanied by large allele frequency changes in three genomic regions associated with earlier maturation and increased somatic growth. Our findings bear out the theoretical prediction that high mortality can drive evolutionary adaptation in target species. Controlling species invasions are worldwide practices that typically remove a substantial proportion of a population during each of many successive generations, hence life history adaptation may be commonplace. Such evolutionary responses could be salient in explaining the widespread failure of invasion control efforts. Genetic and phenotypic monitoring to detect cryptic adaptation and preemptive design of invader eradication programs to deliberately disrupt directional selection for resistance could improve invasion control outcomes.

New York↗
USGS2016

Genetic status and conservation of Westslope Cutthroat Trout in Glacier National Park

Invasive hybridization is one of the greatest threats to the persistence of Westslope Cutthroat Trout Oncorhynchus clarkii lewisi . Large protected areas, where nonhybridized populations are interconnected and express historical life history and genetic diversity, provide some of the last ecological and evolutionary strongholds for conserving this species. Here, we describe the genetic status and distribution of Westslope Cutthroat Trout throughout Glacier National Park, Montana. Admixture between Westslope Cutthroat Trout and introduced Rainbow Trout O. mykiss and Yellowstone Cutthroat Trout O. clarkii bouvieri was estimated by genotyping 1,622 fish collected at 115 sites distributed throughout the Columbia, Missouri, and South Saskatchewan River drainages. Currently, Westslope Cutthroat Trout occupy an estimated 1,465 km of stream habitat and 45 lakes (9,218 ha) in Glacier National Park. There was no evidence of introgression in samples from 32 sites along 587 km of stream length (40% of the stream kilometers currently occupied) and 17 lakes (2,555 ha; 46% of the lake area currently occupied). However, nearly all (97%) of the streams and lakes that were occupied by nonhybridized populations occurred in the Columbia River basin. Based on genetic status (nonnative genetic admixture ≤ 10%), 36 Westslope Cutthroat Trout populations occupying 821 km of stream and 5,482 ha of lakes were identified as “conservation populations.” Most of the conservation populations ( N = 27; 736 km of stream habitat) occurred in the Columbia River basin, whereas only a few geographically restricted populations were found in the South Saskatchewan River ( N = 7; 55 km) and Missouri River ( N = 2; 30 km) basins. Westslope Cutthroat Trout appear to be at imminent risk of genomic extinction in the South Saskatchewan and Missouri River basins, whereas populations in the Columbia River basin are widely distributed and conservation efforts are actively addressing threats from hybridization and other stressors. A diverse set of pro-active management approaches will be required to conserve, protect, and restore Westslope Cutthroat Trout populations in Glacier National Park throughout the 21st century.

Glacier National Park↗
USGS2011

Acetate availability and its influence on sustainable bioremediation of Uranium-contaminated groundwater

Field biostimulation experiments at the U.S. Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, Colorado, have demonstrated that uranium concentrations in groundwater can be decreased to levels below the U.S. Environmental Protection Agency's (EPA) drinking water standard (0.126 μM). During successive summer experiments – referred to as “Winchester” (2007) and “Big Rusty” (2008) - acetate was added to the aquifer to stimulate the activity of indigenous dissimilatory metal-reducing bacteria capable of reductively immobilizing uranium. The two experiments differed in the length of injection (31 vs. 110 days), the maximum concentration of acetate (5 vs. 30 mM), and the extent to which iron reduction (“Winchester”) or sulfate reduction (“Big Rusty”) was the predominant metabolic process. In both cases, rapid removal of U(VI) from groundwater occurred at calcium concentrations (6 mM) and carbonate alkalinities (8 meq/L) where Ca-UO 2 -CO 3 ternary complexes constitute >90% of uranyl species in groundwater. Complete consumption of acetate and increased alkalinity (>30 meq/L) accompanying the onset of sulfate reduction corresponded to temporary increases in U(VI); however, by increasing acetate concentrations in excess of available sulfate (10 mM), low U(VI) concentrations (0.1–0.05 μM) were achieved for extended periods of time (>140 days). Uniform delivery of acetate during “Big Rusty” was impeded due to decreases in injection well permeability, likely resulting from biomass accumulation and carbonate and sulfide mineral precipitation. Such decreases were not observed during the short-duration “Winchester” experiment. Terminal restriction fragment length polymorphism (TRFLP) analysis of 16S rRNA genes demonstrated that Geobacter sp. and Geobacter -like strains dominated the groundwater community profile during iron reduction, with 13 C stable isotope probing (SIP) results confirming these strains were actively utilizing acetate to replicate their genome during the period of optimal U(VI) removal. Gene transcript levels during “Big Rusty” were quantified for Geobacter -specific citrate synthase ( gltA ), with ongoing transcription during sulfate reduction indicating that members of the Geobacteraceae were still active and likely contributing to U(VI) removal. The persistence of reducible Fe(III) in sediments recovered from an area of prolonged (110-day) sulfate reduction is consistent with this conclusion. These results indicate that acetate availability and its ability to sustain the activity of iron- and uranyl-respiring Geobacter strains during sulfate reduction exerts a primary control on optimized U(VI) removal from groundwater at the Rifle IFRC site over extended time scales (>50 days).

Geomicrobiology Journal↗
USGS2011

Patterns of hybridization of nonnative cutthroat trout and hatchery rainbow trout with native redband trout in the Boise River, Idaho

Hybridization is one of the greatest threats to native fishes. Threats from hybridization are particularly important for native trout species as stocking of nonnative trout has been widespread within the ranges of native species, thus increasing the potential for hybridization. While many studies have documented hybridization between native cutthroat trout Oncorhynchus clarkii and nonnative rainbow trout O. mykiss , fewer have focused on this issue in native rainbow trout despite widespread threats from introductions of both nonnative cutthroat trout and hatchery rainbow trout. Here, we describe the current genetic (i.e., hybridization) status of native redband trout O. mykiss gairdneri populations in the upper Boise River, Idaho. Interspecific hybridization was widespread (detected at 14 of the 41 sampled locations), but high levels of hybridization between nonnative cutthroat trout and redband trout were detected in only a few streams. Intraspecific hybridization was considerably more widespread (almost 40% of sampled locations), and several local populations of native redband trout have been almost completely replaced with hatchery coastal rainbow trout O. mykiss irideus ; other populations exist as hybrid swarms, some are in the process of being actively invaded, and some are maintaining genetic characteristics of native populations. The persistence of some redband trout populations with high genetic integrity provides some opportunity to conserve native genomes, but our findings also highlight the complex decisions facing managers today. Effective management strategies in this system may include analysis of the specific attributes of each site and population to evaluate the relative risks posed by isolation versus maintaining connectivity, identifying potential sites for control or eradication of nonnative trout, and long-term monitoring of the genetic integrity of remaining redband trout populations to track changes in their status.

Idaho↗
USGS2006

Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilities

Antibiotics are used at therapeutic levels to treat disease; at slightly lower levels as prophylactics; and at low, subtherapeutic levels for growth promotion and improvement of feed efficiency. Over 88% of swine producers in the United States gave antimicrobials to grower/finisher pigs in feed as a growth promoter in 2000. It is estimated that ca . 75% of antibiotics are not absorbed by animals and are excreted in urine and feces. The extensive use of antibiotics in swine production has resulted in antibiotic resistance in many intestinal bacteria, which are also excreted in swine feces, resulting in dissemination of resistance genes into the environment. To assess the impact of manure management on groundwater quality, groundwater samples have been collected near two swine confinement facilities that use lagoons for manure storage and treatment. Several key contaminant indicators-including inorganic ions, antibiotics, and antibiotic resistance genes-were analyzed in groundwater collected from the monitoring wells. Chloride, ammonium, potassium, and sodium were predominant inorganic constituents in the manure samples and served as indicators of groundwater contamination. Based on these analyses, shallow groundwater has been impacted by lagoon seepage at both sites. Liquid chromatography-mass spectroscopy (LC-MS) was used to measure the dissolved concentrations of tetracycline, chlortetracycline, and oxytetracycline in groundwater and manure. Although tetracyclines were regularly used at both facilities, they were infrequently detected in manure samples and then at relatively trace concentrations. Concentrations of all tetracyclines and their breakdown products in the groundwater sampled were generally less than 0.5 ??g/L.</ p> Bacterial tetracycline resistance genes served as distinct genotypic markers to indicate the dissemination and mobility of antibiotic resistance genes that originated from the lagoons. Applying PCR to genomic DNA extracted from the lagoon and groundwater samples, four commonly occurring tetracycline (tet) resistance genes-tet(M), tet(O), tet(Q), and tet(W)-were detected. The detection frequency of tet genes was much higher in wells located closer to and down-gradient from the lagoons than in wells more distant from the lagoons. These results suggested that in the groundwater underlying both facilities tetracycline resistance genes exist and are somewhat persistent, but that the distribution and potentially the flux for each tet gene varied throughout the study period.

Animal Biotechnology↗