Geology topics

Katy E. Klymus

Publications and source records attributed to Katy E. Klymus.

At least 19 recordsLinked to original sources

USGS2026

Best practice guidelines for targeted environmental DNA-based proficiency testing in non-regulatory contexts

The effective use of environmental DNA (eDNA) tools is contingent on strict adherence to established and validated methods. Differences in eDNA methods and quality assurance protocols may contribute to variability in results. However, quality assurance measures such as proficiency testing can provide independent evaluation of laboratory performance against pre-established test criteria. With this commentary, we discuss how broad implementation of recurring proficiency testing in eDNA laboratories can build decision-maker confidence in eDNA results. It can also create a culture of continuous evaluation and improvement that minimizes error and meets performance requirements to inform the sustainable use or monitoring of natural resources. We provide an overview of proficiency testing across molecular disciplines, review the state of proficiency testing in eDNA applications, and draft a roadmap for the expanded application of proficiency testing informed by best practices for targeted eDNA detection. We suggest that best practice proficiency testing can be conducted by an independent, third-party sample provider. By demonstrating that laboratories are competent and capable of producing reliable results, implementation of proficiency testing best practices should foster confidence in eDNA measurements and its use in decision-making processes. Increased confidence in eDNA methods and a clear expectation of what is considered satisfactory performance are also likely to create more favorable conditions for investments in eDNA-based monitoring.

Environmental DNA↗

USGS2025

Spatial distribution and relative biomass of bigheaded carps in Lake Balaton, Hungary estimated from an environmental DNA survey

Silver carp ( Hypophthalmichthys nobilis ), bighead carp ( H. molitrix ) and their hybrids, collectively known as bigheaded carps, have been introduced to Lake Balaton, Hungary. The current stock sizes are difficult to assess. We investigated environmental DNA (eDNA) techniques targeted for bigheaded carps, assessed the spatial distribution of eDNA in Lake Balaton, compared eDNA concentrations to environmental variables to assess potential habitat selection based on those variables, and provided an estimate of biomass of bigheaded carps relative to eDNA shedding rates per unit biomass observed in controlled experiments. Water samples were collected from 70 sites in an array across the lake. Biomass estimation was calculated using mean eDNA concentration obtained by quantitative PCR of the samples and previously determined eDNA shedding rates of bigheaded carps under controlled conditions in a laboratory. Concentration of eDNA was highly variable between sites, resulting in wide confidence intervals. Basins did not significantly differ in eDNA concentration, and there were no strong relationships between environmental variables and eDNA concentration, indications that bigheaded carps use the entire lake. The model provided an estimate of 4,830 metric tonnes (2,750–8,030 tonnes) of bigheaded carps in Lake Balaton, or 81.0 kg/ha. The eDNA method produced a value close to previous estimates by traditional means of total biomass of bigheaded carps in the lake, and like traditional methods, there was a broad confidence interval on the estimate of the mean. The results of the present study support the utility of aquatic eDNA analysis, and the need for further comparisons with fisheries methods and supporting data from laboratory studies.

Lake Balaton↗

USGS2025

A metadata checklist and data formatting guidelines to make eDNA FAIR (Findable, Accessible, Interoperable and Reusable)

The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding-based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data-driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA-specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready-to-use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user-driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long-term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.

Environmental DNA↗

USGS2025

The complete mitochondrial genomes of the freshwater mussel Ortmanniana ligamentina (Lamarck, 1819): male and female mitotypes

Freshwater mussels of the Unionida order are important to freshwater ecosystems but are highly imperiled worldwide. Improving our understanding of these species is crucial to their continued conservation. Some Unionid mussels exhibit double uniparental inheritance (DUI) in which individuals have two mitochondrial genomes. Of those species with DUI, sequences of the female mitotype are most prevalent in genetic databases. Here, we demonstrate the ability to recover both mitotypes of Ortmanniana ligamentina (Lamarck, 1819) from a non-lethal collection method coupled with high-throughput sequencing. Increased male mitotype sequence representation facilitates understanding Unionid genetic diversity and development of molecular tools for species detection.

Missouri, Pennsylvania↗

USGS2025

What is eDNA method standardization and why do we need it?

The rapid advancement of environmental DNA ( eDNA ) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.

Metabarcoding and Metagenomics↗

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2024

Field trials of an autonomous eDNA sampler in lotic waters

Environmental DNA (eDNA) analysis has become a transformative technology, but sample collection methods lack standardization and sampling at effective frequencies requires considerable field effort. Autonomous eDNA samplers that can sample water at high frequencies offer potential solutions to these problems. We present results from four case studies using a prototype autonomous eDNA sampler as part of the U.S. Geological Survey’s Rapid Environmental eDNA Assessment and Deployment Initiative & Network (READI-Net) project. These case studies involved short-term deployments of an eDNA autosampler (Smith-Root) across a range of riverine habitats with the objectives of (a) identifying what insights could be gained from high-frequency autosampling and (b) benchmarking these autosamples against manually collected samples. The high frequency autosampling revealed high temporal variability of eDNA concentrations and provided valuable insights about eDNA associations with environmental covariates, such as discharge and turbidity. Benchmarking assessments indicated autosamples had similar detection rates to manual samples and obtained similar or greater eDNA quantities. We did find minimal carryover contamination in autosampler field controls. We conclude that eDNA autosamplers have potential to improve freshwater biosurveillance by reducing logistical sampling barriers, standardizing collection methods, and clarifying the influence of environmental covariates on eDNA results.

Idaho, Missouri, Montana, New York↗

USGS2024

Detection and transport of environmental DNA from two federally endangered mussels

Environmental DNA (eDNA) offers a novel approach to supplement traditional surveys and provide increased spatial and temporal information on species detection, and it can be especially beneficial for detecting at risk or threatened species with minimal impact on the target species. The transport of eDNA in lotic environments is an important component in providing more informed descriptions of where and when a species is present, but eDNA transport phenomena are not well understood. In this study, we used species-specific assays to detect eDNA from two federally endangered mussels in two geographically distinct rivers. Using the eDNA concentrations measured from field samples, we developed a one-dimensional (1D) hydrodynamic transport model to predict the downstream fate and transport of eDNA. We detected eDNA from both federally endangered mussels across several seasons and flow rates and up to 3.5 km downstream from the source populations, but the detection rates and eDNA concentrations were highly variable across and within rivers and study reaches. Our 1D transport models successfully integrated the variability of the eDNA field samples into the model predictions and overall model results were generally within ±1 standard error of the eDNA field concentration values. Overall, the results of this study demonstrate the importance of optimizing the spatial locations from where eDNA is collected downstream from a source population, and it highlights the need to improve understanding on the shedding mechanisms and magnitude of eDNA from source populations and biogeomorphic processes that influence eDNA transport.

Missouri, Tennessee↗

USGS2024

Environmental DNA dynamics of three species of unionid freshwater mussels

North American freshwater mussels are of special conservation concern due to their high endemism and the multiple anthropogenic stressors affecting them. Of the over 300 species in North America, nearly one third of these species are federally listed as threatened or endangered. Environmental DNA (eDNA) analysis has been successful in detecting freshwater mussels and could aid in monitoring their populations. Production and degradation rates of eDNA for the species of interest are needed to inform interpretation of eDNA detections, allow possible modeling of relative abundance and population location, and aid in mussel conservation through population identification. Here, we designed and tested qPCR assays for three freshwater mussel species, mucket ( Ortmanniana ligamentina ), fatmucket ( Lampsilis siliquoidea ), and the federally endangered spectaclecase ( Cumberlandia monodonta ). We performed laboratory experiments under controlled conditions to measure eDNA shedding and degradation rates for each species. Different biomasses, temperatures, and food regimens were tested independently to determine if these factors influence the amount of DNA produced by the mussels. Degradation rates of eDNA were measured from experimental tank water after mussels were removed. Overall, we observed low eDNA shedding rates for freshwater mussels compared to previous studies of fish eDNA shedding rates. Furthermore, temperature and feeding showed limited or no significant effects in the species studied. Environmental DNA degradation rates were consistent with those reported in the literature for other taxa. Collectively, our results will be useful for designing eDNA monitoring studies, modeling eDNA dispersal, and interpreting eDNA results to help inform freshwater mussel conservation efforts.

Environmental DNA↗

USGS2024

Species richness and distribution of Sphaeriidae surveyed with Environmental DNA metabarcoding

Freshwater bivalves of the family Sphaeriidae (fingernail, pea, and pill clams) are difficult to survey and identify due to their small size and overlapping morphological traits. Environmental DNA (eDNA) metabarcoding offers a cost-effective method for assessing species richness and distributional patterns at large scales. We evaluated sphaeriid species richness and distribution at 15 sites in the Maumee River, Ohio, USA, based on two eDNA metabarcoding assays (broad and targeted), and we compared our results with those from a traditional benthic macroinvertebrate survey. We detected seven molecular operational taxonomic units (MOTUs) in the Maumee River, including Sphaerium transversum , five MOTUs representing Euglesa spp., and one MOTU representing Odhneripisidum sp. Sphaerium transversum was widely distributed, occurring at 10 sites, but Euglesa and Odhneripisidum were restricted to one to four sites in the upper river. Distributional patterns were broadly similar between both metabarcoding assays and benthic surveys. However, eDNA metabarcoding provided species-level identifications, resulting in higher species richness. Environmental DNA sampling augments and enhances traditional benthic surveys, but greater eDNA sample replication is needed to improve detection, and additional sphaeriid reference sequences are needed to improve species-level identification.

Freshwater Mollusk Biology and Conservation↗

USGS2023

Dead-end hollow fiber ultrafiltration capture of environmental DNA for freshwater mussel (Unionidae) species detection with metabarcoding

Insufficient water sample volumes can be a limiting factor for detecting species with environmental DNA (eDNA) from aquatic habitats. We compared detections of freshwater mussel (Unionidae) communities using large water sample volumes and dead-end hollow fiber ultrafiltration (D-HFUF or DEUF) with traditional eDNA filtration methods that use relatively small water sample volumes. Unionid species were detected in approximately 50-L D-HFUF eDNA samples with two mitochondrial DNA metabarcoding markers (COI and ND1) and compared to species detection results from eDNA captured from commonly used 1-L samples filtered with polyethersulfone (PES) filters at three lotic sites in Georgia and Missouri. Of the 431,560 COI and 1,035,472 ND1 reads from all environmental samples of both filter types that passed quality control, 95% (410,755 reads) of COI reads and 85% (883,472 reads) of ND1 reads were assigned to a unionid species. Nineteen different freshwater mussel species were detected across all D-HFUF samples, and 11 species were detected across all PES samples. Reads assigned to the genus Elliptio could not be resolved beyond the genus level with either marker. From D-HFUF samples, 15 and 16 mussel species were detected with the COI and ND1 markers, respectively. From PES samples, nine and seven species were detected with the COI and ND1 markers, respectively. More mussel species were detected at each site in D-HFUF samples than in PES samples regardless of whether results from both markers were combined or evaluated separately. Our results demonstrate the merit of further exploration and optimization of D-HFUF for capturing eDNA from high-volume water samples to facilitate detection of unionids and likely other aquatic organisms.

Environmental DNA↗

USGS2023

A nitrifier-enriched microbial community contributes to the degradation of environmental DNA

Environmental DNA (eDNA) surveys are a promising alternative to traditional monitoring of invasive species, rare species, and biodiversity. Detecting organism-specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with species abundance can be difficult due to the many abiotic and biotic factors that influence eDNA persistence and degradation. Here, we assessed the impact of a nitrifier-enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt eDNA using experimental aquatic mesocosms and a quantitative PCR approach. The NEM community was cultured from combined sediment and water samples collected from a golf course pond in Columbia, Missouri (USA), and experiments were conducted in the dark at 22°C. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, both in the presence and absence of ammonia nitrogen. Additionally, regardless of ammonia availability, milt eDNA followed a one-phase exponential decay pattern after an initial 24-h plateau in the presence of the NEM community. However, milt eDNA had a shorter half-life (12.5 h) in the absence of exogenous ammonia compared to when ammonia was present (15 h). In sterile mesocosms, eDNA was stable during the 72-h experiment. Together, these results suggest that the presence of microorganisms is necessary for short-term degradation of eDNA. Furthermore, nitrifying microbial communities, which are ubiquitous in most soil and water environments, could limit eDNA persistence in the environment. Understanding the contributions of environmental microbial communities will allow more confidence in sampling design and eDNA result interpretations for biodiversity management applications.

Environmental DNA↗

USGS2023

The Government eDNA Working Group 6th Annual eDNA Technical Exchange Workshop

The 6th annual Environmental DNA (eDNA) Technical Exchange Workshop was a virtual workshop hosted and coordinated by the Government eDNA Working Group (GEDWG) on January 24–26, 2023. GEDWG is a no-cost consortium that focuses on bringing together stakeholders associated with federal, state, provincial, municipal, and other government and non-government agencies interested in eDNA and related fields, for the purposes of sharing technical expertise and experience during monthly discussion meetings and annual workshops. Over 400 participants registered for the virtual Workshop, which featured four keynote speakers, 23 platform talks, eight short-form poster presentations, and an extended discussion session. Workshop attendees represented a broad cross-section of disciplines and backgrounds, including research scientists, natural resource managers, and conservation policy experts, and many different government agencies, private environmental consulting firms, trade organizations, non-governmental organizations, and others in the environmental management sector. Key takeaways from the workshop included moving the application of eDNA into resource management and discovering ways to improve policy uptake in the development of nationwide biodiversity monitoring, some of which is happening in the development of eDNA networks and national strategies. Future research directions discussed include studies of fate and transport, autonomous sampling/sample processing, and reference library curation. Additionally, co-design of studies and improved engagement and communication among scientists and managers are needed to ensure clear expectations and outcomes.

Environmental DNA↗

USGS2023

Toward invasive mussel genetic biocontrol: Approaches, challenges, and perspectives

Invasive freshwater mussels, such as the zebra ( Dreissena polymorpha ), quagga ( Dreissena rostriformis bugensis ), and golden ( Limnoperna fortunei ) mussel have spread outside their native ranges throughout many regions of the North American, South American, and European continents in recent decades, damaging infrastructure and the environment. This review describes ongoing efforts by multiple groups to develop genetic biocontrol methods for invasive mussels. First, we provide an overview of genetic biocontrol strategies that have been applied in other invasive or pest species. Next, we summarize physical and chemical methods that are currently in use for invasive mussel control. We then describe the multidisciplinary approaches our groups are employing to develop genetic biocontrol tools for invasive mussels. Finally, we discuss the challenges and limitations of applying genetic biocontrol tools to invasive mussels. Collectively, we aim to openly share information and combine expertise to develop practical tools to enable the management of invasive freshwater mussels.

iScience↗

USGS2022

Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas

Background The fathead minnow ( Pimephales promelas ) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation. Methods Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950. Results We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow ( P. notatus ) as sister to fathead minnow, with the slim minnow ( P. tenellus ) and bullhead minnow ( P. vigilax ) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (F ST ) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.

PeerJ↗

USGS2022

A comparison of eDNA and visual survey methods for detection of longnose darter Percina nasuta in Missouri

The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA further upstream in the mainstem St. Francis River than previously reported and in a tributary for the first time. Our multi-scale occupancy approach compared models where detection was constant against a model that allowed detection to vary by survey method. The constant model received the most support indicating survey method was not a strong predictor and detection was estimated at 0.70 (0.45–0.86; 95% CI) across both methods. Our study produced effective longnose darter eDNA primers and demonstrated the application of eDNA for sampling small-bodied, cryptic fish. We detected longnose darter eDNA 27 km upstream of their known range and determined that snorkel surveys are the most efficient sampling method if water clarity allows. We recommend target sample sizes to achieve various detection goals for both sample methods and our results inform future design of distributional and monitoring efforts.

Missouri↗

USGS2022

Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database

To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for the verification of eDNA data by working closely with AIS eDNA community practitioners and natural resource managers across government, private and academic sectors. To better inform management decisions, verified AIS eDNA data will be displayed on a separate mapping layer alongside visual sighting data with the inclusion of additional information on the eDNA methods employed to collect and produce the data. To allow for eDNA data display, we produced consensus derived online documents including a submission application and data submission template and are developing a guidance document for detailing the eDNA data submission process. We also developed a communication plan including a mechanism for reporting detections to appropriate managers for consideration prior to display. The products of these efforts are an application and data submission process that will be used in the new environmental DNA data layer on the Nonindigenous Aquatic Species (NAS) database. Herein, we detail how we engaged the eDNA community for consensus of our standards, share lessons learned from the process, and describe the benefits of such an approach at instilling confidence among the research and decision-maker community.

Management of Biological Invasions↗

USGS2021

Editorial: Environmental DNA innovations for conservation

Environmental DNA (eDNA) analysis refers to the collection of bulk environmental samples such as water, sediment, or air, and studying the genetic remnants that organisms have shed into their environment to gain information about species presence.

Frontiers in Ecology and Evolution↗