Geology topics

Christopher M. Merkes

Publications and source records attributed to Christopher M. Merkes.

At least 19 recordsLinked to original sources

USGS2026

Detection of Naegleria fowleri in thermally impacted recreational waters of western United States national parks

Naegleria fowleri is a thermophilic free-living amoeba (FLA) and the causative agent of primary amoebic meningoencephalitis, posing public health risks in warm freshwater environments. This multiyear, multiagency study surveyed 40 thermally impacted recreational waters across five western United States national parks and recreation areas–Yellowstone National Park, Grand Teton National Park, Olympic National Park, Newberry National Volcanic Monument, and Lake Mead National Recreation Area–to assess N. fowleri presence, concentration, and associated environmental conditions. A total of 185 water samples were analyzed by qPCR and Sanger sequencing, revealing widespread detection of N. fowleri in 34% of samples with positive detections from Lake Mead, Yellowstone, and Grand Teton hot springs and thermally impacted waters, with concentrations ranging from 4.9 to 115.7 cells/L. Multiple codetections of N. fowleri with nonpathogenic species including Naegleria australiensis were identified, suggesting they may inhabit similar ecological niches in the natural systems in contrast to engineered systems. These findings indicate that N. fowleri is present in thermally impacted areas across the western United States and underscore the use of enhanced monitoring, public awareness, and risk management strategies in thermally influenced recreational waters.

Arizona, Nevada, Oregon, Washington, Wyoming↗

USGS2025

Evaluation of rapid DNA extraction methods to better enable point-of-use environmental DNA detection

Recent developments in molecular testing have created the opportunity for biologists and managers to detect environmental DNA (eDNA) of target species rapidly and without the requirement of a laboratory. These point-of-use protocols may be especially useful for early detection and rapid response for invasive species or surveillance for at-risk native species, where timely management decisions are critical. Point-of-use eDNA protocols also facilitate wider and less expensive implementation of eDNA methods. One of the key components to an effective point-of-use protocol is a rapid DNA extraction method. Several rapid extraction protocols are suitable for implementation in the field, but information regarding their relative effectiveness is lacking. We evaluated extraction efficiency of four DNA rapid extraction protocols using filters spiked with primary cultured grass carp ( Ctenopharyngodon idella ) gill cells. The extraction methods included two syringe-based column extractions, a lysis and extraction solution, and a divalent cation chelation resin (Chelex) extraction protocol alongside a laboratory-based control kit. We estimated DNA yield using a newly designed quantitative polymerase chain reaction (qPCR) assay targeting the grass carp nuclear genome. We evaluated two additional factors, filter type (mixed cellulose ester [MCE] and polyethersulfone [PES]) and background eDNA source (aquaculture or river). The lysis and extraction solution and Chelex extraction both had the highest overall yield, with MCE filters further increasing Chelex yield while the enzyme extraction yield was dependent on interaction with both filter and eDNA source. Our results indicate that rapid extraction protocols, such as solutions with short heating steps, are effective for DNA isolation and help to increase the overall accessibility of eDNA analyses.

Environmental DNA↗

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

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

Summary of data collected during field efficacy trials of florfenicol and oxytetracycline dihydrate in controlling mortality in walleye (Sander vitreus) because of motile Aeromonad infections

Motile Aeromonad septicemia is a substantial concern during fish propagation and can be catastrophic for fish hatcheries. We tested the efficacy of two different drugs (florfenicol and oxytetracycline) offered with feed as possible treatment options to control mortality because of motile Aeromonad infection. We offered top-coated medicated feeds to hatchery-reared Sander vitreus (walleye) that were naturally infected with motile Aeromonad infection during two separate trials in 2011 and 2012. Substantial walleye mortality occurred before positive clinical outcomes from the medicated feed treatments were observed, and additional treatment measures were taken by hatchery staff to mitigate further mortality in their walleye production tanks. This report summarizes the data that were collected during medicated feed trials. Statistical inferences on treatment efficacy are not included because of the confounding treatments and possible secondary pathogens present throughout this study.

Open-File Report↗

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↗

USGS2023

When are environmental DNA early detections of invasive species actionable?

Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriate response actions to hypothetical eDNA early detections of an introduced aquatic plant in Sebago Lake (Maine, USA). The results were juxtaposed to a recent study that used a similar SDM approach to evaluate response actions to hypothetical eDNA early detections of introduced mussels in Jordanelle Reservoir (Utah, USA). We found that eDNA early detections were not actionable in Sebago Lake because the plant's invasion potential was spatially constrained and the current management activities provided acceptable levels of mitigation. In Jordanelle Reservoir, eDNA detections were actionable due to high invasion potential and analyses supported management actions to contain the invasion. The divergent outcomes of the two case studies are related to the unique attributes of the habitats and species, highlighting the utility of the SDM approach when considering an eDNA monitoring program. We use these two case studies to present a general SDM framework and a set of heuristics that can be efficiently applied to eDNA early detection rapid response scenarios and other instances associated with indeterminant eDNA detections, especially when there is an imperative to make decisions as quickly as possible.

Maine↗

USGS2022

Validation of a portable eDNA detection kit for invasive carps

Loop-mediated isothermal amplification (LAMP) is a rapid molecular detection technique that has been used as a diagnostic tool for detecting human and animal pathogens for over 20 years and is promising for detecting environmental DNA shed by invasive species. We designed a LAMP assay to detect the invasive carps, silver carp ( Hypophthalmichthys molitrix ), bighead carp ( Hypophthalmichthys nobilis ), black carp ( Mylopharyngodon piceus ), and grass carp ( Ctenopharyngodon idella ). To determine the sensitivity of the LAMP assay, we determined limit of detection (LOD) for each invasive carp species and compared with the performance of a grass carp quantitative PCR (qPCR) assay in LOD and in a mesocosm study. We used two grass carp densities, 3 juvenile grass carp in one mesocosm and 33 juvenile grass carp in the other. Prior to adding grass carp to the mesocosms, we added 68 kg of fathead minnows ( Pimephales promelas ) to each mesocosm to simulate farm ponds used for raising bait fish. We filtered 500 mL of water per sample to compare LAMP and qPCR analysis, and we collected 50 mL grab samples that were only analyzed using qPCR to gain additional data using a higher-throughput method to monitor environmental DNA (eDNA) levels throughout the study period. No eDNA for any of the four invasive carp species was detected in water collected from the mesocosms during the three days prior to adding grass carp. Forty-eight hours after grass carp addition to mesocosms, we detected grass carp eDNA in the mesocosm containing 33 grass carp using the LAMP assay. However, we failed to detect any grass carp DNA in the mesocosm containing 3 grass carp with the LAMP assay throughout the study. We analyzed the data using an occupancy model and found that the 500 mL filter samples yielded a higher eDNA capture probability than 50 mL grab samples in the mesocosm containing three grass carp but had similar eDNA capture probability in the mesocosm containing 33 grass carp. Both LAMP and qPCR reliably detected grass carp eDNA 2 days after grass carp addition, but detections were more consistent with qPCR. The LAMP assay may have utility for certain niche uses because it can be used to rapidly analyze eDNA samples and is robust to inhibition, despite having some limitations.

Fishes↗

USGS2022

Using structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA

Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when individuals of that species are not present at the site or a widespread infestation is not imminent. Acting on an erroneous eDNA inference could result in needless costs or reductions in desirable resources. Alternatively, failure to rapidly act on eDNA results that truly indicate invader presence could compound negative impacts and lead to high, long-term costs to manage infestations. We used a structured decision making (SDM) process, which incorporates tradeoffs and uncertainties, to evaluate appropriate response actions following hypothetical eDNA detections of invasive dreissenid mussel ( Dreissena spp.) eDNA in Jordanelle Reservoir, Utah (USA). We worked with decision-makers and stakeholders to identify objectives and discrete management action alternatives to assess consequences and tradeoffs. Alternatives ranged from no action to intensive and expensive control efforts. The best performing alternative was delayed containment described by immediate attempts to confirm the eDNA detections using non-molecular sampling techniques followed by mandatory watercraft exit inspections to prevent dreissenid mussel spread to regional water bodies. Non-molecular sampling increased public support for management by demonstrating a commitment to monitor the invasion state before action, whereas containment decreased likelihood of regional spread to other waters. Delayed containment had the lowest downside risk, and the highest upside gains relative to other alternative actions. Sensitivity analyses showed our results to be robust to parameter and outcome uncertainty.

Management of Biological Invasions↗

USGS2021

Assessment of sea lamprey (Petromyzon marinus) diet using DNA metabarcoding of feces

Sea lamprey ( Petromyzon marinus ) are invasive in the Laurentian Great Lakes, parasitize large-bodied fishes, and therefore are the focus of an international control program. However, damage caused by sea lamprey to modern day fish stocks remains uncertain because diet analysis of juvenile sea lamprey has been challenging; they feed on blood and are difficult to randomly sample in the lakes. Here, both challenges were addressed by showing that DNA metabarcoding of fecal material can be used to identify the diet of actively feeding juvenile sea lamprey, and can also be used to determine what non-feeding adult sea lamprey captured in streams fed on while parasitizing fish. Fecal samples from juvenile sea lamprey that were feeding on lake trout in northern Lake Huron overwhelmingly contained lake trout ( Salvelinus namaycush ) DNA (90%), while smaller percentages contained lake whitefish ( Coregonus clupeaformis ; 5%) and longnose sucker ( Catostomus catostomus ; 5%) DNA. Fecal samples from adult sea lamprey captured from a tributary to northern Lake Huron overwhelmingly contained longnose and white sucker DNA ( Catostomus spp.; 80%), while a smaller percentage contained lake trout DNA (10%). Diet composition of adult sea lamprey sampled in the tributary (Black Mallard Creek) was more diverse than juvenile diet composition. DNA metabarcoding suggests that Catostomus spp. may be an important host fish in northern Lake Huron for sea lamprey prior to spawning. Future research could investigate how diet varies across years and lakes and the prevalence and sources of DNA contamination. Application of DNA metabarcoding for diet assessment may be practical for identifying populations of invasive sea lamprey that feed on highly valued fishes and help guide restoration of lampreys worldwide.

Michigan↗

USGS2020

Robotic environmental DNA bio-surveillance of freshwater health

Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated with traditional sampling since it can automate water sample filtration and preservation of the captured material or homogenize it for immediate analyses in situ. The ESP was originally developed for marine environment applications. Here we evaluated whether the ESP can provide reliable, timely information on environmental (e)DNA detections of human and fish pathogens and introduced fishes at U.S. Geological Survey streamgage sites in freshwater rivers. We compared eDNA collected via ESP at high frequency (e.g., every 3 h) with manual eDNA collections collected at lower frequency (e.g., weekly). We found that water samples filtered and preserved by ESPs successfully detected the DNA of human pathogens, fish pathogens and introduced fishes. Both ESP and manually collected samples provided similar information about target DNA presence. We suggest that the greatest current benefit of the ESP is the cost savings of high frequency, bio-surveillance at remote or hard to access sites. The full potential of robotic technologies like the ESP will be realized when they can more easily execute in situ analyses of water samples and rapidly transmit results to decision-makers.

Idaho, Montana, Wyoming↗

USGS2020

Using environmental DNA (eDNA) to detect the endangered Spectaclecase Mussel ( Margaritifera monodonta )

Margaritifera monodonta , or the Spectaclecase Mussel, is a federally endangered freshwater mussel species that has experienced a 55% reduction in range and is currently concentrated in 3 rivers in the Midwest region of the United States (Gasconade and Meramec rivers, Missouri, and St Croix River, Wisconsin). The detection of new populations by traditional survey methods has been limited because these mussels tend to occur under large rocks and boulders. Environmental DNA (eDNA) technology has been used to detect invasive and rare species, but its use for detection of rare, benthic-dwelling species in large flowing systems has been limited. Here, we propose using eDNA to assess known populations of M. monodonta . We designed a M. monodonta -specific quantitative polymerase chain reaction (qPCR) assay and tested it using water samples from multiple M. monodonta housing tanks, water samples from 2 known mussel beds on the St Croix River, and water samples from 3 known mussel beds on the Mississippi River. We observed higher overall eDNA detection rates on the St Croix River (30.2%) compared to the upper Mississippi River (0.60%). We also observed higher eDNA detection rates (73.3–93.1%) in 2018 for samples collected during the larval release period in May compared to samples collected in August after the reproductive period had ended (55.6–70.8%) on the St Croix River. We tested samples collected at 3 distances downstream from the 2 mussel beds found in the St Croix River, but we did not observe a substantial effect of distance on our detection rates. However, we did observe greater detection rates for samples collected near the bottom compared to at the surface. Our results indicate that this novel qPCR assay can successfully detect M. monodonta eDNA and could be used to rapidly screen locations to guide intensive physical searches for populations in riverine systems.

Wisconsin, Missouri↗

USGS2019

Reporting the limits of detection and quantification for environmental DNA assays

Background Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.

Environmental DNA↗

USGS2019

Refinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations

Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertainties created by imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR). Occurrence models can be used to address these challenges, thus we use an occurrence model to address two objectives: First, determine how many samples were required to detect species using eDNA; Second, examine when and where to take samples. We collected water samples from three different habitat types in the Upper Mississippi River when both Bighead Carp and Silver Carp were known to be present based on telemetry detections. Each habitat type (backwater, tributary, and impoundment) was sampled during April, May and November. Detections of eDNA for both species varied across sites and months, but were generally low, 0 - 19.3% of samples were positive for eDNA. Overall, we found that eDNA-based sampling holds promise to be a powerful monitoring tool for resource managers, however, limitations of eDNA-based sampling include different biological and ecological characteristics of target species such as seasonal habitat usage patterns as well as aspects of different physical environments that impact the implementation of these methods such as water temperature.

Ecological Applications↗

USGS2019

Sampling designs for landscape-level eDNA monitoring programs using three-level occurrence models

Resource managers conduct landscape-level monitoring using environmental DNA (eDNA). These managers must contend with imperfect detection in samples and sub-samples (i.e., molecular analyses). This imperfect detection impacts their ability to both detect species and estimate occurrence. Although occurrence (synonymously occupancy) models can estimate these probabilities, most models and guidance for their application do not consider three levels. We studied this with three aims. First, we examined the number of samples required to detect a species at a site given imperfect detection. Second, we examined the ability of a three-level occurrence model to recover parameter estimates. Third, we examined the number of samples required to reliably recover parameter estimates. We found detecting eDNA in 1 sample at a site required 12 samples under most condition, but detection eDNA in situations that might be expected when looking for species at very low abundance required >50 samples. We found our occupancy model generally recovered known parameters unless detection and sample occurrence probabilities were <0.3. In these situations, >50 samples per site and 8 molecular replicates were required. Conversely, estimating and comparing occurrence and detection probabilities for species with moderate to high abundance may require 4 molecular replicates and 20-30 samples per site. More broadly, our findings illustrate the importance of study design, sample sizes, and molecular replicates for eDNA-based research, monitoring, and management.

Integrated Environmental Assessment and Management↗

USGS2019

Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes

Zebra mussels ( Dreissena polymorpha ) are an aquatic invasive species that plague much of North America and are difficult to impossible to eradicate once they become established. Therefore, prevention and monitoring are key elements in the control of these organisms. Traditional microscopy is commonly used in monitoring but requires the presence of larval veligers. This limits the times when resource managers can monitor for the presence in northern lakes. A new monitoring tool, environmental DNA (eDNA), may allow for a more efficient and cost-effective monitoring program for zebra mussels. We developed and tested an environmental DNA assay in the fall and spring for zebra mussels in two Minnesota lakes, one heavily infested and another newly infested. We found that DNA copy numbers tended to be higher near the lake bottom and DNA was more concentrated in softer substrates. We also found that the amount of zebra mussel DNA sampling in winter resulted in similar results to when sampled in fall. This suggests that one could collect and analyze eDNA for zebra mussels during winter months to help inform future efforts in monitoring and control.

Minnesota↗

USGS2018

Development of a quantitative PCR method for screening ichthyoplankton samples for bigheaded carps

Monitoring ichthyoplankton is useful for identifying reproductive fronts and spawning locations of bigheaded carps (Hypophthalmichthys spp.). Unfortunately, sorting and identifying ichthyoplankton to monitor for bigheaded carp reproduction is time consuming and expensive. Traditional methods require frequent egg-larvae sampling, sorting of all samples to obtain presumptively identified bigheaded carp, and genetic validation of presumptively identified eggs. Quantitative PCR (qPCR) has the potential to streamline this process by identifying samples that likely do or do not contain a target species. Our objective was to develop a genetic screening tool using qPCR with the duplex assays SCTM4/5 and BHTM1/2 to prioritize samples that have a higher likelihood of containing bigheaded carp eggs or larvae. We used tandem ichthyoplankton samples collected for monitoring bigheaded carps in the Upper Mississippi, Illinois, and St. Croix rivers to evaluate the effectiveness of qPCR as a screening tool. Samples with > 10,000 copies of DNA had 100% occurrence of bigheaded carp eggs or larvae in the traditionally sorted samples, whereas samples with < 10 copies of DNA had 0% occurrence of ichthyoplankton from these invasive species. We used a logistic regression model to calculate the probability of finding bigheaded carp eggs or larvae based upon the number of DNA copies; 406 copies corresponded with a 50% probability of having bigheaded carp ichthyoplankton present in a sample. These data can be used to inform management actions (i.e., control, containment) for these invasive fishes, and this tool could be adapted for monitoring for reproduction of other aquatic invasive species.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2018

Assessment of carbon dioxide piscicide treatments

Few chemicals are approved to control or eradicate nuisance fish populations in the United States. Carbon dioxide (CO 2 ) is currently being developed and studied as a new piscicide option for nonselective population control. This study evaluated dry ice (solid state CO 2 ) as a simple CO 2 delivery method during winter piscicide applications. Nonnative Silver Carp Hypophthalmichthys molitrix , Bighead Carp H. nobilis , and native Fathead Minnow Pimephales promelas were overwintered together in ice‐covered ponds treated with 25 kg dry ice/100,000 L (low treatment) or 50 kg dry ice/100,000 L (high treatment). Overwinter fish survival was significantly reduced in ponds treated with dry ice relative to untreated control ponds. Fathead Minnows were less susceptible to CO 2 exposure than the carps, with 26–96% survival in low‐treatment ponds and 4–68% survival in high‐treatment ponds. Silver Carp and Bighead Carp were more sensitive to CO 2 treatments and no individuals of either species survived in ponds with the high‐treatment level. Water samples were also collected in all ponds throughout this study, and we observed notably higher Silver Carp and Bighead Carp environmental DNA (eDNA) concentrations in dry‐ice‐treated ponds relative to untreated control ponds. Distinct changes in eDNA trends correlated with fish mortality, and results indicate that eDNA sampling could be a useful indicator of piscicide efficacy. This study demonstrates that CO 2 administered as dry ice is an effective under‐ice piscicide method.

North American Journal of Fisheries Management↗