Geology topics

Christopher M. Merkes

Publications and source records attributed to Christopher M. Merkes.

24 records · Page 2Linked to original sources

USGS2018

Correlating sea lamprey density with environmental DNA detections in the lab

Invasive sea lamprey (Petromyzon marinus Linnaeus, 1758) are currently managed by the Great Lakes Fishery Commission in an effort to reduce pest populations below levels that cause ecological damage. One technique to improve stream population assessments could be molecular surveillance in the form of environmental DNA (eDNA) monitoring. We developed and validated four probe-based quantitative polymerase chain reaction (qPCR) assays, then used two probes (cytb, nd1) to determine whether eDNA concentration was correlated with adult and larval sea lamprey density in the lab. We found a strong positive correlation between adult sea lamprey densities of 2, 20, and 200 individuals/2000L and eDNA concentrations in tanks using both assays (cytb, nd1). For larval laboratory tank density trials, eDNA concentrations were generally near our limit of quantification and there was no significant difference in copy numbers detected between larval sea lamprey densities of 1, 5, and 25 individuals/28L. Therefore, we examined detection probability rather than concentration with laboratory tank densities. We observed a trend of increasing detection probabilities with increased larval sea lamprey density that approached significance suggesting that when DNA copy numbers are low, detection rates may be more informative in predicting varying densities of larval sea lamprey. The ability to assess sea lamprey densities from a water sample could be a powerful tool to improve traditional assessment and stream ranking techniques. Further refinement of this method in the field may make eDNA surveillance of sea lamprey a reliable part of stream assessments. Rapid eDNA analysis from many streams may help focus traditional assessment efforts, thereby improving the efficiency of invasive sea lamprey control efforts.

Management of Biological Invasions↗

USGS2017

Seasonal trends in eDNA detection and occupancy of bigheaded carps

Bigheaded carps, which include silver and bighead carp, are threatening to invade the Great Lakes. These species vary seasonally in distribution and abundance due to environmental conditions such as precipitation and temperature. Monitoring this seasonal movement is important for management to control the population size and spread of the species. We examined if environmental DNA (eDNA) approaches could detect seasonal changes of these species. To do this, we developed a novel genetic marker that was able to both detect and differentiate bighead and silver carp DNA. We used the marker, combined with a novel occupancy model, to study the occurrence of bigheaded carps at 3 sites on the Wabash River over the course of a year. We studied the Wabash River because of concerns that carps may be able to use the system to invade the Great Lakes via a now closed (ca. 2017) connection at Eagle Marsh between the Wabash River's watershed and the Great Lakes' watershed. We found seasonal trends in the probability of detection and occupancy that varied across sites. These findings demonstrate that eDNA methods can detect seasonal changes in bigheaded carps densities and suggest that the amount of eDNA present changes seasonally. The site that was farthest upstream and had the lowest carp densities exhibited the strongest seasonal trends for both detection probabilities and sample occupancy probabilities. Furthermore, other observations suggest that carps seasonally leave this site, and we were able to detect this with our eDNA approach.

Journal of Great Lakes Research↗

USGS2016

Detecting the movement and spawning activity of bigheaded carps with environmental DNA

Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp movement, hydrography, spawning and eDNA on the Wabash River, IN, USA. We found positive relationships between eDNA and movement and eDNA and hydrography. We did not find a relationship between eDNA and spawning activity in the form of drifting eggs. Our first finding demonstrates how eDNA may be used to monitor species abundance, whereas our second finding illustrates the need for additional research into eDNA methodologies. Current applications of eDNA are widespread, but the relatively new technology requires further refinement.

Molecular Ecology Resources↗

USGS2016

Environmental DNA mapping of Zebra Mussel populations

Environmental DNA (eDNA) has become a popular tool for detecting aquatic invasive species, but advancements have made it possible to potentially answer other questions like reproduction, movement, and abundance of the targeted organism. In this study we developed a Zebra Mussel (Dreissena polymorpha) eDNA protocol. We then determined if this assay could be used to help determine Zebra Mussel biomass in a lake with a well-established population of Zebra Mussels and a lake with an emerging population of mussels. Our eDNA assay detected DNA of Zebra Mussels but not DNA from more than 20 other species of fish and mussels, many commonly found in Minnesota waters. Our assay did not predict biomass. We did find that DNA from Zebra Mussels accumulated in softer substrates in both lakes, even though the mussels were predominately on the harder substrates. Therefore, we concluded that eDNA may be useful to detect the presence of Zebra Mussels in these lakes but our assay/approach could not predict biomass.

Report↗

USGS2015

Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites

The performance of newly developed New Zealand mudsnail ( Potamopyrgus antipodarum ; NZMS) genetic markers for environmental (eDNA) analysis of water were compared across two laboratories. The genetic markers were tested in four quantitative polymerase chain reaction assays targeting two regions of the NZMS mitochondrial genome, specifically the cytochrome c oxidase subunit 1 (coi) and cytochrome b (cytb) genes. In a blind study, analysts tested each sample eight times with each assay. There were 10 expected-negative samples from the Black River in La Crosse, Wisconsin, 10 expected-positive samples from the Black Earth Creek in Black Earth, Wisconsin, and 10 known-positive samples from the Black River spiked with NZMS DNA. Previously extracted samples, kept at the Upper Midwest Environmental Sciences Center, were pooled by sample location and then equal quantities were distributed between the Upper Midwest Environmental Sciences Center and the Molecular Conservation Genetics Laboratory at the University of Wisconsin-Stevens Point for analysis. The assays tested were (1) the assay targeting cytb with a minor groove binder probe described by Goldberg and others (2013), (2) the cytb assay with a modified double-quenched probe, (3) an assay targeting coi with a double-quenched probe, and (4) a duplex reaction combining the modified cytb assay and the coi assay. Samples were considered positive for the presence of NZMS DNA when quantitative polymerase chain reaction amplification and probe signal was higher than the normalized threshold value above baseline fluorescence. For the duplex assay, samples were considered positive only when both probe signals were higher than the normalized threshold value above baseline fluorescence. Positive results were then confirmed by sequencing the products. All four assays detected the DNA of NZMS in all expected-positive and known-positive samples in both labs. The modified cytb assay, the coi assay, and the duplex assay all failed to detect the DNA of NZMS in all expected-negative samples in both labs. The cytb assay, as described by Goldberg and others (2013), failed to detect the DNA of NZMS in all expected-negative samples for the Molecular Conservation Genetics Laboratory, but some reactions resulted in positive detection in late cycles for 9 of the 10 expected-negative samples at the Upper Midwest Environmental Sciences Center. Amplicons for expected-negative samples with positive reactions were sent for sequencing, and none were confirmed as NZMS. Six amplicons failed to give readable sequences, and three gave sequences without similarity to any known sequence in GenBank. Amplicons from each assay for one representative positive sample were sequenced and identified as NZMS with greater than 99 percent identity. The duplex assay was chosen as the most efficient assay and was used at the Upper Midwest Environmental Sciences Center to analyze triplicate samples from 29 streams in Wisconsin, 8 streams in Illinois, and 8 streams in Iowa. In order to verify results, additional triplicate samples were collected from two of the streams in Iowa and two of the streams in Wisconsin for analysis at the Molecular Conservation Genetics Laboratory. All samples at all sites were negative for NZMS DNA.

Illinois, Iowa, Wisconsin↗

USGS2014

Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data

The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp; Hypophthalmichthys molitrix and H. nobilis ) in the Chicago Area Waterway System and Upper Mississippi River. In both systems DNA has been detected from silver carp without the capture of a live fish, which has led to some uncertainty about the source of the DNA. The potential contribution to eDNA by vectors and fomites has not been explored. Because barges move from areas with a high abundance of bigheaded carps to areas monitored for the potential presence of silver carp, we used juvenile silver carp to simulate the barge transport of dead bigheaded carp carcasses, slime residue, and predator feces to determine the potential of these sources to supply DNA to uninhabited waters where it could be detected and misinterpreted as indicative of the presence of live bigheaded carp. Our results indicate that all three vectors are feasible sources of detectable eDNA for at least one month after their deposition. This suggests that current monitoring programs must consider alternative vectors of DNA in the environment and consider alternative strategies to minimize the detection of DNA not directly released from live bigheaded carps.

PLoS ONE↗