Geology topics

Nathan Thompson

Publications and source records attributed to Nathan Thompson.

12 recordsLinked to original sources

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↗

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

Silver Chub spawning confirmed in the Maumee River, a tributary of Lake Erie

Objective Biodiversity is declining due to invasive species and other factors that can affect individual species differently. Silver Chub Macrhybopsis storeriana are declining in their native range, and their conservation status in the Great Lakes ranges from secure to possibly extirpated. Lake Erie once supported a large Silver Chub population until it crashed in the 1950s. Additionally, the spawning behavior and reproductive guild of Silver Chub in Lake Erie is unknown. Our objective was to document Silver Chub spawning in the Maumee River, a Lake Erie tributary. Methods Invasive Grass Carp Ctenopharyngodon idella are known to spawn in the Maumee River during high-flow events from May to July, and the University of Toledo and U.S. Geological Survey regularly sample the lower 24 km for early life stages using paired bongo nets. Contents from paired bongo nets are returned to the laboratory for processing, and a subset of potential Grass Carp eggs are sent for genetic analysis. Result On June 8, 2022, several potential Grass Carp eggs were captured at two sites on the Maumee River during a high-flow event. Fifteen potential Grass Carp eggs were sent for genetic analysis, and DNA sequencing revealed that six of these eggs were Silver Chub. Discussion This was the first known collection of Silver Chub eggs in a Lake Erie tributary, and our findings indicate that Silver Chub likely belong to the pelagophil reproductive guild. Although Grass Carp and Silver Chub spawn under similar conditions, management actions to control Grass Carp in the Maumee River may be unlikely to affect Silver Chub due to electrofishing settings used in the capture of Grass Carp. The verification of Silver Chub spawning in a Western Erie Basin tributary provides insights into their reproductive biology that could be useful in recovery planning in Lake Erie and throughout the Great Lakes.

Ohio↗

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

First documentation of grass carp spawning in Lake Erie’s Central Basin

Grass carp ( Ctenopharyngodon idella ) are non-indigenous to North America having been translocated to the United States in the 1960s as a potential non-chemical solution for nuisance aquatic vegetation. Reproductively viable grass carp now exist in many watersheds in the United States. In the Great Lakes basin, grass carp were first discovered in the 1980s with direct confirmation of successful reproduction in 2015 via collection of fertilized grass carp eggs in the Sandusky River. Early life stage monitoring also confirmed reproduction in the Maumee River in 2017. During 2018–2021, no new spawning tributaries were discovered (18 total sampling events in five Great Lakes tributaries). In 2022, fourteen eggs with characteristics similar to grass carp were identified from the Huron River which is a tributary to Lake Erie’s Central Basin. Eggs were identified to species via DNA sequencing and were determined to be grass carp eggs. The confirmation of spawning in the Huron River represents a third spawning tributary in the Lake Erie basin and expands eastward the geographic extent of known grass carp spawning locations. Presently, the ability of the Huron River to support hatching and survival of larval grass carp is unknown. Discovery of the Huron River as a grass carp spawning tributary identifies the value of continued surveillance in Great Lakes tributaries for early life stages and conducting scientific inquiries evaluating the consistency of tributary use and survival of early life stages.

Ohio↗

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↗

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↗

USGS2020

Metabarcoding assays for the detection of freshwater mussels (Unionida) with environmental DNA

Freshwater mussels of the order Unionida are a widely distributed taxon that are important in maintaining freshwater ecosystems and are also highly imperiled throughout the world. Monitoring of mussel populations with environmental DNA (eDNA) is an attractive alternative to traditional methods because it is noninvasive and requires less labor and taxonomic knowledge from field personnel. We developed eDNA metabarcoding assays specific to freshwater mussels and tested them at six sites in the Clinch River, located in the southeastern United States. Our objective was to determine the utility of eDNA metabarcoding for future monitoring of mussel populations and restoration efforts in this watershed. Two metabarcoding assays that target the mitochondrial DNA regions of the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit (ND1) genes were developed and tested. Our assays appear to be order specific, amplifying members from the two families found in North America, Unionidae and Margaritiferidae, while not amplifying nontarget fish or other bivalve species. From the field collected samples, our assays together detected 19 species, eight of which are listed as federally endangered. The assays also detected 42%, 58%, and 54% of the species identified by recent quantitative visual mussel surveys at three sampling sites. Increased sampling effort by processing a greater water volume or number of samples will likely increase species detections. These eDNA metabarcoding assays may enable enhanced monitoring of freshwater mussel assemblages and subsequently inform conservation efforts.

Virginia↗

USGS2020

Development and testing of species-specific quantitative PCR assays for environmental DNA applications

New, non-invasive methods for detecting and monitoring species presence are being developed to aid in fisheries and wildlife conservation management. The use of environmental DNA (eDNA) samples for detecting macrobiota is one such group of methods that is rapidly becoming popular and being implemented in national management programs. Here we focus on the development of species-specific targeted assays for probe-based quantitative PCR (qPCR) applications. Using probe-based qPCR offers greater specificity than is possible with primers alone. Furthermore, the ability to quantify the amount of DNA in a sample can be useful in our understanding of the ecology of eDNA and the interpretation of eDNA detection patterns in the field. Careful consideration is needed in the development and testing of these assays to ensure the sensitivity and specificity of detecting the target species from an environmental sample. In this protocol we will delineate the steps needed to design and test probe-based assays for the detection of a target species; including creation of sequence databases, assay design, assay selection and optimization, testing assay performance, and field validation. Following these steps will help achieve an efficient, sensitive, and specific assay that can be used with confidence. We demonstrate this process with our assay designed for populations of the mucket ( Actinonaias ligamentina ), a freshwater mussel species found in the Clinch River, USA.

JOVE Journal Of Visualized Experiments↗

USGS2020

Use of environmental DNA to detect grass carp spawning events

The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in determining the presence of aquatic species. The objectives of this project were to assess the use of eDNA collections and quantitative eDNA analysis to assess the potential spawning of grass carp in five reservoir tributaries, and to compare those results to the more traditional method of ichthyoplankton tows. Grass carp eDNA was detected in 56% of sampling occasions and was detected in all five rivers. Concentrations of grass carp eDNA were orders of magnitude higher in June, corresponding to elevated discharge and egg presence. Grass carp environmental DNA flux (copies/h) was lower when no eggs were present and was higher when velocities and discharge increased and eggs were present. There was a positive relationship between grass carp eDNA flux and egg flux. Our results support the further development of eDNA analysis as a method to detect the spawning events of grass carp or other rheophilic spawners.

Fishes↗

USGS2017

Experimental observations on the decay of environmental DNA from bighead and silver carps

Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore decay of eDNA associated with bighead carp ( Hypophthalmichthys nobilis ) biological waste collected from an aquaculture filtration system and with sperm collected from captive silver carp ( H. molitrix ), and how decay may be influenced by differing levels of water turbulence, temperature, microbial load, and pH. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in a decay half-life as much as 5.5× more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5×. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25×, despite relatively little apparent increase in the overall microbial load. This pattern indicated that species constituency of the microbial community, in addition to microbial load, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6× reduction in eDNA halflife. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay condition and a slow decay condition, and tracked eDNA decay over 91 days, we observed a 5.0× greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1× and 3.3×, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate and, thus, the interpretation of eDNA survey results.

Management of Biological Invasions↗