Geology topics

Katy E. Klymus

Publications and source records attributed to Katy E. Klymus.

28 records · Page 2Linked to original sources

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↗

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↗

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↗

USGS2016

Critical considerations for the application of environmental DNA methods to detect aquatic species

Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

Methods in Ecology and Evolution↗

USGS2015

Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix

Wildlife managers can more easily mitigate the effects of invasive species if action takes place before a population becomes established. Such early detection requires sensitive survey tools that can detect low numbers of individuals. Due to their high sensitivity, environmental DNA (eDNA) surveys hold promise as an early detection method for aquatic invasive species. Quantification of eDNA amounts may also provide data on species abundance and timing of an organism’s presence, allowing managers to successfully combat the spread of ecologically damaging species. To better understand the link between eDNA and an organism’s presence, it is crucial to know how eDNA is shed into the environment. Our study used quantitative PCR (qPCR) and controlled laboratory experiments to measure the amount of eDNA that two species of invasive bigheaded carps ( Hypophthalmichthys nobilis and Hypophthalmichthys molitrix ) shed into the water. We first measured how much eDNA a single fish sheds and the variability of these measurements. Then, in a series of manipulative lab experiments, we studied how temperature, biomass (grams of fish), and diet affect the shedding rate of eDNA by these fish. We found that eDNA amounts exhibit a positive relationship with fish biomass, and that feeding could increase the amount of eDNA shed by ten-fold, whereas water temperature did not have an effect. Our results demonstrate that quantification of eDNA may be useful for predicting carp density, as well as densities of other rare or invasive species.

Biological Conservation↗

USGS2015

A reply to Iversen et al.'s comment “Monitoring of animal abundance by environmental DNA - An increasingly obscure perspective”

We appreciate the conversation put forward by Iversen et al. (2015) in their response to our article “Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix ” in the 2015 environmental DNA special issue of Biological Conservation. We agree with Iversen et al.'s concern about overly optimistic conclusions that could be drawn from the current eDNA literature. One hope for eDNA technology is that it can be used in estimating abundance or population density. Evidence suggests that eDNA measurements correlate with total biomass (Takahara et al., 2012) rather than abundance. We demonstrate a similar relationship between biomass and eDNA shedding rates. Nevertheless, without field testing of these methods and specific survey protocols, we cannot make strong conclusions regarding the technique's field applicability. In our manuscript, we attempted to point out areas in which more research is needed.

Biological Conservation↗

USGS2015

Environmental DNA calibration study interim technical review report December 2014

The Environmental DNA Calibration Study (ECALS) is a multi-year study to improve the understanding and interpretation of the detection of Asian carp DNA in environmental samples (eDNA) used in early detection monitoring. eDNA surveillance programs seek to detect the presence of genetic material (DNA in cells sloughed off in slime, feces, urine, etc.) extracted from water samples; the detection of genetic material is linked to the possible presence of Asian carp. The study involves collaboration between the U.S. Army Corps of Engineers, the U.S. Geological Survey, and the U.S. Fish and Wildlife Service. ECALS addresses three major Action Items from the Asian Carp Regional Coordinating Committee (ACRCC) Asian Carp Control Strategy Framework, of which results to date are presented below. Initial ECALS efforts focused on eDNA vectors whereas marker development and calibration experiments received greater attention in 2013.

Report↗

USGS2014

Environmental DNA calibration study. Interim technical review report

Invasive aquatic nuisance species pose a major threat to aquatic ecosystems worldwide. Invasive Asian carps, including bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) have been steadily dispersing upstream through the Mississippi, Illinois, and Des Plaines Rivers since the 1990s. To prevent further movement up the Illinois River into the Chicago Area Waterway System (CAWS, see Figures 1.1.1 to 1.1.3) and possibly Lake Michigan and the Great Lakes ecosystem, an electrical barrier has been operating near Lockport to deter the advance of Asian carp. Although one adult individual has been detected in Lockport pool of the Illinois Waterway, the leading edge of the invasion of bighead and silver carp is considered to be at RM 281.5 in Dresden Island Pool, 15 miles downstream from the barrier and 55 miles from Lake Michigan, and that front has not progressed upstream since 2006. Although spawning activity has been observed in Marseilles pool in 2012, verified capture of eggs and larvae remain downstream in Peoria pool, over 140 miles from Lake Michigan (Figure 1.1.1). Should a sustainable Asian carp population become established in the Great Lakes, native fish populations, as well as many threatened or endangered plant/animal species populations, could be impacted. In response to this threat, the Asian Carp Regional Control Committee (ACRCC) was formed in part to coordinate efforts to understand and organize against the Asian carp threat. The Asian Carp Control Strategy Framework (2012a) outlined major tasks to be completed for a better understanding of factors related to the advance of Asian carp populations towards the Great Lakes. In addition, the ACRCC formed the Monitoring and Rapid Response Workgroup to address Asian carp monitoring and removal (ACRCC 2012b).

Midwest waterways↗

USGS2013

ECALS: Loading studies interim report July 2013

Since the initial detection of Asian carp moving up the Mississippi Basin, the potential for invasion of the Great Lakes by Silver Carp and Bighead Carp has been a major concern to stakeholders. To combat this problem, sampling for environmental DNA (eDNA) is used to monitor the waterways near Lake Michigan. This monitoring area includes the Chicago Area Waterways System (CAWS) and the Des Plaines River. By sampling waters that may be inhabited by Asian carp, the extraction and amplification of carp DNA from the collected cellular debris is possible. This technique has been successfully used in several other contexts (Ficetola et al., 2008; Foote et al., 2008) and is believed to be a highly sensitive method for species detection (Dejean et al., 2012). Compared to traditional methods for surveying aquatic invasive species (fishing, rotenone application, and electrofishing), the increased sensitivity of this method could be a valuable asset. Early detection could lead to a more rapid response to the threat of a Great Lakes invasion by Asian carp.

Report↗