An official website of the United States government
Marine zooplankton are rapid-responders and useful indicators of environmental variability and climate change impacts on pelagic ecosystems on time scales ranging from seasons to years to decades. The systematic complexity and taxonomic diversity of the zooplankton assemblage has presented significant challenges for routine morphological (microscopic) identification of species in samples collected during ecosystem monitoring and fisheries management surveys. Metabarcoding using the mitochondrial Cytochrome Oxidase I (COI) gene region has shown promise for detecting and identifying species of some – but not all – taxonomic groups in samples of marine zooplankton. This study examined species diversity of zooplankton on the Northwest Atlantic Continental Shelf using 27 samples collected in 2002-2012 from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring (EcoMon) Surveys by the NOAA NMFS Northeast Fisheries Science Center. COI metabarcodes were identified using the MetaZooGene Barcode Atlas and Database ( https://metazoogene.org/MZGdb ) specific to the North Atlantic Ocean. A total of 181 species across 23 taxonomic groups were detected, including a number of sibling and cryptic species that were not discriminated by morphological taxonomic analysis of EcoMon samples. In all, 67 species of 15 taxonomic groups had ≥ 50 COI sequences; 23 species had >1,000 COI sequences. Comparative analysis of molecular and morphological data showed significant correlations between COI sequence numbers and microscopic counts for 5 of 6 taxonomic groups and for 5 of 7 species with >1,000 COI sequences for which both types of data were available. Multivariate statistical analysis showed clustering of samples within each region based on both COI sequence numbers and EcoMon counts, although differences among the three regions were not statistically significant. The results demonstrate the power and potential of COI metabarcoding for identification of species of metazoan zooplankton in the context of ecosystem monitoring.
more »
« less
Needles in an ocean haystack: using environmental DNA to study marine mammals in the North Atlantic
Marine mammals in the North Atlantic have experienced severe depletions due to overexploitation. While some species and populations have now recovered, there are numerous other anthropogenic activities impacting their North Atlantic ecosystem. Studying marine mammals is often associated with logistical challenges, and many species have an elusive nature, resulting in substantial knowledge gaps on the distribution, abundance and diversity of marine mammals in the North Atlantic. Environmental DNA (eDNA) is an emerging tool in biodiversity monitoring and has successfully been demonstrated to complement traditional monitoring methods for a wide range of marine taxonomic groups. The promising potential of seawater eDNA is owe to advances within an array of molecular methods used to extract, detect and/or sequence the genetic material of marine organisms from a single seawater sample. We present a literature review of eDNA studies of marine mammals and discuss the potential applications and practical challenges of eDNA in marine mammal research, management and conservation. Environmental DNA has already been introduced to a wide range of applications within marine mammal science, from detection of endangered species to population genetic assessments. Furthermore, eDNA has the power to capture other biologically important species in the marine ecosystem and food web, which could facilitate insight into the spatiotemporal variation of different marine communities in a changing environment. With methodological and technological standardization, eDNA based approaches have a promising potential to be integrated into regular monitoring practices and management strategies.
more »
« less
- Award ID(s):
- 1849227
- PAR ID:
- 10403961
- Date Published:
- Journal Name:
- NAMMCO Scientific Publications
- Volume:
- 12
- ISSN:
- 1560-2206
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.more » « less
-
Abstract Environmental managers need a rapid and cost‐effective monitoring tool for tracking the spread of invasive species, particularly at the onset of introduction. The macroalgaeCaulerpa proliferais considered an invasive species outside its native range, colonizing large patches of seafloor, reducing native species, and altering ecosystem functioning. Here, we developed a droplet digital PCR assay for detection ofC. proliferafrom environmental DNA seawater samples using the internal transcribed spacer (ITS) region. While the assay itself was confirmed to be highly efficient, we discovered concentrations ofC. proliferaeDNA were present below detectable levels in the water column surrounding an outbreak. To understand why, we conducted tank‐based experiments for two California invasive algae species,Caulerpa proliferaandSargassum horneri. The steady‐state eDNA concentration (eDNA copies/ gram of biomass detected) ofC. proliferawas found to be two orders of magnitude lower thanS. horneri. A meta‐analysis of steady‐state concentrations reported in the literature showed a remarkable range from ~104–1011(copies/g), revealing C. proliferato have the lowest recorded steady‐state concentrations of eDNA of any known species. We attributeC. prolifera'slow steady‐state eDNA concentration to its unique biology as a unicellular macroscopic algae which reduces the possible modes of eDNA release compared to similarly sized multicellular organisms. Critically our results demonstrate the potential limits of eDNA approaches, the influence of shedding rates in the reliability of species detections, and the vital importance of benchmarking and validating eDNA assays in both field and laboratory settings.more » « less
-
ABSTRACT The Indo‐Pacific lionfish,Pterois volitans,is an invasive species in the western Atlantic. Since its introduction to Florida in the early 1980s, populations have surged with lionfish now found from North Carolina to Venezuela. As their range expands, these generalist predators threaten native fauna, and while they are primarily a marine species, their tolerance for low salinity conditions may allow them to expand into sensitive estuarine habitats undetected. Traditional approaches for tracking invasive species such as direct observation or trapping are impractical over large spatial scales, making environmental DNA (eDNA) an attractive alternative. Molecular assays, such as those employing quantitative polymerase chain reaction (qPCR), amplify low copy number DNA fragments in environmental samples and are increasingly employed as a complement to traditional methods for the detection of invasive species. Currently, there is one published PCR assay for the detection of lionfish eDNA. However, the specificity of this assay is unverified, and the critical performance parameters limit of detection (LOD) and limit of quantification (LOQ) have not been established. Here we evaluate the efficacy of this assay and show that it is likely to result in false negatives in the western Atlantic. As an alternative, we developed a new TaqMan probe‐based qPCR assay that is species‐specific forP. volitansand highly sensitive with a LOD of 12 copies per reaction and a LOQ of 598 copies per reaction. While our assay does not amplify the closely relatedP. miles, which was also introduced in the western Atlantic, the low prevalence of this species in the invasive population means our assay is effective for most monitoring purposes. We conclude that our assay is a robust method for the detection of lionfish and can be employed in any habitat, offering new opportunities for controlling the spread of invasive lionfish.more » « less
-
Abstract Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.7557/3.6482
