GLORIA

GEOMAR Library Ocean Research Information Access

X

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    Quantifying impacts of an environmental intervention using environmental DNA
    Wiley ; 2023
    In:  Ecological Applications
    Details
    In: Ecological Applications, Wiley
    Abstract: Environmental laws around the world require some version of an environmental‐impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon‐sequencing—also called metabarcoding—of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental‐impact analysis for development projects. Here, we analyze an 18‐month time series of water samples taken before, during, and after two culvert removals in a salmonid‐bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species‐specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout ( Oncorhynchus clarkii ), coho salmon ( Oncorhynchus kisutch ), rainbow trout ( Oncorhynchus mykiss ), and sockeye salmon ( Oncorhynchus nerka ). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court‐mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental‐impact reporting using eDNA that is widely applicable in environments worldwide.
    Type of Medium: Online Resource
    ISSN: 1051-0761 , 1939-5582
    URL: Article
    DOI: 10.1002/eap.2914
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2010123-5
    SSG: 12
    SSG: 23
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 2
    Online Resource
    Online Resource
    Integrating multiple chemical tracers to elucidate the diet and habitat of Cookiecutter Sharks
    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-06-03)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-06-03)
    Abstract: The Cookiecutter shark ( Isistius brasiliensis ) is an ectoparasitic, mesopelagic shark that is known for removing plugs of tissue from larger prey, including teleosts, chondrichthyans, cephalopods, and marine mammals. Although this species is widely distributed throughout the world’s tropical and subtropical oceanic waters, like many deep-water species, it remains very poorly understood due to its mesopelagic distribution. We used a suite of biochemical tracers, including stable isotope analysis (SIA), fatty acid analysis (FAA), and environmental DNA (eDNA), to investigate the trophic ecology of this species in the Central Pacific around Hawaii. We found that large epipelagic prey constituted a relatively minor part of the overall diet. Surprisingly, small micronektonic and forage species (meso- and epipelagic) are the most important prey group for Cookiecutter sharks across the studied size range (17–43 cm total length), with larger mesopelagic species or species that exhibit diel vertical migration also being important prey. These results were consistent across all the tracer techniques employed. Our results indicate that Cookiecutter sharks play a unique role in pelagic food webs, feeding on prey ranging from the largest apex predators to small, low trophic level species, in particular those that overlap with the depth distribution of the sharks throughout the diel cycle. We also found evidence of a potential shift in diet and/or habitat with size and season. Environmental DNA metabarcoding revealed new prey items for Cookiecutter sharks while also demonstrating that eDNA can be used to identify recent prey in stomachs frozen for extended periods. Integrating across chemical tracers is a powerful tool for investigating the ecology of elusive and difficult to study species, such as meso- and bathypelagic chondrichthyans, and can increase the amount of information gained from small sample sizes. Better resolving the foraging ecology of these mesopelagic predators is critical for effective conservation and management of these taxa and ecosystems, which are intrinsically vulnerable to overfishing and exploitation.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-021-89903-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2615211-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 3
    Online Resource
    Online Resource
    Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes
    Wiley ; 2021
    In:  Environmental DNA Vol. 3, No. 2 ( 2021-03), p. 492-514
    Details
    In: Environmental DNA, Wiley, Vol. 3, No. 2 ( 2021-03), p. 492-514
    Abstract: Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus ), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    URL: Article
    DOI: 10.1002/edn3.v3.2
    DOI: 10.1002/edn3.141
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 3001165-6
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 4
    Online Resource
    Online Resource
    Toward a national eDNA strategy for the United States
    Wiley ; 2023
    In:  Environmental DNA
    Details
    In: Environmental DNA, Wiley
    Abstract: Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use‐cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next‐generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Article
    DOI: 10.1002/edn3.432
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 3001165-6
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 5
    Online Resource
    Online Resource
    Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean
    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-10-28)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-10-28)
    Abstract: Increasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-021-00288-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2615211-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 6
    Online Resource
    Online Resource
    Adoption of environmental DNA in public agency practice
    Wiley ; 2023
    In:  Environmental DNA
    Details
    In: Environmental DNA, Wiley
    Abstract: Environmental DNA (eDNA) analysis has matured to the point that it is ready for deployment in many applications, particularly in aquatic environments. But public agencies have yet to adopt eDNA methods into their environmental decision making routines at scale, even when eDNA offers clear advantages to those now in use. This article provides a perspective on this gap by considering adoption of a new technology as a path‐dependent, social process in which some paths lead to outcomes that provide far greater benefits than others. We use the diffusion of innovations to investigate eDNA adoption by government agencies, in an effort to (1) identify likely paths toward institutionalized uptake, and (2) suggest ways of avoiding societally inefficient adoption outcomes. Because—as in any scientific endeavor—the best eDNA practices will continue to change, public agencies must remain open to improvements while building a useful and validated array of methods for routine eDNA application. Here we suggest one mechanism for doing so, which we call collaborative governance.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Article
    DOI: 10.1002/edn3.470
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 3001165-6
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 7
    Online Resource
    Online Resource
    Critical considerations for communicating environmental DNA science
    Wiley ; 2023
    In:  Environmental DNA
    Details
    In: Environmental DNA, Wiley
    Abstract: The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess and monitor aquatic environments. However, instances of inadequate communication from the scientific community about confidence levels, knowledge gaps, reliability, and appropriate parameters of eDNA‐based methods have hindered their uptake in environmental monitoring programs and, in some cases, has created misperceptions or doubts in the management community. To help remedy this situation, scientists convened a session at the Second National Marine eDNA Workshop to discuss strategies for improving communications with managers. These include articulating the readiness of different eDNA applications, highlighting the strengths and limitations of eDNA tools for various applications or use cases, communicating uncertainties associated with specified uses transparently, and avoiding the exaggeration of exploratory and preliminary findings. Several key messages regarding implementation, limitations, and relationship to existing methods were prioritized. To be inclusive of the diverse managers, practitioners, and researchers, we and the other workshop participants propose the development of communication workflow plans, using RACI (Responsible, Accountable, Consulted, Informed) charts to clarify the roles of all pertinent individuals and parties and to minimize the chance for miscommunications. We also propose developing decision support tools such as Structured Decision‐Making (SDM) to help balance the benefits of eDNA sampling with the inherent uncertainty, and developing an eDNA readiness scale to articulate the technological readiness of eDNA approaches for specific applications. These strategies will increase clarity and consistency regarding our understanding of the utility of eDNA‐based methods, improve transparency, foster a common vision for confidently applying eDNA approaches, and enhance their benefit to the monitoring and assessment community.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Article
    DOI: 10.1002/edn3.472
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 3001165-6
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 8
    Online Resource
    Online Resource
    Signal and noise in metabarcoding data
    Public Library of Science (PLoS) ; 2023
    In:  PLOS ONE Vol. 18, No. 5 ( 2023-5-11), p. e0285674-
    Details
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 18, No. 5 ( 2023-5-11), p. e0285674-
    Abstract: Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing—both of which we can model—but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.
    Type of Medium: Online Resource
    ISSN: 1932-6203
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.1371/journal.pone.0285674
    DOI: 10.1371/journal.pone.0285674.g001
    DOI: 10.1371/journal.pone.0285674.g002
    DOI: 10.1371/journal.pone.0285674.g003
    DOI: 10.1371/journal.pone.0285674.g004
    DOI: 10.1371/journal.pone.0285674.s001
    DOI: 10.1371/journal.pone.0285674.s002
    DOI: 10.1371/journal.pone.0285674.s003
    DOI: 10.1371/journal.pone.0285674.s004
    DOI: 10.1371/journal.pone.0285674.s005
    DOI: 10.1371/journal.pone.0285674.s006
    DOI: 10.1371/journal.pone.0285674.s007
    DOI: 10.1371/journal.pone.0285674.r001
    DOI: 10.1371/journal.pone.0285674.r002
    DOI: 10.1371/journal.pone.0285674.r003
    DOI: 10.1371/journal.pone.0285674.r004
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2023
    detail.hit.zdb_id: 2267670-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 9
    Online Resource
    Online Resource
    Toward quantitative metabarcoding
    Wiley ; 2023
    In:  Ecology Vol. 104, No. 2 ( 2023-02)
    Details
    In: Ecology, Wiley, Vol. 104, No. 2 ( 2023-02)
    Abstract: Amplicon‐sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon‐sequencing studies—known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture—struggle to link genetic observations to the underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology, it becomes more important to develop ways to make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying polymerase chain reaction mechanism explains the observed patterns of amplicon data in a general way. By modeling the process through which amplicon‐sequence data arise, rather than transforming the data post hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.
    Type of Medium: Online Resource
    ISSN: 0012-9658 , 1939-9170
    URL: Issue
    URL: Article
    DOI: 10.1002/ecy.v104.2
    DOI: 10.1002/ecy.3906
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 1797-8
    detail.hit.zdb_id: 2010140-5
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...