scholarly journals Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters

2020 ◽  
Vol 287 (1940) ◽  
pp. 20202424
Author(s):  
Ramón Gallego ◽  
Emily Jacobs-Palmer ◽  
Kelly Cribari ◽  
Ryan P. Kelly
Keyword(s):  
Global Change ◽  
Environmental Dna ◽  
Suitable Habitat ◽  
Ecological Communities ◽  
Marine Habitat ◽  
Biological Communities ◽  
Time Space ◽  
Dna Metabarcoding ◽  
Near Term ◽  
Near Future

Studies of the ecological effects of global change often focus on one or a few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use COI mtDNA amplicons from monthly samples of environmental DNA to survey 221 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding more suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.

scholarly journals Environmental DNA Metabarcoding Reveals Winners and Losers of Global Change in Coastal Waters

2020 ◽  
Author(s):  
Ramón Gallego ◽  
Emily Jacobs-Palmer ◽  
Kelly Cribari ◽  
Ryan P. Kelly
Keyword(s):  
Global Change ◽  
Environmental Dna ◽  
Suitable Habitat ◽  
Ecological Communities ◽  
Marine Habitat ◽  
Biological Communities ◽  
Time Space ◽  
Dna Metabarcoding ◽  
Near Term ◽  
Near Future

2AbstractStudies of the ecological effects of global change often focus on one or few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use monthly samples of environmental DNA to survey 222 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen, and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding greater suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.

scholarly journals The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

2021 ◽  
Author(s):  
Bruno Bellisario ◽  
Maria Fais ◽  
Sofia Duarte ◽  
Pedro Vieira ◽  
Carlos Canchaya ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Scale Up ◽  
Environmental Dna ◽  
Taxonomic Diversity ◽  
Ecosystem Functions ◽  
Individual Species ◽  
Ecological Communities ◽  
Spatial Networks ◽  
Dna Metabarcoding ◽  
High Degree

The identification of the patterns and mechanisms behind species distribution is one of the major challenges in ecology, having also important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestimate their real taxonomic diversity due to their high degree of cryptic diversity and inherent diagnosis difficulties, such as meiofaunal communities. Environmental DNA (eDNA) metabarcoding may provide a fast and reliable way to refine and scale-up the characterization of biological diversity in complex environmental samples, allowing to bypass such drawbacks and increase the resolution of biodiversity estimates. Moreover, the possibility of integrating eDNA metabarcoding-derived data with tools and methods rooted in network theory would deepen the knowledge of the structuring processes of ecological communities in ways that cannot be predicted from studying individual species/communities in isolation. Here, a sediment eDNA metabarcoding of mitochondrial cytochrome c oxidase I (COI) and the nuclear hypervariable V4 region of the 18S rDNA (18S) was used to reconstruct the spatial networks of intertidal meiofaunal OTUs from three estuaries of North-Western Iberian Peninsula. Null models were used to identify the role of environmental and spatial constraints on the structure of COI- and 18S-derived spatial networks and to characterize the macroecological features of surveyed phyla. Our results show the feasibility of eDNA metabarcoding, not only to capture a fair amount of diversity hard to detect with standard surveys procedures, but also to identify hierarchical spatial structures in intertidal meiofaunal assemblages. This suggests that exclusivity of occurrence rather than pervasiveness appears to be the norm in meiofaunal organisms and that niche-based processes predominantly drive the spatial aggregation and contemporary distribution of meiofaunal phyla within the system.

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3044 ◽  
Author(s):  
James L. O’Donnell ◽  
Ryan P. Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F. Samhouri ◽  
Natalie C. Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Illumina Platform ◽  
Marine Habitat ◽  
Biological Communities ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

2016 ◽  
Author(s):  
James L O'Donnell ◽  
Ryan P Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F Samhouri ◽  
Natalie C Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Massively Parallel Sequencing ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Marine Habitat ◽  
Biological Communities ◽  
The Face ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to 4 kilometers from shore. Using massively parallel sequencing of 16S amplicons, we identified a diverse community of metazoans and quantified their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

2016 ◽  
Author(s):  
James L O'Donnell ◽  
Ryan P Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F Samhouri ◽  
Natalie C Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Massively Parallel Sequencing ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Marine Habitat ◽  
Biological Communities ◽  
The Face ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to 4 kilometers from shore. Using massively parallel sequencing of 16S amplicons, we identified a diverse community of metazoans and quantified their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

scholarly journals Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae

2020 ◽  
Author(s):  
Emily Jacobs-Palmer ◽  
Ramón Gallego ◽  
Kelly Cribari ◽  
Abigail Keller ◽  
Ryan P. Kelly
Keyword(s):  
Algal Blooms ◽  
Cold Water ◽  
Global Climate ◽  
Puget Sound ◽  
Environmental Dna ◽  
Harmful Algae ◽  
Social Consequences ◽  
Ecological Communities ◽  
Ecological Context ◽  
Dna Metabarcoding

AbstractHarmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. We track trends of presence and abundance in a series of water samples across nearly two years. We find putative harmful algal sequences in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (family Bacillariaceae), as well as multiple harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the saxitoxin-producing genus Alexandrium (family Gonyaulacaceae), two variants from the karlotoxin-producing genus Karlodinium (family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which these species are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of harmful algae, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) provides a tool for monitoring and management moving forward.

scholarly journals Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae

2021 ◽  
Vol 9 ◽  
Author(s):  
Emily Jacobs-Palmer ◽  
Ramón Gallego ◽  
Kelly Cribari ◽  
Abigail G. Keller ◽  
Ryan P. Kelly
Keyword(s):  
Algal Blooms ◽  
Cold Water ◽  
Global Climate ◽  
Puget Sound ◽  
Environmental Dna ◽  
Harmful Algae ◽  
Social Consequences ◽  
Ecological Communities ◽  
Ecological Context ◽  
Dna Metabarcoding

Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of potentially harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. Tracking trends of occurrence in a series of water samples over a period of 19 months, we find algal sequences from genera with harmful members in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (of which some members produce domoic acid; family Bacillariaceae), as well as multiple potentially harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the genus Alexandrium (of which some members produce saxitoxin; family Gonyaulacaceae), two variants from the genus Karlodinium (of which some members produce karlotoxins; family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which they are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of algae from harmful genera, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) suggests a pathway for multispecies monitoring and management moving forward.

scholarly journals Malacological survey in a bottle of water: A comparative study between manual sampling and environmental DNA metabarcoding approaches

2020 ◽  
Author(s):  
Stephen Mulero ◽  
Eve Toulza ◽  
Anaïs Loisier ◽  
Meryl Zimmerman ◽  
Jean-François Allienne ◽  
...  
Keyword(s):  
Anthropogenic Activities ◽  
Environmental Dna ◽  
Freshwater Snail ◽  
Freshwater Ecosystems ◽  
Snail Species ◽  
Ecological Communities ◽  
Bulinus Truncatus ◽  
Galba Truncatula ◽  
Dna Metabarcoding ◽  
Veterinary Importance

AbstractTo assess the effect of anthropogenic activities on ecosystems, it is of prime importance to develop new tools enabling a rapid characterisation of ecological communities. Freshwater ecosystems are particularly impacted and threatened by human activities and need thorough attention to preserve their biodiversity and the ecological services they provide. Studying such ecosystems is generally difficult because the associated organisms are hard to sample and to monitor. We present a ready to use environmental metabarcoding diagnostic tool to characterise and monitor the freshwater malacofauna from water samples. The efficiency of this new tool was compared to a classical malacological survey at 19 sampled sites from 10 distinct rivers distributed over Corsica Island (France). Our eDNA monitoring tool demonstrated a remarkable ability to reconstitute the local malacofauna compared to the malacological survey, with 97.1% of species detection confirmed by both methods. The present tool successfully detected the 11 freshwater snail species previously reported in Corsica by malacological survey but was limited at the genus level for some species. Moreover, our malacological survey allowed an update of the local distribution of a wide diversity of freshwater snails including invasive species (i.e. Potamopyrgus antipodarum and Physa acuta) as well as snail hosts of pathogens of medical and veterinary importance (i.e. Bulinus truncatus and Galba truncatula).

COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (5) ◽  
pp. I_415-I_420 ◽  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  
Keyword(s):  
Comparative Study ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Fish Collection

Environmental DNA for functional diversity

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Functional Groups ◽  
Functional Diversity ◽  
Environmental Dna ◽  
Soil Organisms ◽  
Meaningful Information ◽  
Dna Metabarcoding ◽  
Pros And Cons ◽  
Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

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