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

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.

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The Past, Present, and Future of Tuna at Lake Moāwhitu: Drawing on the two knowledge baskets of Mātauranga Māori and Western Science

10.26686/wgtn.15086241 ◽

2021 ◽

Author(s):

Russleigh Parai

Keyword(s):

Algal Blooms ◽

Human Impacts ◽

Anthropogenic Impacts ◽

Land Use Changes ◽

Environmental Dna ◽

Western Science ◽

Lake Water Quality ◽

Dna Metabarcoding ◽

Remedial Intervention ◽

Life Force

Knowledge generated through experience and understanding relies on the senses, one of which is listening. This thesis provides an opportunity to hear the diminishing voice of tuna utilizing paleolimnological techniques and our natural senses through traditional Indigenous methodologies in order to track the presence of tuna back in time. This study provides historical environmental context of Lake Moāwhitu catchment (Rangitoto ki te Tonga) as a once significant mahinga kai site for manawhenua, Ngāti Koata. The strong connection to place is not lost on Ngāti Koata despite for many their geographic detachment to their turangawaewae. They hear the voice of tuna calling them back to sustain them as they have sustained Māori from the beginning of time. Now considered wāhi tapu due to significant degradation, Moāwhitu is currently undergoing remedial intervention by Ngāti Koata, DoC, Lakes380 and stakeholders to restore the mauri (life force) of the Lake and adjacent wetland ecosystem. Drawing from two distinct knowledge streams of western science and mātauranga Māori, this study draws new (on-site) understandings about the anthropogenic impacts on tuna as well as their status and relationship as tuākana (older sibling) to Māori. Through this journey a ‘te ao Māori’ (Māori worldview) is explored, revealing a historically healthy and abundant tuna population and thriving tuākana-teina relationship up until recent decades. This information complements the environmental reconstruction derived from western science methods applied to a lake Moawhitu sediment core spanning the last 1000 years or so. Through a combination of palynology, hyperspectral scanning and bacterial environmental DNA metabarcoding, it is clear that lake water quality remained high despite various historical land cover and land use changes, until recent decades when deteriorating quality has accompanied a rise in cyanobacteria and toxic algal blooms. These changes appear to coincide with intensified pastoralism accompanying draining of the lake and fringing wetlands since the mid-twentieth century. How tuna have endured these recent human impacts and why their survival and sustainability is important to Aotearoa today is at the heart of this thesis which seeks to explore how two vastly different knowledge streams converge and navigate unchartered waters. The two knowledge baskets (with their respective world views) are held up for the reader to view and consider what an effective collaborative partnership looks like by recognising basic intrinsic values of respect, reciprocity and kindness. The challenge remains to draw out the very best of people (he tangata) as a way to bring about urgent regenerative solutions for our tuākana, tuna, and in turn humanity itself.

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A Halo of Reduced Dinoflagellate Abundances In and Around Eelgrass Beds

10.1101/712612 ◽

2019 ◽

Author(s):

Emily Jacobs-Palmer ◽

Ramón Gallego ◽

Ana Ramón-Laca ◽

Emily Kunselman ◽

Kelly Cribari ◽

...

Keyword(s):

Harmful Algal Blooms ◽

Algal Blooms ◽

Environmental Dna ◽

Ecological Communities ◽

Phylogenetic Groups ◽

Shellfish Aquaculture ◽

Salutary Effect ◽

Eelgrass Habitat ◽

Broad Cross Section ◽

Eelgrass Beds

ABSTRACTSeagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for thirteen major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least fifteen meters outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming Harmful Algal Blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.

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Distribution and seasonal differences in Pacific Lamprey andLampetraspp eDNA across 18 Puget Sound watersheds

PeerJ ◽

10.7717/peerj.4496 ◽

2018 ◽

Vol 6 ◽

pp. e4496 ◽

Cited By ~ 10

Author(s):

Carl O. Ostberg ◽

Dorothy M. Chase ◽

Michael C. Hayes ◽

Jeffrey J. Duda

Keyword(s):

North America ◽

Detection Rate ◽

Puget Sound ◽

Environmental Dna ◽

Probe Design ◽

Significant Finding ◽

Ecological Communities ◽

Detection Rates ◽

Pacific Lamprey ◽

The Pacific

Lampreys have a worldwide distribution, are functionally important to ecological communities and serve significant roles in many cultures. In Pacific coast drainages of North America, lamprey populations have suffered large declines. However, lamprey population status and trends within many areas of this region are unknown and such information is needed for advancing conservation goals. We developed two quantitative PCR-based, aquatic environmental DNA (eDNA) assays for detection of Pacific Lamprey (Entosphenus tridentatus) andLampetraspp, using locked nucleic acids (LNAs) in the probe design. We used these assays to characterize the spatial distribution of lamprey in 18 watersheds of Puget Sound, Washington, by collecting water samples in spring and fall. Pacific Lamprey andLampetraspp were each detected in 14 watersheds and co-occurred in 10 watersheds. Lamprey eDNA detection rates were much higher in spring compared to fall. Specifically, the Pacific Lamprey eDNA detection rate was 3.5 times higher in spring and theLampetraspp eDNA detection rate was 1.5 times higher in spring even though larval lamprey are present in streams year-round. This significant finding highlights the importance of seasonality on eDNA detection. Higher stream discharge in the fall likely contributed to reduced eDNA detection rates, although seasonal life history events may have also contributed. These eDNA assays differentiate Pacific Lamprey andLampetraspp across much of their range along the west coast of North America. Sequence analysis indicates the Pacific Lamprey assay also targets otherEntosphenusspp and indicates theLampetraspp assay may have limited or no capability of detectingLampetrain some locations south of the Columbia River Basin. Nevertheless, these assays will serve as a valuable tool for resource managers and have direct application to lamprey conservation efforts, such as mapping species distributions, occupancy modeling, and monitoring translocations and reintroductions.

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

10.1101/2021.03.16.435605 ◽

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.

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Application of environmental DNA metabarcoding in a lake with extensive algal blooms

Limnology ◽

10.1007/s10201-021-00663-1 ◽

2021 ◽

Author(s):

Qianqian Wu ◽

Masayuki K. Sakata ◽

Deyi Wu ◽

Hiroki Yamanaka ◽

Toshifumi Minamoto

Keyword(s):

Algal Blooms ◽

Environmental Dna ◽

Dna Metabarcoding

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A halo of reduced dinoflagellate abundances in and around eelgrass beds

PeerJ ◽

10.7717/peerj.8869 ◽

2020 ◽

Vol 8 ◽

pp. e8869 ◽

Cited By ~ 2

Author(s):

Emily Jacobs-Palmer ◽

Ramón Gallego ◽

Ana Ramón-Laca ◽

Emily Kunselman ◽

Kelly Cribari ◽

...

Keyword(s):

Harmful Algal Blooms ◽

Algal Blooms ◽

Environmental Dna ◽

Ecological Communities ◽

Phylogenetic Groups ◽

Shellfish Aquaculture ◽

Salutary Effect ◽

Eelgrass Habitat ◽

Broad Cross Section ◽

Eelgrass Beds

Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for 13 major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least 15 m outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming harmful algal blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.

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The Past, Present, and Future of Tuna at Lake Moāwhitu: Drawing on the two knowledge baskets of Mātauranga Māori and Western Science

10.26686/wgtn.15086241.v1 ◽

2021 ◽

Author(s):

Russleigh Parai

Keyword(s):

Algal Blooms ◽

Human Impacts ◽

Anthropogenic Impacts ◽

Land Use Changes ◽

Environmental Dna ◽

Western Science ◽

Lake Water Quality ◽

Dna Metabarcoding ◽

Remedial Intervention ◽

Life Force

Knowledge generated through experience and understanding relies on the senses, one of which is listening. This thesis provides an opportunity to hear the diminishing voice of tuna utilizing paleolimnological techniques and our natural senses through traditional Indigenous methodologies in order to track the presence of tuna back in time. This study provides historical environmental context of Lake Moāwhitu catchment (Rangitoto ki te Tonga) as a once significant mahinga kai site for manawhenua, Ngāti Koata. The strong connection to place is not lost on Ngāti Koata despite for many their geographic detachment to their turangawaewae. They hear the voice of tuna calling them back to sustain them as they have sustained Māori from the beginning of time. Now considered wāhi tapu due to significant degradation, Moāwhitu is currently undergoing remedial intervention by Ngāti Koata, DoC, Lakes380 and stakeholders to restore the mauri (life force) of the Lake and adjacent wetland ecosystem. Drawing from two distinct knowledge streams of western science and mātauranga Māori, this study draws new (on-site) understandings about the anthropogenic impacts on tuna as well as their status and relationship as tuākana (older sibling) to Māori. Through this journey a ‘te ao Māori’ (Māori worldview) is explored, revealing a historically healthy and abundant tuna population and thriving tuākana-teina relationship up until recent decades. This information complements the environmental reconstruction derived from western science methods applied to a lake Moawhitu sediment core spanning the last 1000 years or so. Through a combination of palynology, hyperspectral scanning and bacterial environmental DNA metabarcoding, it is clear that lake water quality remained high despite various historical land cover and land use changes, until recent decades when deteriorating quality has accompanied a rise in cyanobacteria and toxic algal blooms. These changes appear to coincide with intensified pastoralism accompanying draining of the lake and fringing wetlands since the mid-twentieth century. How tuna have endured these recent human impacts and why their survival and sustainability is important to Aotearoa today is at the heart of this thesis which seeks to explore how two vastly different knowledge streams converge and navigate unchartered waters. The two knowledge baskets (with their respective world views) are held up for the reader to view and consider what an effective collaborative partnership looks like by recognising basic intrinsic values of respect, reciprocity and kindness. The challenge remains to draw out the very best of people (he tangata) as a way to bring about urgent regenerative solutions for our tuākana, tuna, and in turn humanity itself.

Download Full-text

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.2424 ◽

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.

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

10.1101/2020.05.21.108589 ◽

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).

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