Environmental DNA reveals seasonal shifts and potential interactions in a marine community

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Янв. 14, 2020

Abstract Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains life, providing critical information about complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing eDNA survey biodiversity from an eighteen-month (2015–2016) time-series seawater samples Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher rank) ranging microorganisms mammals. We inferred changes in composition communities, revealing putative among taxa identifying correlations between these communities environmental properties over time. Community network provided evidence expected predator-prey relationships, linkages, seasonal shifts all life. conclude that eDNA-based analyses can provide detailed marine dynamics identify sensitive biological indicators suggest inform conservation strategies.

Язык: Английский

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MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

Fisheries Science, Год журнала: 2020, Номер 86(6), С. 939 - 970

Опубликована: Сен. 15, 2020

Abstract We reviewed the current methodology and practices of DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies short fragment fish (approx. 170 bp from mitochondrial 12S rRNA gene) across wide variety taxa. This method has mostly been applied to biodiversity monitoring environmental (eDNA) shed and, coupled with next-generation sequencing technologies, enabled massively parallel several hundred eDNA samples simultaneously. Since publication its technical outline in 2015, this widely used various aquatic environments around six continents, MiFish primers have demonstrably outperformed other competing primers. Here, we progress over last 5 years highlight some case studies on marine, freshwater, estuarine communities. Additionally, discuss applications non-fish organisms, single-species detection systems, quantitative monitoring, bulk than eDNA. By recognizing strengths limitations, argue that is useful for ecosystem conservation strategies sustainable use fishery resources “ecosystem-based management” through continuous at multiple sites.

Язык: Английский

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Trawl and eDNA assessment of marine fish diversity, seasonality, and relative abundance in coastal New Jersey, USA

ICES Journal of Marine Science, Год журнала: 2020, Номер 78(1), С. 293 - 304

Опубликована: Ноя. 5, 2020

Abstract Environmental DNA (eDNA) technology potentially improves the monitoring of marine fish populations. Realizing this promise awaits better understanding how eDNA relates to presence and abundance. Here, we evaluate performance by comparing bottom trawl catches from concurrent water samples. In conjunction with New Jersey Ocean Trawl Survey, 1-l samples were collected at surface depth prior tows about one-fourth Survey sites in January, June, August, November 2019. diversity 1 l was same as or higher than 66 M litres swept one tow. Most (70–87%) species detected a given month also eDNA, vice versa, including nearly all (92–100%) abundant species. peak seasonal abundance agreed for ∼70% log-scale comparisons month, reads correlated biomass, more strongly an allometric index calculated biomass. 1-year study, reporting largely concorded monthly estimates richness, composition, seasonality, relative Piggybacking onto existing survey provided relatively low-cost approach understand stock assessment.

Язык: Английский

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Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

The Science of The Total Environment, Год журнала: 2023, Номер 873, С. 162322 - 162322

Опубликована: Фев. 18, 2023

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this only possible an in-depth overview of technological discussion pros cons available methods. We therefore conducted systematic literature review 407 peer-reviewed papers on aquatic published between 2012 2021. observed gradual increase in annual number publications from four (2012) 28 (2018), followed growth 124 This was mirrored tremendous diversification methods all aspects workflow. For example, freezing applied preserve filter samples, whereas we recorded 12 different preservation 2021 literature. Despite ongoing standardisation debate community, field seemingly moving fast opposite direction discuss reasons implications. Moreover, compiling largest PCR-primer database date, provide information 522 141 species-specific metabarcoding primers targeting wide range organisms. works as user-friendly 'distillation' primer that hitherto scattered across hundreds papers, list also reflects which taxa are commonly studied technology environments such fish amphibians, reveals groups corals, plankton algae under-studied. Efforts improve sampling extraction specificity reference databases crucial capture these ecologically important future surveys. In rapidly diversifying field, synthetises procedures can guide users towards best practice.

Язык: Английский

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Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities

Annual Review of Marine Science, Год журнала: 2021, Номер 14(1), С. 161 - 185

Опубликована: Авг. 5, 2021

Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection multiple species) a noninvasive and cost-effective approach monitoring marine fish communities discusses prospects this growing field. coamplifies short fragments across wide variety taxa and, coupled with high-throughput sequencing technologies, allows massively parallel to be performed simultaneously dozens hundreds samples. can predict species richness in given area, detect habitat segregation biogeographic patterns small large spatial scales, monitor spatiotemporal dynamics communities. In addition, it anthropogenic impact on through evaluation their functional diversity. Recognizing strengths limitations will help ensure continuous at sites useful ecosystem conservation sustainable use fishery resources, possibly contributing achieving targets United Nations' Sustainable Development Goal 14 2030.

Язык: Английский

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eDNA metabarcoding as a biomonitoring tool for marine protected areas

PLoS ONE, Год журнала: 2021, Номер 16(2), С. e0238557 - e0238557

Опубликована: Фев. 24, 2021

Monitoring of marine protected areas (MPAs) is critical for ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope effectiveness. Environmental DNA (eDNA) metabarcoding a promising alternative monitoring, but more direct comparisons to needed understand the strengths limitations each approach. This study compares fish communities inside outside Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA underwater census surveys. Results from captured 76% (19/25) species 95% (19/20) genera observed during pairwise census. Species missed by were due inability MiFish 12S barcodes differentiate rockfishes ( Sebastes , n = 4) or low site occupancy rates crevice-dwelling Lythrypnus gobies. However, detected an additional 23 not recorded in paired surveys, previously reported prior highlighting sensitivity eDNA. Significant variation signatures location (50 m) (~1000 demonstrates address key questions such as community composition MPAs. demonstrate utility monitoring ecosystems, providing important complementary tool methods.

Язык: Английский

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Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

The Science of The Total Environment, Год журнала: 2021, Номер 818, С. 151783 - 151783

Опубликована: Ноя. 19, 2021

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification whole communities within a targeted group) is revolutionizing the field aquatic biomonitoring. To date, most studies aiming to assess ecological status ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, has also been applied soft sediment samples, mainly assessing microbial or meiofaunal biota. Compared classical methodologies based manual sorting morphological benthic taxa, offers potentially important advantages environmental quality sediments. The methods protocols utilized can vary considerably among studies, standardization efforts are needed improve their robustness, comparability use regulatory frameworks. Here, we review available information with focus sampling, preservation, extraction steps. We discuss challenges specific analysis, including variety different sources states its persistence in sediment. This paper aims identify good-practice strategies facilitate method harmonization routine future monitoring.

Язык: Английский

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Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Год журнала: 2022, Номер 31(20), С. 5132 - 5164

Опубликована: Авг. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Язык: Английский

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Toward quantitative metabarcoding

Ecology, Год журнала: 2022, Номер 104(2)

Опубликована: Ноя. 2, 2022

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary consist of targeted, amplified fragments sequenced many taxa a mixture-struggle to link genetic observations underlying biology quantitative way, but applications require about or systems under scrutiny. As proliferate it becomes more develop ways make them ensure that their conclusions are adequately supported. Here we previously disparate sets techniques making such quantitative, showing polymerase chain reaction mechanism explains observed patterns amplicon general way. By modeling process through amplicon-sequence arise, rather than transforming post hoc, show how estimate starting proportions mixture taxa. We illustrate calibrate model using mock communities apply approach simulated series empirical examples. Our opens door improve use wide range public health, related fields.

Язык: Английский

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MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

Environmental DNA, Год журнала: 2022, Номер 4(4), С. 894 - 907

Опубликована: Апрель 11, 2022

Abstract Analysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness this approach depends on accuracy taxonomic reference databases. The MIDORI databases, first released in 2017, were built improve for mitochondrial metazoan (animal) sequences. has now been significantly improved and renamed MIDORI2 (available at http://www.reference‐midori.info ). Like MIDORI, from GenBank contains curated sequences thirteen protein‐coding two ribosomal RNA genes. Coverage substantially expanded cover all eukaryotes, including fungi, green algae land plants, other multicellular algal groups, diverse protist lineages. also includes not only species with full binomials, taxa referred by genus left unspecified (“sp.”). Another new feature updating databases approximately every months version numbers corresponding each release. Additional potentially erroneously annotated have removed. Finally, ability export data files BLAST+ added original preformatted five assignment programs, amino acid are made available As a technical validation, we conducted preliminary comparison performance programs. Results suggest that top hits performed better assigning CO1 than alignment‐free methods based compositional features. Comparing commonly sequences, CO‐ARBitrator BOLD, show broader range non‐metazoan taxa. Overall, many contexts, offers clear advantages: higher diversity variety user‐friendly features, regular updates. particularly well‐suited studies target genes broad primers.

Язык: Английский

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