Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(6), P. 1820 - 1835

Published: Jan. 25, 2022

Abstract DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated consistency this technique with traditional morpho‐taxonomic approaches. These individual to assess diversity community structure organisms both in marine freshwater systems globally over last decade. However, a systematic analysis comparability effectiveness DNA‐based across all these has hitherto been lacking. Here, we performed first meta‐analysis available comparing methods measure biological key groups, including plankton, microphytobentos, macroinvertebrates, fish. Across 215 data sets, found that provides richness estimates are consistent those obtained using methods, at local regional scale. also generates species inventories highly congruent Contrastingly, microphytobenthos macroinvertebrates by showed pronounced differences missing some taxa but same time detecting otherwise overseen diversity. The method generally sufficiently advanced study composition fish communities replace more invasive methods. For smaller organisms, like plankton microphytobenthos, may continue give complementary rather than identical compared Systematic comparable collection will increase understanding different aspects complementarity, adequate interpretation results.

Language: Английский

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eDNA metabarcoding detection of nearshore juvenile white sharks (Carcharodon carcharias) and prey fish communities

Journal of Experimental Marine Biology and Ecology, Journal Year: 2025, Volume and Issue: 583, P. 152084 - 152084

Published: Jan. 31, 2025

Language: Английский

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Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(7), P. 2565 - 2579

Published: May 18, 2021

Abstract Bioinformatic analysis of eDNA metabarcoding data is a crucial step toward rigorously assessing biodiversity. Many programs are now available for each the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. We used simulated mock communities real fish to evaluate performance 13 bioinformatic pipelines retrieve occurrence read abundance using 12S mt rRNA gene marker. four indices compare outputs program with samples: sensitivity, F‐measure, root‐mean‐square error (RMSE) on abundances, execution time. found marked differences among only taxonomic assignment step, both in terms F‐measure RMSE. Running time was highly different between step. The fastest best were assembled into pipeline. compared this pipeline constructed from existing toolboxes (OBITools, Barque, QIIME 2). Our Barque obtained all appear be better alternatives analysing when complete reference database available. Analysis also indicated only. This study reveals major during choice algorithm can significant impact diversity estimates should made according objectives study.

Language: Английский

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The future of biodiversity monitoring and conservation utilizing environmental DNA

Environmental DNA, Journal Year: 2020, Volume and Issue: 3(1), P. 3 - 7

Published: Dec. 21, 2020

Technology is often looked to as a means an end. The explosion in use of environmental DNA (eDNA) for species detection great example technological discovery that fueling new possibilities study and quantify the state change, but also recovery resiliency biosphere. articles herein contribute Future Biodiversity Monitoring Conservation Utilizing Environmental DNA, by tackling methodological advances validation, shedding light on ecology different contexts, revealing eDNA observe behavior unravel diversity large hyperdiverse ecosystems. On applied side, several contributions demonstrate detecting invasions restoration populations after habitat restoration. Lastly, make efforts reduce learning curve methods inspire people about biodiversity through using surveys education. Thus, this special issue shows myriad ways which scientific community continually improving utility surveying purpose measuring, monitoring, understanding At forefront, researchers are moving beyond assess population information such abundance testing potential derive functional from RNA. Measuring population's fundamental many conservation management questions. Spear et al. (2021) progress quantities measured water samples culturally economically important sportfish, walleye, 22 lakes Wisconsin. Their observed correlation among best yet natural systems compares with adult biomass estimated mark–recapture surveys. demonstrating concentrations can have strong relationship range uncertainty similar conventional methods. They urge, though, demographic still unknown. But recent studying RNA may change outlook. Tsuri push forward idea specific tissues produce certain messenger RNAs, typing them, we could identify source their production. By tank experiments zebrafish, they mRNAs gills, skin, intestine. While proof-of-concept study, be built technique mRNA-typing eRNA future dig into not only presence abundance, even developmental state, stress, likely other aspects demography when informed biology. Several advancements continue build our established goal improve accuracy, sensitivity, better sampling design habitats. For single species, Williams compare CRISPR-Cas assay against standard qPCR approach Atlantic salmon across two watersheds northern Canada. Both showed agreement, few sites agreement opposite results. Advantages assays done isothermal reactions inhibited assays. latter need highly time-consuming purification These advantages positive more rapid onsite abilities useful contexts. biomonitoring whole communities, challenges faced Leese (2021), derived method target benthic macroinvertebrates used quality assessment. first sequenced river system primers generally amplify both prokaryotic eukaryotic knowledge total then developed desired groups while maximizing differences site-specific nontarget diversity. amplification non-target substantially reduced recovered taxa exceeded detected base morphological identification. good Carraro modeling choice how optimally sample system. Basing model's predictions hydrological terms, strategies needed depending distribution river's catchment decay rates model predictions. Having greater guide effort species. making analysis practical monitoring tool, comparison sensitivity techniques fundamental. Afzali conducted trawling survey demersal fish Estuary Gulf Saint-Lawrence, Canada, compared results metabarcoding. produced 50% consensus relative abundances were significantly correlated each other. Boivin-Delisle gillnet Rupert River, found metabarcoding larger number Moreover, read had significant captured Polanco Fernández underwater visual census bays near Santa Marta, Colombia, wider taxonomic than higher efficiency smaller body sizes those inhabiting deeper water. Overall, it was provide comparable to, or sensitive than, variety To accurate inferences space time studied, environment itself especially extra-organismal source. River particularly understand transport dynamics flow almost immediately separate its individual. Thalinger caged experiment lateral longitudinal once released seasons. show changes seasonally order same location, conditions traits determining lotic environment. most studies focus aquatic systems, Kunadiya spiked soil persistence agricultural soil-borne plant pathogen, Phytophthora cinnamomi. Detection horticulture settings crops including avocado, pineapple, peach, chestnut, macadamia. type, inoculated persist up 378 days, whereas persisted short 1–3 days. This detections indicative presence, would inference recently present soil. Moving occurrence description, increasing showcasing applying gain insights comprises illustrative examples studies. reproductive biology obvious ecological component crucial understand, standpoint. challenging requires laborious work. In contribution, Tsuji Shibata combined experimental field observations spawning (reproductive) events spikes concentration medaka (Oryzias sp.). Besides spike spawning, magnitude depended activities. As such, demonstrates usefulness tool Another facet species' pertains feeding behaviors. Here, dietary plasticity consider key factor allowing cope changes. Yet, spatio-temporal variation diet has been investigated routinely, possibly because logistical constraints. Tournayre analyze prey content nearly 2000 fecal insectivorous horseshoe bat (Rhinolophus ferrumequinum) maternal colonies France. describing diet, tested whether landscape characteristics surrounding at times year influenced composition. much diverse reported previous studies, composed core shared all secondary varied colonies. prime illustration habits elusive Advancing measure broad diversity, population-level exemplified contributions. example, Ratcliffe areas Irish Celtic seas. Concurrent larval netting equivalent estimates richness 75% agreement. Klymus (2020) freshwater mussels unique mussel Clinch watershed southeastern United States. 19 eight federally endangered Oka remarkably high coral reef lagoon Okinawa, Japan. system, clear difference communities between reef's edge shore-side seagrass bed small lagoon, suggesting segregation. Palacios Mejia three primer sets detect fauna flora sediments Mojave Desert springs California, USA. successfully groups, composition data further improvements choices required these habitats complete detection. Székely sampled seawater Disko Bay, West Greenland, bowhead whales newly species-specific real-time PCR assay. observed, enabled them mtDNA control region Sanger sequenced, haplotypes. formed "footprint," where whale just started diving, marked success transect samples. demonstrations move powerful noninvasive usage reliability branches tree life. application evaluate activities emerging provides fast potentially reliable way monitor. advance arena, Duda multiple monitor over four years dam removal project Elwha Washington, Indigenous expanded migrating area upstream side removed non-native Brook Trout suggested expand due removal. Rasmussen fungi arthropod vineyard correspondence strategy integrated, organic, biodynamic. management-dependent resulted fields. Pearman surveillance marine nonindigenous harbors intensive trading increased achieved barcoding markers. continuing accumulation case illustrate biological communities' responses anthropogenic increase restoration/management measures aiming restore conserve complementary addition now undeniable. value being collected undermined current lack standardization guidelines, which, if adopted, allow rigor comparing points time. Minamoto summarize point published "Environmental Sampling Experiment Manual," under initiative Society Japan 2018. particular, authors introduce detailed described manual, selection sites, methods, filtration extraction, report manual will assist users conducting standardized basis collecting data. national international initiatives implement methodologies local monitoring. Leading what hopefully next step standardizing steps differ various protocols collection around world. context global declines facing; becoming urgent crucially engage scale crisis efficient achieve engagement initiatives. ages horizons participate measuring surroundings create awareness. Hupało explore feasibility sequencing rapidly urban educational purposes Norway. identifying 435 15 days performed people, nicely illustrates ease purposes. convincingly openly available resources, sequence raise awareness importance biodiversity. We want honor passing colleague friend dedicating Dr. Cameron R. Turner. His exceptional infused throughout included issue. building off instrumental framework summarized put forth 'Ecology eDNA' (Barnes & Turner, 2016) regarding structure, improvement managing work cited support hypotheses, observations, comparative his keen pushed forward. he no longer us, generated live way. None declared.

Language: Английский

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Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

Environmental DNA, Journal Year: 2021, Volume and Issue: 3(6), P. 1113 - 1127

Published: July 6, 2021

Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring organisms is becoming easier and promises a revolution our approaches to detect changes biodiversity over space time. A cornerstone eDNA approach primer pairs that allow amplifying specific taxonomic groups, which then used link sequence identification. Here, we propose framework for comparing regarding (a) their capacity bind amplify broad coverage species within target clade using silico PCR, (b) not only discriminate between but also genera or families, (c) specificity efficiency across variety environments. As case study, focus on two mitochondrial 12S pairs, MiFish‐U teleo, were designed fishes. We found performance PCRs high both teleo amplified more Actinopterygii, Chondrichthyes, Petromyzontomorphi than MiFish‐U. In contrast, discriminatory power species, genera, families higher likely associated with greater length fragments. The evaluation showed recovered richness compared tropical temperate freshwater environments, generally primers perform well monitor fish species. Since detected when together, those are best combination increase ability detection.

Language: Английский

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Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 289(1973)

Published: April 20, 2022

Increasing speed and magnitude of global change threaten the world's biodiversity particularly coral reef fishes. A better understanding large-scale patterns processes on reefs is essential to prevent fish decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding reconstruct well-known uncover hidden these highly diverse threatened ecosystems. We analysed 226 (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central Southwest Pacific, Coral Triangle Western Indian Ocean) compared those 2047 underwater visual censuses Reef Life Survey 1224 stations. Environmental reveals a higher (16%) biodiversity, with 2650 taxa, 25% more families than surveys. By identifying pelagic, reef-associated crypto-benthic species, eDNA offers fresh view assembly rules across spatial scales. Nevertheless, life survey identified species 47 shared families, which can be due incomplete sequence assignment, possibly combined detection environment, for some species. Combining extensive census novel insights organization richest marine

Language: Английский

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A systematic review of mangrove restoration studies in Southeast Asia: Challenges and opportunities for the United Nation’s Decade on Ecosystem Restoration

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: Sept. 29, 2022

Mangroves provide valuable ecological and socio-economic services. The importance of mangroves is particularly evident in Southeast (SE) Asia where the most extensive diverse forests are found. To recover degraded mangroves, several SE Asian countries have implemented restoration programs. However, to date, there has been no systematic quantitative synthesis on mangrove studies region. Here, we a bibliometric-based analysis understanding trends future directions needed meet biodiversity targets Following Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) protocol, analyzed 335 articles (249 with attributes; 86 social attributes) published until February 2022 from Scopus Web Science databases. Mangrove attributes started around early 1990s mostly Indonesia, Thailand, Malaysia, Vietnam, Philippines. Majority stronger collaboration western rather than within Reasons vary per country, but were intended rehabilitate damaged mangroves. Direct planting was common method used while hydrological rehabilitation less practiced. Research dominated by biodiversity-related focused flora fauna, other ecosystem services (e.g., coastal protection, fisheries production, etc.). Studies only accounted <30% publications, topics related economics. Although apparent, some thematic foci needed. We propose priority research help achieve 2030.

Language: Английский

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Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(4), P. 671 - 682

Published: May 16, 2023

Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems informing policy decision‐making, especially in an era massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at forefront technological advances monitoring, last few years have seen major progress solutions to technical challenges from laboratory bioinformatics. Water eDNA has been shown allow fast efficient recovery signals, but rapid pace development meant that some important principles regarding sampling design, which well established traditional inventories, neglected. Using a spatially explicit river flow model, we illustrate how must be adjusted size watercourse increase quality signal recovered. We additionally investigate effect parameters (volume, number sites, sequencing depth) detection probability empirical data set. Based principles, propose aquatic replication volume scaled match organisms' ecosystems' properties provide reliable estimates. present generalizable conceptual equation describing features as function ecosystem monitored, abundance target organisms, procedure. The aim this formalization enhance standardization critical steps design inventory studies using eDNA. More robust standards will generate more eDNA, necessary method's long‐term plausibility comparability.

Language: Английский

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Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling analytical efforts are needed to improve estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs design effective eDNA monitoring studies. We conducted a water survey of vertebrates Mediterranean watershed identify key factors influencing species richness composition estimates. examined the impacts using high- versus low-capacity filtration capsules, varying levels biological technical replication, pooling PCR replicates before indexing. The primary sources variation identified were capsule capacity site replication across watershed. While within sites also improved effects comparatively smaller. Pooling indexing performed more poorly than analysing them independently. Methodological stronger on terrestrial aquatic species. Based these results, we recommend priority should be given high-capacity multiple sites. Site-level deserves lower priority, especially when filtering large volumes. crucial for detecting rare but balanced with eventually site-level replication. Avoiding important enhance sensitivity Overall, stress importance balancing choices constraints goals, emphasise need assessing different systems.

Language: Английский

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How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(21), P. 14630 - 14643

Published: Oct. 6, 2021

Abstract Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of traces from water samples. However, because eDNA concentration low environments, reliability detect can be limited. Using an approach identify Molecular Taxonomic Units (MOTUs) with single 12S marker, we aimed assess how number sampling replicates filtered volume affect biodiversity estimates. We used paired design 30 L per replicate on 68 reef transects 8 sites 3 regions. quantified local regional variability by comparing MOTU richness, compositional turnover, nestedness. found strong turnover MOTUs between replicated pairs samples undertaken same location, time, conditions. Paired contained non‐overlapping assemblages rather than subsets one another. As result, non‐saturated localized accumulation curves suggest that even 6 (180 L) location underestimate (for area <1 km). using ~25 variable locations (often covering 10 s km) often saturated curves. Our results demonstrate estimates possibly arising heterogeneous distribution seawater, highly skewed frequencies MOTU, addition processing. This high has consequences for monitor temporal spatial changes assemblages. Avoiding false‐negative detections future biomonitoring efforts requires increasing or sampled better inform management eDNA.

Language: Английский

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