Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding

Environmental Advances, Journal Year: 2023, Volume and Issue: 12, P. 100370 - 100370

Published: April 19, 2023

The world is struggling to solve a devastating biodiversity loss that not only affects the extinction of treasured species and irreplaceable genetic variation, but also jeopardizes food production, health, safety people. All initiatives aimed conserve rely heavily on monitoring both populations get accurate spatial patterns overall population assessments. Conventional techniques, such as visual surveys counting individuals, are problematic due challenges in identifying cryptic or immature life stages. Environmental DNA (eDNA) relatively new technology has potential be faster, non-invasive, cost-effective tool for biodiversity, conservation, management practices. eDNA been extracted from materials ancient present, its applications range identification individual study entire ecosystems. In past few years, there substantial increase usage research pertaining ecological preservation conservation. However, several technological problems still need solved. To reduce number false positives and/or negatives produced by current technologies, it necessary improve optimize calibration validation at every stage procedure. There significant greater information about physical constraints use, well synthesis, state, expected lifespan, modes movement. Due widespread use research, essential assess extent breadth these studies. this article, we critically reviewed primary subterranean aquatic invasive species. Through review, readers can better understand limitations metabarcoding.

Language: Английский

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Answers blowing in the wind: Detection of birds, mammals, and amphibians with airborne environmental DNA in a natural environment over a yearlong survey

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(2), P. 375 - 387

Published: Jan. 20, 2023

Abstract Analysis of environmental DNA (eDNA) from passively collected airborne dust has demonstrated broad success for sensitive and robust detection plants. Recent experiments at small spatial scales have suggested that animals can also be detected using eDNA. However, eDNA analysis never been used a long‐term whole‐community assessment natural terrestrial community or with passive collectors. We conducted metabarcoding survey targeting vertebrate carried in the air on an approximately 130‐acre shortgrass prairie over course year. Our wide variety animal forms including amphibian species, several bird both large mammals. found signals changed known patterns activity, wind speed, rainfall. Overall, we demonstrate carries could to detect species environment minimal effort. To develop this as valuable monitoring tool, research needs focus ecology air, which includes origin, state, transport, dispersal, fate environment.

Language: Английский

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Environmental DNA metabarcoding from flowers reveals arthropod pollinators, plant pests, parasites, and potential predator–prey interactions while revealing more arthropod diversity than camera traps

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(3), P. 551 - 569

Published: March 29, 2023

Abstract Arthropods can strongly impact ecosystems through pollination, herbivory, predation, and parasitism. As such, characterizing arthropod biodiversity is vital to understanding ecosystem health, functions, services. Emerging environmental DNA (eDNA) methods targeting trace eDNA left behind on flowers have the potential track interactions. The goal of this study was determine extent which metabarcoding identify plant‐arthropod arthropod‐arthropod interactions assess compared conventional sampling. We deployed camera traps document activity specific flowers, sampled from those same then performed a analysis that targets partial fragment cytochrome c oxidase subunit I gene (COI) all present. found our detected small pollinators, plant pests, parasites, shed light predator–prey while detecting 55 species just 21 trapping. trapping survey, however, larger, more conspicuous nectarivores successfully. also explored ecology residual eDNA, finding rainfall had significant negative effect ability detect eDNA. Preliminary evidence indicates flower may amount be detected. provide clues highlights insights gained future studies. show valuable tool for not only pollinator communities but revealing among plants, predators. Future research should focus how improve detection large pollinators/nectivores studying further explore method's utility.

Language: Английский

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Environmental DNA as an emerging tool in botanical research

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(2)

Published: Jan. 12, 2023

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species communities), means of elucidating biological interaction networks, window into understanding patterns biodiversity. However, only recently potential eDNA realized in botanical world. Here we synthesize state applications systems with emphases on aquatic, ancient, contemporary sediment, airborne systems, focusing both single-species approaches multispecies community metabarcoding. Further, describe how abiotic biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, relative abundance influence utilization interpretation results. Lastly, explore several areas opportunities for further development tools plants, advancing our knowledge efficacy, utility, cost-effectiveness, ultimately facilitating increased adoption analyses systems.

Language: Английский

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Targeting Terrestrial Vertebrates With eDNA: Trends, Perspectives, and Considerations for Sampling

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 1, 2025

ABSTRACT Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations species, rapid, cost‐effective, scalable methods needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA)‐based approaches being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA onto land, presented with new set challenges. This necessitates the development “best‐practice” sample collection guidelines systems purpose detecting vertebrates. address these needs, conducted systematic literature review 143 peer‐reviewed papers applying (excluding Lissamphibia) that were published between 2012 2023. We summarize use biomonitoring, focusing on study design field techniques. Over decade observe steady growth in annual number publications, 3 33 The majority reviewed studies targeted mammals temperate forest regions. While an equal focused metabarcoding approach assess community taxon composition and/or species‐specific detection methods, novel uses increasingly published. These include animal behavior genetics. record three types sampling strategies, eight different substrate types, seven preservation suggesting there is no “one size fits all” eDNA‐based methodology when With multitude aims, across environments, target organisms ecologies, standardization extremely challenging. table known factors influencing Furthermore, identify five key considerations be addressed targeting aim guiding decision making.

Language: Английский

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Airborne eDNA documents a diverse and ecologically complex tropical bat and other mammal community

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(2), P. 350 - 362

Published: Jan. 11, 2023

Abstract Environmental (e)DNA has rapidly become a powerful biomonitoring tool, particularly in aquatic ecosystems. This approach not been as widely adopted terrestrial communities where the methods of vertebrate eDNA collection have varied from use secondary collectors such blood feeding parasites and spider webs, to washing surfaces leaves soil sampling. Recent studies demonstrated potential direct air sampling, but none tested how effective airborne sampling might be biodiverse environment. We used three prototype samplers actively sample mixed neotropical bat community partially controlled assess whether can accurately characterize high diversity with skewed abundances determine if filter design impacts DNA taxonomic recovery. Our study provides evidence for accuracy detection tool highlights its monitoring density, diverse assemblages roosts. Analysis samples recovered >91% species present some limited relationship between abundance read count. data suggests this method depict mixed‐mammal community, when location is contained (e.g., roost, den or burrow) also transfer material on clothing equipment. results demonstrate that simple, inexpensive, battery‐operated homemade collect an air, opening opportunity remote environments.

Language: Английский

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Spider webs capture environmental DNA from terrestrial vertebrates

iScience, Journal Year: 2024, Volume and Issue: 27(2), P. 108904 - 108904

Published: Jan. 30, 2024

Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous environments, the continual exploration of new substrates is crucial. Here we test hypothesis that spider webs can act passive biofilters, capturing eDNA from vertebrates present local environment. Using metabarcoding approach, detected vertebrate all analyzed (N = 49). Spider obtained an Australian woodland locality yielded 32 different species, including native mammals and birds. In contrast, Perth Zoo, less than 50 km away, 61 produced highly distinct species composition, largely reflecting exotic hosted zoo. We show higher animal biomass proximity to enclosures increased detection probability Our results indicate tremendous potential using cost-effective means monitor vertebrates.

Language: Английский

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Capturing marine microbiomes and environmental DNA: A field sampling guide

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 12, 2023

The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection preservation standard practices enable comparative assessments of results across studies facilitate meta-analyses. We support this effort by providing guidelines based on review published methods field sampling experiences. major components considered here are environmental resource considerations, processing strategies, storage options, extraction protocols. It is impossible provide universal recommendations considering the wide range applications; rather, we information design fit-for-purpose To manage scope, focus prokaryotic microeukaryotic eDNA. Even with focused view, practical utility any approach depends multiple factors, including habitat type, available resources, experimental goals. broadly recommend enacting rigorous decontamination protocols, pilot guide filtration volume needed characterize target(s) minimize PCR inhibitor collection, prioritizing freezing over (only) addition buffer. An annotated list that test these parameters included more detailed investigation specific steps. illustrate an demonstrates methodologies, protocol aboard oceanographic vessel. These can aid decision-making process scientists interested sequencing microbiomes and/or

Language: Английский

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Deep‐sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1405 - 1417

Published: Aug. 18, 2023

Abstract The deep‐sea is vast, remote, and largely underexplored. However, methodological advances in environmental DNA (eDNA) surveys could aid the exploration efforts, such as using sponges natural eDNA filters for studying fish biodiversity. In this study, we analyzed from 116 sponge tissue samples compared these to 18 water visual obtained on an Arctic seamount. Across survey methods, revealed approximately 30% of species presumed inhabit area 11 were detected via derived alone. These included commercially important Greenland halibut Atlantic mackerel. Fish detection was highly variable across samples. Highest rates found with low microbial activity those class Hexactinellida. different methods also alternate communities, highlighted by only one overlap between Therefore, conclude that can be a useful tool surveying demersal communities it synergises improving overall biodiversity assessments. Datasets form comprehensive baselines seamounts, which turn inform marine management conservation practices regions where are undertaken.

Language: Английский

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Contrasting seasonal patterns in diet and dung‐associated invertebrates of feral cattle and horses in a rewilding area

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(8), P. 2071 - 2091

Published: Feb. 6, 2023

Abstract Trophic rewilding is increasingly applied in restoration efforts, with the aim of reintroducing ecological functions provided by large‐bodied mammals and thereby promote self‐regulating, biodiverse ecosystems. However, empirical evidence for effects megafauna introductions on abundance richness other organisms such as plants invertebrates, mechanisms involved still need strengthening. In this study, we use environmental DNA (eDNA) metabarcoding dung from co‐existing feral cattle horses to assess seasonal variation plant diet dung‐associated arthropods nematodes. We found consistently high horses, low variability, while generally lower dietary diversity increased substantially during summer. Intriguingly, season‐specific diets differed, a greater proportion trees horses' winter, where relied more shrubs. Graminoids were predominantly but underrepresented compared previous studies, possibly due prevalence forbs study area. Dung‐associated arthropod was higher cattle, largely flies Several species primarily one two herbivores, our data confirmed known patterns activity. Nematode constantly nematode communities markedly different between species. Our results demonstrate complementary through differences invertebrate communities, enhancing understanding large herbivore vegetation associated biodiversity. These are directly applicable decision‐making projects, suggesting biodiversity‐benefits inclusion functionally herbivores.

Language: Английский

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