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

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 873, P. 162322 - 162322

Published: Feb. 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.

Language: Английский

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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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Towards evidence‐based conservation of subterranean ecosystems

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2022, Volume and Issue: 97(4), P. 1476 - 1510

Published: March 21, 2022

ABSTRACT Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness subterranean ecosystems, essential services they provide, and unique conservation challenges, 2021 2022 were designated International Years Caves Karst. As these traditionally been overlooked in global agendas multilateral agreements, a quantitative assessment solution‐based approaches to safeguard biota associated habitats is timely. This allows researchers practitioners understand progress made research needs ecology management. We conducted systematic review peer‐reviewed grey literature focused globally (terrestrial, freshwater, saltwater systems), quantify available evidence‐base for effectiveness interventions. selected 708 publications from years 1964 that discussed, recommended, or implemented 1,954 interventions ecosystems. noted steep increase number studies 2000s while, surprisingly, proportion quantifying impact has steadily significantly decreased recent years. The 31% tested statistically. further highlight 64% reported occurred Palearctic Nearctic biogeographic regions. Assessments heavily biased towards indirect measures (monitoring risk assessment), limited sample organisms (mostly arthropods bats), more accessible systems (terrestrial caves). Our results indicate science field biology does not apply rigorous approach, resulting sparse evidence raises important question how make efforts feasible implement, cost‐effective, long‐lasting. Although there no single remedy, propose suite potential solutions focus our better increasing statistical testing stress importance standardising study reporting facilitate meta‐analytical exercises. also provide database summarising literature, which will help build about likely yield greatest impacts depending upon species interest. view this as starting point shift away tendency recommending based anecdotal expert‐based information rather than scientific evidence, without quantitatively effectiveness.

Language: Английский

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Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 847, P. 157556 - 157556

Published: July 23, 2022

Global food production, supply chains and security are increasingly stressed by human population growth loss of arable land, becoming more vulnerable to anthropogenic environmental perturbations. Numerous mutualistic antagonistic species interconnected with the cultivation crops livestock these can be challenging identify on large scales production systems. Accurate identifications capture this diversity rapid scalable monitoring necessary emerging threats (i.e. pests pathogens), inform ecosystem health soil pollinator diversity), provide evidence for new management practices fertiliser pesticide applications). Increasingly, DNA (eDNA) is providing accurate classifications specific organisms entire assemblages in substrates ranging from air. Here, we aim discuss how eDNA being used agricultural ecosystems, what current limitations exist, could managed expand applications into future. In a systematic review that eDNA-based systems accounts only 4 % all studies. We found majority studies target plant (60 %), predominantly microbes insects %) biased towards Europe (42 %). While uncommon many world's systems, trend most pronounced economies often where at risk. suggest biggest agriculture false negatives resulting degradation assay biases, as well incomplete databases interpretation abundance data. These require silico, vitro, vivo approaches carefully design, test apply reliable taxonomic identifications. explore future opportunities research which further develop useful tool system both developed economies, hopefully improving monitoring, ultimately security.

Language: Английский

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Groundwater is a hidden global keystone ecosystem

Global Change Biology, Journal Year: 2023, Volume and Issue: 30(1)

Published: Dec. 12, 2023

Abstract Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being largest unfrozen freshwater resource, in period depletion by extraction pollution, groundwater environments have been repeatedly overlooked conservation agendas. Disregarding importance as an ignores its critical role preserving surface biomes. To foster timely groundwater, we propose elevating concept keystone species into realm ecosystems, claiming that influences integrity many dependent ecosystems. Our analysis shows over half land areas (52.6%) has medium‐to‐high interaction with reaching up 74.9% when deserts high mountains are excluded. We postulate intrinsic transboundary features for shifting perspectives towards more holistic approaches aquatic ecology beyond. Furthermore, eight key themes develop science‐policy integrated agenda. Given ecosystems above below ground intersect at levels, considering component planetary health pivotal reduce loss buffer against climate change.

Language: Английский

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The application gap: Genomics for biodiversity and ecosystem service management

Biological Conservation, Journal Year: 2023, Volume and Issue: 278, P. 109883 - 109883

Published: Jan. 4, 2023

The conservation of biodiversity from the genetic to community levels is fundamental for continual provision ecosystem services (ES), benefits that ecosystems provide people. Genetic and genomic diversity enhance resilience populations communities underpin functions services. We show genomics applications are mostly limited flagship species their ES management underachieved. propose a framework on how can guide sustainable bridge this genomics-ES 'application gap'. review knowledge in single (relatedness, potentially adaptive variants) or interacting (host-microorganism coevolution, hybridization) effective actions. These include population supplementation, assisted migration hybridization promote climate-adapted variants potential, control invasives, delimitation areas, provenancing strategies restoration, managing microbial function solving trade-offs. Genomics-informed actions improved outcomes supported through synergies between scientists managers at local, regional international levels, development standardized workflows, training incorporation local information. Such facilitate implementation policies such as UN 2030 goals EU Biodiversity strategy 2030, support inclusion ambitious new CBD post-2020 Global Framework hybrids.

Language: Английский

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Perspectives and pitfalls in preserving subterranean biodiversity through protected areas

npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 16, 2024

Subterranean ecosystems (comprising terrestrial, semi-aquatic, and aquatic components) are increasingly threatened by human activities; however, the current network of surface-protected areas is inadequate to safeguard subterranean biodiversity. Establishing protected for challenging. First, there technical obstacles in mapping three-dimensional with uncertain boundaries. Second, rarity endemism organisms, combined a scarcity taxonomists, delays accumulation essential biodiversity knowledge. Third, establishing agreements preserve requires collaboration among multiple actors often competing interests. This perspective addresses challenges preserving through areas. Even face uncertainties, we suggest it both timely critical assess general criteria protection implement them based on precautionary principles. To this end, examine status European discuss solutions improve their coverage ecosystems.

Language: Английский

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Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations

Frontiers in Conservation Science, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 2, 2025

Introduction Rewilding, the facilitation of self-sustaining and resilient ecosystems by restoring natural processes, is an increasingly popular conservation approach potential solution to biodiversity climate crises. Outcomes rewilding can be unpredictable, monitoring essential determine whether are recovering. Metabarcoding, particularly environmental DNA (eDNA), revolutionizing could play important role in understanding impacts but has mostly been applied within aquatic systems. Methods This systematic review focuses on applications eDNA metabarcoding terrestrial monitoring, with additional insights from bulk ingested DNA. We examine publication trends, choice sampling substrate focal taxa, investigate how well performs compared other methods (e.g. camera trapping). Results Terrestrial represented a small proportion total papers, forests most studied system, soil water substrates, vertebrates targeted taxa. Most studies focused measuring species richness, few included analyzes functional diversity. Greater richness was found when using multiple took this approach. Metabarcoding did not consistently outperform terms number vertebrate taxa detected, likely influenced marker, habitat. Discussion Our findings indicate that metabarcoding, eDNA, key rewilding, further ground- truthing needed establish appropriate experimental pipelines for target system interest. Systematic Review Registration https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0 , identifier 38w9q.

Language: Английский

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Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land‐use and geology

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(13), P. 3497 - 3512

Published: April 17, 2023

Abstract Despite being the most important source of liquid freshwater on planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It thus extensively monitored for pollutants and declines in quantity. The organisms living groundwater, however, are rarely target surveillance programmes little known about fauna inhabiting underground habitats. difficulties accessing lack expertise, apparent scarcity these challenge sampling prohibit adequate knowledge fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome limitations but largely unexplored. Here, we sampled water 20 communal spring catchment boxes used drinking provisioning Switzerland, with a high level replication at both filtration amplification steps. We sequenced portion COI mitochondrial gene, which resulted 4917 ASVs, yet only 3% reads could be assigned species, genus, family more than 90% identity. Careful evaluation unassigned corroborated that sequences were true belonging mostly diverse eukaryotic groups, not present reference databases. Principal component analyses showed strong correlation community composition surface land‐use (agriculture vs. forest) geology (fissured rock unconsolidated sediment). While incomplete databases limit assignment taxa eDNA metabarcoding, taxonomy‐free approaches can reveal large hidden diversity couple it major drivers, revealing their imprint chemical biological properties groundwater.

Language: Английский

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Towards invasion ecology for subterranean ecosystems

Biodiversity and Conservation, Journal Year: 2024, Volume and Issue: 33(4), P. 1561 - 1569

Published: March 1, 2024

Abstract Invasive alien species (IAS) are widely recognized as a major threat to ecosystems globally. Despite the growing interest and research effort on biological invasions, impact of IAS both terrestrial aquatic subterranean habitats remains considerably under-studied in comparison other environments. The Convention Biological Diversity (CBD) has established global targets mitigate impacts IAS, emphasizing need for countries, organizations, scientific community identify gaps knowledge, monitoring, management strategies IAS. To this end, we mapped knowledge invasions that emerged from first systematic surveys available information. We suggest there five main restricting our ability understand tackle ecosystems. Given vulnerability lack attention they have received conservation policies, it is crucial increase emphasis This opinion paper aims stimulate such efforts contribute preservation these

Language: Английский

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