Airborne environmental DNA for terrestrial vertebrate community monitoring

Current Biology, Год журнала: 2022, Номер 32(3), С. 701 - 707.e5

Опубликована: Янв. 6, 2022

Biodiversity monitoring at the community scale is a critical element of assessing and studying species distributions, ecology, diversity, movements, it key to understanding tracking environmental anthropogenic effects on natural ecosystems.1Navarro L.M. Fernández N. Guerra C. Guralnick R. Kissling W.D. Londoño M.C. Muller-Karger F. Turak E. Balvanera P. Costello M.J. et al.Monitoring biodiversity change through effective global coordination.Curr. Opin. Environ. Sustain. 2017; 29: 158-169Crossref Scopus (89) Google Scholar, 2Xu H. Cao Y. Yu D. M. He Gill Pereira H.M. Ensuring implementation post-2020 targets.Nat. Ecol. Evol. 2021; 5: 411-418Crossref PubMed (30) 3(2021). High time invest in biodiversity. Nat. 5, 263.Google 4Seibold S. Gossner M.M. Simons N.K. Blüthgen Müller J. Ambarli al.Arthropod decline grasslands forests associated with landscape-level drivers.Nature. 2019; 574: 671-674Crossref (391) Scholar Vertebrates terrestrial ecosystems are experiencing extinctions declines both population numbers sizes due increasing threats from human activities change.5Almond R.E.A. Grooten Petersen T. Living Planet Report 2020: Bending Curve Loss. WWF, 2020Google 6Ceballos G. Ehrlich P.R. Dirzo Biological annihilation via ongoing sixth mass extinction signaled by vertebrate losses declines.Proc. Natl. Acad. Sci. USA. 114: E6089-E6096Crossref (1031) 7Hughes J.B. Daily G.C. Population diversity: its extent extinction.Science. 1997; 278: 689-692Crossref (381) 8Gaston K.J. Fuller R.A. Commonness, depletion conservation biology.Trends 2008; 23: 14-19Abstract Full Text PDF (361) Terrestrial using existing methods generally costly laborious, although DNA (eDNA) becoming tool choice assess biodiversity, few sample types effectively capture diversity. We hypothesized that eDNA captured air could allow straightforward collection characterization communities. filtered three localities Copenhagen Zoo: stable, outside between outdoor enclosures, Rainforest House. Through metabarcoding airborne eDNA, we detected 49 spanning 26 orders 37 families: 30 mammal, 13 bird, 4 fish, 1 amphibian, reptile species. These spanned animals kept zoo, occurring zoo surroundings, used as feed zoo. The comprise range taxonomic families, sizes, behaviors, abundances. found shorter distance sampling device higher animal biomass increase probability detection. hereby show can offer fundamentally new way

Язык: Английский

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Towards the fully automated monitoring of ecological communities

Ecology Letters, Год журнала: 2022, Номер 25(12), С. 2753 - 2775

Опубликована: Окт. 20, 2022

Abstract High‐resolution monitoring is fundamental to understand ecosystems dynamics in an era of global change and biodiversity declines. While real‐time automated abiotic components has been possible for some time, biotic components—for example, individual behaviours traits, species abundance distribution—is far more challenging. Recent technological advancements offer potential solutions achieve this through: (i) increasingly affordable high‐throughput recording hardware, which can collect rich multidimensional data, (ii) accessible artificial intelligence approaches, extract ecological knowledge from large datasets. However, automating the facets communities via such technologies primarily achieved at low spatiotemporal resolutions within limited steps workflow. Here, we review existing data processing that enable communities. We then present novel frameworks combine technologies, forming fully pipelines detect, track, classify count multiple species, record behavioural morphological have previously impossible achieve. Based on these rapidly developing illustrate a solution one greatest challenges ecology: ability generate high‐resolution, standardised across complex ecologies.

Язык: Английский

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Airborne environmental DNA metabarcoding for the monitoring of terrestrial insects—A proof of concept from the field

Environmental DNA, Год журнала: 2022, Номер 4(4), С. 790 - 807

Опубликована: Март 11, 2022

Abstract Biodiversity is in decline due to human‐induced pressures on ecosystems around the world. To be able counteract this alarming trend, it paramount closely monitor biodiversity at global scales. Because practically impossible with traditional methods, last decade has seen a strong push for new solutions. In aquatic ecosystems, monitoring of species from environmental DNA (eDNA) emerged as one most powerful tools our disposal, but terrestrial power eDNA so far been hampered by local scale samples. study, we report successful detection insects airborne samples taken field. We compare results two insect methods (1) light traps moth and (2) transect walks butterflies wild bees. Airborne metabarcoding revealed six classes arthropods, twelve order insects—including representatives four largest orders: Diptera (flies), Lepidoptera (butterflies moths), Coleoptera (beetles), Hymenoptera (bees, wasps, ants). did not detect all observed using suggest further directions development metabarcoding. also recovered nine vertebrates, including frogs, birds, mammals well 12 other phyla. potential become tool monitoring, many impactful applications pests, invasive, or endangered disease vectors.

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

Environmental DNA, Год журнала: 2025, Номер 7(1)

Опубликована: Янв. 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.

Язык: Английский

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Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

Frontiers in Bioinformatics, Год журнала: 2022, Номер 2

Опубликована: Май 26, 2022

Phylogenetic placement refers to a family of tools and methods analyze, visualize, interpret the tsunami metagenomic sequencing data generated by high-throughput sequencing. Compared alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into phylogenetic context using set known reference taking evolutionary history account. Thereby, one can increase accuracy surveys eliminate requirement for having exact or close matches with existing sequence databases. constitutes valuable analysis tool per se , but also entails plethora downstream its results. A common use case is analyze species communities obtained from sequencing, example via taxonomic assignment, diversity quantification, sample comparison, identification correlations environmental variables. In this review, we provide an overview over developed during first 10 years. particular, goals review are 1) motivate usage illustrate some cases, 2) outline full workflow, raw publishable figures, including best practices, 3) introduce most their capabilities, 4) point out pitfalls misconceptions, 5) showcase typical placement-based analyses, how they help data.

Язык: Английский

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Novel community data in ecology-properties and prospects

Trends in Ecology & Evolution, Год журнала: 2023, Номер 39(3), С. 280 - 293

Опубликована: Ноя. 8, 2023

Язык: Английский

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Fungi as environmental bioindicators

The Science of The Total Environment, Год журнала: 2023, Номер 892, С. 164583 - 164583

Опубликована: Июнь 3, 2023

Язык: 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, Год журнала: 2023, Номер 5(2), С. 375 - 387

Опубликована: Янв. 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.

Язык: Английский

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Air-quality networks collect environmental DNA with the potential to measure biodiversity at continental scales

Current Biology, Год журнала: 2023, Номер 33(11), С. R426 - R428

Опубликована: Июнь 1, 2023

Язык: Английский

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