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

---

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

---

Environmental DNA captures native and non-native fish community variations across the lentic and lotic systems of a megacity

Science Advances, Год журнала: 2022, Номер 8(6)

Опубликована: Фев. 11, 2022

Globally, urbanization poses a major threat to terrestrial biodiversity, yet its impact on fish diversity is poorly understood, mainly because of surveying difficulties. In this study, environmental DNA metabarcoding was used survey communities at 109 lentic and lotic sites across Beijing, how variables affect biodiversity fine urban spatial scales investigated. We identified 52 native 23 non-native taxa, with waters harboring both common habitat-specific species. Water quality strongly affected diversity, especially in systems, but had little influence diversity. Fish showed response land cover variation, the relative sequence abundance non-natives increased linearly distance from city center. Our findings illustrate complex effects versus fishes different aquatic habitats highlight distinctive considerations needed conserve biodiversity.

Язык: Английский

---

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, Год журнала: 2023, Номер 12, С. 100370 - 100370

Опубликована: Апрель 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.

Язык: Английский

---

Methodology for fish biodiversity monitoring with environmental DNA metabarcoding: The primers, databases and bioinformatic pipelines

Water Biology and Security, Год журнала: 2022, Номер 1(1), С. 100007 - 100007

Опубликована: Янв. 19, 2022

Environmental DNA (eDNA) originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled monitored using metabarcoding technology, which is revolutionizing fish biodiversity monitoring. Several reviews concerning eDNA have focused on standard sampling methods its applications, though a systematic review marker genes, databases, bioinformatic pipelines has not yet been published. Here, we present comprehensive literature of studies applying technology to for the purpose We systematically provide available universal primers used amplify barcoding sequences eDNA, then discuss reference relevant analyses, as well developed pipelines. The performances their databases are summarized. Combined use multiple primer pairs targeted more than one gene (e.g., 12S, 16S, Cytb, COI), both local public recommended approaches improve sensitivity reliability analyses. also compare effectiveness traditional monitoring highlight challenges future perspectives associated with this new tool. Ultimately, advocate greater incorporation analysis assessments assist environmental managers.

Язык: Английский

---

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, Год журнала: 2022, Номер 289(1973)

Опубликована: Апрель 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

Язык: Английский

---

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Conservation Biology, Год журнала: 2021, Номер 35(6), С. 1944 - 1956

Опубликована: Июль 5, 2021

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing nonlethal approaches based on video environmental DNA alternatives to underwater visual fishing. However, their ability detect multiple biodiversity factors beyond taxonomic diversity still unknown. For bony fishes elasmobranchs, we compared performance eDNA metabarcoding long-term remote assess species' phylogenetic functional diversity. We used 10 samples from 30 L water each 25 hr videos over 4 days Malpelo Island (pacific coast Colombia), protected area. Metabarcoding detected 66% more molecular operational units (MOTUs) than species video. found 66 43 entities with single marker videos, respectively, higher richness for videos. Despite gaps genetic reference databases, also fish videos; accumulation curves showed how 1 transect as much Environmental can be affordably, efficiently, accurately systems. Although assignments limited by coverage use MOTUs highlights potential once databases have expanded.Uso de ADN Ambiental en la Evaluación Diversidad Funcional y Filogenética los Peces Resumen La evaluación del impacto cambios globales efectividad protección es un paso fundamental para el monitoreo peces marinos. mayoría métodos tradicionales censos son demandantes o destructivos, por lo que las estrategias no letales intrusivas basadas videograbaciones ambiental (ADNa) alternativas visuales submarinos pesca. Sin embargo, todavía se conoce habilidad tienen estos detectar diferentes factores biodiversidad más allá diversidad taxonómica. Para óseos elasmobranquios, comparamos desempeño caracterización genética con ADNa remoto larga duración evaluar funcional filogenética especies. Usamos diez muestras tomadas litros agua cada una horas vídeos grabados durante cuatro días Isla (costa Pacífico área marina protegida remota. detectó unidades taxonómicas moleculares operacionales (UTMOs) Encontramos entidades funcionales solo marcador video, respectivamente, riqueza alta A pesar vacíos bases datos genéticos usadas como referencia, también aquella curvas acumulación mostraron cómo transecto tanta puede usarse censar manera asequible, eficiente certera sistemas Aunque atribuciones están limitadas cobertura especies uso UTMOs resalta potencial tiene vez referencia sean expandidas.评估全球变化影响及保护有效性是海洋鱼类监测的关键步骤。然而, 大多数传统种群调查方法都有较高的要求或具有破坏性。基于视频和环境 的非干扰性、非致死性方法则是水下视觉调查或鱼类捕捞的替代方法。然而, 这些方法检测传统分类学多样性之外其它生物多样性因子的能力尚不清楚。本研究关注硬骨鱼类和软骨鱼类, 比较了环境 DNA宏条形码和长期远程视频监测在评估物种的系统发育多样性和功能多样性中的表现情况。我们在一个偏远的海洋保护区--马尔佩洛岛 (哥伦比亚太平洋海岸) , 收集了10个分别取自 升水体的环境 样品, 以及4天共25小时的水下视频。结果发现, 环境 宏条形码比水下视频多检测出66%的分子操作分类单元 。我们利用单一环境DNA标记或视频分别发现了66个和 个功能实体, 利用环境 检测出的功能丰富度高于水下视频。尽管遗传参考数据库仍存在一些空缺, 但环境DNA 还是比视频检测出更高的鱼类系统发育多样性;累积曲线展示了1个环境 样带检测到的系统发育多样性相当于25小时的水下视频。环境 宏条形码可以经济、有效且准确地用于调查海洋系统中的生物多样性因子。尽管分类学鉴定仍受到遗传参考数据库中物种覆盖范围的限制, 但 的使用显现了在参考数据库得到扩充后环境 宏条形码所具备的潜力。【翻译:胡怡思;审校:聂永刚】.

---

A review of applications of environmental DNA for reptile conservation and management

Ecology and Evolution, Год журнала: 2022, Номер 12(6)

Опубликована: Июнь 1, 2022

Abstract Reptile populations are in decline globally, with total reptile abundance halving the past half century, and approximately a fifth of species currently threatened extinction. Research on distributions, population trends, trophic interactions can greatly improve accuracy conservation listings planning for recovery, but data deficiency is an impediment many species. Environmental DNA (eDNA) detect measure community diversity at diverse spatio‐temporal scales, especially useful detection elusive, cryptic, or rare species, making it potentially very valuable herpetology. We aim to summarize utility eDNA as tool informing management discuss benefits limitations this approach. A literature review was conducted collect all studies that used focus ecology, conservation, management. Results search summarized into key discussion points, also draws from other taxa highlight methodological challenges identify future research directions. has had limited application reptiles, relative vertebrate groups, little use regions high richness. techniques have been more successfully applied aquatic reptiles than terrestrial most (64%) focused habitats. Two four reptilian orders dominate existing (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our provides direction emerging ecology when be paired traditional monitoring approaches. Technologies associated rapidly advancing, become sensitive accessible, we expect will increasingly addressing knowledge gaps reptiles.

Язык: Английский

---

Environmental DNA metabarcoding reveals the impact of different land use on multitrophic biodiversity in riverine systems

The Science of The Total Environment, Год журнала: 2022, Номер 855, С. 158958 - 158958

Опубликована: Сен. 21, 2022

Язык: Английский

---

Nematode as a biomonitoring model for evaluating ecological risks of heavy metals in sediments from an urban river

Ecological Indicators, Год журнала: 2023, Номер 147, С. 110013 - 110013

Опубликована: Фев. 16, 2023

Heavy metals have attracted much attention due to their irreversibility, persistence, concealment and bioaccumulation. Biomonitoring method combined chemical analysis can be well evaluate health risks of heavy in the environment. In this study, eleven sediments water samples were collected along Xihe River, which was polluted by Shenyang city China. The content multiple these determined inductively coupled plasma mass spectrometry. 18S rRNA gene sequencing performed identify composition diversity nematodes fine River sediments. biological toxicity water-soluble extracts from further assessed referring different endpoints Caenorhabditis Elegans. results indicated that risk high (potential ecological index = 308.75), Hg Cd are main contributing factors. relative abundance complemented result, Enoplida, Mononchida, Triplonchida, Chromadorida presented a significant positive correlation with concentration metals. Specially, sensitive changes positively correlated As, Pb V. Therefore, such as applied environmental monitoring

Язык: Английский

---