Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(13), P. 2937 - 2958

Published: May 16, 2020

Abstract A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on biodiversity and functioning ecosystems is yet to be implemented by regulatory frameworks. Despite broadly acknowledged potential genomics this end, technical limitations conceptual issues still stand way its broad application end‐users. In addition, multiplicity implementation strategies may contribute a perception that routine methodology premature or “in development”, hence restraining regulators from binding these tools into legal Here, we review recent implementations methods, applied biomonitoring ecosystems. By taking general overview, without narrowing our perspective particular habitats groups organisms, paper aims compare, discuss strengths four for monitoring: (a) Taxonomy‐based analyses focused identification known bioindicators described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; (d) Functional (metagenomics metatranscriptomics). We emphasise utility three latter integrate meiofauna microorganisms are not traditionally utilised because difficult taxonomic identification. Finally, propose roadmap programmes leverage analytical advancements, while pointing out current future research needs.

Language: Английский

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Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 818, P. 151783 - 151783

Published: Nov. 19, 2021

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification whole communities within a targeted group) is revolutionizing the field aquatic biomonitoring. To date, most studies aiming to assess ecological status ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, has also been applied soft sediment samples, mainly assessing microbial or meiofaunal biota. Compared classical methodologies based manual sorting morphological benthic taxa, offers potentially important advantages environmental quality sediments. The methods protocols utilized can vary considerably among studies, standardization efforts are needed improve their robustness, comparability use regulatory frameworks. Here, we review available information with focus sampling, preservation, extraction steps. We discuss challenges specific analysis, including variety different sources states its persistence in sediment. This paper aims identify good-practice strategies facilitate method harmonization routine future monitoring.

Language: Английский

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A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 788, P. 147868 - 147868

Published: May 20, 2021

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced are likely pose an elevated risk of impact native and ecosystems. To inform policy, stakeholders management decisions on threats aquatic ecosystems, 195 assessors representing 120 assessment areas across all six inhabited continents screened 819 from 15 groups organisms (freshwater, brackish, marine plants animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for screening provides with scores under current future climate change conditions that, following statistically based calibration, permits accurate classification into high-, medium- low-risk categories predicted conditions. 1730 screenings undertaken encompassed wide geographical (regions, political entities, parts thereof, water bodies, river basins, lake drainage regions), permitted thresholds be identified almost organismal as well tropical, temperate continental classes, tropical ecoregions. In total, 33 were posing 'very high risk' being or becoming invasive, several these increased conditions, primarily due their thermal tolerances. determined taxonomic zones provide basis against area-specific climate-based calibrated may interpreted. turn, rankings help decision-makers require immediate 'rapid' action (e.g. eradication, control) avoid mitigate adverse impacts, full assessment, restricted banned regard importation and/or sale ornamental aquarium/fishery enhancement.

Language: Английский

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Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

Journal of Applied Ecology, Journal Year: 2020, Volume and Issue: 57(4), P. 707 - 716

Published: March 10, 2020

Abstract Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring in both marine and freshwater ecosystems. However, for semi‐aquatic terrestrial animals, the application of this technique remains relatively untested. We first assess efficiency eDNA detecting mammals natural lotic ecosystems UK by comparing sequence data recovered from water sediment samples to mammalian communities expected historical data. Secondly, using occupancy modelling we compared detection multiple conventional non‐invasive survey methods (latrine surveys camera trapping). detected a large proportion community within each area. Common species areas were at majority sites. Several key conservation concern sampling where authenticated records do not currently exist, but potential false positives also identified. Water‐based provided comparable results per unit effort three (water vole, field vole red deer) models. The comparison between ‘effort’ reach probability ≥.95 revealed that 3–6 replicates would be equivalent 3–5 latrine 5–30 weeks single deployment, depending on species. Synthesis applications . can used generate an initial ‘distribution map’ diversity landscape level. If conducted during times peak abundance, carefully chosen points along river courses provide reliable snapshot are present catchment In order fully capture solitary, rare invasive species, recommend use alongside other surveying (i.e. traps) maximize monitoring efforts.

Language: Английский

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Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: May 20, 2020

Abstract Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability coastal ecosystems in our oceans, but rarely are these changes documented across both time space. The characterisation environmental DNA (eDNA) sediment seawater using metabarcoding offers a powerful molecular lens observe marine biota provides series ‘snapshots’ broad spectrum eukaryotic organisms. Using next-generation tools downstream analytical innovations including machine learning sequence assignment algorithms co-occurrence network analyses, we examined how anthropogenic pressures may have impacted on subtropical coral reefs Okinawa, Japan. Based 18 S ribosomal RNA, not ITS2 data due inconsistent amplification for this marker, as well proxies disturbance, show that richness at the family level significantly increases with medium high disturbance. This change coincides compositional changes, decrease connectedness among taxa, an increase fragmentation taxon networks, shift indicator taxa. Taken together, findings demonstrate ability eDNA act barometer disturbance provide exemplar biotic networks be by activities.

Language: Английский

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Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(13), P. 3175 - 3188

Published: Sept. 25, 2020

In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or setting-up settlement structures. Comparatively much less effort is required to sample water column, which can be accessed remotely. this study we assess feasibility obtaining information from eukaryotic by adjacent layer. We studied two different rocky-substrate with a technique based on quadrat sampling. also took replicate samples at four distances (0, 0.5, 1.5, and 20 m) habitat. Using broad range primers amplify ca. 313 bp fragment cytochrome oxidase subunit I gene, obtained total 3,543 molecular operational taxonomic units (MOTUs). The structure in environments was markedly different, Metazoa, Archaeplastida Stramenopiles being most diverse groups samples, Hacrobia, Metazoa Alveolata water. Only 265 MOTUs (7.5%) were shared between benthos and, these, 180 (5.1%) identified as taxa that left their Most them found immediately benthos, number decreased moved apart It concluded eDNA, even close vicinity poor proxy for analysis structure, methods are monitoring these complex via metabarcoding.

Language: Английский

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Life in a drop: Sampling environmental DNA for marine fishery management and ecosystem monitoring

Marine Policy, Journal Year: 2020, Volume and Issue: 124, P. 104331 - 104331

Published: Dec. 5, 2020

Language: Английский

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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance

Water, Journal Year: 2021, Volume and Issue: 13(8), P. 1113 - 1113

Published: April 18, 2021

The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species management conservation decisions. Developing technologies standard protocols within biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective deposition processes, hydrochemistry pH, contaminating agents. These approaches also provide a robust framework that meets decisions regarding threats human health, environmental resources, economic interests, especially areas limited clean-laboratory resources experienced personnel. This contribution aims facilitate dialogue innovation this by reviewing current sample collection, post-sampling capture concentration eDNA, preservation, extraction, all through monitoring lens.

Language: Английский

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Short‐term temporal variation of coastal marine eDNA

Environmental DNA, Journal Year: 2022, Volume and Issue: 4(4), P. 747 - 762

Published: Feb. 23, 2022

Abstract Temporal variation in eDNA signals is increasingly explored for understanding community ecology aquatic habitats. Seasonal changes have been addressed using sampling, but very little known regarding short‐term temporal that spans hours to days. To address this, we filtered marine water samples from a single coastal site Denmark every hour 32 h. We used metabarcoding target both fish and broader eukaryote diversity evaluated this community. Results revealed species richness (15–27) class (35–64) across the h of further sampling efforts needed reach different levels saturation. Relative read frequency data eukaryotes indicated clear diel change composition, with communities detected during daylight versus dark hours. The abundance our reflected biological rather than stochastic variation, since replicates taken at same were more similar each other those Our compositional results dynamic community, static pool eDNA—even few showed daily pattern relative abundances, uncoupling suggest profiles day can provide valuable information reflecting changes, least highly mobile organism groups. However, also point several pitfalls current experimental design, which are over large areas without time‐consistency or replication. findings shed new light on wide implications study design incorporating temporality into project conceptualization future biodiversity monitoring.

Language: Английский

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Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

Environmental DNA, Journal Year: 2021, Volume and Issue: 3(6), P. 1247 - 1266

Published: July 21, 2021

Abstract While many studies have considered the ability of eDNA to assess animal communities in lacustrine settings, fewer riverine systems, particularly those spanning environmental gradients present large river basins. Such dynamic systems are challenging for biomonitoring due differing transport distances rivers and effects chemistry. To address this challenge, we focused on Thames River system, UK, which has exceptional historical fish records providing a baseline test accuracy metabarcoding recovering community structure across both fresh tidal zones. Two primer sets targeting 12S CO1 regions were used capture catchment, from upper freshwaters mid estuary. was collected at 35 sites, 14 simultaneously paired with traditional surveys direct comparison. We demonstrated that consistently detected more freshwater species than methods, despite extensive sampling effort using latter. In contrast, did not perform as well approaches estuarine waters, although results included novel detection protected sea lamprey. further minor variations recovery all would impact assessment simple ecological models and, thus, some variability between should be viewed serious hindrance uptake. Rather, our findings support growing consensus can reliably detect habitats.

Language: Английский

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