The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations

Diversity, Journal Year: 2023, Volume and Issue: 15(5), P. 631 - 631

Published: May 6, 2023

Aquatic non-indigenous species (NIS) threaten biodiversity, ecosystem functions, and the economy worldwide. Monitoring NIS is of immediate concern to identify newly arriving species, assess efficacy mitigation measures, report long-term indicators introduction, spread, impacts. The challenges associated with conventional methods specimen collection morphological identification have led development alternative methods, such as DNA-based which could offer rapid cost-effective detection NIS. Depending on whether a few (targeted monitoring) or many (passive are being monitored, environmental DNA (eDNA) can infer presence-absence relative abundances, enabling informed decisions actions be made based patterns detection. Compared more eDNA tools increase levels sensitivity for rare elusive even noticeable some taxa when using targeted monitoring. use not only minimizes onus taxonomic expertise reduces resource demands but also sensitive cost-efficient in detecting NIS, thus proving its value an early warning tool. As nucleic acid (DNA/RNA) advance rapidly detection, there must balance between method sensitivity, logistical requirements, costs, factored into future management decisions. While complementary reviews available, our aim emphasize importance incorporating surveys highlight available opportunities this field.

Language: Английский

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Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19158 - e19158

Published: April 14, 2025

DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, their implementation as standardized monitoring is approaching. Evaluating the efficacy reliability these technological crucial for assessments. In this study, we compared three techniques assessing diversity bulk samples from Belgian North Sea. Specifically, amplicon using Illumina MiSeq portable real-time Oxford Nanopore versus shotgun NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served target region analysis. Our results indicate that had similar performances in terms alpha beta diversity, revealing highly location-specific community compositions. metagenomics method also resulted but slightly different compositions approach. Despite differences, were maintained across all platforms. Notably, read counts metagenomic analysis showed weakest correlation size corrected morphological abundance there mismatches between identification DNA based findings which likely caused by a combination factors such primer efficiency an incomplete reference database. underscore critical importance database completeness prior implementing method, especially metagenomics. Nevertheless, our emphasize proves be viable alternative conventional platform monitoring.

Language: Английский

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Benchmarking the discrimination power of commonly used markers and amplicons in marine fish (e)DNA (meta)barcoding

Published: June 3, 2024

Environmental DNA (eDNA) metabarcoding is revolutionizing the study of aquatic ecosystems, enabling high-throughput analysis biodiversity with minimal disturbance. Despite its potential to support fisheries management, species identification and downstream reliability are hindered by lack standardization in fragment choice. This compares discrimination power three markers used marine fish eDNA —12S rRNA, 16S cytochrome oxidase subunit I (COI)— as well two amplicons for each. We analyzed sequences from NCBI GenBank 10 orders Actinopterygii, including mitochondrial genomes. assessed determining percentage monophyletic Neighbor-Joining trees calculating average congeneric divergences data sets: one genomic regions extracted genomes (771 species) another independent each region (3879 species). Among (meta)barcoding amplicons, genomes’ dataset, Folmer Leray-Lobo had highest discriminatory power, 89.2% 87% species, respectively, while 12S Teleo lowest at 71.6%. Conversely, using sequences, percentages 64.8% 63.5%, Ac16S 83.0%. Species influenced marker’s substitution rate, length, target order, quality reference sequence data. recommend considering differences amplicon selection, especially species-level identifications. advise a standard multi-marker approach under certain scenarios, namely when presence close expected.

Language: Английский

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Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach

Marine Environmental Research, Journal Year: 2024, Volume and Issue: 200, P. 106660 - 106660

Published: July 30, 2024

eDNA metabarcoding has been increasingly employed in the monitoring of marine invertebrate non-indigenous species (NIS), particular using filtered seawater. However, comprehensive detection all NIS may require a diversity sampling substrates. To assess effectiveness 5 sample types (hard and artificial substrates, water, zooplankton) on recovery invertebrates' diversity, two marinas were monitored over three time points, COI 18S rRNA genes as DNA markers. We detected total 628 23 NIS, with only up to 9% 17% by types. Hard substrates similar each other but displayed most significant difference when compared water zooplankton. Five are potential first records for Portugal. No seasons, highlighting need varied approaches, consideration temporal variation surveillance.

Language: Английский

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Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Aug. 26, 2024

Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA 16S gene markers, comparison to morphology-based methods fish species identification ichthyoplankton samples. Two transects with four coastal distance categories were sampled along southern coast Portugal, being each sample divided molecular morphological analyses. A total 76 identified by both approaches, overperforming morphology-75 versus 11 species-level identifications. Linking identifications higher taxonomic resolved several uncertainties associated traditional methods. Multi-marker improved detection 20-36% compared a single marker/amplicon, 38 common, reinforcing validity our results. PERMANOVA analysis revealed significant differences communities based on primer set employed, transect location, from coast. Our findings underscore potential assess diversity suggest that its integration routine surveys could enhance accuracy comprehensiveness assessments.

Language: Английский

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Artificial Seaweed Substrates Complement ARMS in DNA Metabarcoding-Based Monitoring of Temperate Coastal Macrozoobenthos

Diversity, Journal Year: 2023, Volume and Issue: 15(5), P. 657 - 657

Published: May 12, 2023

We used DNA metabarcoding to compare macrozoobenthic species colonization between autonomous reef monitoring structures (ARMS) and artificial seaweed systems (ASMS). deployed both substrates in two different locations (Ría de Vigo Ría Ferrol, NW Iberian coast) collected them after 6, 9, 12 months assess composition of the colonizing communities through high-throughput sequencing amplicons within barcode region mitochondrial cytochrome c oxidase I (COI-5P) V4 domain 18S rRNA genes. observed a consistently low similarity substrate types, independently sampling times sites. A large fraction exclusive was recorded for given (up 72%), whereas only up 32% were substrates. The shape structural complexity strongly affected preferences, with ASMS detecting more crustacean gastropod broader diversity taxonomic groups (e.g., Entoprocta Pycnogonida detected exclusively ASMS). demonstrate that despite customary use ARMS macrozoobenthos monitoring, by using we complemented recovery enlarged scope recorded.

Language: Английский

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A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

iScience, Journal Year: 2023, Volume and Issue: 27(1), P. 108588 - 108588

Published: Nov. 25, 2023

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they often biased by inconsistent sampling methods incomplete reference databases. Logistic constraints prompt the development simple, easy-to-deploy samplers. We tested a new device called polyamide mesh organismal (POMPOM) with high surface-to-volume ratio. POMPOMS were deployed inside fishing recreational port Mediterranean alongside conventional settlement plates. also compiled curated database cytochrome oxidase (COI) sequences NIS. COI metabarcoding communities settled POMPOMs captured similar biodiversity than plates, shared molecular operational units (MOTUs) representing ca. 99% reads. 38 NIS detected accounting 26% easy to deploy handle provide an efficient method surveillance.

Language: Английский

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Polychaetes (Annelida) of Cyprus (Eastern Mediterranean Sea): An Updated and Annotated Checklist including New Distribution Records

Diversity, Journal Year: 2023, Volume and Issue: 15(8), P. 941 - 941

Published: Aug. 19, 2023

The diversity and distribution of polychaetes in the coastal area EEZ Republic Cyprus is presented based on both literature records new data acquired a wide range environmental monitoring programmes research projects. A total 585 polychaete species belonging to 49 families were reported waters; among them, 205 (34%) recorded only, 149 (26%) our own data, 231 spp. (40%) from data. 51 identified as non-indigenous; 32 confirmed alien species, 4 considered cryptogenic, 15 questionable there doubts about their identity. Indo-Pacific Schistomeringos loveni was for first time Mediterranean Sea, while four already literature, namely, Bispira melanostigma, Fimbriosthenelais longipinnis Leonnates aylaoberi, Rhodopsis pusilla, added list non-indigenous Sea. current work highlights importance implementing carrying out surveys targeting benthic macrofauna assemblages.

Language: Английский

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Non-indigenous polychaetes along the Salento Peninsula: new records and first molecular data

Mediterranean Marine Science, Journal Year: 2024, Volume and Issue: 25(1), P. 184 - 203

Published: April 15, 2024

The Salento Peninsula represents the eastern-most edge of Italian Peninsula, and one first areas to be invaded by thermophilic non-indigenous species. diversity polychaetes occurring along is reviewed based on literature data new samples. Overall, fifteen were recorded; among them, Syllis similisunzima reported for time in Mediterranean Sea; Lepidonotus tenuisetosus recorded waters; Pseudonereis anomala, until now known only Sicily, from Peninsula; Dorvillea similis a record Ionian Adriatic Sea. 16S rDNA COI sequences obtained eleven species, allowing us some cases confirm their identity and/or geographical origin, while case species they represent molecular ever obtained.

Language: Английский

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Towards a Comprehensive DNA Barcode Library of Stenochironomus Kieffer, 1919 (Diptera: Chironomidae) from China

Diversity, Journal Year: 2024, Volume and Issue: 16(5), P. 257 - 257

Published: April 24, 2024

The adoption of DNA-based assessments for biodiversity monitoring has been on the rise. However, effectiveness taxonomic assignments heavily relies availability and reliability DNA barcode libraries. There is growing demand a comprehensive understanding aquatic critical role Chironomidae, specifically Stenochironomus in freshwater ecosystems. Therefore, our objective to develop reference library China. From 2016 2021, we collected specimens diverse Chinese landscapes using malaise traps, light sweep nets. These were carefully preserved extraction sequencing. Our analysis unveiled 36 unique operational units from 180 COI sequences through Neighbor-Joining tree Automatic Barcode Gap Discovery program, highlighting significant diversity within species. findings emphasize constraints conventional morphological identification methods, especially species with ambiguous morphologies. It also underscores barcoding revealing hidden diversity, known as cryptic Consequently, this study advocates an integrated approach, combining molecular data, refine conservation strategies.

Language: Английский

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