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

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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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Future of DNA-based insect monitoring

Trends in Genetics, Год журнала: 2023, Номер 39(7), С. 531 - 544

Опубликована: Март 10, 2023

Язык: Английский

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Towards exhaustive community ecology via DNA metabarcoding

Molecular Ecology, Год журнала: 2023, Номер 32(23), С. 6320 - 6329

Опубликована: Фев. 10, 2023

Abstract Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability perform inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority published last years used just one or two markers analysed limited number taxonomic groups. Here, we provide overview emerging that can allow all‐taxa biological by combining large specific primers, exploiting power universal primers obtain good information key while limiting overlooked biodiversity. Multiplexes shotgun sequencing capture enrichment may better coverage compared standard metabarcoding, but still require major methodological advances. identify strengths limitations approaches, suggest new development lines might improve broad scale analyses near future. More ecological communities greatly increase value studies, improving understanding consequences ongoing environmental multiple components

Язык: Английский

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A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Molecular Ecology Resources, Год журнала: 2023, Номер 24(5)

Опубликована: Авг. 7, 2023

Abstract Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through require sophisticated processing of high‐throughput sequencing data from taxonomically informative barcodes. Various sets universal and taxon‐specific primers have been developed, extending the usability across archaea, bacteria eukaryotes. Accordingly, multitude analysis tools pipelines also developed. Often, several developed workflows are designed to process same amplicon data, making it somewhat puzzling choose one among plethora existing pipelines. each pipeline its own specific philosophy, strengths limitations, which should be considered depending on aims any study, well bioinformatics expertise user. In this review, we outline input requirements, supported operating systems particular attributes thirty‐two with goal helping users select their projects.

Язык: Английский

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Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Environmental DNA, Год журнала: 2023, Номер 5(6), С. 1133 - 1147

Опубликована: Сен. 28, 2023

Abstract Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range organisms and aquatic systems. Environmental DNA (eDNA) environmental RNA (eRNA), collectively referred to as nucleic acids (eNAs), revolutionized monitoring due their noninvasive nature high‐resolution capabilities when compared traditional survey methods. While eNA applications grown exponentially over past decade, methodological inconsistencies hinder reproducibility comparability. To assess current state methodologies in ecology, we conducted systematic review 300 peer‐reviewed studies that ecological communities diverse Of these papers, 291 examine eDNA, four eRNA, five consider both eDNA eRNA. The small number eRNA highlights field is its infancy. looked at, found clear geographic bias, with approximately 50% all occurring six high‐income countries, while less than 10% occur South America Africa. Further, report lack standardization studies, showing high variability water filtration volume, filter material, pore size, extraction method, marker choice, bioinformatic pipelines. We further highlight incomplete reference sequence databases for limit taxonomic assignment inferences. Finally, identify issue community ecology: missing details, which compromise reproducibility, especially newly emerging applications. facilitate systems permit integration monitoring, recommend improvement alongside guidelines encourage transparency.

Язык: Английский

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Three steps towards comparability and standardization among molecular methods for characterizing insect communities

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1904)

Опубликована: Май 5, 2024

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based large-scale monitoring, to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, provide three recommendations how harmonize efforts biodiversity assessment monitoring via metabarcoding: (i) should adopt use synthetic spike-ins, which will act as positive controls internal standards; (ii) consider using several markers through a multiplex polymerase chain reaction (PCR) approach; (iii) commit publication transparency all protocol-associated metadata standardized fashion. For (i), ready-to-use recipe cytochrome

Язык: Английский

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Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation

Molecular Ecology Resources, Год журнала: 2021, Номер 22(3), С. 847 - 861

Опубликована: Сен. 8, 2021

Metabarcoding of DNA extracted from community samples whole organisms (whole organism DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities provide rapid, accurate high resolution data for novel molecular ecology research. The growth this field has been accompanied by considerable development that builds on microbial metabarcoding methods develop appropriate efficient sampling laboratory protocols communities. However, considerably less attention focused ensuring bioinformatic are adapted comprehensively in wocDNA metabarcoding. In study we examined over 600 papers identified 111 studies performed COI wocDNA. We then systematically reviewed the employed these identify state-of-the-art. Our results show increasing use diversity characterised a clear absence harmonisation, temporal trends little change situation. literature showed (i) heterogeneity across pipelines, tasks tools used, (ii) limited or no adaptation procedures nature fragment, (iii) worrying underreporting tasks, software parameters. Based upon findings propose set recommendations think should consider ensure appropriate, comprehensive comparable. believe adhering will improve long-term integrative potential biodiversity science.

Язык: Английский

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Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

GigaScience, Год журнала: 2022, Номер 11

Опубликована: Янв. 1, 2022

Abstract Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond global change. However, large-scale syntheses may be compromised if workflows differ from each other. There are ongoing efforts improve standardization the reporting inventory harmonization at stage metabarcode has yet addressed. A modular framework harmonized generation a pathway navigate complex structure terrestrial metazoan biodiversity. Here, through our collective expertise practitioners, method developers, researchers leading initiatives we seek initiate generation, arthropod module. We develop initial set submodules covering 5 main steps generation: (i) sample acquisition; (ii) processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, sequencing; (v) sequence metadata deposition, providing backbone To achieve this, identified key points harmonization, reviewed current state art, distilled existing knowledge within submodules, thus promoting best practice by guidelines recommendations reduce universe methodological options. advocate adoption further development encourage modules other fractions step toward synthesis harmonization.

Язык: Английский

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Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects

Parasites & Vectors, Год журнала: 2023, Номер 16(1)

Опубликована: Фев. 14, 2023

Blood-feeding insects are important vectors for an array of zoonotic pathogens. While previous efforts toward generating molecular resources have largely focused on major global medical and veterinary importance, data across a large number hematophagous insect taxa remain limited. Advancements in long-read sequencing technologies associated bioinformatic pipelines provide new opportunities targeted mitochondrial (mt) genomes. For engorged insects, such can be leveraged both mitogenome genome assembly identification vertebrate blood-meal sources. We used nanopore adaptive sampling (NAS) to sequence genomic DNA from four species field-collected, blood-engorged mosquitoes (Aedes Culex spp.) one deer fly (Chrysops sp.). NAS was bioinformatical enrichment mtDNA reads potential hosts using publically available mt genomes as references. also performed experimental control compare results traditional non-NAS the by method. Complete mitogenomes were assembled annotated all five sequenced with NAS: Aedes trivittatus, vexans, restuans, territans fly, Chrysops niger. In comparison generated during our experiment, yielded substantially higher proportion reference-mapped reads, greatly streamlining downstream annotation. The NAS-assembled ranged length 15,582 16,045 bp, contained between 78.1% 79.0% A + T content shared anticipated arrangement 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs. Maximum likelihood phylogenies further characterize each species. Additionally, analysis successful three samples sequenced, mtDNA-based phylogenetic analyses revealing that sources niger, restuans trivittatus human, house sparrow (Passer domesticus) eastern cottontail rabbit (Sylvilagus floridanus), respectively. Our findings show has dual utility simultaneously molecularly identify their hosts. Moreover, indicate facilitate wide mitogenomic systematic studies through novel 'phylogenetic capture' methods. conclude approach great broadly improving blood-feeding answer questions elucidate complex pathways transmission vector-borne

Язык: Английский

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