Environmental (e)RNA advances the reliability of eDNA by predicting its age

Scientific Reports, Год журнала: 2021, Номер 11(1)

Опубликована: Фев. 2, 2021

Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age origin eDNA is complicated by particle transport the presence legacy genetic material, which can obscure interpretation detection quantification. To understand state genomic material within environment, we investigated degradation relationships between (a) size fragments (long vs short), (b) origins (mitochondrial nuclear), (c) nucleic acids (eDNA eRNA), (d) RNA types (messenger (m)RNA ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that eDNA, a mitosis-associated mRNA falling below limits 24 h. Furthermore, ratio eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for material. Thus, quantification increase due to high rRNAs. it may improve positive detections through and/or detecting low abundant mRNAs degrade ~

Язык: Английский

---

Environmental DNA effectively captures functional diversity of coastal fish communities

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 3127 - 3139

Опубликована: Окт. 20, 2020

Abstract Robust assessments of taxonomic and functional diversity are essential components research programmes aimed at understanding current biodiversity patterns forecasting trajectories ecological changes. Yet, evaluating marine along its dimensions is challenging dependent on the power accuracy available data collection methods. Here we combine three traditional survey methodologies (underwater visual census strip transects [UVCt], baited underwater videos [BUV] small‐scale fishery catches [SSFc]), one novel molecular technique (environmental DNA metabarcoding [eDNA]—12S rRNA cytochrome oxidase subunit 1 [COI]) to investigate their efficiency complementarity in assessing fish diversity. We analysed 1,716 multimethod replicates a basin scale measure Mediterranean assemblages. Taxonomic identities were investigated species, genus family levels. Functional assessed using combinations morphological, behavioural trophic traits. show that: (a) SSFc provided higher estimates followed by eDNA, then UVCt BUV; (b) eDNA was only method able gather whole spectrum considered traits, showing most functionally diversified least redundant assemblages; (c) effectiveness describing structure reflected lack selectivity towards any trait. Our findings suggest that reach analysis stretches beyond taxon detection provides new insights into potential studies.

Язык: Английский

---

Species on the move around the Australian coastline: A continental‐scale review of climate‐driven species redistribution in marine systems

Global Change Biology, Год журнала: 2021, Номер 27(14), С. 3200 - 3217

Опубликована: Апрель 9, 2021

Climate-driven changes in the distribution of species are a pervasive and accelerating impact climate change, despite increasing research effort this rapidly emerging field, much remains unknown or poorly understood. We lack holistic understanding patterns processes at local, regional global scales, with detailed explorations range shifts southern hemisphere particularly under-represented. Australian waters encompass world's third largest marine jurisdiction, extending from tropical to sub-Antarctic zones, have warming rates twice average north two four times south. Here, we report results multi-taxon continent-wide review describing observed predicted redistribution around coastline, highlight critical gaps knowledge impeding our of, response to, these considerable changes. Since were first reported region 2003, 198 nine Phyla been documented shifting their distribution, 87.3% which poleward. However, there is little standardization methods metrics shifts, both hindered by baseline data. Our demonstrate importance historical data sets underwater visual surveys, also that approximately one-fifth studies incorporated citizen science. These findings emphasize important role public has had, can continue play, change. Most coastal fish sub-tropical temperate systems, while systems general explored. Moreover, most distributional only described poleward boundary, few considering warmer, equatorward limit. Through identifying limitations, highlights future opportunities for strategic improve representation climate-impact research.

Язык: Английский

---

Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 3140 - 3157

Опубликована: Авг. 8, 2020

Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk sampling and morphological identification. We assessed whether eDNA (2 L filtered seawater) could capture similar Southern Ocean zooplankton conventional CPR (~1,500 seawater per sample). directly compared with (a) (b) of collected (two transects each comparison, 40 44 paired samples, respectively). A metazoan-targeted cytochrome c oxidase I (COI) marker was used to characterize species-level diversity. In 2 this amplified large amounts non-metazoan picoplanktonic algae, but still detected up 1.6 times more species than morphologically analysed samples. COI samples mostly avoided nonmetazoan amplifications recovered metabarcoding. However, roughly two thirds identified taxa contributing community differentiation across subtropical front separating transects. observed diurnal pattern data copepods which perform diel vertical migrations, indicating surprisingly short temporal signal. Compared COI, eukaryote-targeted 18S ribosomal RNA higher proportion, lower diversity, metazoans eDNA. With refinement standardization methodology, become an efficient

Язык: Английский

---

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

Molecular Ecology Resources, Год журнала: 2021, Номер 21(7), С. 2546 - 2564

Опубликована: Июль 8, 2021

Abstract DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate performance MiFish 12S taxonomic assignments using a case study California Current Large Marine Ecosystem fishes to determine best practices metabarcoding. Specifically, use taxonomy cross‐validation by identity framework compare between global database comprised all available sequences curated that only includes from Ecosystem. We demonstrate regional provides higher assignment accuracy than comprehensive database. also document tradeoff misclassification across range cutoff scores, highlighting importance parameter selection classification. Furthermore, compared with without inclusion additionally generated sequences. To this end, sequenced tissue 597 species primers, adding 252 GenBank's existing 550 fish then reads identified seawater environmental samples our references, The addition new references allowed identification 16 additional native taxa representing 17.0% total eDNA samples, including vast ecological economic value. Together these results effective need locus‐specific validation efforts.

Язык: Английский

---

Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification

Molecular Ecology Resources, Год журнала: 2021, Номер 21(7), С. 2565 - 2579

Опубликована: Май 18, 2021

Abstract Bioinformatic analysis of eDNA metabarcoding data is a crucial step toward rigorously assessing biodiversity. Many programs are now available for each the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. We used simulated mock communities real fish to evaluate performance 13 bioinformatic pipelines retrieve occurrence read abundance using 12S mt rRNA gene marker. four indices compare outputs program with samples: sensitivity, F‐measure, root‐mean‐square error (RMSE) on abundances, execution time. found marked differences among only taxonomic assignment step, both in terms F‐measure RMSE. Running time was highly different between step. The fastest best were assembled into pipeline. compared this pipeline constructed from existing toolboxes (OBITools, Barque, QIIME 2). Our Barque obtained all appear be better alternatives analysing when complete reference database available. Analysis also indicated only. This study reveals major during choice algorithm can significant impact diversity estimates should made according objectives study.

Язык: Английский

---

Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes

Environmental DNA, Год журнала: 2021, Номер 4(2), С. 271 - 283

Опубликована: Сен. 27, 2021

Abstract Environmental DNA (eDNA) analysis is a revolutionary tool for non‐invasive, cost‐effective, and highly sensitive monitoring of species distribution abundance; however, there remain some uncertainties related to eDNA detection quantification, as well limitations in terms its ecological interpretation. Although these may be elucidated by better understanding the characteristics dynamics eDNA, insight into such basic information has been limited this decade, contrary advancements applications targeting various taxa environments. This review compiled previous findings regarding macrobial provides insights how knowledge can contribute refinement development biomonitoring stock assessment. A literature survey revealed that studies on cellular molecular state were particularly lacking (18/728 papers from 2008 2020), resulting process transport degradation. highlighted number types beyond short mitochondrial fragments (nuclear longer fragments, larger particles) show improves reliability accuracy abundance estimation, provide more detailed individuals other than their presence abundance. Linking application will advance improve biodiversity, ecosystem function, fisheries resources.

Язык: Английский

---

Meta‐analyses of environmental DNA downstream transport and deposition in relation to hydrogeography in riverine environments

Freshwater Biology, Год журнала: 2022, Номер 67(8), С. 1333 - 1343

Опубликована: Май 10, 2022

Abstract Environmental DNA (eDNA) analysis is a promising tool to monitor species distribution and abundance in aquatic ecosystems. These estimates can be biased lotic environments by the effects of eDNA transport deposition processes. However, our understanding downstream dynamics limited because it fluctuate greatly depending on target quantity source site design sampling. Furthermore, into bottom substrates also determines availability aqueous eDNA, but knowledge about much more limited. Consequently, there little consensus deposition, as well their interactions with hydrogeographic conditions. In this study, we compiled previous papers concerning riverine synthesised deposition. A few studies have recently applied hydrodynamic modelling approach calculated average length ( S w ) velocity V dep ). Referring those studies, manually calculated, or directly extracted, from nine conducted meta‐analyses reveal association these river discharges. simulated mean channel given The estimated values ranged 2.6 13,187.4 m 0.003 1.900 mm/s, respectively. When log‐transformed, median were 10 2.188 (= 154.1) –1.387 0.041) mm/s. maximum distances until 95% 99% particles are deposited 334.0 1,272.7 513.5 1,956.4 m, Moreover, found that discharges positively associated , whereas was lower for natural than mesocosms. This trend could due other environmental factors, such substrates. Our meta‐analysis implied that, under ordinary conditions, most travel less 2 km even when considering resuspension riverbeds. By contrast, study did not consider multiple factors potentially affect would accordingly introduce moderate high degree heterogeneity across studies. issues will addressed future To knowledge, first quantitatively synthesise infer general properties distance velocity. According results, released individuals might effect detection sampling sites downstream. Although further accumulation empirical necessary, findings propose groundwork optimal designs ecosystems reduce false‐positive inference presence false‐negative detection.

Язык: Английский

---

A National Scale “BioBlitz” Using Citizen Science and eDNA Metabarcoding for Monitoring Coastal Marine Fish

Frontiers in Marine Science, Год журнала: 2022, Номер 9

Опубликована: Март 28, 2022

Marine biodiversity is threatened by human activities. To understand the changes happening in aquatic ecosystems and to inform management, detailed, synoptic monitoring of across large spatial extents needed. Such challenging due time, cost, specialized skills that this typically requires. In an unprecedented study, we combined citizen science with eDNA metabarcoding map coastal fish at a national scale. We engaged 360 scientists collect filtered seawater samples from 100 sites Denmark over two seasons (1 p.m. on September 29th 2019 May 10th 2020), sampling nearly exact same time all sites, obtained overview largely unaffected temporal variation. This would have been logistically impossible for involved without help volunteers. high return rate 94% samples, total richness 52 species, representing approximately 80% Danish species 25% marine species. retrieved distribution patterns matching known occurrence both invasive, endangered, cryptic detected seasonal variation accordance phenology. Dissimilarity community compositions increased distance between sites. Importantly, comparing our data National Fish Atlas (the latter compiled century observations) found positive correlation values congruent pattern compositions. These findings support use eDNA-based detect biodiversity, approach readily scalable other countries, or even regional global scales. argue future large-scale biomonitoring will benefit using emerging technology, such be important data-driven management conservation.

Язык: Английский

---

Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Deep Sea Research Part I Oceanographic Research Papers, Год журнала: 2022, Номер 189, С. 103871 - 103871

Опубликована: Сен. 9, 2022

Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater are obtained using Niskin bottles filtered to collect eDNA. However, standard sample volumes small relative the scale environment, conventional collection strategies limited, filtration process time consuming. To overcome these limitations, we developed large – volume eDNA sampler with in situ filtration, capable taking up 12 per deployment. We conducted three deployments our on robotic vehicle Mesobot Flower Garden Banks National Marine Sanctuary northwestern Gulf Mexico collected from 20 400 m depth. compared (∼40–60 L) by (∼2 CTD rosette mounted bottle approach. sequenced V9 region 18S rRNA, which detects broad range invertebrate taxa, found that while both methods detected changes associated depth, approximately 66% more taxa than samples. fraction signal originating metazoans total decreased sampling indicating larger may be especially important detecting mesopelagic deep ocean environments. also noted substantial variability biological replicates sets. Both sets identified other did not although number unique was almost four times those Large particularly when coupled platforms, has great potential surveys, discuss practical methodological considerations future applications.

Язык: Английский

---