Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective ...nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty‐two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km2). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.
Uso Combinado del Metacódigo de Barras de eDNA y Videograbaciones para la Evaluación de la Biodiversidad de Peces
Resumen
El monitoreo de comunidades de peces es importante para el manejo y sustentabilidad de las pesquerías y los ecosistemas marinos. Los sistemas remotos de video submarino con carnada (SRVSC) están entre las técnicas no destructivas más efectivas para el muestreo de peces óseos y elasmobranquios (tiburones, mantarrayas y rayas). Sin embargo, los SRVSC muestrean biota que es conspicua visiblemente; entonces, algunos taxones están mal muestreados o simplemente no se registran en los muestreos. Comparamos la diversidad de peces caracterizada usando SRVSC con la diversidad detectada por medio del metacódigo de barras de ADN ambiental (eDNA, en inglés). Muestreamos el agua de mar y capturamos imágenes con SRVSC en 48 localidades que incluyeron el arrecife y los pastos marinos dentro y fuera de una reserva marina (Bahía Jurien en el oeste de Australia). Se detectaron 83 géneros de peces de 13 órdenes, y la comunidad de peces descrita con el uso combinado del eDNA y el SRVSC produjo >30% riqueza más genérica que cuando cualquiera de los dos métodos se usó individualmente. En lugar de detectar una firma genética homogénea, los ensamblados de eDNA reflejaron la claridad espacial del SRVSC; la diferenciación de los taxones entre los pastos marinos y el arrecife fue clara a pesar la escala geográfica relativamente pequeña del sitio de estudio (∼35 km2). Los taxones que no fueron muestreados por uno de los métodos, por causa de limitaciones y sesgos intrínsecos al método, casi siempre fueron detectados usando el otro método. Por lo tanto, el uso de SRVSC y el eDNA en concreto proporciona una visión más holística de las comunidades marinas de vertebrados en todos los hábitats. Ambos métodos son no invasivos, lo que incrementa su potencial para ser una implementación de uso amplio en la vigilancia de los ecosistemas marinos.
Article impact statement: Use of video and environmental genomics in conservation will greatly improve capacity to effectively monitor fish biodiversity.
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a ...growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate‐related threats and as such there is a pressing need for cost‐effective whole‐ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high‐resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.
While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be ...confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false‐positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along‐shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat‐specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.
Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning ...amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA) it is paramount workflows and analytics are both fit for purpose.
Effective biomonitoring is critical for driving management outcomes that ensure long‐term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with ...metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi‐assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate sampled implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and ...space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of 'snapshots' across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. ...Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological oceanography, as it is capable of identifying a huge phylogenetic range of organisms to species level. Here we develop and apply a novel multi-gene molecular toolkit to eDNA isolated from bulk plankton samples collected over a five-year period from a single site. This temporal scale and level of detail is unprecedented in eDNA studies. We identified consistent seasonal assemblages of zooplankton species, which demonstrates the ability of our toolkit to audit community composition. We were also able to detect clear departures from the regular seasonal patterns that occurred during an extreme marine heatwave. The integration of eDNA analyses with existing biotic and abiotic surveys delivers a powerful new long-term approach to monitoring the health of our world's oceans in the context of a rapidly changing climate.
Aim
Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has ...rarely been tested across large spatial scales or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break and evaluate its use as a regional biomonitoring tool in Australia.
Location
North‐western Australia (NWA).
Methods
We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline.
Results
Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony fish assemblages, were additionally found to differ between the South and North Kimberley regions suggesting previously unrecognized subregional differentiation amongst these taxa. The overall compositional data have been used to update distribution information for a number of endangered, elusive and data‐deficient taxa, including sawfish (family: Pristidae), northern river shark (Glyphis garricki) and wedgefish (genus: Rhynchobatus).
Main conclusions
eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine‐scale patterns across the large‐scale, remote and oceanographically complex region of North‐western Australia. Importantly, this study highlights the potential of integrating broad‐scale eDNA metabarcoding alongside other baseline surveys and long‐term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.
Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct ...New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10–6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs – ...despite the pervasive idea of ‘dino DNA’ from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected ‘small stuff’ – lizards, frogs, and other herpetofauna. But here's the rub – extracting DNA from the bones of this ‘small stuff’ is not only difficult, it often destroys the sample. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate samples held within museum collections.
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