Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA

F, Andrea Polanco; Martinezguerra, Maria Mutis; Marques, Virginie; Villa‐Navarro, Francisco A.; Pérez, Giomar Helena Borrero; Cheutin, Marie-Charlotte; Déjean, Tony; Hocdé, Régis; Juhel, Jean‐Baptiste; Maire, Eva; Manel, Stéphanie; Spescha, Manuel; Valentini, Alice; Mouillot, David; Albouy, Camille; Pellissier, Loïc

doi:10.1111/btp.13009

Cited by 28 publications

(13 citation statements)

References 88 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As a promising method for the assessment of aquatic species diversity ( Ahn et al, 2020 ; Polanco et al, 2021 ; Tsuji et al, 2019 ), eDNA metabarcoding is strongly dependent on a molecular workflow, which involves eDNA capture, extraction, and bioinformatics analyses. Comparative studies have tested the efficiency of eDNA capture using different filtration and extraction methods as well as filtration water volumes in various settings ( Cantera et al, 2019 ; Deiner et al, 2015 ; Djurhuus et al, 2017 ; Shu et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…Adequate water-sampling procedures for aquatic ecosystems are important for eDNA studies. Previous research has demonstrated that a large volume of filtration water is needed to represent real fauna in habitats ( Cantera et al, 2019 ; Polanco et al, 2021 ; Pont et al, 2018 ; Stauffer et al, 2021 ; Valentini et al, 2016 ). The three filtration water volumes tested in this study are commonly used in eDNA metabarcoding studies, with high success rates for species detection ( Sales et al, 2021 ; Valdivia-Carrillo et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

Ruan¹,

Wang²,

Li³

et al. 2022

Zoological Research

View full text Add to dashboard Cite

Environmental DNA (eDNA) integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish diversity. To date, however, no standardized eDNA-based protocol has been established to monitor fish diversity. In this study, we investigated and compared two filtration methods and three DNA extraction methods using three filtration water volumes to determine a suitable approach for eDNA-based fish diversity monitoring in the Pearl River Estuary (PRE), a highly anthropogenically disturbed estuarine ecosystem. Compared to filtration-based precipitation, direct filtration was a more suitable method for eDNA metabarcoding in the PRE. The combined use of DNeasy Blood and Tissue Kit (BT) and traditional phenol/chloroform (PC) extraction produced higher DNA yields, amplicon sequence variants (ASVs), and Shannon diversity indices, and generated more homogeneous and consistent community composition among replicates. Compared to the other combined protocols, the PC and BT methods obtained better species detection, higher fish diversity, and greater consistency for the filtration water volumes of 1 000 and 2 000 mL, respectively. All eDNA metabarcoding protocols were more sensitive than bottom trawling in the PRE fish surveys and combining two techniques yielded greater taxonomic diversity. Furthermore, combining traditional methods with eDNA analysis enhanced accuracy. These results indicate that methodological decisions related to eDNA metabarcoding should be made with caution for fish community monitoring in estuarine ecosystems.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

Ruan¹,

Wang²,

Li³

et al. 2022

Zoological Research

View full text Add to dashboard Cite

show abstract

“…Moving forward, more intensive studies to identify these areas are needed. The discovery of these threatened species highlights the value of eDNA metabarcoding as a tool for assessing biodiversity and represents a promising step towards a holistic conservation in estuaries, mangrove and coastal ecosystems 20,23,41 .…”

Section: Discussionmentioning

confidence: 99%

“…water, soil) 20,21 . It overcomes the shortcomings of conventional survey methods to e ciently characterise sh assemblages in aquatic habitats as have been reported in estuarine [22][23][24] , marine 25,26 , and freshwater ecosystems 27,28 . The use of eDNA as a powerful monitoring instrument is increasingly acknowledged as it reveals greater diversity at a lower cost compared to conventional surveying methods [29][30][31][32] .…”

Section: Introductionmentioning

confidence: 99%

Splash, splash. Who’s there? Advantages and limitations of the environmental DNA (eDNA) metabarcoding in assessing megadiverse but poorly known tropical community of fishes

Abidin

Nor

Lavoué

et al. 2022

Preprint

View full text Add to dashboard Cite

Biodiversity surveys are crucial to monitor the health of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive and frequently only provide rough assessments in complex habitats. Recent advanced molecular methods such as environmental DNA (eDNA) using high-throughput sequencing technology are promising although only few applications in tropical estuarine ecosystems have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species belonging to 127 genera, 68 families, and 25 orders. This approach captured significantly more species than in any previous traditional surveys, including a few species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) a fraction of previously documented specimen-based diversity was not captured by the current method, may be as a consequence of PCR primer specificity, and (3) the detection of non-resident species; stenohaline freshwater taxa (e.g. cyprinids, channids, osphronemids) and marine coral reef taxa (e.g. some sharks, holocentrids and syngnathids), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movement. The community analysis revealed that fish diversity along the estuary is not homogenous, with the upstream more diverse than further downstream. This may be the consequence of the salinity or pollution gradients. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach, in particular the development of a comprehensive reference genetic database.

show abstract

“…West et al ( 2021 ) illustrates the utility of DNA metabarcoding to describe assemblages of aquatic reptiles across northern Australia, where nine aquatic reptile species were detected using a mitochondrial 16S assay designed for reptiles. Polanco et al ( 2021 ) used a mitochondrial 12S assay (VERT01 (Taberlet et al, 2018 )) to describe biodiversity in tropical Columbia in estuaries and marine waters. This primer was designed for all vertebrates, and successfully detected one species of reptile (the spectacled caiman, Caiman crocodilus ) and two families of reptile (Alligatoridae and Kinosternidea), along with several amphibians, birds, mammals, and fish (Polanco et al, 2021 ).…”

Section: Distribution Of Edna Studiesmentioning

confidence: 99%

A review of applications of environmental DNA for reptile conservation and management

Nordstrom

Mitchell

Byrne

et al. 2022

Ecology and Evolution

View full text Add to dashboard Cite

Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.

show abstract

Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA

Cited by 28 publications

References 88 publications

Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

Splash, splash. Who’s there? Advantages and limitations of the environmental DNA (eDNA) metabarcoding in assessing megadiverse but poorly known tropical community of fishes

A review of applications of environmental DNA for reptile conservation and management

Contact Info

Product

Resources

About