Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding

Alexander, Jason B.; Bunce, Michael; White, Nicole E.; Wilkinson, Shaun P.; Adam, Arne A. S.; Berry, Tina E.; Stat, Michael; Thomas, Lynda; Newman, Stephen J.; Dugal, Laurence; Richards, Zoe T.

doi:10.1007/s00338-019-01875-9

Cited by 62 publications

(90 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the inability to quantify dietary items in terms of biomass or relative abundance (Nielsen et al 2017) makes diet metabarcoding problematical for characterizing complex, phylogenetically disparate diets such as those of parrotfishes. Biases among potential prey taxa in gene copy number, DNA extraction and amplification (Alberdi et al 2019;Deagle et al 2019;Lamb et al 2019) and contamination of ingesta with environmental DNA (Shinzato et al 2018;Alexander et al 2020) currently limit metabarcoding approaches.…”

Section: Methodology For Diet Studiesmentioning

confidence: 99%

Resolving resource partitioning in parrotfishes (Scarini) using microhistology of feeding substrata

Nicholson

Clements

2020

Coral Reefs

View full text Add to dashboard Cite

Parrotfishes (Scarini) are considered key agents in coral reef health and recovery, but the drivers of parrotfish-coral dynamics remain contentious. The prevailing view of parrotfishes as ecosystem engineers is based on the perceived removal of algal turf, macroalgae and sediment, but these are effects of feeding, not causes. The recent proposal that most parrotfishes are 'microphages' that target microscopic photoautotrophs (particularly cyanobacteria) identifies the need to resolve dietary targets at a microscopic scale. Here, we investigate parrotfish dietary targets by posing the following two questions: (1) are microscopic photoautotrophs the most consistent and dominant elements of the prey community, and (2) do the prey community and substratum taphonomy vary between parrotfish species? In order to identify and quantify dietary targets, five parrotfish species were followed until focused feeding was observed at Lizard Island on the Great Barrier Reef, Australia. Feeding sites were photographed in situ and extracted as substratum bite cores. Cores were analysed microscopically to identify and quantify all epilithic photoautotrophs. Endolithic photoautotrophs accessible to excavating parrotfish were also investigated by vacuumembedding cores with epoxy resin followed by decalcification to expose endolith microborings. The dominant functional groups of epilithic biota on the cores were tufted cyanobacteria, turfing algae and crustose coralline algae (CCA). The only consistent feature across all cores was the high density of filamentous cyanobacteria, supporting the view that these parrotfishes target microphotoautotrophs. Macroalgae was absent or a minor component on cores, supporting the hypothesis that parrotfishes avoid larger algae. The microchlorophyte Ostreobium was the dominant photoautotrophic euendolith (true borer) in the cores of the excavating parrotfish Chlorurus microrhinos. Significant differences in CCA coverage, turf height and substrate taphonomy were found among the five parrotfish species, suggesting that interspecific resource partitioning is based on successional stage of feeding substrata.

show abstract

Section: Methodology For Diet Studiesmentioning

confidence: 99%

Resolving resource partitioning in parrotfishes (Scarini) using microhistology of feeding substrata

Nicholson

Clements

2020

Coral Reefs

View full text Add to dashboard Cite

show abstract

“…Given that marine ecosystems are dynamic, conducting eDNA and visual surveys at different times could result in capturing different communities (Beenties et al, 2019). This possibility would be easily tested by including eDNA sampling as part of any fish visual census protocol (Alexander et al, 2020) and doing so could add value to visual surveys as eDNA may provide insight into parts of the fish community (e.g., blennies) that are difficult to fully capture in visual surveys (Alexander et al, 2020; Stat et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…While eDNA may revolutionize monitoring of marine biodiversity, to date most marine eDNA studies have focused on relatively low diversity temperate marine environments (Bohmann et al, 2014; McElroy et al, 2020; Rees et al, 2017; Thomsen et al, 2012a). Similarly, most coral reef eDNA studies to date have occurred in Japan, Central Pacific, Western Australia, and the Red Sea (Alexander et al 2020;Bessey et al 2020; DiBattista et al 2017; Lafferty et al 2020; Oka et al 2020;Stat et al 2017; Stat et al 2019; West et al 2020), where fish biodiversity is far lower than the Coral Triangle (Bellwood & Meyer, 2009; Roberts et al, 2002). Most recently, Juhel et al (2020) used eDNA to examine fish diversity in Raja Ampat, Indonesia, home to the world’s most diverse reef fish fauna (Allen, 2002), reporting a strong correlation between eDNA results and checklists from visual data.…”

Section: Introductionmentioning

confidence: 99%

“…Similarly, most coral reef eDNA studies to date have occurred in Japan, Central Pacific, Western Australia, and the Red Sea (Alexander et al 2020;Bessey et al 2020;DiBattista et al 2017;Lafferty et al 2020;Oka et al 2020;Stat et al 2017;Stat et al 2019;West et al 2020), where fish biodiversity is far lower than the Coral Triangle (Bellwood & Meyer, 2009;Roberts et al, 2002).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

Marwayana

Gold

Barber

2021

Preprint

View full text Add to dashboard Cite

Indonesia is the heart of the Coral Triangle, the world's most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. This study uses environmental DNA (eDNA) to survey fish communities across a pronounced biodiversity gradient in Indonesia. A total of 12,939,690 sequence reads of MiFish 12S rRNA from 39 sites spanning 7 regions of Indonesia revealed 4,146 Amplified Sequence Variants (ASVs). Regional patterns of fish diversity based on eDNA broadly conformed to expectations based on traditional biodiversity survey methods, with the highest fish biodiversity in Raja Ampat and generally lower diversity in Western Indonesia. However, eDNA performed relatively poorly compared to visual survey methods in site-by-site comparisons, both in terms of total number of taxa recovered and ability to assign species names to ASVs. This result stands in a stark contrast to eDNA studies of temperate and tropical ecosystems with lower diversity. Analyses show that while sequencing depth was sufficient to capture all fish diversity within individual seawater samples, variation among samples from individual localities was high, and sampling effort was insufficient to capture all fish diversity at a given sampling site. Interestingly, mean ASVs recovered per one-liter seawater was surprisingly similar across sites, despite substantial differences in total diversity, suggesting a limit to total ASVs (~200) per one-liter eDNA sample. Combined, results highlight two major challenges of eDNA in highly diverse ecosystems such as the Coral Triangle. First, reference databases are incomplete and insufficient for effective ASV taxonomic assignment. Second, eDNA sampling design developed from lower diversity temperate marine ecosystems are inadequate to fully capture diversity of biodiversity hotspots like the Coral Triangle.

show abstract

“…In contrast, the enormous biodiversity in aquatic ecosystems, which include a myriad of unknown species, cannot automatically be monitored like physical attributes, making continuous biodiversity monitoring difficult (Fujikura et al 2010;DiBattista et al 2017;Alexander et al 2019). Regarding fish, over 32,000 species are known from aquatic environments worldwide, and an average of around 400 new species were described annually between 2005(Nelson et al 2016.…”

Section: Introductionmentioning

confidence: 99%

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

2020

View full text Add to dashboard Cite

We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.

show abstract

Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding

Cited by 62 publications

References 60 publications

Resolving resource partitioning in parrotfishes (Scarini) using microhistology of feeding substrata

Resolving resource partitioning in parrotfishes (Scarini) using microhistology of feeding substrata

Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

Contact Info

Product

Resources

About