Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

Ahn, Hyojin; Kume, Manabu; Terashima, Yuki; Feng, Ye; Kameyama, Shuichi; Miya, Masaki; Yamashita, Yoh; Kasai, Atsushi

doi:10.1101/2020.03.22.997809

Cited by 6 publications

(9 citation statements)

References 47 publications

(61 reference statements)

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“…This is supported by the timing of our sampling during high tide, when the ocean level reaches its maximum and seawater freely enters the estuary. 22 demonstrated that species from the surrounding marine and freshwater habitats are more easily detected during this period.…”

Section: Discussionmentioning

confidence: 88%

“…Our ndings agree with 16 who likewise found the greatest abundance of sh species in the midstream of the Merbok Estuary. This is an indicator that optimal conditions to support high biodiversity warrants a pristine environment 22 . The NMDS ordination allied with PERMANOVA based on read counts of the two metabarcoding assays, con rming clustering results that three distinct sh communities were distinguishable by the designated zones.…”

Section: Diversity Patterns and Compositionmentioning

confidence: 99%

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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

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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.

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Section: Discussionmentioning

confidence: 88%

Section: Diversity Patterns and Compositionmentioning

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

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“…Despite their importance, estuarine ecosystems are susceptible to anthropogenic effects and are suffering from severe alterations, degradation, or losses (Wingard and Lorenz 2014). In light of this critical situation in estuarine ecosystems, three papers on biodiversity monitoring using the MiFish metabarcoding methods from East Asian countries have been consecutively published in the past 6 months (Zhang et al 2019;Zou et al 2020;Ahn et al 2020).…”

Section: Estuarine Fish Communitymentioning

confidence: 99%

“…More recently, Ahn et al (2020) conducted biodiversity monitoring using MiFish eDNA metabarcoding at five estuaries with a broader geographic scale along the Japanese archipelago. Water samples were collected from river mouths and adjacent coastal areas of two and three estuaries with high and low degrees of development, respectively (Ahn et al 2020). A total of 182 fish species across 67 families were detected, 11 of which occurred in all of the rivers.…”

Section: Estuarine Fish Communitymentioning

confidence: 99%

“…Species richness apparently decreased with increasing the degree of human development along each river, while species composition varied among rivers, reflecting the distribution and migration of fishes. Ahn et al (2020) concluded that further development of the eDNA technique will offer an alternative method for accurate and non-invasive monitoring of aquatic life.…”

Section: Estuarine Fish Communitymentioning

confidence: 99%

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

2020

Self Cite

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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.

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Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Yoshida

Kawato²,

Fujiwara³

et al. 2023

Front. Mar. Sci.

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Deep-sea ecosystems present difficulties in surveying and continuous monitoring of the biodiversity of deep-sea ecosystems because of the logistical constraints, high cost, and limited opportunities for sampling. Environmental DNA (eDNA) metabarcoding analysis provides a useful method for estimating the biodiversity in aquatic ecosystems but has rarely been applied to the study of deep-sea fish communities. In this study, we utilized pumped deep-sea water for the continuous monitoring of deep-sea fish communities by eDNA metabarcoding. In order to develop an optimum method for continuous monitoring of deep-sea fish biodiversity by eDNA metabarcoding, we determined the appropriate amount of pumped deep-sea water to be filtered and the practical number of filtered sample replicates required for biodiversity monitoring of deep-sea fish communities. Pumped deep-sea water samples were filtered in various volumes (5–53 L) at two sites (Akazawa: pumping depth 800 m, and Yaizu: pumping depth 400 m, Shizuoka, Japan) of deep-sea water pumping facilities. Based on the result of evaluations of filtration time, efficiency of PCR amplification, and number of detected fish reads, the filtration of 20 L of pumped deep-sea water from Akazawa and filtration of 10 L from Yaizu were demonstrated to be suitable filtration volumes for the present study. Fish biodiversity obtained by the eDNA metabarcoding analyses showed a clear difference between the Akazawa and Yaizu samples. We also evaluated the effect of the number of filter replicates on the species richness detected by eDNA metabarcoding from the pumped deep-sea water. At both sites, more than 10 sample replicates were required for the detection of commonly occurring fish species. Our optimized method using pumped deep-sea water and eDNA metabarcoding can be applied to eDNA-based continuous biodiversity monitoring of deep-sea fish to better understand the effects of climate change on deep-sea ecosystems.

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Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

Cited by 6 publications

References 47 publications

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

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

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

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

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