Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

Mapping Intimacies ◽

10.1101/864710 ◽

2019 ◽

Author(s):

Natalia Fraija-Fernández ◽

Marie-Catherine Bouquieaux ◽

Anaïs Rey ◽

Iñaki Mendibil ◽

Unai Cotano ◽

...

Keyword(s):

Marine Fish ◽

Environmental Dna ◽

Distribution Patterns ◽

Abundant Species ◽

Fish Diversity ◽

12S Rrna ◽

Rrna Gene ◽

Ecological Knowledge ◽

Diversity Assessment ◽

The Common

AbstractCurrent methods for monitoring marine fish diversity mostly rely on trawling surveys, which are invasive, costly and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we explore the potential of environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5L-water samples were collected onboard a wide-scale oceanographic survey covering about 120,000 square kilometres in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality-filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel and blue whiting), but eDNA metabarcoding resulted in more detected fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fish biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.

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MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Royal Society Open Science ◽

10.1098/rsos.150088 ◽

2015 ◽

Vol 2 (7) ◽

pp. 150088 ◽

Cited By ~ 268

Author(s):

M. Miya ◽

Y. Sato ◽

T. Fukunaga ◽

T. Sado ◽

J. Y. Poulsen ◽

...

Keyword(s):

Fish Species ◽

Survey Methods ◽

Hypervariable Region ◽

Environmental Dna ◽

Pcr Primers ◽

12S Rrna ◽

Rrna Gene ◽

Sufficient Information ◽

Diverse Range ◽

Spatial And Temporal Scales

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.

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

Fisheries Science ◽

10.1007/s12562-020-01461-x ◽

2020 ◽

Vol 86 (6) ◽

pp. 939-970

Author(s):

Masaki Miya ◽

Ryo O. Gotoh ◽

Tetsuya Sado

Keyword(s):

Fishery Management ◽

Massively Parallel Sequencing ◽

Simultaneous Detection ◽

Environmental Dna ◽

Single Species ◽

Conservation Strategies ◽

Estuarine Fish ◽

12S Rrna ◽

Rrna Gene ◽

Biodiversity Monitoring

Abstract 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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Fish diversity assessment in the headwaters of the Volga River using environmental DNA metabarcoding

Aquatic Conservation Marine and Freshwater Ecosystems ◽

10.1002/aqc.3163 ◽

2019 ◽

Vol 29 (10) ◽

pp. 1785-1800 ◽

Cited By ~ 7

Author(s):

Laurène A. Lecaudey ◽

Martin Schletterer ◽

Vyacheslav V. Kuzovlev ◽

Christoph Hahn ◽

Steven J. Weiss

Keyword(s):

Environmental Dna ◽

Fish Diversity ◽

Volga River ◽

Diversity Assessment ◽

Dna Metabarcoding

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Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d201241 ◽

2019 ◽

Vol 20 (12) ◽

Cited By ~ 1

Author(s):

Sapto Andriyono ◽

MD. JOBAIDUL ALAM ◽

HYUN-WOO KIM

Keyword(s):

Marine Fish ◽

Molecular Identification ◽

Environmental Dna ◽

Fish Diversity ◽

Morphological Identification ◽

Fish Samples ◽

Identification Of Species ◽

Seawater Samples ◽

Next Generation Sequencing Ngs ◽

Diversity Study

Abstract. Andriyono S, Jobaidul Alam Md, Kim HW. 2019. Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia. Biodiversitas 20: 3772-3781. Molecular identification of species is now fast growing and currently widely applied method in the diversity estimation of aquatic biota; even though morphological identification is still carried out. The molecular approach is beneficial complementing on regular surveys, e.g. use of nets, traps, fishing rods, and even with poisons. In this study, the eDNA metabarcoding was applied to water samples around the Pondok Dadap fish landing station, Indonesia to determine the diversity of fish around the waters and also to identify marine fish landed in this area. Molecular identification was carried out on fish samples obtained from the fish market improved GenBank database on COI and ITS. While, seawater samples were carried out by using the next-generation sequencing (NGS) platform to obtain the eDNA metabarcoding data for the first time. Molecular identification obtained 34 species (68 sequences of COI and ITS regions) belonging to 28 genera, 18 families, 4 orders, while the eDNA metabarcoding approach identified 53 marine fish species by using the MiFish pipeline representing 38 genera, 27 families, and 7 orders. From the present study, we can able to estimated fish diversity by eDNA metabarcoding, and this finding will be helpful for baseline data preparation for future effective management of resources in this area.

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Short Communication Universal primers to amplify the complete mitochondrial 12S rRNA gene in marine fish species

Genetics and Molecular Research ◽

10.4238/2013.october.15.6 ◽

2013 ◽

Vol 12 (4) ◽

pp. 4575-4578

Author(s):

X.X. Jin ◽

S.L. Zhao ◽

R.X. Wang

Keyword(s):

Marine Fish ◽

Fish Species ◽

Short Communication ◽

Universal Primers ◽

12S Rrna ◽

Rrna Gene ◽

Marine Fish Species ◽

12S Rrna Gene ◽

Mitochondrial 12S Rrna

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eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

10.1101/2021.01.05.425493 ◽

2021 ◽

Author(s):

Jake M Jackman ◽

Chiara Benvenuto ◽

Ilaria Coscia ◽

Cintia O Carvalho ◽

Jonathan S Ready ◽

...

Keyword(s):

Water Samples ◽

Gap Analysis ◽

Environmental Dna ◽

Threshold Value ◽

Taxonomic Resolution ◽

12S Rrna ◽

Rrna Gene ◽

Neotropical Fish ◽

Β Diversity ◽

Α Diversity

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α-diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

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Application of Environmental DNA (eDNA) Metabarcoding Method to Identify Threatened Sulawesi Mammal Based on 12S rRNA Gene

HAYATI Journal of Biosciences ◽

10.4308/hjb.29.1.114-121 ◽

2021 ◽

Vol 29 (1) ◽

pp. 114-121

Author(s):

Bambang Suryobroto ◽

Ahmad Abdul Jabbar ◽

Puji Rianti

Keyword(s):

Species Identification ◽

High Throughput Sequencing ◽

Genetic Material ◽

Environmental Dna ◽

Reference Sequence ◽

12S Rrna ◽

Rrna Gene ◽

Mammal Species ◽

Terrestrial Mammals ◽

Salt Licks

Species detection and identification is a crucial steps in biodiversity assessment. Traditional methods are often invasive and resource intensive. The number of studies demonstrating successful of eDNA metabarcoding approach in species identification has increased rapidly in recent years. Some of large terrestrial mammals have reportedly utilize natural salt licks as a source of minerals in the diet and its genetic material left in the environment can be used to identify species from this site. An eDNA metabarcoding protocol had been carried out to identify Sulawesi mammals from Adudu natural salt-licks, Nantu Wildlife Reserve, Gorontalo. Environmental DNA were extracted from water samples, Amplicon libraries were prepared by PCR amplification and Illumina MiSeq high throughput sequencing. Reads processing and taxonomic assignment carried out in two bioinformatics packages, PipeCraft-1.0 and OBITools-2.11. Two endangered Sulawesi mammals species had been identified, i.e. lowland anoa (Bubalus depressicornis) and babirusa (Babyrousa babyrussa). The accuracy of mammal species identification using eDNA metabarcoding is affected by rigorous experimental procedures, DNA marker reliability, and availability of reference sequence database.

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