Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

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

10.1101/2021.02.19.432056 ◽

2021 ◽

Author(s):

Onny N. Marwayana ◽

Zachary Gold ◽

Paul H. Barber

Keyword(s):

Survey Methods ◽

Marine Ecosystem ◽

Sampling Site ◽

Environmental Dna ◽

Marine Biodiversity ◽

Fish Diversity ◽

Sampling Effort ◽

Coral Triangle ◽

Regional Patterns ◽

Biodiversity Survey

AbstractIndonesia 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 MiFish12SrRNA 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.

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Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

10.22541/au.163252330.05592688/v1 ◽

2021 ◽

Author(s):

Nicole Foster ◽

Kor-jent Dijk ◽

Ed Biffin ◽

Jennifer Young ◽

Vicki Thomson ◽

...

Keyword(s):

Dna Sequences ◽

Dna Barcode ◽

Environmental Dna ◽

Reference Sequence ◽

Reference Database ◽

Chloroplast Gene ◽

Coastal Plants ◽

Reference Databases ◽

Targeted Capture ◽

Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

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Effect of monsoon on coastal fish diversity of Goa: an example from the gillnet fishery

Indian Journal of Fisheries ◽

10.21077/ijf.2016.2016.63.2.45862-02 ◽

2016 ◽

Vol 63 (2) ◽

Cited By ~ 1

Author(s):

G. B. Sreekanth ◽

N. Manju Lekshmi ◽

Sushanta Kumar Chakraborty ◽

Ashok Kumar Jaiswar ◽

P. U. Zacharia ◽

...

Keyword(s):

Fish Diversity ◽

Coastal Fish

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Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65449 ◽

2021 ◽

Vol 4 ◽

Author(s):

O. Nurul Fizatul Nabilah ◽

A. R. Ramizah ◽

A. B. Adibah ◽

S. Syazwan ◽

A.G. Intan Faraha ◽

...

Keyword(s):

Dna Sequences ◽

Environmental Dna ◽

Coi Gene ◽

Alien Invasive Species ◽

Survey Method ◽

Specific Primers ◽

Invasive Fishes ◽

Specific Amplification ◽

Species Specific ◽

High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

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Environmental DNA effectively captures functional diversity of coastal fish communities

Molecular Ecology ◽

10.1111/mec.15661 ◽

2020 ◽

Author(s):

Giorgio Aglieri ◽

Charles Baillie ◽

Stefano Mariani ◽

Carlo Cattano ◽

Antonio Calò ◽

...

Keyword(s):

Functional Diversity ◽

Fish Communities ◽

Environmental Dna ◽

Coastal Fish

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MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

BMC Genomics ◽

10.1186/1471-2164-11-461 ◽

2010 ◽

Vol 11 (1) ◽

pp. 461 ◽

Cited By ~ 81

Author(s):

Manuel Stark ◽

Simon A Berger ◽

Alexandros Stamatakis ◽

Christian von Mering

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Environmental Dna

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Metabolic network-guided binning of metagenomic sequence fragments

Bioinformatics ◽

10.1093/bioinformatics/btv671 ◽

2015 ◽

Vol 32 (6) ◽

pp. 867-874 ◽

Cited By ~ 4

Author(s):

Matthew B. Biggs ◽

Jason A. Papin

Keyword(s):

Metabolic Network ◽

Dna Sequences ◽

Metabolic Networks ◽

Human Microbiome ◽

Environmental Dna ◽

Human Microbiome Project ◽

Supplementary Information ◽

Metagenomic Sequence ◽

Connectivity Score ◽

Genome Scale

Abstract Motivation: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health. Results: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks. Availability and implementation: The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

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