Environmental DNA (eDNA) Metabarcoding as a Sustainable Tool of Coastal Biodiversity Assessment

Abstract

Global biodiversity loss represents one of the most serious environmental crises of the 21st centuries, with substantial impact on both ecosystem services and the health of our environment. 52% of global biodiversity decline was recorded between 1970 and 2010, and this loss was even higher for freshwater populations than for marine or terrestrial ecosystems (WWF 2014). Undeniably, Malaysian coastal ecosystem harbour extraordinary biodiversity having this country is recognised as one of the megadiverse country. However, unsustainable development of the Malaysian coastal area has led to the decline of the aquatic biodiversity. There is limited knowledge on the extent of biodiversity and the genetic resources in the aquatic environment some of them could already be extinct before we could identify them. Therefore, by implementing the Living Lab concept accustomed to the university, a non-invasive alternative method called environmental DNA or eDNA metabarcoding with an aid of Next Generation Sequencing (NGS) was introduced to identify species diversity of fish in a coastal ecosystem. In this study, the eDNA metabarcoding tool is applied in assessing water samples for fish species detection. This new, time and cost-effective method enables the acquisition of large datasets, paving the way for a finer understanding of fish diversity in different river landscape, with major implications for sustainable fisheries management and conservation, in parallel to goal fourteen (14) of the United Nations Sustainable Development Goals—Life Below Water.

Glossary

Amplicon

A fragment of DNA or RNA derived from replication process or amplification, either naturally or artificially, through for example a PCR process.

Biomonitoring

Biodiversity assessment that is done in repeats across space and time that may focus on a target organism such as invasive or at-risk species.

DNA Barcoding

The use of a short, standardised DNA fragments in taxonomic identification by comparing the DNA sequence to a reference database.

DNA Sequencing

A process whereby the order of nucleotides within a DNA sequence is determined.

Environmental DNA (eDNA)

Trace of DNA in environmental samples—water, soil or faeces. eDNA is a mixture of potentially degraded DNA from many different organisms and be in different physical states (intraorganismal, intramembranous, particulate, adsorbed or free) (Taberlet et al. 2012).

Marker

A gene or a region of DNA with a known location in the genome and can utilised in identifying individuals or species.

Metabarcoding

identification of taxon from DNA extracted from a sample containing many different organisms.

Molecular Operational Taxonomic Unit (MOTU)

The working proxy for “species” in molecular ecology. It is the taxonomic level of sampling defined by the researcher in a study. MOTUs are generated by comparing sequences against each other to form a distance matrix, followed by clustering groups of sequences with a specified amount of variability allowed within each MOTU (Bohmann et al. 2014).

Next Generation Sequencing

Parallel sequencing technologies which produce thousands to billions of DNA sequences in a single sequencing run—e.g. Illumina Genome Analyser Series, Roche 454, Life Technologies SOLiD, Ion Torrent and PacBio.

PCR

Polymerase chain reaction is a method used to amplify a single copy or a few copies of a fragment of DNA generating thousands to millions of copies of a particular DNA sequence.

Primers

Short oligonucleotides that are complimentary to a particular region of the genome and are the starting point of DNA replication in PCR process.

Taxon

An organism identified to any taxonomic rank; from kingdom to species level.