Environmental DNA (eDNA) Metabarcoding as a Sustainable Tool …
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ecosystem while increasing stress and predation risk to the animals itself (Rottmann
et al. 1992). Fish survey in natural aquatic ecosystem covers multiple components
which includes estimating the total area of the habitat, total fish numbers, and species
composition (including identifying introduced species) (Hankin and Reeves 1988).
In Malaysia specifically, there are a variety of methods that is used to sample fish in
the coastal area which includes the rivers, streams and estuaries. Gill net, hook-andline, bag net, trammel net, lift net, traps, dip net, hyke net, angling, visual census and
electrofishing are the most common methods in conducting fish surveys (Fisheries
2011). While these common methods are traditionally used, the molecular approach
has revolutionised a pathway by using environmental DNA (eDNA). Application of
eDNA metabarcoding for biodiversity assessments/surveys has gained much attention because of its efficiency in ecosystem biomonitoring. A comprehensive monitoring program should account for knowledge of a species’ distribution, their habitat
and allowing adaptive management to be practiced. One of the earliest, successful
eDNA surveys utilising water samples is done by Ficetola et al. (2008) where they
utilise eDNA in detecting invasive species of the bullfrog, Rana catesbeiana in natural wetland ponds for the purpose of biomonitoring. This study marks the novel
application of eDNA in conservation genetics to document occurrences of aquatic
invasive species.
Environmental DNA (eDNA) has effectively detects the presence of fish species
in both freshwater and marine ecosystem (Bohmann et al. 2014; Rees et al. 2014).
Recent studies also have shown that eDNA is far more sensitive in detecting rare
or uncommon species as compared to capture-based survey methods (Jerde et al.
2013; Laramie et al. 2015) and several researches have proven that eDNA is useful
for detecting species that would be difficult to find using traditional methods due
to either low density or trap shyness (Shaw et al. 2016; Simpfendorfer et al. 2016).
Environmental DNA (eDNA) surveillance is not only essential for detection of invasive species but can also be useful in the discovery of endangered species. Research
utilising eDNA in the field of endangered species has shown positive detection of
both amphibians (Dejean et al. 2012; Ficetola et al. 2008; Pilliod et al. 2013; Rees
et al. 2014) and freshwater fishes (Bylemans et al. 2017; Eva et al. 2016). A summary of several applications of eDNA in biodiversity monitoring, specifically in fish
surveys is presented in Table 1.
4 General Methodologies of eDNA Metabarcoding
Generally, eDNA metabarcoding approach of biodiversity assessment begin with
the collection of environment sample, extracting the DNA within the environmental
sample, and developing a DNA library that either comprises of a random subset of the
DNA present (by using shortgun sequencing) or targets specific and informative DNA
fragments (amplicon sequencing) (Shaw et al. 2017). Next Generation Sequencing
(NGS) platforms were then being used in generating the DNA sequences before the
sequence reads is run through the bioinformatics analyses in taxonomic identification
215
ecosystem while increasing stress and predation risk to the animals itself (Rottmann
et al. 1992). Fish survey in natural aquatic ecosystem covers multiple components
which includes estimating the total area of the habitat, total fish numbers, and species
composition (including identifying introduced species) (Hankin and Reeves 1988).
In Malaysia specifically, there are a variety of methods that is used to sample fish in
the coastal area which includes the rivers, streams and estuaries. Gill net, hook-andline, bag net, trammel net, lift net, traps, dip net, hyke net, angling, visual census and
electrofishing are the most common methods in conducting fish surveys (Fisheries
2011). While these common methods are traditionally used, the molecular approach
has revolutionised a pathway by using environmental DNA (eDNA). Application of
eDNA metabarcoding for biodiversity assessments/surveys has gained much attention because of its efficiency in ecosystem biomonitoring. A comprehensive monitoring program should account for knowledge of a species’ distribution, their habitat
and allowing adaptive management to be practiced. One of the earliest, successful
eDNA surveys utilising water samples is done by Ficetola et al. (2008) where they
utilise eDNA in detecting invasive species of the bullfrog, Rana catesbeiana in natural wetland ponds for the purpose of biomonitoring. This study marks the novel
application of eDNA in conservation genetics to document occurrences of aquatic
invasive species.
Environmental DNA (eDNA) has effectively detects the presence of fish species
in both freshwater and marine ecosystem (Bohmann et al. 2014; Rees et al. 2014).
Recent studies also have shown that eDNA is far more sensitive in detecting rare
or uncommon species as compared to capture-based survey methods (Jerde et al.
2013; Laramie et al. 2015) and several researches have proven that eDNA is useful
for detecting species that would be difficult to find using traditional methods due
to either low density or trap shyness (Shaw et al. 2016; Simpfendorfer et al. 2016).
Environmental DNA (eDNA) surveillance is not only essential for detection of invasive species but can also be useful in the discovery of endangered species. Research
utilising eDNA in the field of endangered species has shown positive detection of
both amphibians (Dejean et al. 2012; Ficetola et al. 2008; Pilliod et al. 2013; Rees
et al. 2014) and freshwater fishes (Bylemans et al. 2017; Eva et al. 2016). A summary of several applications of eDNA in biodiversity monitoring, specifically in fish
surveys is presented in Table 1.
4 General Methodologies of eDNA Metabarcoding
Generally, eDNA metabarcoding approach of biodiversity assessment begin with
the collection of environment sample, extracting the DNA within the environmental
sample, and developing a DNA library that either comprises of a random subset of the
DNA present (by using shortgun sequencing) or targets specific and informative DNA
fragments (amplicon sequencing) (Shaw et al. 2017). Next Generation Sequencing
(NGS) platforms were then being used in generating the DNA sequences before the
sequence reads is run through the bioinformatics analyses in taxonomic identification