Environmental DNA (eDNA) technology: Fisheries and aquaculture perspectives

Abstract

The use of environmental DNA (eDNA) technology has emerged as a pioneering tool in the fields of fisheries and aquaculture, offering novel approaches for the monitoring and management of aquatic ecosystems. This study explores the potential of eDNA technology usage in the research and management of aquatic ecosystems. The importance of this method is discussed in relation to a number of ecological scenarios, including the assessment of biodiversity, monitoring of fish populations and pathogens, early detection of invasive fish species, and evaluation of water quality. Additionally, it addresses the challenges and obstacles that arise in the utilization of eDNA and discusses the ethical considerations that should be taken into account in future applications. This can underscore its significance as a non-intrusive, economical, and exceptionally responsive tool for advancing sustainable fisheries and aquaculture practices. This comprehensive review provides an in-depth analysis of the several applications of eDNA technology within the domains of fisheries and aquaculture.

Full text

Indian J Anim Health (2023), 62(2)- Special Issue
DOI: https://doi.org/10.36062/ijah.2023.spl.02623
Environmental DNA (eDNA) technology: Fisheries and aquaculture perspectives
N. Chouhan1, D. Dekari1, B. Choudhary1, A. Singh2 and T. Gon Choudhury1*
1College of Fisheries, Central Agricultural University, Lembucherra- 799 210, Tripura, India; 2ICAR-Central Institute
of Fisheries Education, Andheri West, Mumbai- 400061, Maharashtra, India
Abstract
The use of environmental DNA (eDNA) technology has emerged as a pioneering tool in the fields of fisheries and
aquaculture, offering novel approaches for the monitoring and management of aquatic ecosystems. This study explores the
potential of eDNA technology usage in the research and management of aquatic ecosystems. The importance of this method
is discussed in relation to a number of ecological scenarios, including the assessment of biodiversity, monitoring of fish
populations and pathogens, early detection of invasive fish species, and evaluation of water quality. Additionally, it addresses
the challenges and obstacles that arise in the utilization of eDNA and discusses the ethical considerations that should be
taken into account in future applications.This canunderscore itssignificance as a non-intrusive, economical, and exceptionally
responsive tool for advancing sustainable fisheries and aquaculture practices. This comprehensive review provides an in-
depth analysis of the several applications of eDNA technology within the domains of fisheries and aquaculture.
Keywords: Aquaculture, Aquatic ecosystems, Environmental DNA, Invasive fish, Pathogen detection
Highlights
eDNA: Revolutionizing fisheries and aquaculture management with precision
From biodiversity to ethics: eDNA’s multifaceted role in aquatic sciences
eDNA tech: Pioneering sustainable fisheries and ecosystem monitoring
The power of eDNA: Transforming aquatic conservation efforts
Invited Review Article
*Corresponding Author, E-mail: tanmoygc@gmail.com
INTRODUCTION
The concept of eDNA technology garnered more
attention and progress in recent years, resulting in an
increase in techniques for the recovery, amplification
and sequencing of DNA from environmental materials.
The utilisation of eDNA has emerged as a potent
tec h nique in cont e mpora ry ec o logic al st udies ,
facilitating the acquisition of information pertaining to
speci es occ urrence, po pul atio n siz e and sp ati a l
distribution. These aspects were historically difficult to
ascertain through conventional survey techniques. The
initial groundwork in the domains of fisheries and
aquaculture established the basis for the subsequent
development of eDNAtechnology. Its non-intrusive
characteristics and capacity to furnish valuable insights
into aquatic ecosystems contributed to its recognition
in thisfield. Through the examination of gene ti c
material, researchers are able to get valuable insights
pertaining to the existence, population size and general
ecological well-being of many species.
To meet the world’s growing fish demand and
maintain aquacult ure output and food biosecuri ty,
pa tho gen dete ction metho ds must be deve lop ed
(Mugimba et al., 2021). Aquatic pathogens include
ba cte ria , viru ses, and fungi thre aten worl dwide
aquaculture. Aquafarms need early diagnosis and health
monitoring to prevent disease spread. Disease research
and outbreak control are hampered by the volume of
organ samples that must be processed (Sieber et al.,
2020). Target-spec ifi c pri mers ca n amplify th e
pathogenic agent’s DNA, which can subsequently be
detected by sequencing. The third generation of DNA
sequencing (Liu et al., 2020) has brought high-
throughput genetic tools and eDNA technology as a bio-
monitoring tool. eDNA technology is one of numerous
advanced diagnostic methods that use genetic markers
specific to the target taxon or taxa. DNA or RNA from
nucleic acid (small DNA fragments) lost by a living entity
can be detected in soil, water, ice, sediment, and air
without isolating it (Díaz-Ferguson and Moyer, 2014;
Thomsen and Willerslev, 2015). Due to DNA’s greater
stability than RNA, eDNA detection in the environment
is easier and less laborious. In freezing, dry permafrost,
DNA degrades over thousands of years (Willerslev
et al., 2003), but in temperate water, it takes weeks
(Thomsen et al., 20 12). Standard eDNA sample
com p osit i on tes t s inc l ude DN A extr a ction ,
purification,filtration, polymerase chain reaction (PCR)
amplification and DNA sequencing are the mai n
components of this approach.
Using eDNA for species identification is a great
example of a technology innovation that opens up new

ways to study and quantify biosphere change, recovery,
and resilience (Thomsen et al., 2012). Early monitoring
method s improve precision and standardisation in
identifying cryptic, inaccessible, and low-abundance
organisms (Thomsen et al., 2012). eDNA from ancient
and modern materials can identify a single species or
analyze entire ecosystems. This can also measure farmed
fish, parasite, bacteria, fungi and other organism. As
crucial as it is to detect pathogens, it is also important to
determine if target pathogenic organisms breach food
safety or wat er quality. eDNA rese arch began in
microbiology since culture-based methods greatly alter
the natural range of bacteria (Thomsen and Willerslev,
2015). Species quantification is still the goal of eDNA
research, and many authors have made success in aquatic
organisms (Nathan et al., 2014), but this method can
easily identify harmful algae and pathogens.
After sediments were analyzed for ancient and
contempora ry animal and plant DNA, eDNA was
obtained from a range of terrestrial and aquatic
environmental samples to assess macro-organismal
diversity. eDNA methods have helped researchers to
investigate ancient habitats and monitor contemporary
biodive rsit y in terrestri al and marine ecosystems
(Thomsen and Willerslev, 2015). After discharge, eDNA
may persist in the environment, be picked up by organic
and inorganic particles, decay, or be altered by bacteria.
There was a correlation between species abundance,
body size and DNA release and degradation. Few abiotic
factors impact eDNA stability, inclu ding oxygen
concentration, nuclease activity, pH, conductivity, UV
light, and temperature (Shapiro, 2008). Alvarez et al.
(1996) suggest researching target eDNA fragment size
since smaller fragments survive for weeks or years.
Potentially harmful organisms in the environment and
near aquaculture facilities must be regularly monitored
with eDNA metabarcoding to prevent economic losses
due to infections. The development of technology has
made it simpler to identify various living beings without
negatively affecting either the environment or the
organisms themselves (Bohara et al., 2022). Antibiotic
resistance genes (ARGs) are highly concerned due to the
intensive use of antibiotics in aquaculture species to
prevent and cure bacterial diseases. So, this review shows
how the scientific community is constantly increasing
the use of eDNA surveys as an advantageous tool in
aquaculture perspectives.
Overview of eDNA technology
Collecting samples, extracting DNA, amplifying it,
and sequencing it are all foundational steps in eDNA
Fig. 1. Overview of the sequential processes involved in environmental DNA (eDNA) technology
2Indian Journal of Animal Health, Special Issue, 2023

technology (Fig. 1). First, soil and water samples are
taken from the area of interest. Next, specific procedures
are used to extract the DNA from these samples with the
goal of isolating and purifying the eDNA. The DNA
sections serving as genetic markers for the species of
interest are subsequently amplified using PCR. High-
throughput sequencing and other modern sequencing
technologies have made it possible to analyze many
genetic markers in a single sample. DNA sequences are
compared to databases to determine what kinds of species
live in the area being studied. A quantitative study can
show how common or rare each species is. Due to the
sensitivity of eDNA technology, it is possible to find
uncommon or cryptic species that would otherwise go
undetected by more conventional survey techniques. In
addition, eDNA investigations can track changes in
species diversity in real time because of its high temporal
resolution.
Assessment of biodiversity, conservation biology,
and monitoring of aquatic ecosystems are just few of
the ecological fields that might benefit from eDNA
techno l og y . It hel ps s c i e n t i st s monit o r t h e
whereabouts of threatened species, find the carriers
of dise a se, and evaluat e th e eff ects of h uman
interference with natural environments. However,
the r e are sti l l obs t acles to overcom e , su c h as
contamination, degradation, and differences in eDNA
shedding rates. To perfect procedures, standardize
methods, and set up stringent quality controls, further
study is needed. However, the vast volume of sea water
promotes dilution and dispersion of the eDNA, making
detection more difficult than in freshwater ecosystems
(Díaz-Ferguson and Moyer, 2014). The quantity of
eDNA in aquatic ecosystems is highly dependent on
th e diversity of speci es pre se nt and the rate of
degradation by biotic and abiotic factors. Diet and
trophic investigations can be carried out using eDNA
fragments or metabarcoding techniques without the
need to see or identify prey in the stomach or faces by
employing stomach contents as target DNA (Zarzoso-
Lacoste et al., 2013).
Application of eDNA technology in fisheries and
aquaculture
eDNA is fish DNA lost in the environment, such as
sk i n , s c a l e s , f e c e s, gametes, dead c ell s, etc.
Un d e r st anding a quatic sp e c ie s divers i t y and
distribution is crucial to managing and monitoring
aquatic habitats. Jo et al. (2019) suggest it hel ps
discover spatial variations in coastal ecosystem species
communities. Numerous aquatic creatures are hidden
under the water; therefore, their accessibility is being
studied (Ardura et al., 2015). As eDNA technology
advances, it can be used to examine a wider aquatic
environment and easily identify creatures (Hänfling
et al., 2016). As monitoring this resource under climate
change is crucial, eDNA allows rapid monitoring of
va st ecosyste ms like the oc e an a nd its bot tom
distribution, which is rich in biodiversity. Since it
detects eDNA in the water, not the fish, it may give a
false positive if the source water contains the parasite.
DNA metabarcoding may help explain freshwater
pl a n kton commu n it y st ructu r e and disp e rsion .
Microorganisms and macroalgae inhibit harmful algal
blooms through biological processes that need further
study using eDNA analysis. Researchers can also
evaluate aquaculture ARGs prevalence by focusing on
certain genes. To accurately detect species in
aquacul ture , thi s techn olog y mu st be puri f ied,
amplified, bioinformatics analyzed, DNA extracted, and
sampled. Standardization of methods is essential for
data comparabili ty and dependability, and eDNA
technology raises ethical and regulatory issues for
responsible management, including privacy, data
sharing, and species discovery. This section covered
aquaculture applications of eDNA technology.
Detection of fish pathogens: The risk of infection and
disease spread is higher in fish farms than in natural
habitats because farmed animals are often kept in high
density and are subject to constant stress and a variety
of pollutants. So, the use of eDNA technology for the
detection of fish diseases has emerged as a game-
changing approach to aquatic health monitoring and
disease management. Bacteria, viruses, and parasites
are some of the fish diseases that can have devastating
effects on both wild and farmed fish populations. The
release of genetic material from bacteria into the
extracellular media has been documented by Bohara
et al.(2022).
So m e bacter i a extrude dama g ed DN A and
manufacture new DNA in water to survive, whereas others
lyse their cells and release their DNA (Battista, 1997).
Rainwater and groundwater intrusion may transfer the
fungus to surrounding lakes and rivers, but cannot be
traced accurately because fungal DNA is less studied
than bacterial DNA (Martins et al., 2010). Traditionally,
fish were collec ted a nd euthaniz ed before be ing
examined for endoparasites, which was time-consuming
and cruel. However, eDNA technology has made this
process more efficient. Several studies (Taengphu et al.,
2022) have shown that eDNA or eRNA may detect viral
DNA and RNA (Ip et al., 2023). The number of different
bacteria varies with temperature, but eDNA can detect
3
eDNA technology for fisheries and aquaculture

Table 1. Fish diseases identified by using eDNA technology
Disease Pathogens detected Source Country References
Red seabream iridovirus Seawater Singapore Minamoto et al., 2009;
Ip et al., 2023
Nervous necrosis virus Seawater Singapore Ip et al., 2023
Viral Cyprinus herpes virus Lake, Pond, River Japan Minamoto et al., 2009
pathogens (CyHV-3)
Tilapia tilapine virus Pond water Thailand Taengphu et al., 2022
Ranavirus Pond water France Miaud et al., 2019
Scale drop disease virus Pond water Singapore Kiat et al., 2023
Renibacterium River and pond Sweden Persson et al., 2022
Bacterial salmoninarum water
pathogens Aeromonas spp. River Korea Fong et al., 2016
Flavobacterium River Japan Tenma et al., 2021
psychrophilum
Recirculatory
Yersinia ruckeri aquaculture Norway Lewin et al., 2020
system (RAS)
Fungal Saprolegnia parasitica River France Rocchi et al., 2017
pathogens
Myxosporean River Spain Lisnerová et al., 2023
Chilodonella hexasticha Pond water Australia Gomes et al., 2017
Pseudoloma neurophilia RAS United States Schuster et al., 2023
Gyrodactylus salaris River and pond Norway Rusch et al., 2018
water
Schistocephalus solidus Seawater Canada Berger and Aubin-
Horth, 2018
Parasitic Nematodeand Lakes New Zealand Thomas et al., 2022
pathogens Platyhelminths
Dactylogyrus spp. Fish consignment Australia Trujillo-González
et al., 2019
Myxobolus cerebralis River California Richey et al., 2018
Tetracapsuloides River Switzerland Carraro et al., 2018
bryosalmonae
Ceratonova shasta River California Richey et al., 2020
Neoparamoeba perurans Seawater Australia Bridle et al., 2010
Cryptocaryon irritans Marine fish farm Hong Kong Tsang et al., 2021
Sphaerothecum destruens River and pond Great Britain Sana et al., 2018
water
it. Table 1 lists several fish diseases found by this method.
Invasive and time-consuming approaches often used
to identify these infections may be stressful for fish and
prevent early diagnosis. In order to identify fish diseases
quickly and accurately, eDNA technology provides a
non-invasive, extremely sensitive alternative. eDNA-
based virus detection works on the premise that infected
fish leak genetic material into the environment (Kawato
et al., 2021). Researchers can now easily isolate the
eDNA, and allows for a comprehensive assessment of
the range of pathogens present in each body of water or
aquaculture facility. This eDNA monitoring reduces
stress during surveillance while providi ng a more
th oroug h eval uation of dis ease pre valence than
conventional sample approaches.
Eu t roph icat i on and alga e bloo ms cont r ol:
Eutrophication, which harms aquatic ecosystems, is
caused by algal blooms due to addition of excess
nutrients into water body. To address this problem eDNA
Indian Journal of Animal Health, Special Issue, 2023
4

technology is helpful. Human activities and nutrient
imports have been linked to eutrophication, which may
degrade water quality, diminish biodiversity, and pose
risks to human health. Genetic material discharged by
orga nisms is used for in-depth species monitoring
without direct observation. When it comes to controlling
algal blooms, eDNA can help by seeing the first
symptoms of a bloom-forming and determining which
species are most prevalent. Timely treatments, such
altering nutrient inputs or deploying targeted algicides,
are made possible by timely information. Safeguarding
water quality and the delicate balance of aquatic habitats,
eDNA technology provides a non-intrusive, cost-
ef fec tiv e sol uti on to monitoring and mit iga ting
eutrophication and algal blooms. In the 1990s, eDNA
techniques were used to track phytoplankton blooms
and evaluate the impact of environmental factors on
bacterial community biomass (Bailiff and Karl, 1991).
We can use species compositions to find ecological
indicators to reduce aquatic eutrophication and HABs
in freshwater and marine habitats. Due to their toxicity
and quick development, harmful algal blooms, induced
by phytoplankton, hypoxia, or a lack of local flora and
fauna (Smith and Schindler, 2009), destroy aquatic food
webs (Wiegand and Pflugmacher, 2005). Algicidal
chemical and biological approaches for plankton
management are time-consuming, expensive, and only
used when algae are visible (He et al., 2012). Their
presence has already degraded water quality by lowering
oxygen levels and restricting nutrient cycling and light
(Paerl and Otten, 2013), but eDNA can detect them at
extremely low levels and allow early treatment. Imai
et al. (2010) found that cyanobacteria toxins harm
animals, plants, and humans. Thus, rapid eDNA advances
should help monitor and avoid marine HABs. Lowering
N and P inputs in too-fertile aquatic systems can stop
eut r ophi c a tion and HAB s. eD NA could l ocate
microorganisms that efficiently absorb and change
nutrients like N and P in waterbodies to reduce their
concentration (Liu et al., 2020). Identifying bacteria that
suppress toxic algal growth is crucial. Species diversity
and environmental characteristics like pH, N, and P must
be monitored throughout time to determine microbe
preferences. Early warning systems and HAB prevention
can be achieved by purposely encouraging such bacteria
to multiply before an epidemic.
DNA content in coastal waters has been shown to
correspond with the spatial and temporal fluctuations
of bacterial and phytoplankton populations during
blooming episodes (Bailiffand Karl, 1991). Combining
eDNA procedures with additional approaches, such as
physical and chemical st udies, may provide more
complete information.
Fish biodiversity monitoring: Fish species were detected
by direct observation to determine their distributions,
patterns, and abundances (Thomsen et al., 2012).
However, these methods are laborious and expensive,
so new molecular methods for aquatic organism
detection have emerged. There are many ways to use
eDNA in conse rvation biology. Fish biodiversit y
monitoring, analysis, and conservation a re greatly
improved by eDNA technology. Monitoring of fish
populations, species ranges, and habitat changes is
necessary. These analyses inform ecosystem status and
conservation efforts. Studying fish populations helps
researchers conserve, identify threatened species, and
assess environmental stressors. Genetic analysis and
eDNA sampling offer novel biodiversity assessment
methods. This innovative method allows non-intrusive
sam pling of aquatic ecosystems to complet e fish
population studies and also estimates population. This
kn o wledg e aids fishe ries mana g e ment , habi t at
degradation assessments, and conservation. eDNA
technology makes fish biodiversity research fast, cheap,
and scalable, preserving aquatic ecosystems and fish
populations for future generations. Maintaining healthy
fisheries, food supplies, and aquatic ecosystems’ delicate
ba l a nce re qui r es pro t ecting fish pop u lation s.
Researc hers examine d biologi cal life events like
spawning and larval settling in fish and shrimp to
determine when and where a species’ life history event
occurred (Díaz-Ferguson and Moyer, 2014). eDNA and
water quality assessments of planktonic species may help
researchers develop technologies with the data.
Because short DNA sequences can persist for long
periods in cold environments with reduced exposure or
no light, ancient eDNA in sediments, ice cores, and other
environmental sources can help scientists reconstruct
community structure and historical ecological processes
(Willerslev et al., 2003). Most of Earth’s species haven’t
been formally described by scientists, compounding this
problem. Since fish eDNA was 8-1,800 times more
concentrated in sediment than water and surficial
sediments than surface water, sediment was used to
identify fish species (Turner et al., 2015). Directly
collecting and observing many species or samples is
imp o ssi ble. Many clos ely relate d sp ecie s lack
morphological distinguishing features, making visual
differentiation difficult (Ko et al., 2013). Monitoring
species and populations provides reliable distribution
patterns and population size estimates, which helps
conserve biodiversity (Thomsen and Willerslev, 2015).
As eDNA metabarcoding detected a broader range of
taxonomic groups than the visual surveys (Afzali et al.,
2021), it was found that eDNA metabarcoding can
provide monitoring results that are comparable to, or
5
eDNA technology for fisheries and aquaculture

more sensitive than, a variety of conventional monitoring
methods. The fauna and vegetation of springs in the
Mojave Desert of California, USA, were detected using
three different eDNA metabarcoding primer sets by
Palacios Mejia et al. (2021). Székely et al. (2021) took
water samples from the ocean to look for bowhead whales
using a recently developed real-time PCR technique.
To better forecast geographic and temporal biodiversity
trends, eDNA-based techniques are likely to transition
in the future from single-marker assessments of species
or groups to meta-genomic surveys of whole ecosystems.
The biological, geological, and environmental sciences
may all benefit from these developments (Thomsen and
Willerslev, 2015).
Ecology and environment: eDNA technology is a game-
changer in the fields of ecology and environmental
management since it provides a fast, non-invasive way
to measure biodiversity and monitor ecosystem vitality.
It includes the collection of genetic material that animals
shed into the environment, which reveals information
on the existence, distribution, and inte ractions of
different species. This enables scientists to keep an eye
on sensitive or i naccessible environments without
causing any damage. Its accuracy and scalability make
it a powerful resource for monitoring ecosystems and
predicting future changes. By facilitating sustainable
practices that protect biodiversity and environmental
integrity, eDNA technology enables a proactive strategy
for managing ecosystems.
This metho d wa s used to det e rmine ha b itat
connectivity for fish migration between the sea and river
(Yamanaka and Minamoto, 2016) and to easily identify
the presence or absence of the targeted species during
seasonal migration pattern identification to maintain fish
diversity and river ecosystem functions. Tsuji and
Shibata (2021) demonstrated how their eDNA method
can study fish reproductive biology. It could be useful
for assessing river-artificial barrier effects before and after
construction (Yamanaka and Minamoto, 2016). Using
eDNA analysis to predict comm unity composition
(Minamoto et al., 2012), quantify species abundance
(Pilliod et al., 2013), and detect aquatic species has
advanced rapidly. Higher species extinction rates than
pre-human times (Barnosky et al., 2011) threaten human
health and the planet’s future (Diaz et al., 2006). Long-
term data can provide innovative conservation and
management guidelines for aquatic ecosystems. Better
aquat ic ecos ystem mana gem e nt would im prov e
freshwater and saltwater biodiversity and quality. These
traits would boost biodiversity, the economy, and health
(Liu et al., 2020).
Early detection of invasive species: This technique
greatly improves the early identification of invasive
species. Rapid and sensitive identification of species
that cannot be directly seen is made possible by eDNA
via the collection of genetic material shed into the
environm ent. This non-invasiv e method improves
monitoring efficiency and accuracy, both of which are
essential for preventing further harm from incursions.
Rare and elusive species may be found with the use of
eDNA, as an invasive species and the effe cts of
environmental changes. Even in difficult settings, eDNA
enables more thorough collection. It’s useful for spotting
invasive species in their early stages when they’re often
hard to notice using conventional approaches. The
ability to implement quick reaction techniques is greatly
enhanced by early discovery, which helps to minimize
additional ecological harm. According to Yamanaka and
Minamoto (2016), eDNA technology is an excellent tool
fo r fis h moni tori n g si n ce it e nable s pr oactiv e
management and protects native ecosystems from the
detrimental consequences of alien species.
Locating an invasive alien species’ range is the first
step in addressing the difficulties it causes. However, it
might be challenging to research species in aquatic
habitats (Fujiwara et al., 2016). The abundance of food
in their new settings has allowed many invasive fish
species to rapidly expand their biomass via breeding.
These fish may eventually displace local species by
outcompeting them for food and other resources. It has
been claimed that eDNA detection may be used to
distinguish between fish species in water (Minamoto
et al., 2012). The introduction of invasive alien species
may have negative consequences on native ecosystems
and fisheries, contributing to the worldwide loss of
biodiversity that has been identified as a pressing issue.
With this technology, invading species may be found in
their early stages by tracing their genetic footprints in
water bodies. In North America, eDNA has been shown
to be an effective detection method for invasive species
in freshwater systems by researchers Jerde et al. (2011).
Asian carp (Hypophthalmichthys molitrix and H. nobilis)
were the primary research subjects in this investigation
of their detection methods. When problems are identified
quickly, solutions may be implemented to slow or stop
their growth. Assessing ecosystem health may be done
indirectly via the use of eDNA to track shifts in
community makeup and declines in species diversity.
Water quality monitoring: The prosperity of fishing
and farming in water requires pristine aquatic habitats.
By measuring the existence and quantity of indicator
species, eDNA may be used to keep tabs on water quality.
6Indian Journal of Animal Health, Special Issue, 2023

Lake water quality can be measured by phytoplankton
biomass and species composition (Chen et al., 2017).
Pollution, habitat degradation, and other environmental
stresses may all be deduced from variations in eDNA
signals. Parameters of water quality such as temperature,
oxygen content, pH, and pollution levels must be kept
optima l fo r aqua tic life to th rive . Overa ll f ish
productivity may be hampered by poor water quality
due to stress, sickness, and decreased reproduction.
Specifically, changes in species variety might impact
the distribution of submerg ed mac rophytes, water
quality (Didham et al., 2005), and the general dynamics
of an ecosystem. Therefore, eDNA may prove to be a
valuable resource in future risk-based decision making
for nat ural re sourc es and envir onmental impact
assessments (Veldhoen et al., 2012).
Diatom has high protein and fat content, which aids
in the development of fish and shrimp, and this is also
used to monitor the water quality. Miyata et al. (2022)
evaluated a diatom eDNA-based approach and employed
eDNA/eRNA from algae and arthropods to assess
biodiversity and water quality. Sedimentary eDNA was
employed by Sun et al. (2021) to make connection
be twe en reservoi r wa ter qua lity and long-t erm
mi crobiologi cal pr ofil es, andobse rve d bacte ria l
communities of sediments provided a historical window
into the effects that human activities had on water quality.
Detecting antibiotic resistance genes using DNA: The
efficacy of antibiotics used in animal treatment may be
diminished if bacteria in aquatic settings acquire the
ability to transmit ARGs to native bacterial populations.
The wide spread use of antibiotics in aquaculture
contributes to a worldwide health crisis known as
antibiotic resistance (AR). Aquatic and terrestrial
ecosystems are equally impacted by the development of
AR due to the horizontal transmission of ARGs across
bacteria in aquaculture settings. The health of aquatic
creatures may be impacted, and the delicate equilibrium
of microbial communities in aquatic environments may
be upset if these genes are introduced. There may be
serious ecological and public health consequences if
antibiotic-resistant bacteria are accidentally released
int o the en viron m ent. Comp a rison of cli n ical,
agricultural, or eDNA sequences to collections of
reference AMR sequences is the backbone of AMR
surveillance and genome analysis, underscoring the
significance of well-curated AMR databases (McArthur
and Tsang, 2017).
It has been suggested that the acquisition of genes
from several sources may lead to multidrug resistance in
certain bacteria (Saavedr a et al., 2018). Possible
mechanisms for the emergence of AMR includ e
spontaneous mutations and the horizontal transfer of
genes from resistant bacteria through transformation,
transduction, and conjugation. Transformation involves
the transfer of cell-free DNA to bacteria that are receptive
or comp etent ; tran sdu ctio n involve s the use of
bacteriophages; and conjugation involves the transfer
of mobile genetic elements like plasmids through direct
cell-to-cell contact. Antimicrobial usage may provide a
selection pressure that favours the survival and spread
of drug-resistant microorganisms. Water use in irrigation,
animal farms, and aquaculture all pose risks for spreading
AMR. This is because water may carry pathogens from
one location to another. In addition, long-distance
travellers like seagulls and other wild animals are known
to spread resistant bacteria to new ecosystems.
Aquaculture facilities and their surrounding water
bodies may be sampled for eDNA analysis, eliminating
the requirement for time-consuming and laborious
culture-based approaches for detecting antibiotic-
resistant bacteria and ARGs. AMR research in surface
waters may utilize molecular methods that evaluate the
DNA of a bacterium for related ARGs (Chang et al.,
2017). This is because environmental bacteria might
represent key resistance reservoirs, and their culture is
also not straightforward; thus, they evade detection. By
analyzing the retrieved eDNA using molecular tools like
PCR or metagenomic approaches, scientists get insight
in to the preva len ce, dive rsity, and dynamics of
antibiotic-resistant populations. qPCR experiments
di r e cted at i ndiv i dual AR Gs that also prov ide
information on the prevalence of resistance genes in
aquaculture settings. As shown by Chang et al. (2017),
qPCR data may be used as a reliable substitute for ARG
transferability. Depending on the DNA extraction
method, qPCR may reveal the abundance of the targeted
ARGs in diverse genetic settings, such as live bacteria,
mobile DNA fragments like MGEs (Mobile genetic
element), and “free” ambient DNA, i.e., extracellular
DNA (Eramoet al., 2019).
Future directions
Future advances in fisheries and aquaculture with
eDNA technology are likely to continue. More research
is needed to perfect the technique, increase detection
sensitivity, and expand uses. Academics and industry
must collaborate to maximize eDNA’s potential. Future
species identification will require optimizing molecular
tests and verifying positive samples, both eDNA-related
challenges. Optimizing eDNA for disease diagnosis is still
difficult, and to ensure that eDNA comes from active
infection but not from discarded DNA fragments. For
accurate results, sample collection, processing, and
analysis must minimize contamination. Validation and
7
eDNA technology for fisheries and aquaculture

standardization of eDNA-based assays are improving their
reliability. Another way to reduce eDNA false positive
ambiguity is to Sanger sequence every positive eDNA.
This technique can only provide information on
organisms discovered from genetic material, so reference
DNA databases may limit its use for certain species, and
we needed species-specific primer sets so that we could
ide n tify o ther s pecies a lso. I f eDNA anal y sis
technologies improve, metabarcoding with universal
primers, it can estimate fish biomass and biodiversity.
These advances will help us protect endangered species
and eradicate invasive ones. Deep-sea community
composition is unknown due to the rarity of hadal
ecosystem studies, so this method allows us to identify
deep oceanic aquatic fauna.
Aquaculture and host species repatriation may
benefit from eDNA infection testing to stop infectious
agents from spreading to wild fish populations. Thus,
Sana et al. (2018) addressed a major fi she r ies
conservation issue. eDNA tools need more work before
they can fully replace conventional pathogen abundance
detection methods (Rusch et al., 2018), but researchers
say they will cut costs, improve surveillance, and speed
up risk mitigation if they return positive.
Conclusion
Fisheries and aquaculture research and management
are changing rapidly due to eDNA technology. Its use
in biodiversity assessment, pathogen screening, fish
population monitoring, HAB detection, invasive species
identification, and water quality monitoring shows its
forging potential. As genetic methods are being refined
with the advancement of genomic technologies, eDNA
can help to promote sustainable practices and protect
aquatic ecosystems. Sustainable methods are needed to
reduce aquaculture ARG transfer risks. This includes
prudent antibiotic use, probiotics, vaccinations, and
strict biosecurity. Using eDNA to monitor ARGs may
help develop and evaluate preventative measures. Due
to its wide coverage, eDNA technology for fish pathogen
identification is a paradigm shift in aquatic disease
monitoring, protecting both wild and cultivated fish
populations. Despite its ability to reliably detect target
species, eDNA’s use in the real world is limited by its
inability to accurately assess the prevalence of non-
targeted agents in the environment.
Conflict of Interest: The authors declare no competing
interests.
Au thor ’ s cont r ibut ions : NC : Inv e stig a t ion,
conceptualization, review and editing; DD: Review and
editing; BC: Tabulation; AS: Formal analysis, review
and editing; TGC: Conceptualization, validation,
supervision, review and editing.
ACKNOWLEDGEMENT
T h e a u t h o r s si n c er e l y t h an k t h e V i c e
Chancellor, Central Agricultural University, Imphal
and Dean, College of Fishe ries, CAU, Tripura for
providing all necessary resour ces pertaining to this
review artic le
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Received- 22.09.2023, Accepted- 06.11.2023, Published- 24.11.2023 (Online)
Section Editor: Dr. D. Kamilya, Member, Editorial Board
eDNA technology for fisheries and aquaculture 11