Scientific Reports,
Journal Year:
2024,
Volume and Issue:
14(1)
Published: Nov. 21, 2024
Abstract
The
Arctic
Ocean
(AO)
is
changing
at
an
unprecedented
rate,
with
ongoing
sea
ice
loss,
warming
and
freshening
impacting
the
extent
duration
of
primary
productivity
over
summer
months.
Surface
microbial
eukaryotes
are
vulnerable
to
such
changes,
but
basic
knowledge
spatial
variability
surface
communities
limited.
Here,
we
sampled
in
waters
Beaufort
Sea
from
four
contrasting
environments:
Canada
Basin
(open
ocean),
Mackenzie
Trough
(river-influenced),
Nuvuk
region
(coastal)
under-ice
system
Basin.
Microbial
community
structure
composition
varied
significantly
among
systems,
most
phylogenetically
diverse
being
found
more
coastal
systems.
Further
analysis
environmental
factors
showed
potential
vulnerability
change
specialised
community,
which
was
samples
taken
water
immediately
beneath
ice,
where
distinguished
by
rare
species.
In
context
ice-associated
assemblages
may
transition
towards
generalist
assemblages,
implications
for
eventual
loss
biodiversity
associated
ecosystem
function
Ocean.
ICES Journal of Marine Science,
Journal Year:
2024,
Volume and Issue:
81(8), P. 1536 - 1548
Published: Aug. 7, 2024
Abstract
Quantifying
the
biomass,
or
number
of
individuals,
diversity,
and
distribution
marine
species
is
a
critical
aspect
understanding
managing
ecosystems.
In
recent
years,
there
has
been
growing
interest
in
using
environmental
DNA
(eDNA)
for
ecosystem
management
biodiversity
assessment.
However,
main
challenge
hindering
eDNA
applicability
inability
to
infer
absolute
abundances
from
multispecies
analysis
(eDNA
metabarcoding).
this
study,
we
demonstrate
way
forward
by
estimating
abundance
commercially
important
fish
Norwegian
fjord
joint
Bayesian
statistical
model
traditional
trawl-catch
data
molecular
derived
eDNA.
Using
model,
accurately
predict
out-of-sample
trawl
catches
alone.
Moreover,
our
provides
empirical
estimates
key
processes
linking
concentration
population
estimated
observations,
including
catchability,
shedding,
degradation,
dilution,
transport,
recovery
rate,
isolation
efficiency.
These
processes,
amplification
efficiencies
correcting
Polymerase
Chain
Reaction
(PCR)
bias,
are
species-specific
enable
translation
metabarcoding
into
abundances.
findings
have
broad
implications
use
conservation
efforts.
Royal Society Open Science,
Journal Year:
2024,
Volume and Issue:
11(2)
Published: Feb. 1, 2024
Mesophotic
coral
ecosystems
(MCEs)
are
light-dependent
tropical
or
subtropical
communities
occurring
at
depths
of
30–150
m.
Broader
surveys
MCEs
needed
to
better
understand
stony
corals,
the
keystone
species
coral-reef
ecosystems.
While
have
been
studied
by
professional
SCUBA
divers
and
with
deep-sea
robots,
comprehensive
required.
An
eDNA
metabarcoding
method
has
recently
used
survey
scleractinian
corals
in
shallow
reefs.
We
tested
whether
might
be
more
comprehensively
surveyed
collecting
seawater
samples
using
an
underwater
mini-remote
operated
vehicle
(mini-ROV).
Seawater
was
collected
1–2
m
above
reef
tops
20–80
24
sites
six
locations
around
Zamami
Islands
(Okinawa,
Japan).
Water
were
then
subjected
coral-specific
amplification.
Metabarcoding
analyses
amplicons
showed
that
except
for
one
site,
from
approximately
0.5
l
sufficient
identify
genera.
The
proportion
Acropora
higher
reefs
upper
ridges
slopes,
while
Porites
increased
mesophotic
.
Although
further
technical
improvements
required,
this
study
suggests
it
may
possible
monitor
generic
level
mini-ROVs.
Environmental DNA,
Journal Year:
2024,
Volume and Issue:
6(5)
Published: Sept. 1, 2024
ABSTRACT
Environmental
DNA
(eDNA)
has
significant
potential
to
improve
the
efficiency
of
biological
sampling
and
detect
species
that
pose
challenges
for
traditional
methods.
However,
a
key
obstacle
in
utilizing
eDNA
data
ecosystem
management
is
uncertainty
surrounding
ability
estimate
abundance
or
biomass
multiple
simultaneously.
In
this
study,
we
use
experimental
trials
with
known
biomasses
explore
feasibility
(1)
estimating
proportions
from
metabarcoding
(2)
absolute
concentrations
by
scaling
single
obtained
qPCR.
The
focal
study
were
three
gadid
fishes
are
components
marine
ecosystems
Alaska
vary
their
distribution
habitat
use:
Walleye
pollock
(
Gadus
chalcogrammus
),
Pacific
cod
macrocephalus
Arctic
Boreogadus
saida
).
After
designing
gadid‐specific
primers
accounting
PCR
biases
data,
found
corrected
read
closely
approximated
true
species.
Furthermore,
strong
positive
relationships
between
concentration
using
quantitative
combined
estimates
derived
These
findings
suggest
it
possible
accurately
quantify
compositions
metrics
gadids
real‐world
scenarios.
work
provides
framework
developing
analytical
approaches
can
be
applied
other
utility
eDNA.
Metabarcoding and Metagenomics,
Journal Year:
2024,
Volume and Issue:
8
Published: Dec. 30, 2024
Environmental
DNA
(eDNA)
and
RNA
(eRNA)
metabarcoding
has
become
a
popular
tool
for
assessing
biodiversity
from
environmental
samples,
but
inconsistent
documentation
of
methods,
data
metadata
makes
results
difficult
to
reproduce
synthesise.
A
working
group
scientists
have
collaborated
produce
set
minimum
reporting
guidelines
the
constituent
steps
workflows,
physical
layout
laboratories
through
archiving.
We
emphasise
how
suite
should
adhere
findable,
accessible,
interoperable
reproducible
(FAIR)
standards,
thereby
providing
context
evaluating
understanding
study
results.
An
overview
considerations
each
workflow
step
is
presented
then
summarised
in
checklist
that
can
accompany
published
or
report.
Ensuring
workflows
are
transparent
documented
critical
research
allow
more
efficient
uptake
into
management
decision-making.
ICES Journal of Marine Science,
Journal Year:
2025,
Volume and Issue:
82(2)
Published: Jan. 20, 2025
Abstract
In
this
study,
we
evaluated
how
well
DNA
metabarcoding
of
environmental
samples
captures
changes
in
marine
mesozooplankton
community
composition
to
optimize
the
use
sequencing
data
for
studying
seasonal
dynamics.
Although
is
increasingly
used
monitor
distribution
communities,
there
a
lack
standardized
methods,
and
it
remains
uncertain
what
extent
reflects
patterns
dynamics
observed
by
other
methods.
Zooplankton
net
were
collected
every
second
week
throughout
2017
northern
Salish
Sea,
British
Columbia.
We
compared
two
genetic
markers
(18S
targeting
eukaryotes
cytochrome
oxidase
I
invertebrates)
with
microscopic
assessments
zooplankton
collected.
also
transformation
using
relative
abundance,
presence/absence,
eDNA-index,
affects
linearity
between
morphological
Despite
low
taxonomic
agreement
microscopy,
found
most
biomass
dominating
genera
be
represented.
Using
generally
good
congruence
cycles
microscopy
DNA,
that
discrete
water
analyzed
can
provide
information
on
vertical
distributions
genera.
conclude
presenting
guidelines
future
studies
aim
study
Molecular Ecology Resources,
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 15, 2025
ABSTRACT
DNA
metabarcoding
is
subject
to
observation
bias
associated
with
PCR
and
sequencing,
which
can
result
in
observed
read
proportions
differing
from
actual
species
the
extract.
Here,
we
amplify
sequence
a
mock
community
of
known
composition
containing
marine
fishes
cetaceans
using
four
different
primer
sets
variety
conditions.
We
first
compare
observations
two
expected
based
on
total
genomic
target
mitochondrial
template
DNA.
find
that
calibrating
concentration
most
appropriate
as
it
isolates
amplification
bias;
calibration
results
be
attributed
both
ratios
then
model
remaining
approximately
60%
explained
by
inherent
species‐specific
characteristics.
These
include
primer‐template
mismatches,
amplicon
fragment
length,
GC
content,
vary
somewhat
across
Taq
polymerases.
Finally,
investigate
how
protocols
influence
regardless
changing
strongly
templates
mismatches.
Our
findings
suggest
pairs
without
mismatches
targeting
narrow
taxonomic
group
yield
more
repeatable
accurate
estimates
species'
true,
underlying
proportions.
identify
key
factors
should
considered
when
designing
studies
aim
apply
data
quantitatively.
Scientific Reports,
Journal Year:
2025,
Volume and Issue:
15(1)
Published: June 2, 2025
Near
real-time
data
across
taxa
are
necessary
for
quantifying
biodiversity
at
regional
to
continental
scales
and
evaluating
conservation
measures.
Yet,
standardized
methods
globally
distributed
infrastructure
still
lacking.
In
this
study,
we
conducted
the
first
national
survey
of
terrestrial
using
a
metabarcoding
approach
on
airborne
environmental
DNA
collected
by
ambient
air
quality
monitoring
network.
Our
goal
was
perform
multi-taxonomic
assessment
scale,
compare
detections
with
those
another
large-scale
(citizen
sciences)
estimate
tentative
minimum
eDNA
transportation
distance.
We
identified
over
1,100
taxa,
including
vertebrates,
invertebrates,
protists,
fungi
plants
covering
wide
range
life
history
traits
ecological
niches.
Citizen
science
were
complementary,
better
mapping
less
charismatic
difficult
spot
demonstrating
its
potential
align
global
goals.
Airborne
signals
relatively
local
(<
80
km),
likely
due
deposition
larger
particles
from
shorter
distances
limited
wind
near
ground
level.
Overall,
our
results
show
that
molecular
protocols
integrated
into
existing
networks
can
provide
standardized,
low
field
cost,
broad
scalability.
Ecological Applications,
Journal Year:
2023,
Volume and Issue:
33(8)
Published: Aug. 29, 2023
Abstract
Environmental
laws
around
the
world
require
some
version
of
an
environmental‐impact
assessment
surrounding
construction
projects
and
other
discrete
instances
human
development.
Information
requirements
for
these
assessments
vary
by
jurisdiction,
but
nearly
all
analysis
biological
elements
ecosystems.
Amplicon‐sequencing—also
called
metabarcoding—of
environmental
DNA
(eDNA)
has
made
it
possible
to
sample
amplify
genetic
material
many
species
present
in
those
environments,
providing
a
tractable,
powerful,
increasingly
common
way
doing
development
projects.
Here,
we
analyze
18‐month
time
series
water
samples
taken
before,
during,
after
two
culvert
removals
salmonid‐bearing
freshwater
stream.
We
also
sampled
multiple
control
streams
develop
robust
background
expectation
against
which
evaluate
impact
this
intervention
treatment
generate
calibrated,
quantitative
metabarcoding
data
from
amplifying
12s
MiFish
mtDNA
locus
complementary
species‐specific
PCR
yield
multispecies
estimates
absolute
eDNA
concentrations
across
time,
creeks,
sampling
stations.
then
use
linear
mixed
effects
model
reveal
patterns
over
estimate
removal
on
salmonids
creek.
focus
our
four
salmonid
species:
cutthroat
trout
(
Oncorhynchus
clarkii
),
coho
salmon
kisutch
rainbow
mykiss
sockeye
nerka
).
find
that
one
creek
seemed
have
no
while
second
had
large
fish
passage.
The
itself
only
transient
during
events.
In
context
billions
dollars
court‐mandated
road
replacements
taking
place
Washington
State,
USA,
results
suggest
replacement
can
be
conducted
with
minimal
key
management
concern.
Furthermore,
methods
effective
efficient
approach
monitoring
hundreds
culverts
prioritize
are
required
replaced.
More
broadly,
demonstrate
rigorous,
method
reporting
using
is
widely
applicable
environments
worldwide.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Oct. 5, 2023
Abstract
Metabarcoding
analyses
have
recently
undergone
significant
development
due
to
the
power
of
this
technique
in
biodiversity
monitoring.
However,
it
is
still
difficult
draw
accurate
quantitative
conclusions
about
ecosystems
studied,
mainly
because
biases
inherent
environmental
DNA
or
introduced
during
experimental
process.
These
alter
relationship
between
amount
observed
and
biomass
number
individuals
species
detected.
Two
metabarcoding
been
measured:
ratio
total
target
concentrations,
PCR
amplification
bias.
A
method
for
their
correction
proposed.
All
tests
were
performed
on
mock
alpine
plant
communities
using
marker
Sper01
,
which
expected
low
bias
its
highly
conserved
priming
sites.
Our
approach
combines
standard
techniques
(qPCR
digital
droplet
PCR)
with
a
realistic
stochastic
model
dynamics
that
accounts
saturation.
The
was
used
estimate
efficiencies
each
infer
true
proportions
from
read
relative
frequencies.
corrections
are
easy
implement
can
be
applied
previously
generated
data.
This
work
demonstrates
importance
two
considered
an
open
door
data,
although
many
other
remain
considered.