ABSTRACT
Recent
studies
demonstrated
that
integrating
allometric
scaling
could
strengthen
the
relationship
between
environmental
DNA
(eDNA)
concentration
and
organism
abundance.
The
finding
has
been
supported
mainly
by
field
surveys
but
not
verified
sufficiently
at
individual
level
in
a
controlled
experimental
condition.
In
addition,
it
remains
unknown
whether
only
eDNA
also
RNA
(eRNA)
production
scales
allometrically
with
body
mass.
To
address
knowledge
gaps,
we
conducted
long‐term
rearing
experiment
using
ayu
(
Plecoglossus
altivelis
)
to
monitor
of
their
messenger
ribosomal
eRNA
growth
from
larvae
adults.
Water
samples
were
collected
tanks
P.
(eNAs)
concentrations
water
estimated
quantitative
real‐time
PCR
mitochondrial
nuclear
gene
markers.
parallel
each
sampling,
number
fish
individuals
total
biomass
tank
recorded.
Regardless
types,
individual‐level
eNA
related
scaled
mass
(ASM),
coefficient
b
=
0.75,
more
strongly
than
mean
result
indicated
larger
produces
lesser
mass‐specific
particles,
supporting
relevance
population
observed
surveys.
Moreover,
ratios
some
significantly
decreased
tank.
may
relate
changes
intracellular
physiology
and/or
aging,
having
potential
indicate
population's
average
size.
Our
study
offered
insights
into
various
particles
depending
on
size
metabolic
rate
implications
for
better
understanding
ecology
effective
stock
management.
Frontiers in Conservation Science,
Год журнала:
2025,
Номер
5
Опубликована: Янв. 2, 2025
Introduction
Rewilding,
the
facilitation
of
self-sustaining
and
resilient
ecosystems
by
restoring
natural
processes,
is
an
increasingly
popular
conservation
approach
potential
solution
to
biodiversity
climate
crises.
Outcomes
rewilding
can
be
unpredictable,
monitoring
essential
determine
whether
are
recovering.
Metabarcoding,
particularly
environmental
DNA
(eDNA),
revolutionizing
could
play
important
role
in
understanding
impacts
but
has
mostly
been
applied
within
aquatic
systems.
Methods
This
systematic
review
focuses
on
applications
eDNA
metabarcoding
terrestrial
monitoring,
with
additional
insights
from
bulk
ingested
DNA.
We
examine
publication
trends,
choice
sampling
substrate
focal
taxa,
investigate
how
well
performs
compared
other
methods
(e.g.
camera
trapping).
Results
Terrestrial
represented
a
small
proportion
total
papers,
forests
most
studied
system,
soil
water
substrates,
vertebrates
targeted
taxa.
Most
studies
focused
measuring
species
richness,
few
included
analyzes
functional
diversity.
Greater
richness
was
found
when
using
multiple
took
this
approach.
Metabarcoding
did
not
consistently
outperform
terms
number
vertebrate
taxa
detected,
likely
influenced
marker,
habitat.
Discussion
Our
findings
indicate
that
metabarcoding,
eDNA,
key
rewilding,
further
ground-
truthing
needed
establish
appropriate
experimental
pipelines
for
target
system
interest.
Systematic
Review
Registration
https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0
,
identifier
38w9q.
Frontiers in Physiology,
Год журнала:
2024,
Номер
14
Опубликована: Фев. 15, 2024
New
Zealand’s
green-lipped
mussel
(
Perna
canaliculus
)
is
an
ecologically
and
economically
important
species.
Marine
heatwaves
are
increasing
in
frequency
around
NZ’s
coastline,
these
events
correlated
with
increased
stress
mortality
of
some
aquaculture
This
study
aimed
to
identify
general
biomarkers
heat
P.
assess
whether
responses
differed
between
genetically
distinct
selectively
bred
mussels.
We
exposed
three
families
mussels
(families
A,
B
C)
seawater
temperature
regimes
the
laboratory:
1)
a
“control”
treatment
(ambient
12°C),
2)
26°C
challenge
subsequent
recovery
period,
3)
sustained
no
recovery.
investigated
survival,
immune
response
(hemocyte
concentration
viability,
oxidative
total
antioxidant
capacity),
hemocyte
gene
expression
gill
microbiome
during
challenges.
In
heat-stress
treatment,
family
A
had
highest
survival
rate
(42%
compared
25%
5%
for
C
B,
respectively).
Gene
levels
significantly
shifted
thermal
families,
more
dissimilar
than
C.
Family
substantially
genes
impacted
by
timepoint
other
while
very
little
genes/pathways
that
responded
stress.
Genes
related
shock
proteins
(e.g.,
AIF1,
CTSC,
TOLL8,
CASP9,
FNTA,
AHCY,
CRYAB,
PPIF)
were
upregulated
all
Microbiome
species-richness
before
heat-stress,
having
distinctly
different
flora
families.
Microbial
diversity
changed
similarly
prolonged
species
Vibrio
Campylobacter
Our
highlights
use
non-lethal
sampling
hemocytes
as
diagnostic
tool
explore
mussels,
predict
their
ocean
warming.
approach
can
potential
thermotolerant
candidates
further
selective
breeding,
which
may
increase
resilience
industry
warming
ocean.
Molecular Ecology,
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 5, 2024
ABSTRACT
Genetic
mechanisms
have
been
at
the
forefront
of
our
exploration
into
substrate
adaptive
evolution
and
phenotypic
diversification.
However,
genetic
variation
only
accounts
for
a
fraction
variation.
In
last
decade,
significance
RNA
modification
has
become
more
apparent
in
context
organismal
adaptation
to
rapidly
changing
environments.
m
6
A
methylation,
most
abundant
form
modification,
is
emerging
as
potentially
significant
player
various
biological
processes.
Despite
its
fundamental
function
regulate
other
major
post‐transcriptional
such
microRNA
alternative
splicing,
role
ecology
understudied.
This
review
highlights
potential
importance
methylation
ecological
adaptation,
emphasising
need
further
research,
especially
natural
systems.
We
focus
on
how
not
affects
mRNA
fate
but
also
influences
miRNA‐mediated
gene
regulation
contributing
adaptation.
The
aim
this
synthesise
key
background
information
enhance
understanding
driving
species
survival
dynamic
environments
motivate
future
research
dynamics
methylation.
The
sources
and
degradation
profiles
of
dissolved
environmental
RNAs
from
fish
in
water
remain
unknown.
In
this
study,
laboratory
experiments
mathematical
modelling
were
conducted
to
investigate
the
permeability
RNA
extracted
zebrafish
cells
through
filters,
release
live
dying
cells,
a
non-sterile
aqueous
environment.
This
research
aimed
provide
biological
ecological
insights
into
water.
results
showed
that
most
was
detected
filtrates
after
passage
0.45
µm
filters.
Over
course
6-day
experiment,
dynamic
levels
liquid
environment
containing
or
determined.
rates
calculated
using
modelling.
degraded
tubes,
2
months,
more
than
15%
remained
detectable.
half-life
tubes
approximately
20
~
43
days.
suggest
natural
waters
aquariums
could
be
so
low
it
would
difficult
detect
them
current
techniques.
obtained
study
will
help
develop
new
methods
for
measuring
dynamics
determining
their
significance.
Abstract
Environmental
RNA
(eRNA)
has
the
potential
as
a
non‐invasive
tool
for
assessing
physiological
status
of
macro‐organisms,
yet
quantitative
method
relative
gene
expression
analysis
is
still
underexplored.
To
bridge
this
gap,
study
introduces
quantification
eRNA,
employing
PCR
(qPCR)
to
evaluate
antioxidant
gene,
catalase
(
cat
),
in
Japanese
medaka
Oryzias
latipes
exposed
two
toxic
chemicals
96
h:
chlorpyrifos
(CPS)
and
carbamazepine.
Our
results
showed
that,
genes
frequently
used
reference
tissue
or
cells
conventional
correlated
with
each
other.
Also,
one
them
elfa
)
exhibited
less
variability,
showing
its
suitability
eRNA
analyses.
Additionally,
levels
increased
increasing
CPS
concentrations,
concentration‐response
manner.
These
suggest
promising
qPCR
applications
monitoring
an
organism's
health
response
environmental
changes.
However,
we
observed
disparities
beta‐actin
actb
between
whole
fish
body,
indicating
might
have
biased
origin.
Further
research
needed
uncover
origin
determine
limitations
applicability
domain
analysis.
Molecular Ecology Resources,
Год журнала:
2024,
Номер
24(4)
Опубликована: Март 19, 2024
The
analyses
of
environmental
DNA
(eDNA)
and
RNA
(eRNA)
released
by
organisms
into
their
surrounding
environment
(water,
soil
air)
have
emerged
as
powerful
tools
for
monitoring
biodiversity.
While
eDNA
has
been
widely
adopted
the
non‐invasive
detection
species
characterization
community
composition,
utilization
eRNA
is
still
in
its
infancy.
Due
to
functional
nature,
holds
intriguing
potential
biodiversity
offering
new
avenues
research
beyond
detection.
For
example,
conspecifics
that
are
almost
genetically
identical
can
exhibit
distinct
transcriptomic
differences
depending
on
life
stage.
In
this
issue
Molecular
Ecology
Resources
,
Parsley
Goldberg
(2024)
demonstrate,
through
a
lab‐validated
field
study,
be
used
detect
stages
amphibians.
This
study
elegantly
demonstrates
not
only
invasive
or
endangered
but
also
reveal
population
demographic
information
important
guiding
effective
conservation
strategies.
Archives of Insect Biochemistry and Physiology,
Год журнала:
2024,
Номер
116(4)
Опубликована: Авг. 1, 2024
Abstract
Fluctuations
in
temperature
are
recognized
as
a
potent
driver
of
selection
pressure,
fostering
genomic
variations
that
crucial
for
the
adaptation
and
survival
organisms
under
selection.
Notably,
water
is
pivotal
factor
influencing
aquatic
organism
persistence.
By
comprehending
how
respond
to
shifts
temperature,
we
can
understand
their
potential
physiological
adaptations
environmental
change
one
or
multiple
species.
This,
turn,
contributes
formulation
biologically
relevant
guidelines
landscape
scale
transcriptome
profile
lotic
systems.
Here,
investigated
distinct
responses
seven
stream
stonefly
species,
collected
from
four
geographical
regions
across
Japan,
including
atmospheric
temperatures.
We
achieved
this
by
assessing
differences
gene
expression
through
RNA‐sequencing
within
individual
species
exploring
patterns
community‐genes
among
different
identified
735
genes
exhibited
differential
expressions
gradient.
Remarkably,
community
displayed
levels
respiration
metabolic
genes.
Additionally,
diversity
molecular
functions
appeared
be
linked
spatial
variation,
with
potentially
contributing
overall
functional
found
22
consistent
response
variations.
These
related
respiration,
metabolism
development
clear
gradient
providing
robust
evidence
divergent
adaptive
temperature.
Our
findings
underscore
local
conditions,
suggesting
shared
may
occur
similar
conditions.
This
study
emphasizes
significance
considering
various
when
impacts
changes
on
insect
communities
understanding
mechanisms
cope
such
changes.
