PLoS ONE,
Journal Year:
2021,
Volume and Issue:
16(9), P. e0257510 - e0257510
Published: Sept. 21, 2021
Anthropogenic
activities
are
changing
the
state
of
ecosystems
worldwide,
affecting
community
composition
and
often
resulting
in
loss
biodiversity.
Rivers
among
most
impacted
ecosystems.
Recording
their
current
with
regular
biomonitoring
is
important
to
assess
future
trajectory
Traditional
monitoring
methods
for
ecological
assessments
costly
time-intensive.
Here,
we
compared
macroinvertebrates
based
on
environmental
DNA
(eDNA)
sampling
traditional
kick-net
biodiversity
patterns
at
92
river
sites
covering
all
major
Swiss
catchments.
From
data,
a
biotic
index
(IBCH)
145
indicator
taxa
had
been
established.
The
was
matched
by
taxonomically
annotated
eDNA
data
using
machine
learning
approach.
Our
comparison
diversity
only
uses
zero-radius
Operational
Taxonomic
Units
assigned
taxa.
Overall,
found
strong
congruence
between
both
assessment
total
(gamma
diversity).
However,
when
assessing
site
level
(alpha
diversity),
were
less
consistent
gave
complementary
composition.
Specifically,
retrieved
significantly
fewer
per
than
Importantly,
however,
subsequent
classification
rivers
detected
indicators
resulted
similar
scores
that
classified
random
forest
majority
predictions
(72%)
from
same
status
categories
as
Thus,
validly
communities
and,
combined
learning,
provided
reliable
classifications
rivers.
while
gives
macroinvertebrate
approach,
subsequently
calculated
indices
nevertheless
directly
comparable
consistent.
Molecular Ecology,
Journal Year:
2020,
Volume and Issue:
29(22), P. 4258 - 4264
Published: Sept. 23, 2020
The
last
decade
brought
a
spectacular
development
of
so-called
environmental
(e)DNA
studies.
In
general,
"environmental
DNA"
is
defined
as
DNA
isolated
from
samples,
in
contrast
to
genomic
that
extracted
directly
specimens.
However,
the
variety
different
sources
eDNA
and
range
taxonomic
groups
are
targeted
by
studies
large,
which
has
led
some
discussion
about
breadth
concept.
particular,
there
recent
trend
restrict
use
term
"eDNA"
macro-organisms,
not
physically
present
samples.
this
paper,
we
argue
such
distinction
may
be
ideal,
because
signal
can
come
organisms
across
whole
tree
life.
Consequently,
advocate
should
used
its
generic
sense,
originally
defined,
encompassing
all
including
microbial,
meiofaunal
macrobial
taxa.
We
first
suggest
specifying
origin
sample,
water
eDNA,
sediment
or
soil
eDNA.
A
second
specification
would
then
define
group
through
polymerase
chain
reaction
amplification,
fish
invertebrate
bacterial
This
terminology
does
also
require
assumptions
specific
state
sampled
(intracellular
extracellular).
hope
will
help
better
scope
studies,
especially
for
managers,
who
them
reference
routine
biomonitoring
bioassessment.
Molecular Ecology,
Journal Year:
2020,
Volume and Issue:
30(13), P. 2937 - 2958
Published: May 16, 2020
Abstract
A
decade
after
environmental
scientists
integrated
high‐throughput
sequencing
technologies
in
their
toolbox,
the
genomics‐based
monitoring
of
anthropogenic
impacts
on
biodiversity
and
functioning
ecosystems
is
yet
to
be
implemented
by
regulatory
frameworks.
Despite
broadly
acknowledged
potential
genomics
this
end,
technical
limitations
conceptual
issues
still
stand
way
its
broad
application
end‐users.
In
addition,
multiplicity
implementation
strategies
may
contribute
a
perception
that
routine
methodology
premature
or
“in
development”,
hence
restraining
regulators
from
binding
these
tools
into
legal
Here,
we
review
recent
implementations
methods,
applied
biomonitoring
ecosystems.
By
taking
general
overview,
without
narrowing
our
perspective
particular
habitats
groups
organisms,
paper
aims
compare,
discuss
strengths
four
for
monitoring:
(a)
Taxonomy‐based
analyses
focused
identification
known
bioindicators
described
taxa;
(b)
De
novo
bioindicator
analyses;
(c)
Structural
community
metrics
including
inferred
ecological
networks;
(d)
Functional
(metagenomics
metatranscriptomics).
We
emphasise
utility
three
latter
integrate
meiofauna
microorganisms
are
not
traditionally
utilised
because
difficult
taxonomic
identification.
Finally,
propose
roadmap
programmes
leverage
analytical
advancements,
while
pointing
out
current
future
research
needs.
Environment International,
Journal Year:
2019,
Volume and Issue:
131, P. 104986 - 104986
Published: July 9, 2019
Due
to
the
limitations
of
current
extraction
methods,
extracellular
DNA
(eDNA)
is
rarely
discerned
from
intracellular
(iDNA)
despite
having
unique
contributions
antibiotic
resistance
genes
(ARGs)
propagation.
Furthermore,
eDNA
may
be
free
(f-eDNA)
or
adsorbed
suspended
solids,
including
cells
(a-eDNA),
which
affects
ARG
persistence
and
transmissivity.
We
developed
a
novel
method
using
magnetic
beads
separate
iDNA,
a-eDNA,
f-eDNA
assess
how
these
physical
states
ARGs
change
across
wastewater
treatment
plant.
This
efficiently
extracted
(>85.3%)
with
higher
recovery
than
methods
such
as
alcohol
precipitation,
CTAB-based
extraction,
kits
(<10%).
Biological
UV
disinfection
decreased
concentration
(iARGs)
(a-eARGs),
causing
an
increase
released
(f-eARGs).
More
were
discharged
through
wasted
biosolids
in
effluent;
iARGs
a-eARGs
are
prevalent
((73.9
±
22.5)
%
(23.4
15.3)
total
respectively),
while
f-eARGs
effluent
((90.3
16.5)
%).
Bacterial
community
analysis
showed
significant
correlations
between
specific
genera
(e.g.,
Aeromonas,
Pseudomonas
Acinetobacter
strongly
correlated
multidrug-resistance
gene
blaTEM).
system
discharge
receiving
environments,
however,
increased
eARG
concentrations
present
effluent,
contribute
environmental
resistome.
Environmental DNA,
Journal Year:
2020,
Volume and Issue:
3(1), P. 261 - 276
Published: Dec. 21, 2020
Abstract
DNA
metabarcoding
of
freshwater
communities
typically
relies
on
PCR
amplification
a
fragment
the
mitochondrial
cytochrome
c
oxidase
I
(COI)
gene
with
degenerate
primers.
The
advantage
COI
is
its
taxonomic
resolution
and
availability
an
extensive
reference
database.
However,
when
universal
primers
are
used
environmental
(eDNA)
isolated
from
water,
benthic
invertebrate
read
OTU
numbers
“watered
down,”
that
is,
under
represented,
compared
to
whole
specimen
“bulk
samples”
due
greater
co‐amplification
abundant
nontarget
taxa
(e.g.,
fungi,
algae,
bacteria).
Because
stream
prime
importance
for
regulatory
biomonitoring,
more
effective
ways
capture
their
diversity
via
eDNA
water
important.
In
this
study,
we
aimed
improve
assessment
by
minimizing
amplification.
Therefore,
generated
data
using
BF2/BR2
samples
collected
throughout
15
months
German
Long‐Term
Ecological
Research
site
(Rhine‐Main‐Observatory,
Kinzig
River)
identify
most
taxa.
Based
these
data,
designed
new
reverse
primer
(EPTDr2n)
3’‐specificity
toward
validated
specificity
in
silico
together
forward
fwhF2
available
GenBank
BOLD.
We
then
performed
situ
tests
20
River
samples.
found
percentage
target
reads
was
much
higher
combination
two
pairs,
fwhF2/fwhR2n
(99.6%
versus
25.89%
39.04%,
respectively).
Likewise,
number
detected
species
substantially
(305
113
185)
exceeded
153
identified
expert
taxonomists
at
nearby
sites
across
decades
sampling.
While
few
taxa,
such
as
flatworms,
were
not
detected,
show
optimized
avoids
bias
thus
significantly
improves
detection
eDNA.
Global Change Biology,
Journal Year:
2020,
Volume and Issue:
26(12), P. 6867 - 6879
Published: Sept. 16, 2020
Abstract
Human‐induced
global
change
dramatically
alters
individual
aspects
of
river
biodiversity,
such
as
taxonomic,
phylogenetic
or
functional
diversity,
and
is
predicted
to
lead
losses
associated
ecosystem
functions.
Understanding
these
dependencies
are
critical
human
well‐being.
Until
now,
however,
most
studies
have
only
looked
either
at
organismal
groups
single
functions,
little
known
on
the
effect
activities
multitrophic
biodiversity
multifunctionality
in
riverine
ecosystem.
Here
we
profiled
from
bacteria
invertebrates
based
environmental
DNA
(hereafter,
‘eDNA’)
samples
across
a
major
catchment
China,
analysed
their
with
multiple
especially
linked
C/N/P‐cycling.
Firstly,
found
spatial
cross‐taxon
congruence
pattern
communities'
structure
network
Shaying
river,
which
was
related
strong
filtering
due
land
use.
Secondly,
use
explained
decline
multifaceted
but
increased
redundancy
Thirdly,
function
relationships
an
integrative
level
showed
concave‐up
(non‐saturating)
shape.
Finally,
structural
equation
modeling
suggested
that
affects
functions
through
biodiversity‐mediated
pathways,
including
loss
altered
community
interdependence
groups.
Our
study
highlights
value
complete
inclusive
assessment
for
integrated
land‐use
management
ecosystems.
Molecular Ecology Resources,
Journal Year:
2021,
Volume and Issue:
22(4), P. 1231 - 1246
Published: Sept. 22, 2021
Abstract
Metabarcoding
of
DNA
extracted
from
environmental
or
bulk
specimen
samples
is
increasingly
used
to
profile
biota
in
basic
and
applied
biodiversity
research
because
its
targeted
nature
that
allows
sequencing
genetic
markers
many
parallel.
To
achieve
this,
PCR
amplification
carried
out
with
primers
designed
target
a
taxonomically
informative
marker
within
taxonomic
group,
sample‐specific
nucleotide
identifiers
are
added
the
amplicons
prior
sequencing.
The
latter
enables
assignment
sequences
back
they
originated
from.
Nucleotide
can
be
during
metabarcoding
“library
preparation”,
is,
when
prepared
for
Different
strategies
this
labelling
exist.
All
have
advantages,
challenges
limitations,
some
which
lead
misleading
results,
worst
case
compromise
fidelity
data.
Given
range
questions
addressed
using
metabarcoding,
ensuring
data
generation
robust
fit
chosen
purpose
critically
important
practitioners
seeking
employ
assessments.
Here,
we
present
an
overview
three
main
workflows
library
preparation
studies
on
Illumina
platforms;
one‐step
PCR,
two‐step
tagged
PCR.
Further,
distill
key
considerations
researchers
select
appropriate
strategy
their
specific
study.
Ultimately,
by
gaining
insights
into
consequences
different
workflows,
hope
further
consolidate
power
as
tool
assess
across
applications.
Oikos,
Journal Year:
2020,
Volume and Issue:
129(5), P. 607 - 618
Published: Jan. 13, 2020
Uncovering
biodiversity
as
an
inherent
feature
of
ecosystems
and
understanding
its
effects
on
ecosystem
processes
is
one
the
most
central
goals
ecology.
Studying
organisms’
occurrence
patterns
in
natural
has
spurred
discovery
foundational
ecological
rules,
such
species–area
relationship,
general
scientific
interest.
Recent
global
changes
add
relevance
urgency
to
diversity
organisms,
their
respective
roles
processes.
While
information
properties
abiotic
environmental
conditions
are
now
available
at
unprecedented,
highly‐resolved
spatial
temporal
scales,
fundamental
variable
–
itself
still
often
studied
a
local
perspective,
generally
not
wide
taxonomic
breadth,
high
scale
coverage.
This
limiting
capacity
impact
ecology
field
science.
In
this
forum
article,
we
propose
that
complete
assessments
should
be
inclusive
across
functional
groups,
space,
time
better
understand
emergent
properties,
functioning.
We
use
riverine
case
example
because
they
among
biodiverse
worldwide,
but
also
highly
threatened,
in‐depth
these
systems
critically
needed.
Furthermore,
structure
requires
multiscale
perspective
consideration
autocorrelation
structures
commonly
ignored
biodiversity–ecosystem
functioning
studies.
show
how
recent
methodological
advances
DNA
(eDNA)
provide
novel
opportunities
uncover
broad
link
it
processes,
with
potential
revolutionize
sciences.
then
outline
roadmap
for
using
technique
assess
manner.
Our
proposed
approach
will
help
get
associated
scales
relevant
landscape
managers.
Environment International,
Journal Year:
2019,
Volume and Issue:
135, P. 105307 - 105307
Published: Dec. 24, 2019
As
the
largest
semi-closed
marine
ecosystem
in
world,
Black
Sea
has
been
heavily
affected
by
human
activities
for
a
long
time.
Describing
biodiversity
of
multi-trophic
biota
pelagic
zone
and
identifying
dominant
environmental
factors
are
prerequisites
protecting
sustainability
ecosystems.
However,
up
to
now,
taxonomic
distributional
information
about
is
not
clear.
Here,
we
employed
Tree-of-Life
metabarcoding
analyze
eight
communities
Sea,
investigated
their
biogeographical
distribution,
further
analyzed
influence
biological
abiotic
on
large
scales.
We
found
that,
(1)
Over
8900
OTUs
were
detected
which
630
species
identified,
covering
holistic
from
single-celled
(bacteria
5620
141
species;
algae
1096
185
protozoa
546
146
species)
multicellular
organisms
(invertebrate
metazoans
150
34
fishes
1369
76
mammals
39
5
species).
(2)
Higher
trophic
(fishes
mammals)
distributed
more
evenly
space
than
lower
(microorganisms,
invertebrates).
For
organisms,
vertical
stratification
was
obvious
horizontal
(vertical
p
<
0.02,
0.05).
(3)
The
bottom
algae)
food
web
significantly
distribution
composition
others
through
interactions
(Mantel
(4)
At
level
factors,
effect
local
sorting
15%
higher
that
mass
dispersal
effect.
first
time,
this
study
monitored
profiled
provided
technological
advances
preliminary
knowledge
ongoing
protection
efforts.