Molecular Ecology Resources,
Год журнала:
2023,
Номер
24(1)
Опубликована: Июль 27, 2023
The
current
biodiversity
and
climate
crises
highlight
the
need
for
efficient
tools
to
monitor
terrestrial
ecosystems.
Here,
we
provide
evidence
use
of
airborne
eDNA
analyses
as
a
novel
method
detecting
vertebrate
communities
in
nature.
Metabarcoding
143
samples
collected
during
3
days
mixed
forest
Denmark
yielded
64
bird,
mammal,
fish
amphibian
taxa,
which
detected
57
'wild'
taxa
represent
over
quarter
around
210
vertebrates
that
occur
overall
area.
We
spatial
movement
temporal
patterns
influence
weather
conditions
on
detections.
This
study
demonstrates
high-resolution
biomonitoring
systems
elucidates
its
potential
guide
global
nature
management
conservation
efforts
ongoing
crisis.
Current Biology,
Год журнала:
2022,
Номер
32(3), С. 701 - 707.e5
Опубликована: Янв. 6, 2022
Biodiversity
monitoring
at
the
community
scale
is
a
critical
element
of
assessing
and
studying
species
distributions,
ecology,
diversity,
movements,
it
key
to
understanding
tracking
environmental
anthropogenic
effects
on
natural
ecosystems.1Navarro
L.M.
Fernández
N.
Guerra
C.
Guralnick
R.
Kissling
W.D.
Londoño
M.C.
Muller-Karger
F.
Turak
E.
Balvanera
P.
Costello
M.J.
et
al.Monitoring
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H.
Cao
Y.
Yu
D.
M.
He
Gill
Pereira
H.M.
Ensuring
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Evol.
2021;
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411-418Crossref
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(30)
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High
time
invest
in
biodiversity.
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263.Google
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S.
Gossner
M.M.
Simons
N.K.
Blüthgen
Müller
J.
Ambarli
al.Arthropod
decline
grasslands
forests
associated
with
landscape-level
drivers.Nature.
2019;
574:
671-674Crossref
(391)
Scholar
Vertebrates
terrestrial
ecosystems
are
experiencing
extinctions
declines
both
population
numbers
sizes
due
increasing
threats
from
human
activities
change.5Almond
R.E.A.
Grooten
Petersen
T.
Living
Planet
Report
2020:
Bending
Curve
Loss.
WWF,
2020Google
6Ceballos
G.
Ehrlich
P.R.
Dirzo
Biological
annihilation
via
ongoing
sixth
mass
extinction
signaled
by
vertebrate
losses
declines.Proc.
Natl.
Acad.
Sci.
USA.
114:
E6089-E6096Crossref
(1031)
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J.B.
Daily
G.C.
Population
diversity:
its
extent
extinction.Science.
1997;
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689-692Crossref
(381)
8Gaston
K.J.
Fuller
R.A.
Commonness,
depletion
conservation
biology.Trends
2008;
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14-19Abstract
Full
Text
PDF
(361)
Terrestrial
using
existing
methods
generally
costly
laborious,
although
DNA
(eDNA)
becoming
tool
choice
assess
biodiversity,
few
sample
types
effectively
capture
diversity.
We
hypothesized
that
eDNA
captured
air
could
allow
straightforward
collection
characterization
communities.
filtered
three
localities
Copenhagen
Zoo:
stable,
outside
between
outdoor
enclosures,
Rainforest
House.
Through
metabarcoding
airborne
eDNA,
we
detected
49
spanning
26
orders
37
families:
30
mammal,
13
bird,
4
fish,
1
amphibian,
reptile
species.
These
spanned
animals
kept
zoo,
occurring
zoo
surroundings,
used
as
feed
zoo.
The
comprise
range
taxonomic
families,
sizes,
behaviors,
abundances.
found
shorter
distance
sampling
device
higher
animal
biomass
increase
probability
detection.
hereby
show
can
offer
fundamentally
new
way
Ecology Letters,
Год журнала:
2022,
Номер
25(12), С. 2753 - 2775
Опубликована: Окт. 20, 2022
Abstract
High‐resolution
monitoring
is
fundamental
to
understand
ecosystems
dynamics
in
an
era
of
global
change
and
biodiversity
declines.
While
real‐time
automated
abiotic
components
has
been
possible
for
some
time,
biotic
components—for
example,
individual
behaviours
traits,
species
abundance
distribution—is
far
more
challenging.
Recent
technological
advancements
offer
potential
solutions
achieve
this
through:
(i)
increasingly
affordable
high‐throughput
recording
hardware,
which
can
collect
rich
multidimensional
data,
(ii)
accessible
artificial
intelligence
approaches,
extract
ecological
knowledge
from
large
datasets.
However,
automating
the
facets
communities
via
such
technologies
primarily
achieved
at
low
spatiotemporal
resolutions
within
limited
steps
workflow.
Here,
we
review
existing
data
processing
that
enable
communities.
We
then
present
novel
frameworks
combine
technologies,
forming
fully
pipelines
detect,
track,
classify
count
multiple
species,
record
behavioural
morphological
have
previously
impossible
achieve.
Based
on
these
rapidly
developing
illustrate
a
solution
one
greatest
challenges
ecology:
ability
generate
high‐resolution,
standardised
across
complex
ecologies.
Environmental DNA,
Год журнала:
2022,
Номер
4(4), С. 790 - 807
Опубликована: Март 11, 2022
Abstract
Biodiversity
is
in
decline
due
to
human‐induced
pressures
on
ecosystems
around
the
world.
To
be
able
counteract
this
alarming
trend,
it
paramount
closely
monitor
biodiversity
at
global
scales.
Because
practically
impossible
with
traditional
methods,
last
decade
has
seen
a
strong
push
for
new
solutions.
In
aquatic
ecosystems,
monitoring
of
species
from
environmental
DNA
(eDNA)
emerged
as
one
most
powerful
tools
our
disposal,
but
terrestrial
power
eDNA
so
far
been
hampered
by
local
scale
samples.
study,
we
report
successful
detection
insects
airborne
samples
taken
field.
We
compare
results
two
insect
methods
(1)
light
traps
moth
and
(2)
transect
walks
butterflies
wild
bees.
Airborne
metabarcoding
revealed
six
classes
arthropods,
twelve
order
insects—including
representatives
four
largest
orders:
Diptera
(flies),
Lepidoptera
(butterflies
moths),
Coleoptera
(beetles),
Hymenoptera
(bees,
wasps,
ants).
did
not
detect
all
observed
using
suggest
further
directions
development
metabarcoding.
also
recovered
nine
vertebrates,
including
frogs,
birds,
mammals
well
12
other
phyla.
potential
become
tool
monitoring,
many
impactful
applications
pests,
invasive,
or
endangered
disease
vectors.
Environmental DNA,
Год журнала:
2022,
Номер
4(4), С. 894 - 907
Опубликована: Апрель 11, 2022
Abstract
Analysis
of
environmental
DNA
is
increasingly
used
to
characterize
ecological
communities,
but
the
effectiveness
this
approach
depends
on
accuracy
taxonomic
reference
databases.
The
MIDORI
databases,
first
released
in
2017,
were
built
improve
for
mitochondrial
metazoan
(animal)
sequences.
has
now
been
significantly
improved
and
renamed
MIDORI2
(available
at
http://www.reference‐midori.info
).
Like
MIDORI,
from
GenBank
contains
curated
sequences
thirteen
protein‐coding
two
ribosomal
RNA
genes.
Coverage
substantially
expanded
cover
all
eukaryotes,
including
fungi,
green
algae
land
plants,
other
multicellular
algal
groups,
diverse
protist
lineages.
also
includes
not
only
species
with
full
binomials,
taxa
referred
by
genus
left
unspecified
(“sp.”).
Another
new
feature
updating
databases
approximately
every
months
version
numbers
corresponding
each
release.
Additional
potentially
erroneously
annotated
have
removed.
Finally,
ability
export
data
files
BLAST+
added
original
preformatted
five
assignment
programs,
amino
acid
are
made
available
As
a
technical
validation,
we
conducted
preliminary
comparison
performance
programs.
Results
suggest
that
top
hits
performed
better
assigning
CO1
than
alignment‐free
methods
based
compositional
features.
Comparing
commonly
sequences,
CO‐ARBitrator
BOLD,
show
broader
range
non‐metazoan
taxa.
Overall,
many
contexts,
offers
clear
advantages:
higher
diversity
variety
user‐friendly
features,
regular
updates.
particularly
well‐suited
studies
target
genes
broad
primers.
ABSTRACT
Terrestrial
vertebrates
are
experiencing
worldwide
population
declines
and
species
extinctions.
To
effectively
conserve
remaining
populations
species,
rapid,
cost‐effective,
scalable
methods
needed
to
complement
longstanding
monitoring
methods.
Increasingly,
environmental
DNA
(eDNA)‐based
approaches
being
used
for
terrestrial
vertebrate
biomonitoring
within
a
range
of
environments.
However,
as
we
move
eDNA
onto
land,
presented
with
new
set
challenges.
This
necessitates
the
development
“best‐practice”
sample
collection
guidelines
systems
purpose
detecting
vertebrates.
address
these
needs,
conducted
systematic
literature
review
143
peer‐reviewed
papers
applying
(excluding
Lissamphibia)
that
were
published
between
2012
2023.
We
summarize
use
biomonitoring,
focusing
on
study
design
field
techniques.
Over
decade
observe
steady
growth
in
annual
number
publications,
3
33
The
majority
reviewed
studies
targeted
mammals
temperate
forest
regions.
While
an
equal
focused
metabarcoding
approach
assess
community
taxon
composition
and/or
species‐specific
detection
methods,
novel
uses
increasingly
published.
These
include
animal
behavior
genetics.
record
three
types
sampling
strategies,
eight
different
substrate
types,
seven
preservation
suggesting
there
is
no
“one
size
fits
all”
eDNA‐based
methodology
when
With
multitude
aims,
across
environments,
target
organisms
ecologies,
standardization
extremely
challenging.
table
known
factors
influencing
Furthermore,
identify
five
key
considerations
be
addressed
targeting
aim
guiding
decision
making.
Frontiers in Bioinformatics,
Год журнала:
2022,
Номер
2
Опубликована: Май 26, 2022
Phylogenetic
placement
refers
to
a
family
of
tools
and
methods
analyze,
visualize,
interpret
the
tsunami
metagenomic
sequencing
data
generated
by
high-throughput
sequencing.
Compared
alternative
(e.
g.,
similarity-based)
methods,
it
puts
metabarcoding
sequences
into
phylogenetic
context
using
set
known
reference
taking
evolutionary
history
account.
Thereby,
one
can
increase
accuracy
surveys
eliminate
requirement
for
having
exact
or
close
matches
with
existing
sequence
databases.
constitutes
valuable
analysis
tool
per
se
,
but
also
entails
plethora
downstream
its
results.
A
common
use
case
is
analyze
species
communities
obtained
from
sequencing,
example
via
taxonomic
assignment,
diversity
quantification,
sample
comparison,
identification
correlations
environmental
variables.
In
this
review,
we
provide
an
overview
over
developed
during
first
10
years.
particular,
goals
review
are
1)
motivate
usage
illustrate
some
cases,
2)
outline
full
workflow,
raw
publishable
figures,
including
best
practices,
3)
introduce
most
their
capabilities,
4)
point
out
pitfalls
misconceptions,
5)
showcase
typical
placement-based
analyses,
how
they
help
data.
Environmental DNA,
Год журнала:
2023,
Номер
5(2), С. 375 - 387
Опубликована: Янв. 20, 2023
Abstract
Analysis
of
environmental
DNA
(eDNA)
from
passively
collected
airborne
dust
has
demonstrated
broad
success
for
sensitive
and
robust
detection
plants.
Recent
experiments
at
small
spatial
scales
have
suggested
that
animals
can
also
be
detected
using
eDNA.
However,
eDNA
analysis
never
been
used
a
long‐term
whole‐community
assessment
natural
terrestrial
community
or
with
passive
collectors.
We
conducted
metabarcoding
survey
targeting
vertebrate
carried
in
the
air
on
an
approximately
130‐acre
shortgrass
prairie
over
course
year.
Our
wide
variety
animal
forms
including
amphibian
species,
several
bird
both
large
mammals.
found
signals
changed
known
patterns
activity,
wind
speed,
rainfall.
Overall,
we
demonstrate
carries
could
to
detect
species
environment
minimal
effort.
To
develop
this
as
valuable
monitoring
tool,
research
needs
focus
ecology
air,
which
includes
origin,
state,
transport,
dispersal,
fate
environment.