Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils
Soil Biology and Biochemistry,
Год журнала:
2025,
Номер
unknown, С. 109741 - 109741
Опубликована: Фев. 1, 2025
Язык: Английский
The performance of different methods in characterizing soil live prokaryotic diversity and abundance is highly variable
iMetaOmics.,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 28, 2025
Abstract
The
long‐term
persistence
of
extracellular
DNA
in
soils
is
well‐documented,
yet
its
impacts
on
analyzing
soil
microbial
abundance
and
diversity
remain
controversial.
This
primarily
arises
from
our
limited
comprehension
regarding
the
reliability
various
methods
for
studying
live
microbiotas.
In
this
study,
we
systematically
compared
assessed
commonly
used
diversity,
including
alkaline
buffer
washing,
propidium
monoazide
(PMA)
treatment,
DNase
pre‐digestion,
rRNA‐based
analysis,
using
collected
a
wide
range
locations
across
China.
We
found
that
elimination
substantially
influenced
analysis
prokaryotic
abundance,
community
profiles,
co‐occurrence
patterns,
but
not
assembly
mechanisms.
However,
effects
varied
considerably
different
methods.
pre‐digestion
PMA
treatment
led
to
significant
decreases
while
washing
had
negligible
effects.
As
richness,
significantly
decreased
increased
it,
respectively.
Although
67.8%
amplicon
sequence
variants
were
shared,
differences
their
relative
observed
While
removal
simplified
network,
it
also
enhanced
robustness.
According
assessment
experiments,
showed
highest
efficiency
characterizing
accuracy.
Concerns
other
include
low
efficiency,
instability,
uncertainties
result
explanation.
study
suggests
characterized
by
exhibit
high
variability,
recommended
communities.
These
findings
provide
crucial
information
optimizing
microbiome
research
methodologies.
Язык: Английский
Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire
Microbiology Resource Announcements,
Год журнала:
2024,
Номер
13(6)
Опубликована: Май 16, 2024
We
examined
the
dynamics
of
soil
microbiomes
under
heat
press
disturbance
from
an
underground
coal
mine
fire
in
Centralia,
PA.
Here,
we
present
metagenomic
sequencing
and
assembly
data
across
seven
consecutive
years
at
repeatedly
sampled
fire-affected
sites
along
with
unaffected
reference
sites.
Язык: Английский
Bacterial community response to novel and repeated disturbances
Environmental Microbiology Reports,
Год журнала:
2024,
Номер
16(5)
Опубликована: Окт. 1, 2024
Disturbance
response
and
recovery
are
increasingly
important
in
microbial
ecology,
as
microbes
may
recover
from
disturbances
differently
than
macro
communities.
Past
can
alter
community
structure
their
to
subsequent
disturbance
events,
but
it
remains
unclear
if
the
same
patterns
persist
after
long-term
exposure
stress.
Here,
we
compare
bacterial
composition
a
that
experienced
2
years
of
monthly
salinity
addition
with
has
not
additions.
We
then
track
an
additional
based
on
past
exposure.
tested
following
hypotheses:
first,
communities
repeated
history
will
have
different
without
history;
second,
exposed
undergo
trajectory
experiencing
novel
disturbance.
find
affect
years,
primarily
through
increased
resistance.
This
work
enhances
our
understanding
temporal
dynamics
suggests
pose
threat
function.
Язык: Английский
Resting for Viability: Gordonia Polyisoprenivorans Zm27, a Robust Generalist for Petroleum Bioremediation Under Hypersaline Stress
Опубликована: Янв. 1, 2024
The
intrinsic
issue
associated
with
applying
microbes
for
practical
pollution
remediation
is
maintaining
the
expected
activity
of
engaged
strains
or
consortiums
as
effectively
under
laboratory
conditions.
Faced
various
stress
factors,
degraders
dormancy
ability
are
more
likely
to
survive
and
exhibit
degradation
activity.
In
this
study,
a
hydrocarbonoclastic
halotolerant
strain,
Gordoniapolyisoprenivorans
ZM27,
was
isolated
via
stimulation
resuscitation-promoting
factor
(Rpf).
Long-term
dual
10%
NaCl
incubation
starvation
could
induce
ZM27
into
viable
but
nonculturable
(VBNC)-like
state,
cells
be
resuscitated
by
Rpf
stimulation.
Notable
changes
in
both
morphological
physiological
characteristics
between
VBNC-like
confirmed
response
its
robust
resistance
against
harsh
environments.
Whole-genome
sequencing
analysis
indicated
generalist
degrader
ability.
Subsequently,
applied
soil
microcosm
experiment
investigate
application
potential
combined
exhibited
most
effective
biodegradation
performance,
initial
n-hexadecane
content
(1,000
mg
kg-1)
decreased
63.29%
after
14-day
incubation.
Based
on
16S
rRNA
analysis,
Gordonia
positive
stimulation,
significant
competitiveness
niches.
absolute
abundance
genus
negatively
correlated
that
Alcanivorax,
obligate
hydrocarbon
top
during
profile
community
may
efficient
than
specialist
Alcanivorax
including
sustainable
culturability
long-term
stress,
performance
microcosm,
valuable
remediating
petroleum
stressful
Our
work
validated
importance
remediation.
Язык: Английский
Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Май 27, 2024
Abstract
Viruses
are
important
components
of
the
soil
microbiome,
influencing
microbial
population
dynamics
and
functions
their
hosts.
However,
relationships
feedbacks
between
virus
dynamics,
host
environmental
disturbance
is
not
understood.
Centralia,
PA,
USA,
site
an
underground
coal
seam
fire
that
has
been
burning
for
over
60
years.
As
moves
along
seam,
previously
heated
soils
cool
to
ambient
temperature,
creating
a
gradient
heat
intensity
recovery.
We
examined
annual
viral
seven
consecutive
years
in
Centralia
using
untargeted
metagenome
sequencing.
Viral
communities
changed
time
were
distinct
fire-affected
reference
sites.
Dissimilarity
was
greater
across
sites
(space)
than
within
(time),
cumulative
diversity
more
rapidly
stabilized
year
There
also
changes
CRISPR
investment
as
cooled,
corresponding
shifts
diversity.
Finally,
there
differences
viral-encoded
auxiliary
metabolic
genes
These
results
indicate
despite
high
site-to-site
diversity,
surprising
community
consistency
shifting
host-viral
interactions
recovering
from
disturbance.
Together,
these
provide
insights
into
how
collectively
respond
unpredicted
Highlights
In
seven-year
study
temperate
affected
by
fire,
displayed
variability
(spatial)
(temporal).
unheated
throughout
sampling.
Soil
bacterial
composition
correlated
composition,
though
this
relationship
weakened
when
accounting
edaphic
properties
temperature
pH.
may
be
less
resilient
press
communities.
Viral-host
shift
during
recovery
long-term
heating.
Язык: Английский
Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment
Trends in Microbiology,
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 1, 2024
Microbial
environmental
DNA
and
RNA
(collectively
'eNA')
originate
from
a
diverse
abundant
array
of
microbes
present
in
samples.
These
eNA
signals,
largely
representing
whole
organisms,
serve
as
powerful
complement
to
signals
derived
fragments
or
remnants
larger
organisms.
Integrating
microbial
data
into
the
toolbox
ecosystem
assessments
biotic
indices
therefore
has
potential
transform
how
we
use
understand
biodiversity
dynamics
functions,
inform
next
generation
monitoring.
Incorporating
holobiont
Tree
Life
approaches
analyses
offers
further
holistic
insight
range
ecological
interactions
between
other
paving
way
for
advancing
our
understanding
of,
ultimately
manipulating
properties
pertinent
management,
conservation,
wildlife
health,
food
production.
Язык: Английский