FEMS Microbiology Ecology,
Journal Year:
2024,
Volume and Issue:
100(3)
Published: Feb. 14, 2024
Different
types
of
inlet
water
are
expected
to
affect
microbial
communities
lake
ecosystems
due
changing
environmental
conditions
and
the
dispersal
species.
However,
knowledge
effects
changes
in
export
assemblages
on
is
limited,
especially
for
glacier-fed
lakes.
Here,
we
collected
samples
from
surface
a
its
two
fed
streams
Tibetan
Plateau
investigate
importance
glacial
non-glacial
as
sources
diversity
bacterial
communities.
Results
showed
that
stream
was
an
important
source
microorganisms
studied
lake,
contributing
45.53%
total
community
water,
while
only
19.14%
seeded
by
stream.
Bacterial
were
significantly
different
between
streams.
pH,
conductivity,
dissolved
solids,
temperature
nitrogen
had
significant
effect
spatial
turnover,
together
explained
36.2%
variation
distribution
among
habitats.
Moreover,
co-occurrence
associations
tended
be
stronger
than
Collectively,
this
study
may
provide
reference
assessing
contributions
Nature Microbiology,
Journal Year:
2021,
Volume and Issue:
6(3), P. 354 - 365
Published: Jan. 25, 2021
Abstract
Candidate
phyla
radiation
(CPR)
bacteria
and
DPANN
archaea
are
unisolated,
small-celled
symbionts
that
often
detected
in
groundwater.
The
effects
of
groundwater
geochemistry
on
the
abundance,
distribution,
taxonomic
diversity
host
association
CPR
has
not
been
studied.
Here,
we
performed
genome-resolved
metagenomic
analysis
one
agricultural
seven
pristine
microbial
communities
recovered
746
genomes
total.
sites,
which
serve
as
local
sources
drinking
water,
contained
up
to
31%
4%
archaea.
We
observed
little
species-level
overlap
metagenome-assembled
(MAGs)
across
indicating
may
be
differentiated
according
physicochemical
conditions
populations.
Cryogenic
transmission
electron
microscopy
imaging
genomic
analyses
enabled
us
identify
lineages
reproducibly
attach
cells
showed
growth
seems
stimulated
by
attachment
host-cell
surfaces.
Our
reveals
site-specific
coexist
with
diverse
hosts
aquifers.
Given
organisms
have
identified
human
microbiomes
their
presence
is
correlated
diseases
such
periodontitis,
our
findings
relevant
considerations
water
quality
health.
Nature Communications,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: Nov. 11, 2023
Abstract
Soil
harbors
a
vast
expanse
of
unidentified
microbes,
termed
as
microbial
dark
matter,
presenting
an
untapped
reservoir
biodiversity
and
genetic
resources,
but
has
yet
to
be
fully
explored.
In
this
study,
we
conduct
large-scale
excavation
soil
matter
by
reconstructing
40,039
metagenome-assembled
genome
bins
(the
SMAG
catalogue)
from
3304
metagenomes.
We
identify
16,530
21,077
species-level
(SGBs)
unknown
SGBs
(uSGBs),
which
expand
archaeal
bacterial
diversity
across
the
tree
life.
also
illustrate
pivotal
role
uSGBs
in
augmenting
microbiome’s
functional
landscape
intra-species
diversity,
providing
large
proportions
43,169
biosynthetic
gene
clusters
8545
CRISPR-Cas
genes.
Additionally,
determine
that
contributed
84.6%
previously
unexplored
viral-host
associations
catalogue.
The
catalogue
provides
useful
genomic
resource
for
further
studies
investigating
resources.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: July 17, 2024
Abstract
With
the
continuous
expansion
of
saline
soils
under
climate
change,
understanding
eco-evolutionary
tradeoff
between
microbial
mitigation
carbon
limitation
and
maintenance
functional
traits
in
represents
a
significant
knowledge
gap
predicting
future
soil
health
ecological
function.
Through
shotgun
metagenomic
sequencing
coastal
along
salinity
gradient,
we
show
contrasting
directions
bacteria
archaea
that
manifest
changes
to
genome
size
potential
microbiome.
In
salt
environments
with
high
requirements,
exhibit
reduced
sizes
associated
depletion
metabolic
genes,
while
display
larger
genomes
enrichment
salt-resistance,
metabolic,
carbon-acquisition
genes.
This
suggests
conserve
energy
through
streamlining
when
facing
stress,
invest
pathways
broaden
their
resource
usage.
These
findings
suggest
divergent
adaptations
stress
amongst
clades
serve
as
foundation
for
response
microbiomes
escalating
change.
Frontiers in Microbiology,
Journal Year:
2025,
Volume and Issue:
16
Published: Feb. 4, 2025
Introduction
Organic
fertilizer
offers
significant
advantages
for
sustainable
agricultural
development
compared
to
inorganic
fertilizers
and
is
increasingly
becoming
the
predominant
strategy.
Functional
traits
gut
microbiota
of
soil
fauna
are
recognized
as
potential
indicators
environmental
changes.
However,
there
a
dearth
research
examining
correlation
between
functional
intestinal
microorganisms
in
response
organic
fertilizer.
Methods
In
this
study,
we
selected
Entomobrya
proxima
Folsom,
collembolan
species
found
cropland
across
North
China,
our
subject
study.
We
set
treatments
with
no
(CK)
three
different
concentrations
at
1%
(O1),
6%
(O2),
10%
(O3).
Stereomicroscopy
high-throughput
amplicon
sequencing
were
employed
elucidate
through
host
associated
microbial
communities.
Results
The
results
indicated
that
impact
on
collembolans
was
closely
linked
input
concentration.
Specifically,
low
positively
influenced
all
Folsom;
conversely,
higher
exerted
an
overall
detrimental
effect.
For
bacterial
community,
addition
resulted
decrease
abundance,
adversely
affected
α
-diversity,
significantly
altered
structure
community
CK.
effect
concentration
these
parameters.
composition
varied
due
fertilizer,
changes
observed
relative
abundances
six
phyla
genera.
Furthermore,
body
length
foreleg
may
serve
characterizing
proportions
Alcanivorax
Sphingobacterium
community.
Additionally,
assembly
process
strongly
by
amount
added;
led
narrowing
niche
width
believed
contribute
increase
richness.
Discussion
conclusion,
adding
multiple
impacts
fauna,
sizes
related
its
These
findings
provide
insights
conserving
animals
while
maximizing
their
ecological
functions
offer
perspectives
optimizing
management
practices.
Environmental Science & Technology,
Journal Year:
2021,
Volume and Issue:
55(15), P. 10862 - 10874
Published: July 20, 2021
The
global
rise
and
spread
of
antibiotic
resistance
greatly
challenge
the
treatment
bacterial
infections.
Wastewater
plants
(WWTPs)
harbor
discharge
genes
(ARGs)
as
environmental
contaminants.
However,
knowledge
gap
on
host
identity,
activity,
functionality
ARGs
limits
transmission
health
risk
assessment
WWTP
resistome.
Hereby,
a
genome-centric
quantitative
metatranscriptomic
approach
was
exploited
to
realize
high-resolution
qualitative
analyses
hosts
(i.e.,
multiresistance,
pathogenicity,
niches)
in
12
urban
WWTPs.
We
found
that
∼45%
248
recovered
genomes
expressed
against
multiple
classes
antibiotics,
among
which
bacitracin
aminoglycoside
Proteobacteria
were
most
prevalent
scenario.
Both
potential
pathogens
indigenous
denitrifying
bacteria
transcriptionally
active
ARGs.
almost
unchanged
relative
expression
levels
resistant
populations
(66.9%)
surviving
ARG
including
globally
emerging
(e.g.,
Aliarcobacter
cryaerophilus)
treated
effluent
prioritize
future
examination
risks
related
propagation
human
exposure
receiving
environment.
Microbiome,
Journal Year:
2021,
Volume and Issue:
9(1)
Published: Oct. 18, 2021
Abstract
Background
Winter
carbon
loss
in
northern
ecosystems
is
estimated
to
be
greater
than
the
average
growing
season
uptake
and
primarily
driven
by
microbial
decomposers.
Viruses
modulate
cycling
via
induced
mortality
metabolic
controls,
but
it
unknown
whether
viruses
are
active
under
winter
conditions
(anoxic
sub-freezing
temperatures).
Results
We
used
stable
isotope
probing
(SIP)
targeted
metagenomics
reveal
genomic
potential
of
soil
populations
simulated
conditions,
with
an
emphasis
on
virus-host
dynamics.
Arctic
peat
soils
from
Bonanza
Creek
Long-Term
Ecological
Research
site
Alaska
were
incubated
anoxic
H
2
18
O
or
natural
abundance
water
for
184
370
days.
sequenced
23
SIP-metagenomes
measured
dioxide
(CO
)
efflux
throughout
experiment.
identified
46
bacterial
(spanning
9
phyla)
243
viral
that
actively
took
up
respired
CO
incubation.
Active
represented
only
a
small
portion
detected
community
capable
fermentation
organic
matter
degradation.
In
contrast,
large
one
third
linked
populations.
86
auxiliary
genes
other
environmentally
relevant
genes.
The
majority
these
carried
had
diverse
functions
such
as
utilization
scavenging
could
provide
their
host
fitness
advantage
utilizing
much-needed
sources
acquiring
essential
nutrients.
Conclusions
Overall,
there
was
stark
difference
identity
function
compared
unlabeled
would
have
been
overlooked
non-targeted
standard
metagenomic
analysis.
Our
results
illustrate
substantial
interactions
occur
highlight
major
community-structuring
agent
likely
modulates
during
winter,
which
may
pivotal
understanding
future
fate
arctic
soils'
vast
stocks.
