Briefings in Bioinformatics,
Год журнала:
2024,
Номер
25(6)
Опубликована: Сен. 23, 2024
Abstract
Metagenomic
analyses
facilitate
the
exploration
of
microbial
world,
advancing
our
understanding
roles
in
ecological
and
biological
processes.
A
pivotal
aspect
metagenomic
analysis
involves
assessing
quality
metagenome-assembled
genomes
(MAGs),
crucial
for
accurate
insights.
Current
machine
learning–based
methods
often
treat
completeness
contamination
prediction
as
separate
tasks,
overlooking
their
inherent
relationship
limiting
models’
generalization.
In
this
study,
we
present
DeepCheck,
a
multitasking
deep
learning
framework
simultaneous
MAG
contamination.
DeepCheck
consistently
outperforms
existing
tools
accuracy
across
various
experimental
settings
demonstrates
comparable
speed
while
maintaining
high
predictive
even
new
lineages.
Additionally,
employ
interpretable
techniques
to
identify
specific
genes
pathways
that
drive
model’s
predictions,
enabling
independent
investigation
assessment
these
elements
deeper
Frontiers in Plant Science,
Год журнала:
2025,
Номер
15
Опубликована: Янв. 16, 2025
Excessive
utilization
of
chemical
fertilizers
degrades
the
quality
medicinal
plants
and
soil.
Bio-organic
(BOFs)
including
microbial
inoculants
microalgae
have
garnered
considerable
attention
as
potential
substitutes
for
fertilizer
to
enhance
yield.
In
this
study,
a
field
experiment
was
conducted
investigate
effects
BOF
partially
substituting
on
growth
plant
Polygala
tenuifolia.
The
parameters,
bioactive
component
contents,
soil
properties
composition
rhizosphere
microorganisms
were
measured.
results
indicated
that
40%
with
showed
most
pronounced
growth-promoting
effect,
leading
29.30%
increase
in
underground
biomass
19.72%
3,6'-disinapoylsucrose
(DISS)
content.
Substituting
20%
improved
quality,
significantly
increasing
organic
matter
content
by
15.68%
(p<0.05).
Microalgae
addition
affected
bacterial
community
P.
tenuifolia,
reducing
relative
abundance
Cladosporium
33.33%
57.93%,
while
Chloroflexi
31.06%
38.27%,
under
reduction,
respectively.
positively
correlated
both
DISS
(p<0.05),
indicating
may
stimulate
species
associated
carbon
cycling,
thereby
enhancing
fertility,
nutrient
absorption,
ultimately
increased
accumulation
production
components
addition,
there
no
significant
difference
contents
between
reduced
dosage
combined
solid
inoculant
(SMI)
polyglutamic
(PMI),
compared
100%
fertilizer.
Correlation
analysis
revealed
PMI
could
phosphorus
availability
through
Streptomyces
recruitment.
conclusion,
our
findings
demonstrated
bio-organic
can
substitute
improve
microorganisms,
This
provides
theoretical
basis
productivity
reduction.
Frontiers in Microbiology,
Год журнала:
2025,
Номер
16
Опубликована: Март 7, 2025
Introduction
Cadmium
(Cd),
a
toxic
heavy
metal,
has
increasingly
impacted
vineyard
soils
and
grapevine
(
Vitis
vinifera
)
production
in
recent
years.
Intercropping
with
the
hyperaccumulator
plant
Solanum
nigrum
emerged
as
promising
strategy
to
improve
soil
health
increase
resilience
Cd-contaminated
soil.
Methods
This
study
investigated
effects
of
intercropping
S.
(IntVVSN)
on
enzyme
activity
microbial
community.
Results
Compared
monocultures
grapevine,
IntVVSN
increased
activities
sucrase,
urease,
cellulase,
decreased
amylase,
neutral
phosphatase.
The
community
showed
higher
abundances
beneficial
groups
such
Acidobacteriota,
Actinobacteriota,
Chloroflexi.
These
were
involved
metal
detoxification
nutrient
cycling,
indicating
their
potential
role
enhancing
Cd
tolerance.
Kyoto
Encyclopedia
Genes
Genomes
(KEGG)
pathway
enrichment
analysis
revealed
distinct
metabolic
adaptations
under
soil,
significant
upregulation
pathways
related
secondary
metabolite
synthesis,
carbohydrate
metabolism,
glycan
biosynthesis,
nucleotide
protein
processing.
changes
composition,
along
enhanced
cycling
indicated
by
activities,
suggest
healthier
more
resilient
environment.
This,
turn,
contributes
improved
tolerance
grapevines.
Conclusion
highlights
phytoremediation
intercropping,
which
promotes
sustainable
agricultural
practices
improving
growth
stress.
ABSTRACT
Effects
of
fire
on
soil
viruses
and
virus–host
dynamics
are
largely
unexplored,
despite
known
microbial
contributions
to
biogeochemical
processes
ecosystem
recovery.
Here,
we
assessed
how
viral
prokaryotic
communities
responded
a
prescribed
burn
in
mixed
conifer
forest.
We
sequenced
91
viral-size
fraction
metagenomes
(viromes)
115
16S
rRNA
gene
amplicon
libraries
from
120
samples:
four
samples
at
five
timepoints
(two
before
three
after
fire)
six
sites
(four
treatment,
two
control).
hypothesized
that
compositional
differences
would
be
most
significant
between
burned
unburned
soils,
but
instead,
plot
location
best
distinguished
communities,
more
than
treatment
(burned
or
not),
depth
(0–3
3–6
cm),
timepoint.
For
both
prokaryotes,
some
resembled
controls,
while
others
were
significantly
different,
revealing
heterogeneous
responses
fire.
These
patterns
explained
by
severity,
here
defined
chemistry.
Viral
not
richness
decreased
with
low
viromic
DNA
yields
indicated
substantial
loss
biomass
higher
severity.
The
relative
abundances
Firmicutes,
Actinobacteriota,
the
predicted
infect
them
increased
suggesting
survival
infection
these
fire-responsive
potentially
spore-forming
taxa.
degree
severity
experienced
each
patch
soil,
rather
status
alone,
differed
over
mere
meters
same
Therefore,
our
analyses
highlight
importance
high-resolution,
paired
data
explain
community
IMPORTANCE
impact
microbiome,
particularly
understudied
warrants
investigation,
given
collected
forest
assess
impacts
this
disturbance
communities.
show
simple
categorical
comparisons
areas
insufficient
reveal
underlying
response
patterns.
patchy
nature
(indicated
chemistry
data)
led
changes
composition
high
lower
indistinguishable
those
controls.
Our
results
considering
highly
resolved
measurements,
even
nearby
soils
fire,
order
understand
burns.
Soil Use and Management,
Год журнала:
2025,
Номер
41(1)
Опубликована: Янв. 1, 2025
Abstract
Soil
microbes
play
a
significant
role
in
the
carbon
cycle.
However,
our
understanding
of
how
soil
respond
to
different
substrates
is
still
limited.
Here,
we
investigated
ecological
mechanisms
behind
overall
metabolism
differences
under
fertilizations
paddy
ecosystem.
Four
fertilization
treatments,
no
fertilizers
(CK),
mineral
nitrogen,
phosphorus
and
potassium
(NPK),
plus
organic
manures
(NPKM)
straw
return
(NPKS)
were
set
up.
Our
results
indicated
that
drove
shifts
microbial
community
structure,
with
reduction
abundance
Actinobacteriota
an
increase
Chloroflexi
.
NPKS
CK
exhibited
higher
utilization
capacity
across
various
sources,
particularly
metabolic
activity
for
carbohydrates
than
NPK
NPKM
treatments.
The
weighted
gene
co‐expression
network
analysis
(WGCNA)
was
used
evaluate
correlation
between
modules
WGCNA
metabolism.
We
found
are
important
contributors
variations
It
key
species
module
affecting
carbohydrate
C0119
,
which
belongs
Ktedonobacteria
suggest
could
mediate
core
bacterial
affect
finally
function.
Microbiology Research,
Год журнала:
2025,
Номер
16(3), С. 64 - 64
Опубликована: Март 10, 2025
The
study
of
the
metagenomes
bacterial
communities
in
saline
areas
is
relevant
connection
with
global
salinization
agricultural
lands.
aim
this
was
to
investigate
biodiversity
and
structure
rhizobacterial
associated
halophyte
S.
marina
from
low
moderate
sulfate–chloride
salinity
habitats.
community
bulk
rhizosphere
soil
analyzed
using
high-throughput
sequencing
V1–V9
region
16S
rRNA
by
Oxford
Nanopore
Technologies.
Alpha
beta
diversity
indices
were
calculated.
A
total
55
phyla
309
genera
bacteria
identified,
among
which
Proteobacteria
Bacteroidetes
dominated.
occurrence
Planctomycetes,
Verrucomicrobia,
Acidobacteria
higher
than
soil.
Bacterial
alpha
decreased
increasing
salinity,
while
it
increased
rhizosphere.
proportion
halotolerant
Flavobacterium
Alteromonas
significantly
grew
both
In
addition,
rhizosphere,
percentage
Comamonas,
Methylibium,
Lysobacter,
Planctomyces,
Sphingomonas,
Stenotrophomonas,
Lewinella
increased.
Among
them,
several
included
plant
growth
promoting
rhizobacteria
(PGPR).
more
soil,
Bacillus,
Salinimicrobium,
Marinobacter,
Clostridium,
Euzebya,
KSA1,
Halorhodospira
also
compared
site.
Thus,
changed
taxonomic
Journal of Marine Science and Engineering,
Год журнала:
2025,
Номер
13(4), С. 653 - 653
Опубликована: Март 25, 2025
The
Okinawa
Trough
(OT)
has
been
a
focus
of
scientific
research
for
many
years
due
to
the
presence
vibrant
hydrothermal
and
cold
seep
activity
within
its
narrow
basin.
However,
spatial
distribution
environmental
drivers
microbial
communities
in
OT
sediments
remain
poorly
understood.
present
study
aims
address
this
knowledge
gap
by
investigating
diversity
abundance
at
ten
different
sampling
sites
transitional
zone
between
vents
seeps
OT.
community
two
(G08
G09)
close
proximity
showed
high
degree
similarity.
lower
bacterial
archaeal
abundances
were
found
these
sites.
groups,
classified
as
Hydrothermarchaeota
Thermoplasmata,
comparatively
higher
relative
In
addition,
ammonia-oxidizing
archaea
(AOA),
from
family
Nitrosopumilaceae,
have
surface
G03,
G04,
G05,
G06,
G07.
This
result
suggests
that
ammonia
oxidation
may
be
actively
occurring
areas.
Furthermore,
Methylomirabilaceae,
which
are
responsible
methane
coupled
with
nitrite
reduction,
dominated
three
(G07,
G08,
G09),
implying
N-DAMO
play
an
important
role
mitigating
emissions.
Using
FAPROTAX
database,
we
predicted
prokaryotic
functional
groups
involved
methyl-reducing
methanogenesis
hydrogenotrophic
most
abundant
G08
G09.
At
G01
G02,
such
hydrocarbon
degradation,
methanotrophy,
methanol
oxidation,
denitrification,
sulfate
respiration,
sulfur
more
abundant.
Nitrogen
content
is
factor
determining
sediments.
These
results
expand
our
Environmental Technology,
Год журнала:
2025,
Номер
unknown, С. 1 - 12
Опубликована: Апрель 2, 2025
The
complexity
of
ecological
remediation
technology
restricts
its
long-term
application
in
engineering
practice.
In
this
study,
a
simple
top-down
mussels-bacteria
(TDMB)
integrated
system
used
for
river
water
quality
improvement
was
constructed,
and
the
operation
performances
accompanied
by
corresponding
mechanisms
were
investigated.
results
showed
that
during
161
days
operation,
average
removal
efficiency
achieved
75.45%
COD,
79.41%
ammonia
nitrogen
70%
total
(TN),
while
contribution
proportions
mussels
immobilized
microorganisms
TN
28.07%
69.77%,
respectively.
High-throughput
sequencing
revealed
dominant
immobilization
norank_SC-I-84
(10.52%),
norank_PHOS-HE36
(9.58%),
norank_Anaerolineaceae
(3.04%),
Nitrospira
(2.64%),
norank_Gemmatimonadaceae
(2.36%)
norank_Pirellulaceae
(2.113%),
all
which
involved
removal.
This
study
provided
promising
strategy
gained
insight
into
polluted
rivers.