Environmental Microbiology,
Journal Year:
2024,
Volume and Issue:
26(6)
Published: June 1, 2024
Abstract
Carbon‐fixing
micro‐organisms
(CFMs)
play
a
pivotal
role
in
soil
carbon
cycling,
contributing
to
uptake
and
sequestration
through
various
metabolic
pathways.
Despite
their
importance,
accurately
quantifying
the
absolute
abundance
of
these
soils
has
been
challenging.
This
study
used
digital
droplet
polymerase
chain
reaction
(ddPCR)
approach
measure
key
emerging
CFMs
pathways
fen
bog
at
different
depths,
ranging
from
0
15
cm.
We
targeted
total
prokaryotes,
oxygenic
phototrophs,
aerobic
anoxygenic
phototrophic
bacteria
chemoautotrophs,
optimizing
conditions
achieve
quantification
genes.
Our
results
revealed
that
phototrophs
were
most
abundant
CFMs,
making
up
15%
prokaryotic
abundance.
They
followed
by
chemoautotrophs
10%
9%.
observed
higher
gene
concentrations
than
bog.
There
also
variations
depth,
which
differed
between
for
all
findings
underscore
peatlands,
challenging
previous
estimates
relied
solely
on
microbial
dioxide
fixation
assessments.
Incorporating
is
essential
comprehensive
understanding
contributions
processes.
sheds
light
complex
mechanisms
functioning
peatlands.
Ecology and Evolution,
Journal Year:
2025,
Volume and Issue:
15(2)
Published: Feb. 1, 2025
ABSTRACT
Evaluating
field‐sourced
samples
with
poor‐quality
and
low‐quantity
DNA,
like
animal
feces,
presents
significant
challenges
in
the
field
of
molecular
biology.
Nonetheless,
recent
innovations
PCR
technology
are
promoted
as
effective
tools
to
overcome
many
these
issues.
Here,
we
evaluate
efficiency
droplet
digital
(ddPCR)
a
method
for
color
vision
assessment
from
feces
white‐faced
capuchins
(
Cebus
imitator
)
report
frequencies
alleles
genotypes
wild
population.
The
sex‐linked
polymorphism
monkeys
Americas
is
driven
by
single
nucleotide
polymorphisms
(SNPs)
opsin
genes
at
up
three
tuning
sites.
DNA
was
extracted
fecal
collected
211
(53.1%
males)
Sector
Santa
Rosa,
Costa
Rica:
56
were
evaluated
ddPCR,
24
both
ddPCR
Sanger
sequencing,
141
sequencing
(historical
dataset).
same
opsins
derived
each
monkey
using
ddPCR;
however,
latter
far
more
sensitive
required
fewer
reach
definitive
genotype.
Overall,
most
frequent
phenotypes
red
green/red.
distribution
was:
Females
N
=
99):
green/red
(35.4%),
red/red
(33.3%),
green/yellow
(14.1%),
yellow/red
(12.1%),
yellow/yellow
(4.0%),
green/green
(1.0%);
Males
112):
(60.7%),
yellow
(23.2%),
green
(16.1%).
reliable
evaluating
noninvasively
advantage
excellent
sensitivity
high‐throughput.
highly
robust
inhibitors
can
be
potentially
used
identify
other
disease‐related
SNP
mutations
animals.
Molecular Ecology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 15, 2025
ABSTRACT
Hot
spring
microbial
mats
represent
intricate
biofilms
that
establish
self‐sustaining
ecosystems,
hosting
diverse
communities
which
facilitate
a
range
of
biochemical
processes
and
contribute
to
the
structural
functional
complexity
these
systems.
While
community
structuring
across
mat
depth
has
received
substantial
attention,
mechanisms
shaping
horizontal
spatial
composition
structure
remain
understudied.
Here,
we
explored
contributions
species
source,
local
environment
interaction
assembly
in
six
regions
following
flow
direction
with
temperature
decreasing
from
73.3°C
52.8°C.
Surprisingly,
found
despite
divergent
structures
potential
functions
different
mats,
large
proportions
members
(45.50%–80.29%)
recipient
originated
same
source
at
upper
limit
for
photosynthetic
life.
This
finding
indicated
were
dispersed
water
subsequently
filtered
shaped
by
environmental
factors.
Furthermore,
critical
specific
attributes
played
pivotal
role
influencing
interactions
other
microorganisms.
Therefore,
dispersal
via
flow,
variables,
jointly
governed
assembly,
elucidating
dimension
hot
providing
insights
into
within
extreme
biospheres.
Metagenomics
holds
promise
as
a
comprehensive,
nontargeted
tool
for
environmental
monitoring.
However,
one
key
limitation
is
that
the
quantitative
capacity
of
metagenomics
not
well-defined.
Here,
we
demonstrated
metagenomic
technique
and
benchmarked
approach
wastewater-based
surveillance
antibiotic
resistance
genes.
To
assess
variability
low-abundance
oligonucleotide
detection
across
sample
matrices,
spiked
DNA
reference
standards
(meta
sequins)
into
replicate
wastewater
extracts
at
logarithmically
decreasing
mass-to-mass
percentages
(m/m%).
Meta
sequin
ladders
exhibited
strong
linearity
input
concentrations
low
2
×
10–3
m/m%
(R2
>
0.95),
with
little
to
no
length
or
GC
bias.
At
mean
sequencing
depth
94
Gb,
limits
quantification
(LoQ)
were
calculated
be
1.3
103
1
gene
copy
per
μL
extract,
respectively.
In
influent,
activated
sludge,
secondary
effluent
samples,
27.3,
47.7,
44.3%
detected
genes
≤LoQ,
Volumetric
log
removal
values
statistically
equivalent
between
ddPCR
16S
rRNA,
intI1,
sul1,
CTX-M-1,
vanA.
The
benchmark
here
step
toward
establishing
high-throughput,
nontargeted,
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
16
Published: April 25, 2025
Tobacco
black
shank
(TBS)
disease,
caused
by
Phytophthora
nicotianae
(P.
nicotianae),
poses
a
significant
threat
to
global
agriculture
and
results
in
substantial
economic
losses.
Traditional
methods,
like
culture-based
techniques
quantitative
polymerase
chain
reaction
(qPCR),
aid
pathogen
identification
but
can
be
less
sensitive
for
complex
samples
with
low
loads.
Here,
we
developed
validated
droplet
digital
PCR
(ddPCR)
assay
high
sensitivity
specificity
detecting
P.
nicotianae.
ddPCR
qPCR
revealed
comparable
analytical
performance
including
limit
of
blank
(LoB),
detection
(LoD),
quantitation
(LoQ).
For
the
68
infectious
tobacco
root
145
surrounding
soil
samples,
demonstrated
greater
sensitivity,
higher
positive
rate
96.4%
vs
83.9%.
Receiver
operating
characteristic
(ROC)
analysis
showed
an
area
under
curve
(AUC)
was
0.913,
compared
0.885
qPCR.
Moreover,
provided
better
quantification
accuracy
concentrations
soil,
suggesting
tolerance
potential
inhibitors
soil.
These
highlight
as
robust
reliable
tool
early
diagnosis
offering
valuable
improving
disease
management
strategies.
Research Square (Research Square),
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 6, 2025
Abstract
Background
The
current
gold
standard
for
the
detection
of
bloodstream
infections
has
several
limitations,
including
a
low
positivity
rate,
high
contamination
and
lengthy
flow
cycle.
Droplet
digital
polymerase
chain
reaction
(ddPCR),
novel
technique
offering
sensitivity
specificity
ability
to
provide
absolute
quantification,
not
been
extensively
investigated
in
context
infections.
Methods
A
prospective
study
was
conducted
on
77
patients
with
suspected
infections,
blood
cultures
ddPCR
used
investigate
presence
four
pathogens.
Additionally,
general
characteristics
relevant
routine
tests
were
collected
analysed
assess
diagnostic
efficacy
Results
from
intensive
care
medicine,
respiratory
other
departments
considering
BSIs
enrolled.
Blood
identified
24
positive
samples,
8
Staphylococcus
aureus,
12
Enterococcus
species,
1
Streptococcus
3
Candida
species..
assay
demonstrated
100%
all
pathogen
categories
specificities
94.20%,
92.31%,
93.42%,
94.59%,
respectively.
In
addition,
simultaneously
detected
4
cases
polymicrobial
14
negative
cultures,
which
verified
by
Sanger
sequencing.
assay's
time
significantly
shorter
than
that
an
average
4.31
±
0.94
hours
compared
68.40
2.50
(p
<
0.01).
Conclusion
present
demonstrates
droplet
(ddPCR)
reduces
turnaround
culture
specimens.
Furthermore,
it
sensitivity,
predictive
value,
enables
early
diagnosis
larger
number
samples
is
required
validate
correlation
between
quantification
patient
severity
prognosis.
