Research Square (Research Square),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Sept. 14, 2023
Single
cell
sequencing
is
useful
for
resolving
complex
systems
into
their
composite
types
and
computationally
mining
them
unique
features
that
are
masked
in
pooled
sequencing.
However,
while
commercial
instruments
have
made
single
analysis
widespread
mammalian
cells,
analogous
tools
microbes
limited.
Here,
we
present
EASi-seq
(Easily
Accessible
microbe
sequencing).
By
adapting
the
workflow
of
Mission
Bio
Tapestri
instrument,
this
method
allows
efficient
individual
microbes'
genomes.
thousands
to
be
sequenced
per
run
and,
as
show,
can
generate
detailed
atlases
human
environmental
microbiomes.
The
ability
capture
large
shotgun
genome
datasets
from
provides
new
opportunities
discovering
analyzing
species
subpopulations.
To
facilitate
this,
develop
a
companion
bioinformatic
pipeline
clusters
by
similarity,
improving
whole
assembly,
strain
identification,
taxonomic
classification,
gene
annotation.
In
addition,
demonstrate
integration
metagenomic
contigs
with
reduce
bias
increase
coverage.
Overall,
enables
high
quality
genomic
data
microbiome
samples
using
an
accessible
on
commercially
available
platform.
Cells,
Journal Year:
2023,
Volume and Issue:
12(14), P. 1875 - 1875
Published: July 17, 2023
Unmasking
the
subtleties
of
immune
system
requires
both
a
comprehensive
knowledge
base
and
ability
to
interrogate
that
with
intimate
sensitivity.
That
task,
considerable
extent,
has
been
handled
by
an
iterative
expansion
in
flow
cytometry
methods,
technological
capability
also
accompanying
advances
informatics.
As
field
fluorescence-based
cytomics
matured,
it
reached
barrier
at
around
30
parameter
analyses,
which
stalled
until
spectral
created
fundamental
transformation
will
likely
lead
potential
100
simultaneous
analyses
within
few
years.
The
advance
informatics
now
become
watershed
moment
for
as
competes
mature
systematic
approaches
such
genomics
proteomics,
allowing
take
seat
multi-omics
table.
In
addition,
recent
try
combine
speed
systems
other
detection
addition
fluorescence
alone,
make
flow-based
instruments
even
more
indispensable
any
biological
laboratory.
This
paper
outlines
current
cell
analysis
discusses
traditional
microfluidic
sorting
well
next-generation
instruments,
provides
early
look
future
opportunities
are
arise.
Science Advances,
Journal Year:
2025,
Volume and Issue:
11(3)
Published: Jan. 17, 2025
Following
30
years
of
sequencing,
we
assessed
the
phylogenetic
diversity
(PD)
>1.5
million
microbial
genomes
in
public
databases,
including
metagenome-assembled
(MAGs)
uncultivated
microbes.
As
compared
to
vast
uncovered
by
metagenomic
sequences,
cultivated
taxa
account
for
a
modest
portion
overall
diversity,
9.73%
bacteria
and
6.55%
archaea,
while
MAGs
contribute
48.54%
57.05%,
respectively.
Therefore,
substantial
fraction
bacterial
(41.73%)
archaeal
PD
(36.39%)
still
lacks
any
genomic
representation.
This
unrepresented
manifests
primarily
at
lower
taxonomic
ranks,
exemplified
134,966
species
identified
18,087
samples.
Our
study
exposes
hotspots
freshwater,
marine
subsurface,
sediment,
soil,
other
environments,
whereas
human
samples
yielded
minimal
novelty
within
context
existing
datasets.
These
results
offer
roadmap
future
genome
recovery
efforts,
delineating
uncaptured
underexplored
environments
underscoring
necessity
renewed
isolation
sequencing.
Horticulturae,
Journal Year:
2023,
Volume and Issue:
9(12), P. 1306 - 1306
Published: Dec. 5, 2023
Nowadays,
legal
regulations
and
social
environmental
concerns
are
converging
towards
the
promotion
of
more
sustainable
agriculture
based
on
organic
compounds
soil
preservation.
These
trends
fuelling
growth
biofertilizers,
which
beneficial
preparations
containing
microorganisms
able
to
enhance
a
plant’s
ability
uptake
essential
nutrients.
Their
production
commercialization
encompass
multitude
critical
steps
deeply
reviewed
in
this
manuscript
through
an
exhaustive
overview
key
stages,
such
as
microorganism
selection,
new
sources,
upscaling
field
trials,
encapsulation,
current
application
systems
regulatory
considerations.
However,
although
economical
expectations
promising,
several
methodological,
environmental,
undermining
their
advancement.
The
redefinition
international
frameworks,
enhancement
trending
technologies,
fostering
multidisciplinary
collaboration
across
sectors
players
promote
biofertilizers
eco-friendly
cost-effective
alternatives
chemical
fertilizers.
Journal of Hazardous Materials Advances,
Journal Year:
2024,
Volume and Issue:
14, P. 100425 - 100425
Published: March 28, 2024
The
current
study
comprehensively
reviews
the
ecological
niche
and
pathogenicity
shift
in
freshwater
microbial
community
response
to
stress
induced
by
a
high
pollution
load.
provides
unique
understanding
of
how
change
oxygen
level
tends
affect
survival
aquatic
biota
delving
into
an
increase
pollutant
load
affects
stability.
review
indicated
that
loads
alter
balance
resources
such
as
organic
matter,
dissolved
gases,
light
penetration,
essential
nutrients.
This
causes
dynamics
species-dependent
microorganisms
environments.
also
alteration
genome
microorganisms,
leading
development
antibiotic
resistance
genes
thereby
increasing
microorganisms.
dynamic
created
lowers
natural
defence
strategies
environment,
efficacy
pathogens
infest
respective
host.
A
detailed
mechanisms
involved
exotoxins
production
interaction
with
will
give
important
insight
effect
exotoxin.
is
importance
both
environmental
medical
interests.
because
not
only
detrimental
organisms
but
resists
improperly
treated
drinking
water.
Such
water
could
retrogress
wellness
quality
life
when
used
continuously.
An
extensive
on
specific
pollutants
cause
microbiota
provide
impact
stability
environment.
Heliyon,
Journal Year:
2024,
Volume and Issue:
10(7), P. e27930 - e27930
Published: March 21, 2024
Despite
the
diligent
efforts
of
libraries,
archives,
and
similar
institutions
to
preserve
cultural
monuments,
biodeterioration
continues
pose
a
significant
threat
these
objects.
One
main
sources
microorganisms
responsible
for
process
is
presence
airborne
microorganisms.
Therefore,
this
research
aims
monitor
compare
outcomes
both
culture-dependent
(utilising
various
cultivation
strategies)
culture-independent
approaches
(RNA-based
sequencing)
identifying
metabolically
active
in
archives
Czech
Republic.
Through
study,
several
species
that
have
potential
risks
heritage
objects
health
institution
employees
were
found.
Additionally,
efficacy
different
media
was
demonstrated
be
varied
across
archive
rooms,
highlighting
necessity
employing
multiple
comprehensive
analyses.
Of
noteworthy
importance,
resuscitating-promoting
factor
(Rpf)
proved
pivotal
tool,
increasing
bacterial
culturability
by
up
30%
when
synergistically
employed
Reasoner's
2A
agar
(R2A)
R2A
+
Rpf
media.
Next,
study
emphasises
importance
integrating
approaches.
The
overlap
between
genera
identified
approach
those
also
from
33%
surpassing
94%,
with
maximum
alignment
exceeding
94%
only
one
case.
Our
results
highlight
actively
monitoring
assessing
levels
microbial
air
contamination
prevent
further
deterioration
promote
improved
conditions
institutions.
Bionatura journal :,
Journal Year:
2025,
Volume and Issue:
2(1), P. 1 - 19
Published: Jan. 11, 2025
La
presente
investigación
tuvo
por
objeto
evaluar
el
proceso
de
descomposición
los
residuos
orgánicos
proveniente
juguerías
un
mercado
zonal,
mediante
uso
microorganismos
montaña
(MM)
y
microrganismos
eficientes
(ME)
para
determinar
macronutrientes,
propiedades
físicas
químicas
del
producto
(compost).
metodología
utilizada
fue
la
descomponer
al
mismo
tiempo
una
cierta
cantidad
con
ME
MM,
manera
independiente,
verificar
rapidez
e
intensidad
olor
en
proceso.
Se
evaluó
constantemente,
tres
veces
semana,
permitiendo
recopilación
datos
observación
progresiva.
Los
resultados
indican
que
materia
orgánica
compost
se
incrementó
364,29
%
trabajo
MM
incremento
296,43
ME;
arena
experimenta
14,15%
10,52
aumento
ME.
densidad
aparente
2,09
incorporación
eficientes.
El
nitrógeno
467,46
472,62
a
las
siete
semanas
descomponen
98
100
Palabras
clave:
compost;
descomposición;
olor;
orgánica;
ISME Communications,
Journal Year:
2025,
Volume and Issue:
5(1)
Published: Jan. 1, 2025
Abstract
Mitigation
of
the
negative
environmental
consequences
excess
anthropogenic
nitrogen
input
requires
a
thorough
understanding
processes
driving
biogeochemical
cycle.
Nitrification
is
one
key
nitrogen-cycling
and
performed
by
ammonia-oxidizing
bacteria
archaea,
nitrite-oxidizing
bacteria,
complete
nitrifiers.
However,
fastidious
growth
nitrifiers
largely
hampered
their
isolation
using
classical
cultivation
techniques,
as
most
do
not
grow
on
solid
media.
Here,
we
present
workflow
for
targeted
enrichment
canonical
combining
function-specific
in
vivo
fluorescent
labeling
with
cell
sorting.
Optimized
floc
disruption
techniques
enlarged
fraction
planktonic
cells
signal
intensity,
respectively,
while
maintaining
viability.
Sorted
fractions
were
incubated
ammonium-containing
mineral
media
screened
nitrite
nitrate
production.
Nitrifying
cultures
upscaled
characterized
16S
ribosomal
ribonucleic
acid
amoA
gene-targeted
polymerase
chain
reactions
fluorescence
situ
hybridization.
Overall,
obtained
axenic
enriched
Nitrosomonas,
seven
comammox
Nitrospira
from
five
bioreactors,
recirculating
aquaculture
system
biofilter,
agricultural
soil.
In
conclusion,
presented
enables
fast
retrieval
ammonia
oxidizers
complex
samples,
allowing
in-depth
physiological
characterization.
ISME Communications,
Journal Year:
2025,
Volume and Issue:
5(1)
Published: Jan. 1, 2025
Abstract
Microbes
in
soil
navigate
interactions
by
recognizing
kin,
forming
social
groups,
exhibiting
antagonistic
behavior,
and
engaging
competitive
kin
rivalry.
Here,
we
investigated
a
novel
phenomenon
of
self-growth
suppression
(sibling
rivalry)
observed
Bradyrhizobium
diazoefficiens
USDA
110.
Swimming
colonies
110
developed
distinct
demarcation
line
inter-colony
zone
when
inoculated
adjacent
to
each
other.
In
addition
self,
suppressed
growth
other
strains
several
bacteria.
We
demonstrated
that
the
sibling
rivalry
is
due
but
not
cell
death.
The
cells
were
culturable
had
reduced
respiratory
activity,
ATP
levels,
motility.
was
presence
diffusible
effector
compound.
This
labile,
preventing
extraction,
identification,
it
unlikely
protein
or
strong
acid
base.
counterintuitive
suggests
strategic
adaptation
for
conserving
energy
resources
environments.
Bradyrhizobium’s
utilization
antagonism
including
likely
provides
advantage
long-term
success
ecosystems.
