bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Фев. 18, 2024
In
a
recent
publication,
we
introduce
the
PGPT
ontology
and
PGPT-db
of
bacterial
plant
growth-promotion
traits
associated
database
protein
sequences,
provide
several
tools
for
genome
analysis
on
PLaBAse
server.
Here,
extend
scope
to
perform
metagenomic
datasets.
First,
mgPGPT-db,
an
extended
39,
582,
183
sequences
obtained
computationally
by
including
proteins
from
AnnoTree.
With
this,
have
integrated
into
our
metagenome
tool
MEGAN
mapping
files
identify
PGPT-related
genes
using
results
DIAMOND
alignment
reads
against
either
new
mgPGPT-db
database,
NCBI-nr
or
AnnoTree
database.
We
demonstrate
compare
these
different
approaches
in
detail
example
data
set
evince
improvement
compared
PGPT-db.
also
inferred
content
samples
taken
environments
reveal
specific
clustering.
IMPORTANCE:
A
deeper
understanding
growth-promoting
bacteria
is
important
enlight
enhance
native
plant-beneficial
functional
diversity
regarding
environmental
stress
adaption
ability
suppress
even
food-borne
pathogens
strain
inoculation
dedicated
agriculture
other
production
systems.
The
work
presented
here
extends
beyond
individual
allow
assessment
potential
metagenomes
samples.
Microorganisms,
Год журнала:
2024,
Номер
12(4), С. 779 - 779
Опубликована: Апрель 11, 2024
Plant
phenotype
is
a
complex
entity
largely
controlled
by
the
genotype
and
various
environmental
factors.
Importantly,
co-evolution
has
allowed
plants
to
coexist
with
biotic
factors
in
their
surroundings.
Recently,
plant
endophytes
as
an
external
phenotype,
forming
part
of
plethora
microbial
assemblage,
have
gained
immense
attention
from
scientists.
Functionally,
impact
many
ways,
including
increasing
nutrient
availability,
enhancing
ability
cope
both
abiotic
stress,
accumulation
important
secondary
metabolites.
The
current
state
research
been
devoted
evaluating
phenotypic
impacts
on
host
plants,
direct
influence
metabolite
stress
response.
However,
there
knowledge
gap
how
genetic
interaction
pathogens,
other
communities,
eventually
controlling
extended
phenotype.
This
review
will
summarize
can
abundance
functional
diversity
endophytic
community,
gene
expression,
host–endophyte–pathogen
disease
triangle.
information
provide
novel
insights
into
breeders
could
specifically
target
plant–endophyte
for
crop
improvement.
Biology,
Год журнала:
2024,
Номер
13(2), С. 96 - 96
Опубликована: Фев. 3, 2024
Symbiotic
nitrogen
fixation
is
a
major
contributor
of
N
in
agricultural
ecosystems,
but
the
establishment
legume–rhizobium
symbiosis
highly
affected
by
soil
salinity.
Our
interest
focused
on
use
non-rhizobial
endophytes
to
assist
between
chickpea
and
its
microsymbiont
under
salinity
avoid
loss
production
fertility.
aims
were
(1)
investigate
impact
both
symbiotic
partners;
including
early
events
Mesorhizobium-chickpea
symbiosis,
(2)
evaluate
potential
four
isolated
from
legumes
native
arid
regions
(Phyllobacterium
salinisoli,
P.
ifriqiyense,
Xanthomonas
translucens,
Cupriavidus
respiraculi)
promote
growth
nodulation
results
show
significant
reduction
seed
germination
rate
Mesorhizobium
ciceri
LMS-1
different
levels
The
composition
phenolic
compounds
root
exudates
significantly
changed
when
plants
subjected
salinity,
which
turn
nod
genes
expression
LMS-1.
Furthermore,
response
exudate
stimuli
was
suppressed
presence
(250
mM
NaCl).
On
contrary,
upregulation
exoY
otsA
genes,
are
involved
exopolysaccharide
trehalose
biosynthesis,
respectively,
registered
salt-stressed
cells.
In
addition,
co-inoculation
with
along
consortium
containing
two
bacterial
endophytes,
salinisoli
X.
resulted
improvement
performance
These
indicate
that
this
endophytic
may
be
an
appropriate
ecological
safe
tool
improve
adaptation
salt-degraded
soils.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Фев. 18, 2024
In
a
recent
publication,
we
introduce
the
PGPT
ontology
and
PGPT-db
of
bacterial
plant
growth-promotion
traits
associated
database
protein
sequences,
provide
several
tools
for
genome
analysis
on
PLaBAse
server.
Here,
extend
scope
to
perform
metagenomic
datasets.
First,
mgPGPT-db,
an
extended
39,
582,
183
sequences
obtained
computationally
by
including
proteins
from
AnnoTree.
With
this,
have
integrated
into
our
metagenome
tool
MEGAN
mapping
files
identify
PGPT-related
genes
using
results
DIAMOND
alignment
reads
against
either
new
mgPGPT-db
database,
NCBI-nr
or
AnnoTree
database.
We
demonstrate
compare
these
different
approaches
in
detail
example
data
set
evince
improvement
compared
PGPT-db.
also
inferred
content
samples
taken
environments
reveal
specific
clustering.
IMPORTANCE:
A
deeper
understanding
growth-promoting
bacteria
is
important
enlight
enhance
native
plant-beneficial
functional
diversity
regarding
environmental
stress
adaption
ability
suppress
even
food-borne
pathogens
strain
inoculation
dedicated
agriculture
other
production
systems.
The
work
presented
here
extends
beyond
individual
allow
assessment
potential
metagenomes
samples.
