Plant Cell & Environment,
Год журнала:
2019,
Номер
42(10), С. 2860 - 2870
Опубликована: Июль 29, 2019
Plant
roots
interact
with
an
enormous
diversity
of
commensal,
mutualistic,
and
pathogenic
microbes,
which
poses
a
big
challenge
to
distinguish
beneficial
microbes
from
harmful
ones.
Plants
can
effectively
ward
off
pathogens
following
immune
recognition
conserved
microbe-associated
molecular
patterns
(MAMPs).
However,
such
elicitors
are
essentially
not
different
those
neutral
that
abundantly
present
in
the
root
microbiome.
Recent
studies
indicate
plant
system
plays
active
role
influencing
rhizosphere
microbiome
composition.
Moreover,
it
has
become
increasingly
clear
root-invading
including
rhizobia
arbuscular
mycorrhiza,
evade
or
suppress
host
immunity
establish
mutualistic
relationship
their
host.
Evidence
is
accumulating
many
free-living
microbiota
members
responses,
highlighting
suppression
as
important
function
Thus,
gate
keeping
functions
restricted
warding
but
also
extend
microbiota,
likely
promote
colonization
by
prevent
growth-defense
tradeoffs
triggered
MAMP-rich
environment.
Protein & Cell,
Год журнала:
2020,
Номер
12(5), С. 315 - 330
Опубликована: Май 11, 2020
Abstract
Advances
in
high-throughput
sequencing
(HTS)
have
fostered
rapid
developments
the
field
of
microbiome
research,
and
massive
datasets
are
now
being
generated.
However,
diversity
software
tools
complexity
analysis
pipelines
make
it
difficult
to
access
this
field.
Here,
we
systematically
summarize
advantages
limitations
methods.
Then,
recommend
specific
for
amplicon
metagenomic
analyses,
describe
commonly-used
databases,
help
researchers
select
appropriate
tools.
Furthermore,
introduce
statistical
visualization
methods
suitable
analysis,
including
alpha-
beta-diversity,
taxonomic
composition,
difference
comparisons,
correlation,
networks,
machine
learning,
evolution,
source
tracing,
common
styles
informed
choices.
Finally,
a
step-by-step
reproducible
guide
is
introduced.
We
hope
review
will
allow
carry
out
data
more
effectively
quickly
order
efficiently
mine
biological
significance
behind
data.
Frontiers in Plant Science,
Год журнала:
2020,
Номер
10
Опубликована: Янв. 24, 2020
Plants
host
a
mesmerizing
diversity
of
microbes
inside
and
around
their
roots,
known
as
the
microbiome.
The
microbiome
is
composed
mostly
fungi,
bacteria,
oomycetes,
archaea
that
can
be
either
pathogenic
or
beneficial
for
plant
health
fitness.
To
grow
healthy,
plants
need
to
surveil
soil
niches
roots
detection
microbes,
in
parallel
maximize
services
nutrients
uptake
growth
promotion.
employ
palette
mechanisms
modulate
including
structural
modifications,
exudation
secondary
metabolites
coordinated
action
different
defence
responses.
Here,
we
review
current
understanding
on
composition
activity
root
how
molecules
shape
structure
root-associated
microbial
communities.
Examples
are
given
interactions
occur
rhizosphere
between
soilborne
fungi.
We
also
present
some
well-established
examples
harnessing
highlight
fitness
by
selecting
Understanding
manipulate
aid
design
next-generation
inoculants
targeted
disease
suppression
enhanced
growth.
Frontiers in Plant Science,
Год журнала:
2021,
Номер
12
Опубликована: Март 2, 2021
Plant
secondary
metabolites
(PSMs)
play
many
roles
including
defense
against
pathogens,
pests,
and
herbivores;
response
to
environmental
stresses,
mediating
organismal
interactions.
Similarly,
plant
microbiomes
participate
in
of
the
above-mentioned
processes
directly
or
indirectly
by
regulating
metabolism.
Studies
have
shown
that
plants
can
influence
their
microbiome
secreting
various
and,
turn,
may
also
impact
metabolome
host
plant.
However,
not
much
is
known
about
communications
between
interacting
partners
phenotypic
changes.
In
this
article,
we
review
patterns
potential
underlying
mechanisms
interactions
PSMs
microbiomes.
We
describe
recent
developments
analytical
approaches
methods
field.
The
applications
these
new
increased
our
understanding
relationships
Though
current
studies
primarily
focused
on
model
organisms,
results
obtained
so
far
should
help
future
agriculturally
important
facilitate
development
manipulate
PSMs–microbiome
with
predictive
outcomes
for
sustainable
crop
productions.
Land
degradation
reduces
soil
functioning
and,
consequently,
the
services
that
provides.
Soil
hydrological
functions
are
critical
to
combat
and
promote
restoration.
microorganisms
affect
hydrology,
but
role
of
microbiota
in
forming
sustaining
is
not
well
explored.
Case
studies
indicate
potential
as
game-changers
restoring
functions.
We
review
state
art
microorganism
use
land
restoration
technology,
groups
with
greatest
for
restoration,
knowledge
effect
on
physical
properties,
proposed
strategies
long-term
degraded
lands.
also
emphasize
need
advance
emerging
research
field
biophysical
landscape
interactions
support
soil-plant
ecosystem
practices.
Journal of Agricultural and Food Chemistry,
Год журнала:
2020,
Номер
68(18), С. 5024 - 5038
Опубликована: Апрель 7, 2020
Microorganisms
colonizing
the
plant
rhizosphere
provide
a
number
of
beneficial
functions
for
their
host.
Although
an
increasing
investigations
clarified
great
functional
capabilities
microbial
communities,
understanding
precise
mechanisms
underlying
impact
microbiome
assemblies
is
still
limited.
Also,
not
much
known
about
various
microbiome.
In
this
review,
we
summarize
current
knowledge
biotic
and
abiotic
factors
that
shape
as
well
traits
are
to
plants
growth
disease-resistance.
We
give
particular
emphasis
on
root
metabolites
how
contributes
growth,
yield,
Finally,
introduce
new
perspective
novel
method
showing
synthetic
community
construction
provides
effective
approach
unravel
plant–microbes
microbes–microbes
interplays.
Annual Review of Microbiology,
Год журнала:
2020,
Номер
74(1), С. 81 - 100
Опубликована: Июнь 12, 2020
Methodological
advances
over
the
past
two
decades
have
propelled
plant
microbiome
research,
allowing
field
to
comprehensively
test
ideas
proposed
a
century
ago
and
generate
many
new
hypotheses.
Studying
distribution
of
microbial
taxa
genes
across
habitats
has
revealed
importance
various
ecological
evolutionary
forces
shaping
microbiota.
In
particular,
selection
imposed
by
strongly
shapes
diversity
composition
microbiota
leads
adaptation
associated
with
navigating
immune
system
utilizing
plant-derived
resources.
Reductionist
approaches
demonstrated
that
interaction
between
immunity
is,
in
fact,
bidirectional
plants,
microbiota,
environment
shape
complex
chemical
dialogue
collectively
orchestrates
plantmicrobiome.
The
next
stage
research
will
require
integration
reductionist
establish
general
understanding
assembly
function
both
natural
managed
environments.
Chemical Society Reviews,
Год журнала:
2021,
Номер
50(14), С. 8003 - 8049
Опубликована: Янв. 1, 2021
Technological
developments
enable
the
discovery
of
novel
enzymes,
advancement
enzyme
cascade
designs
and
pathway
engineering,
moving
biocatalysis
into
an
era
technology
integration,
intelligent
manufacturing
enzymatic
total
synthesis.
