bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Сен. 16, 2023
ABSTRACT
Xanthomonas
translucens,
the
causal
agent
of
bacterial
leaf
streak
disease
(BLS)
in
cereals,
is
a
re-emerging
pathogen
that
becoming
increasingly
destructive
across
world.
While
BLS
has
caused
yield
losses
past,
there
anecdotal
evidence
newer
isolates
may
be
more
virulent.
We
observed
two
translucens
collected
from
sites
Colorado
are
aggressive
on
current
wheat
and
barley
varieties
compared
to
older
isolates,
we
hypothesize
genetic
changes
between
recent
contribute
differences
isolate
aggressiveness.
To
test
this,
phenotyped
genetically
characterized
X.
2018,
which
designated
CO236
(from
barley)
CO237
wheat).
Using
pathovar-specific
phenotyping
PCR
primers,
determined
belongs
pathovar
undulosa.
sequenced
full
genomes
using
Oxford
Nanopore
long-read
sequencing,
their
whole
against
published
genomes.
This
analysis
confirmed
our
designations
for
Xtt
Xtu
CO237,
showed
that,
at
whole-genome
level,
were
no
obvious
genomic
structural
other
respective
Focusing
undulosa
(Xtu
CO237),
then
putative
Type
III
effectors
among
all
available
found
they
highly
conserved.
However,
striking
presence
sequence
various
transcription
activator-like
(TALE)
genomes,
correlate
with
virulence.
Here,
explore
potential
implications
these
virulence
factors,
provide
possible
explanations
increased
recently-emerged
isolates.
Data
Summary
A
list
accessions
used
this
study
can
Supplemental
Table
S1.
sequences
deposited
GenBank
(Accession:
PRJNA1017868
PRJNA1017870,
respectively).
Software
packages
custom
Conda
environment
S4.
The
dataset
MinION
reads
Dryad,
https://doi.org/10.5061/dryad.d51c5b06q
.
Custom
bash
Python
scripts
effector
(
https://github.com/robertslabcsu/xanthanalysis.git
).
Impact
statement
destructive,
cereal
crops
known
resistance
or
methods
chemical
control.
Recent
have
emphasizes
need
understand
how
evolves,
interacts
its
host,
find
new
ways
manage
disease.
identify
factors
aggressiveness
recently
impacts
understanding
host
range
evolution.
Genome Biology and Evolution,
Год журнала:
2024,
Номер
16(4)
Опубликована: Апрель 1, 2024
The
genus
Xanthomonas
has
been
primarily
studied
for
pathogenic
interactions
with
plants.
However,
besides
host
and
tissue-specific
strains,
this
also
comprises
nonpathogenic
strains
isolated
from
a
broad
range
of
hosts,
sometimes
in
association
other
environments,
including
rainwater.
Based
on
their
incapacity
or
limited
capacity
to
cause
symptoms
the
isolation,
xanthomonads
can
be
further
characterized
as
commensal
weakly
pathogenic.
This
study
aimed
understand
diversity
evolution
compared
counterparts
based
cooccurrence
phylogenetic
relationship
identify
genomic
traits
that
form
basis
life
history
framework
groups
by
ecological
strategies.
We
sequenced
genomes
83
spanning
phylogeny
identified
eight
novel
species,
indicating
unexplored
diversity.
While
some
species
have
experienced
recent
loss
type
III
secretion
system,
specifically
hrp2
cluster,
we
observed
an
apparent
lack
cluster
lifestyles
diverse
species.
performed
analysis
large
data
set
337
explain
how
may
established
plants
across
continuum
commensals
weak
pathogens
pathogens.
Presence
distinct
transcriptional
regulators,
nutrient
utilization
assimilation
genes,
chemotaxis
genes
lifestyle-specific
adaptations
xanthomonads.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2022,
Номер
72(6)
Опубликована: Июнь 9, 2022
The
genus
Xanthomonas
contains
a
set
of
diverse
bacterial
strains,
most
which
are
known
for
their
pathogenicity
on
annual
crops
and
fruit
trees
causing
economically
important
plant
diseases.
Recently,
five
strains
were
isolated
from
Agrobacterium-induced
crown
gall
tissues
amaranth
(Amaranthus
sp.)
weeping
fig
(Ficus
benjamina)
plants
in
Iran.
Phenotypic
characteristics
(i.e.
biochemical
tests
features)
whole
genome
sequence-based
core-genome
phylogeny
followed
by
average
nucleotide
identity
digital
DNA-DNA
hybridization
calculations
suggested
that
these
gall-associated
belong
to
two
new
species
within
the
Xanthomonas.
In
this
study,
we
provide
formal
description
where
bonasiae
sp.
nov.
is
proposed
with
FX4T
(=CFBP
8703T=DSM
112530T)
as
type
strain.
name
youngii
AmX2T
8902T=DSM
112529T)
Microbiology Spectrum,
Год журнала:
2024,
Номер
12(4)
Опубликована: Фев. 21, 2024
ABSTRACT
Fruit
bodies
(sporocarps)
of
wild
mushrooms
growing
in
natural
environments
play
a
substantial
role
the
preservation
microbial
communities,
for
example,
clinical
and
food-poisoning
bacteria.
However,
as
reservoirs
plant
pathogenic
bacteria
remains
almost
entirely
unknown.
Furthermore,
bacterial
transmission
from
mushroom
species
to
agricultural
plants
has
rarely
been
recorded
literature.
In
September
2021,
creamy-white
Gram-negative
strain
was
isolated
sporocarp
Suillus
luteus
(slippery
jack)
Bermuda
grass
(
Cynodon
dactylon
)
lawn
Southern
Iran.
A
similar
same
fungus
area
2022.
Both
strains
were
identified
Burkholderia
gladioli
based
on
phenotypic
features
well
phylogeny
16S
rRNA
three
housekeeping
genes.
The
not
only
white
button
Agaricus
bisporus
but
also
induced
hypersensitive
reaction
(HR)
tobacco
common
bean
leaves
caused
soft
rot
set
diverse
species,
that
is,
chili
pepper,
pod,
cucumber,
eggplant,
garlic,
gladiolus,
narcissus,
onion,
potato,
spring
okra,
kohlrabi,
mango,
watermelon.
Isolation
B.
S.
two
consecutive
years
could
be
indicative
this
bacterium
environment.
associated
with
naturally
potentially
invade
neighboring
crops,
vegetables
ornamentals.
potential
phytopathogenic
is
further
discussed.
IMPORTANCE
genus
contains
biologically
heterogeneous
can
habitats,
soil,
water,
diseased
material,
specimens.
study,
pectinolytic
sporocarps
2021
Molecular
phylogenetic
analyses
revealed
both
belonged
complex
,
while
pathovar
status
remained
undetermined.
Biological
investigations
accomplished
pathogenicity
host
range
assays
showed
ranging
ornamentals
monocotyledonous
dicotyledonous
vegetables.
Thus,
considered
an
infectious
pathogen
capable
being
transmitted
annual
crops.
Our
results
raise
hypothesis
.
Applied and Environmental Microbiology,
Год журнала:
2024,
Номер
90(9)
Опубликована: Авг. 19, 2024
ABSTRACT
Xanthomonas
species
are
major
pathogens
of
plants
and
have
been
studied
extensively.
There
is
increasing
recognition
the
importance
non-pathogenic
within
same
genus.
With
this
came
need
to
understand
genomic
functional
diversity
(NPX)
at
strain
level.
This
study
reports
isolation
investigation
into
variation
in
NPX
isolates,
chiefly
indica
,
a
newly
discovered
from
rice.
The
establishes
relationship
X.
strains
clade
I
Xanthomonads
with
another
species,
sontii
also
associated
rice
seeds.
Identification
highly
diverse
strains,
open-pan
genome,
systematic
hyper-variation
lipopolysaccharide
biosynthetic
locus
when
compared
pathogenic
indicates
acquisition
new
functions
for
adaptation.
Furthermore,
comparative
genomics
studies
established
absence
virulence
genes
such
as
type
III
secretion
system
effectors,
which
present
pathogens,
presence
known
bacterial-killing
IV
(X-T4SS).
were
found
protect
bacterial
leaf
blight
pathogen,
oryzae
pv.
(Xoo).
phenotype
an
X-T4SS
mutant
suggests
redundancy
genetic
basis
mechanisms
involved
bioprotection
function,
may
include
multiple
loci,
putative
bacteriocin-encoding
gene
clusters
involvement
other
factors
nutrient
niche
competition
apart
induction
innate
immunity
through
shared
microbial-associated
molecular
patterns.
rice-NPX
community
its
counterpart
can
be
promising
model
understanding
plant-microbe-microbiome
interaction
studies.
IMPORTANCE
group
bacteria
characteristic
lifestyle
phytopathogen.
However,
discovery
shift
bacteria.
Multi-strain,
in-depth
genomic,
evolutionary
on
each
these
still
lacking.
provides
novel
insights
genome
diversity,
dynamics,
trends
microbiome
relatives
that
form
sub-clade.
Interestingly,
we
uncovered
species.
plant
protection
property
shows
their
part
healthy
microbiome.
finding
open
pan-genome
large-scale
significant
role
host
findings
high-quality
resources
will
allow
further
host-associated
microbial
health.
Phytopathology,
Год журнала:
2022,
Номер
112(8), С. 1630 - 1639
Опубликована: Фев. 23, 2022
Xanthomonas
arboricola
comprises
a
number
of
economically
important
fruit
tree
pathogens
classified
within
different
pathovars.
Dozens
nonpathogenic
and
taxonomically
unvalidated
strains
are
also
designated
as
X.
arboricola,
leading
to
complicated
taxonomic
status
in
the
species.
In
this
study,
we
have
evaluated
whole-genome
resources
all
available
spp.
public
databases
refine
members
species
based
on
DNA
similarity
indexes
core
genome-based
phylogeny.
Our
results
show
that,
nine
validly
described
pathovars
pathotype
seven
genuine,
belonging
clade
regardless
their
pathogenicity
host
isolation
(thus
validity
pathovar
status).
However,
pv.
guizotiae
populi
do
not
belong
because
low
similarities
between
type
strain
these
two
Thus,
propose
elevate
rank
sp.
nov.
with
CFBP
7408T
populina
3123T.
addition,
other
mislabeled
were
scattered
that
previously
or
represent
novel
await
formal
description.
Plant Pathology,
Год журнала:
2023,
Номер
72(7), С. 1260 - 1271
Опубликована: Апрель 24, 2023
Abstract
Soft
rot‐inducing
bacterial
pathogens
are
considered
among
the
main
biotic
constraints
on
vegetables
and
annual
crops.
Most
of
soft
rot
members
Pectobacterium
spp.
Dickeya
,
with
former
genus
encompassing
a
continuously
increasing
number
species
varying
in
geographic
distribution
host
isolation.
In
Iran,
have
rarely
been
investigated
using
high‐throughput
nucleotide
sequence‐based
techniques,
leaving
genetic
diversity
these
mostly
undetermined.
During
2021,
crops
symptoms
maceration
were
collected
from
Fars,
Hamedan,
Isfahan,
Khuzestan
Kohgiluyeh‐Boyer‐Ahmad
provinces
Iran.
Forty‐four
pectinolytic
strains
isolated
symptomatic
tissues
bell
pepper,
cabbage,
carrot,
lettuce,
potato
zucchini.
The
subjected
to
pathogenicity
range
assays,
specific
PCR
tests
phylogenetic
analysis
three
housekeeping
genes
(
dnaX
gapA
leuS
).
All
pathogenic
their
Among
44
strains,
26
identified
as
based
primer
pair
Y1/Y2.
Multilocus
sequence
confirmed
latter
belonging
revealed
that
scattered
into
four
species:
P
.
brasiliense
(five
strains),
carotovorum
(eight
polaris
strains)
versatile
strains).
P.
not
previously
reported
country.
Host
assays
showed
broader
than
other
two
species.
Phytopathology,
Год журнала:
2023,
Номер
113(11), С. 2024 - 2036
Опубликована: Апрель 18, 2023
Bacterial
leaf
streak
of
small-grain
cereals
is
an
economically
important
disease
wheat
and
barley
crops.
The
occurs
in
many
countries
across
the
globe,
with
particular
importance
regions
characterized
by
high
precipitation
or
areas
which
sprinkler
irrigation
used.
Three
genetically
distinct
lineages
Gram-negative
bacterium
Xanthomonas
translucens
(X.
pv.
undulosa,
X.
translucens,
cerealis)
are
responsible
for
most
bacterial
infections
on
Considering
seedborne
nature
pathogens,
they
included
A2
(high-risk)
list
quarantine
organisms
some
European
countries;
hence,
under
strict
control
zero
tolerance.
Due
to
taxonomic
complexities
within
exact
geographic
distribution
each
pathovar
has
not
yet
been
determined.
In
this
mini
review,
we
provide
updated
overview
detection
diagnosis
pathogens.
First,
a
short
history
pathogens
provided,
followed
symptomology
host
range
causal
agents.
Then,
utility
conventional
methods
high-throughput
molecular
approaches
precise
identification
explained.
Finally,
highlight
role
inspections
early
pathogen
combating
risk
21st
century's
small-grains
cereals'
industry.
Phytopathology,
Год журнала:
2022,
Номер
113(2), С. 150 - 159
Опубликована: Сен. 22, 2022
Mycopathogenic
bacteria
play
a
pivotal
role
in
the
productivity
of
edible
mushrooms
grown
under
controlled
conditions.
In
this
study,
we
carried
out
comprehensive
farm
survey
and
sampling
(2018
to
2021)
on
button
mushroom
(Agaricus
bisporus)
farms
15
provinces
Iran
monitor
status
bacterial
pathogens
infecting
crop.
strains
were
isolated
from
pins,
stems,
caps,
as
well
casing
layer
38
farms.
The
incited
symptoms
caps
ranging
faint
discoloration
dark
brown
blotch
inoculated
surfaces.
Among
inciting
disease
bottom
mushroom,
40
identified
Ewingella
americana
based
biochemical
assays
phylogeny
16S
rRNA
gyrB
gene.
E.
differed
their
aggressiveness
stipes,
where
corresponding
ranged
deep
yellow
brown.
phylogenetic
analyses,
all
study
clustered
monophyletic
clade
closely
related
nonpathogenic
environmental
species.
BOX-PCR-based
fingerprinting
revealed
intraspecific
diversity.
Using
cutoff
level
73
76%
similarity,
formed
six
clusters.
A
chronological
pattern
was
observed,
2018
differentiated
those
2020
2021.
Taken
together,
due
multifaceted
nature
pathogen,
such
widespread
occurrence
could
be
an
emerging
threat
for
industry
country.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июнь 5, 2023
Abstract
The
genus
Xanthomonas
has
been
primarily
studied
for
pathogenic
interactions
with
plants.
However,
besides
host
and
tissue
specific
strains,
this
also
comprises
nonpathogenic
strains
isolated
from
a
broad
range
of
hosts,
sometimes
in
association
other
environments,
including
rainwater.
Based
on
their
incapacity
or
limited
capacity
to
cause
symptoms
the
isolation,
xanthomonads
can
be
further
characterized
as
commensal
weakly
pathogenic.
This
study
aimed
understand
diversity
evolution
compared
counterparts
based
co-occurrence
phylogenetic
relationship
identify
genomic
traits
that
form
basis
life-history
framework
groups
by
ecological
strategies.
We
sequenced
genomes
83
spanning
phylogeny
identified
eight
novel
species,
indicating
unexplored
diversity.
While
some
species
have
experienced
recent
loss
type
III
secretion
system,
specifically,
hrp2
cluster,
we
observed
an
apparent
lack
cluster
lifestyles
diverse
species.
gathered
evidence
gene
flow
among
co-occurring
suggesting
potential
act
reservoir
adaptive
vice
versa.
enriched
nonpathogens
suggest
strategy
stress
tolerance,
rather
than
avoidance,
during