Research in Microbiology,
Journal Year:
2023,
Volume and Issue:
175(1-2), P. 104133 - 104133
Published: Sept. 6, 2023
Rare
earth
element
(REE)
recovery
from
waste
streams,
mine
tailings
or
recyclable
components
using
bioleaching
is
gaining
traction
due
to
the
shortage
and
security
of
REE
supply
as
well
environmental
problems
that
occur
processing
refining.
Four
heterotrophic
microbial
species
with
known
phosphate
solubilizing
capabilities
were
evaluated
for
their
ability
leach
a
high-grade
monazite
when
provided
either
galactose,
fructose
maltose.
Supplying
resulted
in
greatest
amount
leached
ore
largest
acid
organic
produced.
Gluconic
was
dominant
identified
produced
by
cultures,
followed
acetic
acid.
The
proved
difficult
different
carbon
sources,
preferential
Ce
over
La,
Nd
Pr.
Current Opinion in Microbiology,
Journal Year:
2023,
Volume and Issue:
73, P. 102297 - 102297
Published: March 30, 2023
The
rhizosphere
is
a
chemically
complex
environment
that
harbors
strikingly
diverse
microbial
community.
past
few
decades
have
seen
rapid
growth
in
the
body
of
literature
on
plant–microbe–microbe
interactions
and
plant
health.
Thus,
aim
this
paper
to
review
current
knowledge
(specifically
bacteria)
how
these
influence
microbiomes
impact
This
article
discusses
(i)
recruits
beneficial
bacteria
ii)
competition
between
mechanisms/weapons
employed
bacteria–bacteria
shapes
microbiome
turn
affects
heath.
discussion
mainly
focuses
interference
competition,
characterized
by
production
specialized
metabolites
(antibacterial
compounds)
exploitative
where
bacterial
strain
restricts
competitor's
access
nutrients
such
as
through
secretion
siderophores
could
allude
cooperation.
Understanding
mechanisms
plant–bacteria
provide
insights
into
manipulate
for
improved
agricultural
outcomes.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Jan. 29, 2024
Abstract
Intercropping
has
the
potential
to
improve
plant
nutrition
as
well
crop
yield.
However,
exact
mechanism
promoting
improved
nutrient
acquisition
and
role
rhizosphere
microbiome
may
play
in
this
process
remains
poorly
understood.
Here,
we
use
a
peanut/maize
intercropping
system
investigate
of
root-associated
microbiota
iron
these
crops,
combining
profiling,
strain
substance
isolation
functional
validation.
We
find
that
increases
peanut
but
not
maize
plants
composition
changes
converges
between
two
tested
experiments.
identify
Pseudomonas
secreted
siderophore,
pyoverdine,
improves
glasshouse
field
Our
results
suggest
presence
siderophore-secreting
intercropped
plays
an
important
nutrition.
These
findings
could
be
used
envision
future
practices
aiming
Science Advances,
Journal Year:
2025,
Volume and Issue:
11(3)
Published: Jan. 15, 2025
Bacterial
social
interactions
play
crucial
roles
in
various
ecological,
medical,
and
biotechnological
contexts.
However,
predicting
these
from
genome
sequences
is
notoriously
difficult.
Here,
we
developed
bioinformatic
tools
to
predict
whether
secreted
iron-scavenging
siderophores
stimulate
or
inhibit
the
growth
of
community
members.
Siderophores
are
chemically
diverse
can
be
stimulatory
inhibitory
depending
on
bacteria
have
lack
corresponding
uptake
receptors.
We
focused
1928
representative
Pseudomonas
genomes
an
experimentally
validated
coevolution
algorithm
match
encoded
siderophore
synthetases
receptor
groups.
derived
community-level
iron
interaction
networks
show
that
siderophore-mediated
differ
across
habitats
lifestyles.
Specifically,
dense
sharing
competition
were
observed
among
environmental
nonpathogenic
species,
while
small,
fragmented
occurred
human-associated
pathogenic
species.
Together,
our
sequence-to-ecology
approach
empowers
analyses
thousands
bacterial
strains
offers
opportunities
for
targeted
intervention
microbial
communities.
Ecology Letters,
Journal Year:
2021,
Volume and Issue:
25(1), P. 138 - 150
Published: Nov. 9, 2021
Microbial
invasions
can
compromise
ecosystem
services
and
spur
dysbiosis
disease
in
hosts.
Nevertheless,
the
mechanisms
determining
invasion
outcomes
often
remain
unclear.
Here,
we
examine
role
of
iron-scavenging
siderophores
driving
Pseudomonas
aeruginosa
into
resident
communities
environmental
pseudomonads.
Siderophores
be
'public
goods'
by
delivering
iron
to
individuals
possessing
matching
receptors;
but
they
also
bads'
withholding
from
competitors
lacking
these
receptors.
Accordingly,
should
either
promote
or
impede
invasion,
depending
on
their
effects
invader
growth.
Using
supernatant
feeding
assays,
show
that
success
indeed
increased
when
could
use
its
inhibit
(public
bad)
rather
than
stimulate
good)
Conversely,
decreased
more
was
inhibited
residents'
siderophores.
Our
findings
identify
as
a
major
driver
dynamics
bacterial
under
iron-limited
conditions.
The ISME Journal,
Journal Year:
2024,
Volume and Issue:
18(1)
Published: Jan. 1, 2024
Abstract
Microorganisms
living
in
soil
maintain
intricate
interactions
among
themselves,
forming
the
microbiota
that
influences
rhizosphere
microbiome
and
plant
growth.
However,
mechanisms
underlying
microbial
remain
unclear.
Streptomyces
Mesorhizobium
are
commonly
found
serve
as
growth-promoting
rhizobacteria
(PGPR).
Here,
we
identified
an
unprecedented
interaction
between
colonies
of
red-soil-derived
sp.
FXJ1.4098
BAC0120
referred
to
it
“proximity-based
defensive
mutualism
(PBDM).”
We
metabolite-mediated
iron
competition
sharing
two
microorganisms
were
responsible
for
PBDM.
produced
a
highly
diffusible
siderophore,
desferrioxamine,
which
made
unavailable
co-cultured
BAC0120,
thereby
inhibiting
its
also
released
poorly
iron-porphyrin
complexes,
could
be
utilized
by
restoring
growth
nearby
BAC0120.
Furthermore,
ternary
interactions,
PBDM
strategy
contributed
protection
close
from
other
competitors,
resulting
coexistence
these
PGPR.
A
scale-up
pairwise
screening
suggested
may
common
Streptomyces.
These
results
demonstrate
key
role
complex
provide
novel
insights
into
PGPR
soil.
BioMetals,
Journal Year:
2022,
Volume and Issue:
36(4), P. 777 - 797
Published: Dec. 12, 2022
Iron
is
important
for
bacterial
growth
and
survival,
as
it
a
common
co-factor
in
essential
enzymes.
Although
iron
very
abundant
the
earth
crust,
its
bioavailability
low
most
habitats
because
ferric
largely
insoluble
under
aerobic
conditions
at
neutral
pH.
Consequently,
bacteria
have
evolved
plethora
of
mechanisms
to
solubilize
acquire
from
environmental
host
stocks.
In
this
review,
I
focus
on
Pseudomonas
spp.
first
present
main
uptake
taxa,
which
involve
direct
ferrous
via
importers,
production
iron-chelating
siderophores,
exploitation
siderophores
produced
by
other
microbial
species,
use
compounds
plants
animals.
second
part
elaborate
how
these
affect
interactions
between
communities,
their
hosts.
This
live
diverse
communities
certain
iron-uptake
strategies
might
not
only
nutrient,
but
also
gain
relative
advantages
over
competitors
race
iron.
Thus,
an
integrative
understanding
acquisition
eco-evolutionary
dynamics
they
drive
community
level
prove
useful
understand
why
spp.,
particular,
many
general,
such
repertoires.
Analytical and Bioanalytical Chemistry,
Journal Year:
2022,
Volume and Issue:
414(8), P. 2671 - 2685
Published: Jan. 27, 2022
Microbial
secondary
metabolites
represent
a
rich
source
for
drug
discovery,
plant
protective
agents,
and
biotechnologically
relevant
compounds.
Among
them
are
siderophores,
iron-chelating
molecules,
that
show
great
influence
on
bacterial
community
assembly
the
potential
to
control
pathogen
invasions.
One
of
such
siderophore
is
pyoverdine
produced
by
fluorescent
Pseudomonas
members
consists
different
peptide
chains
specific
each
species.
The
identification
structural
elucidation
suites
siderophores
remain
widely
underexplored
as
general
high-throughput
analytical
protocols
missing.
Therefore,
dedicated
method
was
established
allowing
rapid
localization
pyoverdines.
Liquid
culture
samples
were
purified
an
easy
small-scale
solid-phase
extraction
(SPE).
Ultra-high-performance
liquid
chromatography
high-resolution
tandem
mass
spectrometry
(UHPLC-HR-MS/MS)
separated
highly
polar
pyoverdines
their
derivatives.
All
ion
fragmentation
(AIF)
generated
spectra
containing
characteristic
fragments
biological
precursor
pyoverdine,
ferribactin.
This
led
revelation
secreted
Targeted
MS/MS
experiments
at
multiple
collision
energies
accomplished
full
structure
chain.
A
calculator
predictor
facilitated
greatly
interpretation
providing
accurate
masses
straightforward
comparison
measured
theoretical
values.
successfully
validated
using
four
well-known
with
various
chains.
Finally,
applicability
proven
analysis
13
unknown
sampled
cultures.
these,
4
novel
discovered
herein
reported
first
time.
The
global
rise
of
antibiotic
resistance
calls
for
new
drugs
against
bacterial
pathogens.
A
common
approach
is
to
search
natural
compounds
deployed
by
microbes
inhibit
competitors.
Here,
we
show
that
the
iron-chelating
pyoverdines,
siderophores
produced
environmental
Pseudomonas
spp.,
have
strong
antibacterial
properties
inducing
iron
starvation
and
growth
arrest
in
screen
320
isolates
used
12
human
pathogens
uncovered
several
pyoverdines
with
particularly
high
distinct
chemical
characteristics.
most
potent
pyoverdine
effectively
reduced
Acinetobacter
baumannii
,
Klebsiella
pneumoniae,
Staphylococcus
aureus
a
concentration-
iron-dependent
manner.
Pyoverdine
increased
survival
infected
Galleria
mellonella
host
larvae
showed
low
toxicity
host,
mammalian
cell
lines,
erythrocytes.
Furthermore,
experimental
evolution
combined
whole-genome
sequencing
revealed
limited
compared
an
antibiotic.
Thus,
from
strains
potential
become
class
sustainable
antibacterials
specific
Microbial
secondary
metabolites
are
a
rich
source
for
pharmaceutical
discoveries
and
play
crucial
ecological
functions.
While
tools
exist
to
identify
metabolite
clusters
in
genomes,
precise
sequence-to-function
mapping
remains
challenging
because
neither
function
nor
substrate
specificity
of
biosynthesis
enzymes
can
accurately
be
predicted.
Here,
we
developed
knowledge-guided
bioinformatic
pipeline
solve
these
issues.
We
analyzed
1928
genomes
Pseudomonas
bacteria
focused
on
iron-scavenging
pyoverdines
as
model
metabolites.
Our
predicted
188
chemically
different
with
nearly
100%
structural
accuracy
the
presence
94
distinct
receptor
groups
required
uptake
iron-loaded
pyoverdines.
unveils
an
enormous
yet
overlooked
diversity
siderophores
(151
new
structures)
receptors
(91
groups).
approach,
combining
feature
sequence
phylogenetic
approaches,
is
extendable
other
microbial
genera,
thus
emerges
powerful
tool
reconstruct
bacterial
metabolism
pathways
based
data.
ISME Communications,
Journal Year:
2024,
Volume and Issue:
4(1)
Published: Jan. 1, 2024
How
to
derive
principles
of
community
dynamics
and
stability
is
a
central
question
in
microbial
ecology.
Bottom-up
experiments,
which
small
number
bacterial
species
are
mixed,
have
become
popular
address
it.
However,
experimental
setups
typically
limited
because
co-culture
experiments
labor-intensive
difficult
distinguish.
Here,
we
use
four-species
show
that
information
from
monoculture
growth
inhibitory
effects
induced
by
secreted
compounds
can
be
combined
predict
the
competitive
rank
order
community.
Specifically,
integrative
parameters
allow
building
preliminary
order,
then
adjusted
using
supernatant
assays.
While
our
procedure
worked
for
two
different
media,
observed
differences
orders
between
media.
We
parameterized
computer
simulations
with
empirical
data
higher
interactions
largely
follow
predicted
pairwise
one
important
exception.
The
impact
was
reduced
communities
their
negative
were
spread
across
multiple
target
species.
Altogether,
formulated
three
simple
rules
how
assay
establish
an