Applied and Environmental Microbiology,
Journal Year:
2024,
Volume and Issue:
90(6)
Published: May 21, 2024
ABSTRACT
Polycyclic
tetramate
macrolactams
(PTMs)
are
bioactive
natural
products
commonly
associated
with
certain
actinobacterial
and
proteobacterial
lineages.
These
molecules
have
been
the
subject
of
numerous
structure-activity
investigations
since
1970s.
New
members
continue
to
be
pursued
in
wild
engineered
bacterial
strains,
advances
PTM
biosynthesis
suggest
their
outwardly
simplistic
biosynthetic
gene
clusters
(BGCs)
belie
unexpected
product
complexity.
To
address
origins
this
complexity
understand
its
influence
on
discovery,
we
engaged
a
combination
bioinformatics
systematically
classify
BGCs
PTM-targeted
metabolomics
compare
select
BGC
types.
By
comparing
groups
producers
mutants,
exposed
knowledge
gaps
that
complicate
bioinformatics-driven
predictions.
In
sum,
provide
new
insights
into
evolution
while
accounting
for
PTMs
discovered
thus
far.
The
combined
computational
metabologenomic
findings
presented
here
should
prove
useful
guiding
future
discovery.
IMPORTANCE
macrolactam
(PTM)
pathways
frequently
found
within
genomes
biotechnologically
important
bacteria,
including
Streptomyces
Lysobacter
spp
.
Their
molecular
typically
bioactive,
having
substantial
agricultural
therapeutic
interest.
Leveraging
genomics
discovery
related
is
desirable,
but
drawing
accurate
structural
predictions
from
alone
remains
challenging.
This
difficulty
stems
previously
underappreciated
remaining
gaps,
compounded
by
stream
yet-uncharacterized
loci
gleaned
recently
sequenced
genomes.
We
following
study
create
framework
cataloging
historic
clusters,
identifying
cluster
variations,
tracing
evolutionary
paths
these
molecules.
Our
data
chemistry
discoverable
nature.
However,
our
metabolomic
mutational
analyses
emphasize
practical
limitations
genomics-based
exposing
hidden
Environmental Science & Technology,
Journal Year:
2021,
Volume and Issue:
55(16), P. 11294 - 11307
Published: Aug. 2, 2021
Understanding
the
degradation
of
dissolved
organic
matter
(DOM)
is
vital
for
optimizing
DOM
control.
However,
microbe-mediated
transformation
during
wastewater
treatment
remains
poorly
characterized.
Here,
microbes
and
along
full-scale
biotreatment
processes
were
simultaneously
characterized
using
comparative
genomics
high-resolution
mass
spectrometry-based
reactomics.
Biotreatments
significantly
increased
DOM's
aromaticity
unsaturation
due
to
overproduced
lignin
polyphenol
analogs.
was
diversified
by
over
five
times
in
richness,
with
thousands
nitrogenous
sulfur-containing
compounds
generated
through
oxidoreduction,
functional
group
transfer,
C–N
C–S
bond
formation.
Network
analysis
demonstrated
microbial
division
labor
transformation.
their
roles
determined
traits
rather
than
taxa.
Specifically,
network
module
hubs
exhibited
rapid
growth
potentials
broad
substrate
affinities
but
deficient
xenobiotics-metabolism-associated
genes.
They
mainly
correlated
liable
consumption
its
recalcitrant
compounds.
In
contrast,
connectors
peripherals
potential
degraders
slow
growth.
showed
specialized
associations
fewer
molecules
probably
fed
on
metabolites
hub
microbes.
Thus,
developing
technologies
(e.g.,
carriers)
selectively
enrich
peripheral
consequently
decouple
may
advance
removal.
ISME Communications,
Journal Year:
2023,
Volume and Issue:
3(1)
Published: Feb. 22, 2023
Abstract
Developing
low-cadmium
(Cd)
rice
cultivars
has
emerged
as
a
promising
avenue
for
food
safety
in
Cd-contaminated
farmlands.
The
root-associated
microbiomes
of
have
been
shown
to
enhance
growth
and
alleviate
Cd
stress.
However,
the
microbial
taxon-specific
resistance
mechanisms
underlying
different
accumulation
characteristics
between
remain
largely
unknown.
This
study
compared
low-Cd
cultivar
XS14
hybrid
YY17
with
five
soil
amendments.
results
showed
that
was
characterized
by
more
variable
community
structures
stable
co-occurrence
networks
soil-root
continuum
YY17.
stronger
stochastic
processes
assembly
(~25%)
rhizosphere
than
(~12%)
suggested
may
higher
changes
properties.
Microbial
machine
learning
models
jointly
identified
keystone
indicator
microbiota,
such
Desulfobacteria
Nitrospiraceae
Meanwhile,
genes
involved
sulfur
cycling
nitrogen
were
observed
among
microbiome
these
two
cultivars,
respectively.
Microbiomes
root
diversity
functioning,
significant
enrichment
functional
related
amino
acid
carbohydrate
transport
metabolism,
cycling.
Our
findings
revealed
differences
similarities
communities
associated
well
bacterial
biomarkers
predictive
Cd-accumulation
capacity.
Thus,
we
provide
new
insights
into
recruitment
strategies
under
stress
highlight
utility
offering
clues
enhancing
crop
resilience
stresses
future.
Water Research,
Journal Year:
2023,
Volume and Issue:
246, P. 120700 - 120700
Published: Oct. 6, 2023
The
tremendous
progress
in
sequencing
technologies
has
made
DNA
routine
for
microbiome
studies.
Additionally,
advances
mass
spectrometric
techniques
have
extended
conventional
proteomics
into
the
field
of
microbial
ecology.
However,
systematic
studies
that
provide
a
better
understanding
complementary
nature
these
'omics'
approaches,
particularly
complex
environments
such
as
wastewater
treatment
sludge,
are
urgently
needed.
Here,
we
describe
comparative
metaomics
study
on
aerobic
granular
sludge
from
three
different
plants.
For
this,
employed
metaproteomics,
whole
metagenome,
and
16S
rRNA
amplicon
to
same
granule
material
with
uniform
size.
We
furthermore
compare
taxonomic
profiles
using
Genome
Taxonomy
Database
(GTDB)
enhance
comparability
between
approaches.
Though
major
taxonomies
were
consistently
identified
samples,
composition
obtained
by
omics
varied
significantly
at
lower
levels,
which
impacts
interpretation
nutrient
removal
processes.
Nevertheless,
demonstrated
genera
all
cover
majority
protein
biomass.
established
data
contig
classification
pipeline
publicly
available,
provides
valuable
resource
further
metabolic
processes
sludge.
