Towards synthetic ecology: strategies for the optimization of microbial community functions
Frontiers in Synthetic Biology,
Journal Year:
2025,
Volume and Issue:
3
Published: March 18, 2025
Microbial
communities
are
able
to
carry
out
myriad
functions
of
biotechnological
interest,
ranging
from
the
degradation
industrial
waste
synthesis
valuable
chemical
products.
Over
past
years,
several
strategies
have
emerged
for
design
microbial
and
optimization
their
functions.
Here
we
provide
an
accessible
overview
these
strategies.
We
highlight
how
principles
synthetic
biology,
originally
devised
engineering
individual
organisms
sub-organismal
units
(e.g.,
enzymes),
influenced
development
field
ecology.
With
this,
aim
encourage
readers
critically
evaluate
insights
biology
should
guide
our
approach
community-level
engineering.
Language: Английский
Defense Heterogeneity in Host Populations Gives Rise to Pathogen Diversity
The American Naturalist,
Journal Year:
2024,
Volume and Issue:
204(4), P. 370 - 380
Published: June 28, 2024
AbstractHost
organisms
can
harbor
microbial
symbionts
that
defend
them
from
pathogen
infection
in
addition
to
the
resistance
encoded
by
host
genome.
Here,
we
investigated
how
variation
defenses,
generated
genetic
background
and
symbiont
presence,
affects
emergence
of
diversity
across
evolutionary
time.
We
passaged
opportunistic
Language: Английский
Ecological dynamics explain modular denitrification in the ocean
Proceedings of the National Academy of Sciences,
Journal Year:
2024,
Volume and Issue:
121(52)
Published: Dec. 18, 2024
Microorganisms
in
marine
oxygen
minimum
zones
(OMZs)
drive
globally
impactful
biogeochemical
processes.
One
such
process
is
multistep
denitrification
(NO
3
–
→NO
2
→NO→N
O→N
),
which
dominates
OMZ
bioavailable
nitrogen
(N)
loss
and
nitrous
oxide
(N
O)
production.
Denitrification-derived
N
typically
measured
modeled
as
a
single
step,
but
observations
reveal
that
most
denitrifiers
OMZs
contain
subsets
(“modules”)
of
the
complete
pathway.
Here,
we
identify
ecological
mechanisms
sustaining
diverse
denitrifiers,
explain
prevalence
certain
modules,
examine
implications
for
loss.
We
describe
microbial
functional
types
carrying
out
modules
by
their
underlying
redox
chemistry,
constraining
traits
with
thermodynamics
pathway
length
penalties,
an
idealized
ecosystem
model.
Biomass
yields
single-step
increase
along
when
organic
matter
(OM)
limits
growth,
explains
viability
populations
respiring
NO
O
-filled
ocean.
Results
predict
denitrifier
community
succession
environmental
gradients:
Pathway
increases
limiting
substrate
shifts
from
OM
to
N,
suggesting
niche
short
module
free-living,
OM-limited
communities,
particle-associated
consistent
observations.
The
model
captures
mechanistically
observed
dominance
higher
tolerance
module.
also
capture
dominant
source
O.
Our
framework
advances
mechanistic
understanding
relationship
between
ecology
ocean
can
be
extended
other
processes
environments.
Language: Английский
Pattern and Process in a Rapidly Changing World: Ideas and Approaches
The American Naturalist,
Journal Year:
2024,
Volume and Issue:
204(4), P. 361 - 369
Published: June 28, 2024
AbstractScience
is
as
dynamic
the
world
around
us.
Our
ideas
continually
change,
do
approaches
we
use
to
study
science.
Few
things
remain
invariant
in
this
changing
landscape,
but
a
fascination
with
pattern
and
process
one
that
has
endured
throughout
history
of
Paying
homage
long-held
tradition,
2023
Vice
Presidential
Symposium
American
Society
Naturalists
focused
on
role
ecology
evolution.
It
brought
together
group
early-career
researchers
working
topics
ranging
from
genetic
diversity
microbes
patterns
species
interactions
geological
record.
Their
work
spanned
taxonomic
spectrum
mammals,
temporal
dimension
Cenozoic
present,
manipulative
experiments
comparative
approaches.
In
introductory
article,
I
discuss
how
these
diverse
are
linked
by
common
thread
elucidating
processes
underlying
they
collectively
generate
novel
insights
into
maintenance
at
different
levels
organization.
Language: Английский