Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Nov. 28, 2024
Abstract
Perturbations
such
as
climate
change,
invasive
species
and
pollution,
impact
the
functioning
diversity
of
ecosystems.
However
has
many
meanings,
ecosystems
provide
a
plethora
functions.
Thus,
on
top
various
perturbations
that
global
change
represents,
there
are
also
ways
to
measure
perturbation’s
ecological
impact.
This
leads
an
overwhelming
response
variability,
which
undermines
hopes
prediction.
Here,
we
show
this
variability
can
instead
insights
into
hidden
features
functions
responses
perturbations.
By
analysing
dataset
experiments
in
microbial
soil
systems
first
functional
is
not
random;
mechanistically
similar
tend
respond
coherently.
Furthermore,
metrics
broad
(e.g.
total
biomass)
systematically
opposite
ways.
We
then
formalise
these
observations
demonstrate,
using
geometrical
arguments,
simulations,
theory-driven
analysis
empirical
data,
only
predictable,
but
be
used
access
useful
information
about
contributions
population-level
Our
research
offers
powerful
framework
for
understanding
complexity
change.
Annual Review of Biophysics,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 19, 2025
All
biological
systems
are
subject
to
perturbations:
due
thermal
fluctuations,
external
environments,
or
mutations.
Yet,
while
composed
of
thousands
interacting
components,
recent
high-throughput
experiments
show
that
their
response
perturbations
is
surprisingly
low-dimensional:
confined
only
a
few
stereotyped
changes
out
the
many
possible.
Here,
we
explore
unifying
dynamical
framework
-
soft
modes
explain
and
analyze
low-dimensionality
in
biology,
from
molecules
eco-systems.
We
argue
this
one
makes
non-trivial
predictions
generalize
classic
ideas
developmental
biology
disparate
systems,
namely:
phenocopying,
dual
buffering,
global
epistasis.
While
some
these
have
been
borne
experiments,
discuss
how
allow
for
far-reaching
which
data
protein
biophysics
microbial
ecology.
Trends in Microbiology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 1, 2025
The
structure
and
function
of
microbial
communities
is
shaped
by
intricate
ecological
interactions
amongst
the
constituent
microorganisms.
Thus,
a
mechanistic
understanding
emergent
community-level
functions
requires
knowledge
on
how
architecture
underlying
interaction
networks
affects
these
properties.
To
address
this,
researchers
employ
different
sequencing-based
experimental
approaches
to
infer
topology
given
network.
However,
it
remains
generally
unclear
which
method
best
suited
for
quantifying
critical
network
parameters.
Here
we
provide
comparative
overview
serving
this
purpose,
with
particular
emphasis
their
strengths
weaknesses.
In
way,
our
work
can
help
guide
design
studies
that
aim
at
unraveling
structure-function
relationships
in
communities.
Microbial Biotechnology,
Journal Year:
2025,
Volume and Issue:
18(3)
Published: March 1, 2025
Winemaking
has
leveraged
microbiology
to
enhance
wine
quality,
typically
by
engineering
and
inoculating
individual
yeast
strains
with
desirable
traits.
However,
do
not
grow
alone
during
fermentation,
rather
they
are
embedded
in
diverse
evolving
microbial
communities
exhibiting
complex
ecological
dynamics.
Understanding
predicting
the
interplay
between
community
over
course
of
species
succession
chemical
matrix
can
benefit
from
recognising
that
wine,
like
all
ecosystems,
is
subject
general
evolutionary
rules.
In
this
piece,
we
outline
how
conceptual
methodological
frameworks
ecology
biology
assist
researchers
improving
fermentation
processes
understanding
mechanisms
governing
population
dynamics,
these
important
microcosms,
unlocking
genetic
potential
for
strain
development.
Molecular Systems Biology,
Journal Year:
2023,
Volume and Issue:
19(9)
Published: Aug. 7, 2023
Predictively
linking
taxonomic
composition
and
quantitative
ecosystem
functions
is
a
major
aspiration
in
microbial
ecology,
which
must
be
resolved
if
we
wish
to
engineer
consortia.
Here,
have
addressed
this
open
question
for
an
ecological
function
of
biotechnological
relevance:
alcoholic
fermentation
wine
yeast
communities.
By
exhaustively
phenotyping
extensive
collection
naturally
occurring
strains,
find
that
most
ecologically
industrially
relevant
traits
exhibit
phylogenetic
signal,
allowing
functional
communities
predicted
from
taxonomy.
Furthermore,
demonstrate
the
contributions
individual
strains
complex
followed
simple
rules.
These
regularities
can
integrated
quantitatively
predict
newly
assembled
Besides
addressing
theoretical
questions
our
results
methodologies
provide
blueprint
rationally
managing
processes
relevance.
Biological Theory,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 9, 2025
Abstract
The
organism
is
the
central
entity
in
biological
science.
However,
consensus
with
regard
to
definition
of
underlying
concept
lacking.
Moreover,
several
ambiguous
life
forms
exist
that
challenge
current
definitions
term.
Based
on
a
comprehensive
analysis
available
literature,
we
provide
an
overview
criteria
and
approaches
have
been
previously
used
define
organismality.
In
addition,
highlight
non-paradigmatic
entities
identify
problems
organismal
units.
To
address
these
issues,
propose
cross-disciplinary
list
key
allow
both
paradigmatic
cases
be
unequivocally
classified.
this
way,
our
work
not
only
provides
newcomers
exciting
field,
but
also
enhances
communication
across
disciplines.
Environmental Microbiology,
Journal Year:
2025,
Volume and Issue:
27(1)
Published: Jan. 1, 2025
Ecological
assembly-the
process
of
ecological
community
formation
through
species
introductions-has
recently
seen
exciting
theoretical
advancements
across
dynamical,
informational,
and
probabilistic
approaches.
However,
these
theories
often
remain
inaccessible
to
non-theoreticians,
they
lack
a
unifying
lens.
Here,
I
introduce
the
assembly
graph
as
an
integrative
tool
connect
emerging
theories.
The
visually
represents
dynamics,
where
nodes
symbolise
combinations
edges
represent
transitions
driven
by
introductions.
Through
lens
graphs,
review
how
processes
reduce
uncertainty
in
random
arrivals
(informational
approach),
identify
graphical
properties
that
guarantee
coexistence
examine
class
dynamical
models
constrain
topology
graphs
(dynamical
quantify
transition
probabilities
with
incomplete
information
(probabilistic
approach).
To
facilitate
empirical
testing,
also
methods
decompose
complex
into
smaller,
measurable
components,
well
computational
tools
for
deriving
graphs.
In
sum,
this
math-light
progress
aims
catalyse
research
towards
predictive
understanding
assembly.
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.
