PLoS ONE,
Journal Year:
2019,
Volume and Issue:
14(2), P. e0212355 - e0212355
Published: Feb. 14, 2019
Microbial
communities
control
numerous
biogeochemical
processes
critical
for
ecosystem
function
and
health.
Most
analyses
of
coastal
microbial
focus
on
the
characterization
bacteria
present
in
either
sediment
or
seawater,
with
fewer
studies
characterizing
both
seawater
together
at
a
given
site,
even
including
information
about
non-bacterial
communities.
As
result,
knowledge
ecological
patterns
biodiversity
across
domains
habitats
is
limited-despite
fact
that
archaea,
bacteria,
eukaryotes
are
known
to
interact
habitats.
To
better
understand
ecosystems,
we
characterized
three
sites
along
coastline
Puerto
Nuevo,
Baja
California,
Mexico
using
16S
18S
rRNA
gene
amplicon
sequencing.
We
found
hosted
approximately
500-fold
more
operational
taxonomic
units
(OTUs)
than
(p
<
0.001).
Distinct
phyla
were
versus
samples.
Of
top
ten
most
abundant
classes,
Cytophagia
(bacterial)
Chromadorea
(eukaryal)
specific
environment,
whereas
Cyanobacteria
Bacteroidia
Chlorophyceae
environment.
A
total
47
unique
genera
observed
comprise
core
taxa
community
environment
types
sites.
No
archaeal
as
part
taxa.
significant
differences
composition
between
For
bacterial
was
statistically
different
Major
Outlet
site
0.05),
closest
residential
area,
eukaryal
all
0.05).
Our
findings
highlight
distinct
spatial
heterogeneity
region
Mexico.
Microbial Ecology,
Journal Year:
2022,
Volume and Issue:
85(2), P. 669 - 683
Published: Feb. 2, 2022
Abstract
Soil
is
one
of
the
most
important
assets
planet
Earth,
responsible
for
maintaining
biodiversity
and
managing
ecosystem
services
both
managed
natural
ecosystems.
It
encompasses
large
proportion
microscopic
biodiversity,
including
prokaryotes
eukaryotes.
microbiome
critical
in
soil
functions,
but
their
activities
have
diminutive
recognition
few
systems
like
desert
land
forest
highly
dependent
on
abiotic
biotic
factors
pH,
carbon
content,
structure,
texture,
vegetation,
it
can
notably
vary
with
ecosystems
respective
inhabitants.
Thus,
unboxing
this
black
box
essential
to
comprehend
basic
components
adding
supported
services.
Recent
advancements
field
molecular
microbial
ecology
delivered
commanding
tools
examine
genetic
trove
biodiversity.
Objective
review
provide
a
evaluation
work
microbiome,
especially
since
advent
NGS
techniques.
The
also
focuses
advances
our
understanding
communities,
interactions,
functional
capabilities
along
role
maneuvering
biogeochemical
cycle
while
underlining
tapping
unprecedented
metagenomics
data
infer
ecological
attributes
yet
undiscovered
microbiome.
This
key
research
directions
that
could
shape
future
applied
into
has
led
us
understand
difficult
generalize
plays
substantiated
shaping
networks
indeed
vital
resource
sustaining
functioning.
Exploring
will
help
unlocking
roles
various
network.
be
resourceful
exploring
forecasting
its
impacts
dealing
alleviating
problems
rapid
climate
change.
Biological reviews/Biological reviews of the Cambridge Philosophical Society,
Journal Year:
2019,
Volume and Issue:
95(2), P. 350 - 364
Published: Nov. 15, 2019
Soil
is
one
of
the
most
biodiverse
terrestrial
habitats.
Yet,
we
lack
an
integrative
conceptual
framework
for
understanding
patterns
and
mechanisms
driving
soil
biodiversity.
One
underlying
reasons
our
poor
biodiversity
relates
to
whether
key
theories
(historically
developed
aboveground
aquatic
organisms)
are
applicable
Here,
present
a
systematic
literature
review
investigate
how
(species-energy
relationship,
theory
island
biogeography,
metacommunity
theory,
niche
neutral
theory)
can
explain
observed
We
then
discuss
two
spatial
compartments
nested
within
at
which
be
applied
acknowledge
scale-dependent
nature
Philosophical Transactions of the Royal Society B Biological Sciences,
Journal Year:
2020,
Volume and Issue:
375(1798), P. 20190249 - 20190249
Published: March 23, 2020
Heterogeneity
is
a
fundamental
property
of
soil
that
often
overlooked
in
microbial
ecology.
Although
it
generally
accepted
the
heterogeneity
underpins
emergence
and
maintenance
diversity,
profound
far-reaching
consequences
can
have
on
many
aspects
ecology
activity
yet
to
be
fully
apprehended
not
been
integrated
into
our
understanding
functioning.
In
this
contribution
we
first
discuss
how
environment,
consequent
uncertainty
associated
with
acquiring
resources,
may
affected
metabolism,
motility
interactions
evolved
and,
ultimately,
overall
represented
ecosystem
models,
such
as
heterotrophic
decomposition
or
respiration.
We
then
present
an
analysis
predicted
metabolic
pathways
for
bacteria,
obtained
from
MetaCyc
pathway/genome
database
collection
(https://metacyc.org/).
The
suggests
while
there
relationship
between
phylogenic
affiliation
catabolic
range
bacterial
taxa,
does
appear
trade-off
16S
rRNA
gene
copy
number,
taken
proxy
potential
growth
rate,
strains
substrates
used.
Finally,
simple,
spatially
explicit
model
used
understand
decomposers
environmental
affect
organic
matter,
suggesting
might
important
variability
process.
This
article
part
theme
issue
'Conceptual
challenges
community
ecology'.
Biological reviews/Biological reviews of the Cambridge Philosophical Society,
Journal Year:
2020,
Volume and Issue:
95(4), P. 1073 - 1096
Published: April 20, 2020
ABSTRACT
Organismal
movement
is
ubiquitous
and
facilitates
important
ecological
mechanisms
that
drive
community
metacommunity
composition
hence
biodiversity.
In
most
existing
theories
models
in
biodiversity
research,
represented
simplistically,
ignoring
the
behavioural
basis
of
consequently
variation
behaviour
at
species
individual
levels.
However,
as
human
endeavours
modify
climate
land
use,
processes
organisms
response
to
these
changes,
including
movement,
become
critical
understanding
resulting
loss.
Here,
we
draw
together
research
from
different
subdisciplines
ecology
understand
impact
individual‐level
on
community‐level
patterns
coexistence.
We
join
framework
with
key
concepts
theory,
assembly
modern
coexistence
theory
using
idea
micro–macro
links,
where
various
aspects
emergent
scale
up
local
regional
mobility
mobile‐link‐generated
abiotic
biotic
environmental
conditions.
These
turn
influence
both
and,
timescales,
such
dispersal
limitation,
filtering,
niche
partitioning.
conclude
by
highlighting
challenges
promising
future
avenues
for
data
generation,
analysis
complementary
modelling
approaches
provide
a
brief
outlook
how
new
behaviour‐based
view
becomes
responses
communities
under
ongoing
change.
The ISME Journal,
Journal Year:
2021,
Volume and Issue:
15(6), P. 1782 - 1793
Published: Jan. 19, 2021
How
do
fungi
navigate
through
the
complex
microscopic
maze-like
structures
found
in
soil?
Fungal
behaviour,
especially
at
hyphal
scale,
is
largely
unknown
and
challenging
to
study
natural
habitats
such
as
opaque
soil
matrix.
We
monitored
growth
behaviour
strategies
of
seven
Basidiomycete
litter
decomposing
species
a
micro-fabricated
"Soil
Chip"
system
that
simulates
principal
aspects
pore
space
its
micro-spatial
heterogeneity.
The
hyphae
were
faced
with
micrometre
constrictions,
sharp
turns
protruding
obstacles,
examined
have
profoundly
different
responses
terms
foraging
range
persistence,
spatial
exploration
ability
pass
obstacles.
Hyphal
was
not
predictable
solely
based
on
ecological
assumptions,
our
results
obtained
level
trait
information
scale
cannot
be
fully
explained
using
classical
concepts
exploitation
phalanx/guerrilla
strategies.
Instead,
we
propose
multivariate
analysis,
acknowledging
trade-offs
microscale
fungal
mycelia
exhibit.
Our
provide
novel
insights
about
well
an
additional
understanding
habitat
colonisation,
their
niche
partitioning
environment.
Environmental Science & Technology,
Journal Year:
2022,
Volume and Issue:
56(2), P. 711 - 731
Published: Jan. 5, 2022
Investigating
environmental
processes,
especially
those
occurring
in
soils,
calls
for
innovative
and
multidisciplinary
technologies
that
can
provide
insights
at
the
microscale.
The
heterogeneity,
opacity,
dynamics
make
soil
a
"black
box"
where
interactions
processes
are
elusive.
Recently,
microfluidics
has
emerged
as
powerful
research
platform
experimental
tool
which
create
artificial
micromodels,
enabling
exploring
on
chip.
Micro/nanofabricated
microfluidic
devices
mimic
some
of
key
features
with
highly
controlled
physical
chemical
microenvironments
scale
pores,
aggregates,
microbes.
combination
various
techniques
makes
an
integrated
approach
observation,
reaction,
analysis,
characterization.
In
this
review,
we
systematically
summarize
emerging
applications
platforms,
from
investigating
interfacial
microbial
to
analysis
high-throughput
screening.
We
highlight
how
used
new
into
mechanisms,
effects
microscale,
contribute
interrogation
systems
across
different
scales.
Critical
discussions
practical
limitations
platforms
perspectives
future
directions
summarized.
envisage
will
represent
technological
advances
toward
microscopic,
controllable,
situ
research.
