ABSTRACT
Microbial
communities
typically
contain
many
rare
taxa
that
make
up
the
majority
of
observed
membership,
yet
contribution
this
microbial
“rare
biosphere”
to
community
dynamics
is
unclear.
Using
16S
rRNA
amplicon
sequencing
3,237
samples
from
42
time
series
nine
different
ecosystems
(air;
marine;
lake;
stream;
adult
human
skin,
tongue,
and
gut;
infant
brewery
wastewater
treatment),
we
introduce
a
new
method
detect
occasionally
become
very
abundant
(conditionally
[CRT])
then
quantify
their
contributions
temporal
shifts
in
structure.
We
discovered
CRT
made
1.5
28%
represented
broad
diversity
bacterial
archaeal
lineages,
explained
large
amounts
dissimilarity
(i.e.,
97%
Bray-Curtis
dissimilarity).
Most
were
detected
at
multiple
points,
though
also
identified
“one-hit
wonder”
only
one
point.
case
study
temperate
lake,
gained
additional
insights
into
ecology
by
comparing
routine
disturbance
events.
Our
results
reveal
contribute
greater
amount
than
apparent
low
proportional
abundances.
This
observation
was
true
across
wide
range
ecosystems,
indicating
these
are
essential
for
understanding
changes
over
time.
IMPORTANCE
processes
foundations
ecosystems.
The
ecological
roles
microorganisms
largely
unknown,
but
it
thought
they
stability
acting
as
reservoir
can
rapidly
respond
environmental
changes.
investigated
occurrence
more
prominent
(“conditionally
rare”).
quantified
conditionally
variety
not
present
all
examples,
contributed
disproportionately
when
most
abundant.
result
indicates
an
important
general
role
within
communities.
Science,
Journal Year:
2016,
Volume and Issue:
353(6305), P. 1272 - 1277
Published: Sept. 15, 2016
Microbial
metabolism
powers
biogeochemical
cycling
in
Earth’s
ecosystems.
The
taxonomic
composition
of
microbial
communities
varies
substantially
between
environments,
but
the
ecological
causes
this
variation
remain
largely
unknown.
We
analyzed
and
functional
community
profiles
to
determine
factors
that
shape
marine
bacterial
archaeal
across
global
ocean.
By
classifying
>30,000
microorganisms
into
metabolic
groups,
we
were
able
disentangle
from
variation.
find
environmental
conditions
strongly
influence
distribution
groups
by
shaping
niches,
only
weakly
within
individual
groups.
Hence,
structure
constitute
complementary
roughly
independent
“axes
variation”
shaped
markedly
different
processes.
Science,
Journal Year:
2015,
Volume and Issue:
348(6237)
Published: May 22, 2015
Microbes
are
dominant
drivers
of
biogeochemical
processes,
yet
drawing
a
global
picture
functional
diversity,
microbial
community
structure,
and
their
ecological
determinants
remains
grand
challenge.
We
analyzed
7.2
terabases
metagenomic
data
from
243
Tara
Oceans
samples
68
locations
in
epipelagic
mesopelagic
waters
across
the
globe
to
generate
an
ocean
reference
gene
catalog
with
>40
million
nonredundant,
mostly
novel
sequences
viruses,
prokaryotes,
picoeukaryotes.
Using
139
prokaryote-enriched
samples,
containing
>35,000
species,
we
show
vertical
stratification
composition
driven
by
temperature
rather
than
other
environmental
factors
or
geography.
identify
core
functionality
reveal
that
>73%
its
abundance
is
shared
human
gut
microbiome
despite
physicochemical
differences
between
these
two
ecosystems.
BMC Bioinformatics,
Journal Year:
2012,
Volume and Issue:
13(1)
Published: May 30, 2012
Understanding
the
interaction
among
different
species
within
a
community
and
their
responses
to
environmental
changes
is
central
goal
in
ecology.
However,
defining
network
structure
microbial
very
challenging
due
extremely
high
diversity
as-yet
uncultivated
status.
Although
recent
advance
of
metagenomic
technologies,
such
as
throughout
sequencing
functional
gene
arrays,
provide
revolutionary
tools
for
analyzing
structure,
it
still
difficult
examine
interactions
based
on
high-throughput
metagenomics
data.
Here,
we
describe
novel
mathematical
bioinformatics
framework
construct
ecological
association
networks
named
molecular
(MENs)
through
Random
Matrix
Theory
(RMT)-based
methods.
Compared
other
construction
methods,
this
approach
remarkable
that
automatically
defined
robust
noise,
thus
providing
excellent
solutions
several
common
issues
associated
with
We
applied
determine
communities
subjected
long-term
experimental
warming
pyrosequencing
data
16
S
rRNA
genes.
showed
constructed
MENs
under
both
unwarming
conditions
exhibited
topological
features
scale
free,
small
world
modularity,
which
were
consistent
previously
described
networks.
Eigengene
analysis
indicated
eigengenes
represented
module
profiles
relatively
well.
In
consistency
many
studies,
major
traits
including
temperature
soil
pH
found
be
important
determining
examined.
To
facilitate
its
application
by
scientific
community,
all
these
methods
statistical
have
been
integrated
into
comprehensive
Molecular
Ecological
Network
Analysis
Pipeline
(MENAP),
open-accessible
now
(
http://ieg2.ou.edu/MENA
).
The
RMT-based
provides
powerful
elucidate
changes,
are
fundamentally
research
ecology
microbiology.
Microbiology and Molecular Biology Reviews,
Journal Year:
2013,
Volume and Issue:
77(3), P. 342 - 356
Published: Sept. 1, 2013
Recent
research
has
expanded
our
understanding
of
microbial
community
assembly.
However,
the
field
ecology
is
inaccessible
to
many
ecologists
because
inconsistent
and
often
confusing
terminology
as
well
unnecessarily
polarizing
debates.
Thus,
we
review
recent
literature
on
assembly,
using
framework
Vellend
(Q.
Rev.
Biol.
85:183-206,
2010)
in
an
effort
synthesize
unify
these
contributions.
We
begin
by
discussing
patterns
biogeography
then
describe
four
basic
processes
(diversification,
dispersal,
selection,
drift)
that
contribute
also
discuss
different
combinations
where
when
they
may
be
most
important
for
shaping
communities.
The
spatial
temporal
scales
assembly
are
discussed
relation
processes.
Throughout
this
paper,
highlight
differences
between
microbes
macroorganisms
generate
hypotheses
describing
how
end
implications
ecosystem
function
biodiversity.
Frontiers in Microbiology,
Journal Year:
2012,
Volume and Issue:
3
Published: Jan. 1, 2012
Microbial
communities
are
at
the
heart
of
all
ecosystems,
and
yet
microbial
community
behavior
in
disturbed
environments
remains
difficult
to
measure
predict.
Understanding
drivers
stability,
including
resistance
(insensitivity
disturbance)
resilience
(the
rate
recovery
after
is
important
for
predicting
response
disturbance.
Here,
we
provide
an
overview
concepts
stability
that
relevant
communities.
First,
highlight
insights
from
ecology
useful
defining
measuring
stability.
To
determine
whether
general
disturbance
responses
exist
communities,
next
examine
representative
studies
literature
investigated
press
(long-term)
pulse
(short-term)
disturbances
a
variety
habitats.
Then
discuss
biological
features
individual
microorganisms,
populations,
may
govern
overall
We
conclude
with
thoughts
about
unique
systems
perspectives
-
informed
by
meta-omics
data
New Phytologist,
Journal Year:
2010,
Volume and Issue:
188(1), P. 223 - 241
Published: June 16, 2010
•
Here,
we
describe
a
new
database,
MaarjAM,
that
summarizes
publicly
available
Glomeromycota
DNA
sequence
data
and
associated
metadata.
The
goal
of
the
database
is
to
facilitate
description
distribution
richness
patterns
in
this
group
fungi.
Small
subunit
(SSU)
rRNA
gene
sequences
metadata
were
collated
from
all
suitable
taxonomic
ecological
publications.
These
have
been
made
accessible
an
open-access
(http://maarjam.botany.ut.ee).
Two
hundred
eighty-two
SSU
virtual
taxa
(VT)
described
based
on
comprehensive
phylogenetic
analysis
sequences.
Two-thirds
VT
showed
limited
ranges,
occurring
single
current
or
historic
continents
climatic
zones.
Those
with
taxonomically
wide
range
host
plants
also
tended
geographical
distribution,
vice
versa.
No
relationships
detected
between
latitude,
elevation
vascular
plant
richness.
molecular
diversity
suggest
ranges
most
positive
relationship
width
taxon's
its
range.
Inconsistencies
traditional
taxonomy
Glomeromycota,
shortage
major
ecosystems,
are
highlighted.