Fungal Diversity,
Journal Year:
2018,
Volume and Issue:
90(1), P. 135 - 159
Published: May 1, 2018
High-throughput
sequencing
studies
generate
vast
amounts
of
taxonomic
data.
Evolutionary
ecological
hypotheses
the
recovered
taxa
and
Species
Hypotheses
are
difficult
to
test
due
problems
with
alignments
lack
a
phylogenetic
backbone.
We
propose
an
updated
phylum-
class-level
fungal
classification
accounting
for
monophyly
divergence
time
so
that
main
ranks
more
informative.
Based
on
phylogenies
estimates,
we
adopt
phylum
rank
Aphelidiomycota,
Basidiobolomycota,
Calcarisporiellomycota,
Glomeromycota,
Entomophthoromycota,
Entorrhizomycota,
Kickxellomycota,
Monoblepharomycota,
Mortierellomycota
Olpidiomycota.
accept
nine
subkingdoms
accommodate
these
18
phyla.
consider
kingdom
Nucleariae
(phyla
Nuclearida
Fonticulida)
as
sister
group
Fungi.
also
introduce
perl
script
newick-formatted
backbone
assigning
into
hierarchical
framework,
using
this
or
any
other
system.
provide
example
testing
evolutionary
based
global
soil
data
set.
Microbiome,
Journal Year:
2018,
Volume and Issue:
6(1)
Published: May 17, 2018
Taxonomic
classification
of
marker-gene
sequences
is
an
important
step
in
microbiome
analysis.
We
present
q2-feature-classifier
(
https://github.com/qiime2/q2-feature-classifier
),
a
QIIME
2
plugin
containing
several
novel
machine-learning
and
alignment-based
methods
for
taxonomy
classification.
evaluated
optimized
commonly
used
implemented
1
(RDP,
BLAST,
UCLUST,
SortMeRNA)
new
(a
scikit-learn
naive
Bayes
classifier,
consensus
based
on
VSEARCH,
BLAST+)
bacterial
16S
rRNA
fungal
ITS
amplicon
sequence
data.
The
naive-Bayes,
BLAST+-based,
VSEARCH-based
classifiers
meet
or
exceed
the
species-level
accuracy
other
designed
marker
gene
that
were
this
work.
These
evaluations,
19
mock
communities
error-free
simulations,
including
simulated
"novel"
sequences,
are
available
our
extensible
benchmarking
framework,
tax-credit
https://github.com/caporaso-lab/tax-credit-data
).
Our
results
illustrate
importance
parameter
tuning
optimizing
classifier
performance,
we
make
recommendations
regarding
choices
these
under
range
standard
operating
conditions.
both
free,
open-source,
BSD-licensed
packages
GitHub.
Science,
Journal Year:
2014,
Volume and Issue:
346(6213)
Published: Nov. 28, 2014
Fungi
play
major
roles
in
ecosystem
processes,
but
the
determinants
of
fungal
diversity
and
biogeographic
patterns
remain
poorly
understood.
Using
DNA
metabarcoding
data
from
hundreds
globally
distributed
soil
samples,
we
demonstrate
that
richness
is
decoupled
plant
diversity.
The
plant-to-fungus
ratio
declines
exponentially
toward
poles.
Climatic
factors,
followed
by
edaphic
spatial
variables,
constitute
best
predictors
community
composition
at
global
scale.
show
similar
latitudinal
gradients
to
other
organisms,
with
several
notable
exceptions.
These
findings
advance
our
understanding
permit
integration
fungi
into
a
general
macroecological
framework.
Nucleic Acids Research,
Journal Year:
2018,
Volume and Issue:
47(D1), P. D259 - D264
Published: Oct. 12, 2018
UNITE
(https://unite.ut.ee/)
is
a
web-based
database
and
sequence
management
environment
for
the
molecular
identification
of
fungi.
It
targets
formal
fungal
barcode-the
nuclear
ribosomal
internal
transcribed
spacer
(ITS)
region-and
offers
all
∼1
000
public
ITS
sequences
reference.
These
are
clustered
into
∼459
species
hypotheses
assigned
digital
object
identifiers
(DOIs)
to
promote
unambiguous
reference
across
studies.
In-house
third-party
curation
annotation
have
resulted
in
more
than
275
improvements
data
over
past
15
years.
serves
as
provider
range
metabarcoding
software
pipelines
regularly
exchanges
with
major
databases
other
community
resources.
Recent
include
redesigned
handling
unclassifiable
hypotheses,
integration
taxonomic
backbone
Global
Biodiversity
Information
Facility,
support
an
unlimited
number
parallel
classification
systems.
Microbiology and Molecular Biology Reviews,
Journal Year:
2015,
Volume and Issue:
79(3), P. 293 - 320
Published: July 2, 2015
All
plants
are
inhabited
internally
by
diverse
microbial
communities
comprising
bacterial,
archaeal,
fungal,
and
protistic
taxa.
These
microorganisms
showing
endophytic
lifestyles
play
crucial
roles
in
plant
development,
growth,
fitness,
diversification.
The
increasing
awareness
of
information
on
endophytes
provide
insight
into
the
complexity
microbiome.
nature
plant-endophyte
interactions
ranges
from
mutualism
to
pathogenicity.
This
depends
a
set
abiotic
biotic
factors,
including
genotypes
microbes,
environmental
conditions,
dynamic
network
within
biome.
In
this
review,
we
address
concept
endophytism,
considering
latest
insights
evolution,
ecosystem
functioning,
multipartite
interactions.
New Phytologist,
Journal Year:
2015,
Volume and Issue:
205(4), P. 1406 - 1423
Published: Feb. 2, 2015
Summary
Almost
all
land
plants
form
symbiotic
associations
with
mycorrhizal
fungi.
These
below‐ground
fungi
play
a
key
role
in
terrestrial
ecosystems
as
they
regulate
nutrient
and
carbon
cycles,
influence
soil
structure
ecosystem
multifunctionality.
Up
to
80%
of
plant
N
P
is
provided
by
many
species
depend
on
these
symbionts
for
growth
survival.
Estimates
suggest
that
there
are
c
.
50
000
fungal
250
species.
The
development
high‐throughput
molecular
tools
has
helped
us
better
understand
the
biology,
evolution,
biodiversity
associations.
Nuclear
genome
assemblies
gene
annotations
33
now
available
providing
fascinating
opportunities
deepen
our
understanding
lifestyle,
metabolic
capabilities
symbionts,
dialogue
between
evolutionary
adaptations
across
range
Large‐scale
surveys
have
novel
insights
into
diversity,
spatial
temporal
dynamics
communities.
At
ecological
level,
network
theory
makes
it
possible
analyze
interactions
plant–fungal
partners
complex
underground
multi‐species
networks.
Our
analysis
suggests
nestedness,
modularity
specificity
networks
vary
type.
Mechanistic
models
explaining
partner
choice,
resource
exchange,
coevolution
been
developed
being
tested.
This
review
ends
major
frontiers
further
research.
Contents
1406
I.
Introduction
1407
II.
Biodiversity
1408
III.
Carbon
cycling
multifunctionality
1410
IV.
Mycorrhizal
1411
V.
Evolution
selection
1413
VI.
genomics
crosstalk
1416
VII.
Conclusions
future
research
1418
Acknowledgements
References
1419
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2016,
Volume and Issue:
unknown
Published: Oct. 15, 2016
Abstract
Amplicon
sequencing
of
tags
such
as
16S
and
ITS
ribosomal
RNA
is
a
popular
method
for
investigating
microbial
populations.
In
experiments,
sequence
errors
caused
by
PCR
are
difficult
to
distinguish
from
true
biological
variation.
I
describe
UNOISE2,
an
updated
version
the
UNOISE
algorithm
denoising
(error-correcting)
Illumina
amplicon
reads
show
that
it
has
comparable
or
better
accuracy
than
DADA2.
Nature Communications,
Journal Year:
2018,
Volume and Issue:
9(1)
Published: July 10, 2018
Abstract
By
changing
soil
properties,
plants
can
modify
their
growth
environment.
Although
the
microbiota
is
known
to
play
a
key
role
in
resulting
plant-soil
feedbacks,
proximal
mechanisms
underlying
this
phenomenon
remain
unknown.
We
found
that
benzoxazinoids,
class
of
defensive
secondary
metabolites
are
released
by
roots
cereals
such
as
wheat
and
maize,
alter
root-associated
fungal
bacterial
communities,
decrease
plant
growth,
increase
jasmonate
signaling
defenses,
suppress
herbivore
performance
next
generation.
Complementation
experiments
demonstrate
benzoxazinoid
breakdown
product
6-methoxy-benzoxazolin-2-one
(MBOA),
which
accumulates
during
conditioning
phase,
both
sufficient
necessary
trigger
observed
phenotypic
changes.
Sterilization,
profiling
complementation
reveal
MBOA
acts
indirectly
altering
microbiota.
Our
results
mechanism
determine
composition
rhizosphere
microbiota,
plant-herbivore
interactions
