The ISME Journal,
Journal Year:
2021,
Volume and Issue:
16(1), P. 272 - 283
Published: July 27, 2021
Abstract
Nitrification,
the
oxidation
of
ammonia
to
nitrate,
is
an
essential
process
in
biogeochemical
nitrogen
cycle.
The
first
step
nitrification,
oxidation,
performed
by
three,
often
co-occurring
guilds
chemolithoautotrophs:
ammonia-oxidizing
bacteria
(AOB),
archaea
(AOA),
and
complete
oxidizers
(comammox).
Substrate
kinetics
are
considered
be
a
major
niche-differentiating
factor
between
these
guilds,
but
few
AOA
strains
have
been
kinetically
characterized.
Here,
kinetic
properties
12
representing
all
cultivated
phylogenetic
lineages
were
determined
using
microrespirometry.
Members
genus
Nitrosocosmicus
lowest
affinity
for
both
total
ammonium
any
characterized
AOA,
values
similar
previously
affinities
AOB.
This
contrasts
previous
assumptions
that
possess
much
higher
substrate
than
their
comammox
or
AOB
counterparts.
correlated
with
cell
surface
area
volume
ratios.
In
addition,
measurements
across
range
pH
supports
hypothesis
that—like
AOB—ammonia
not
monooxygenase
enzyme
comammox.
Together,
data
will
facilitate
predictions
interpretation
oxidizer
community
structures
provide
robust
basis
establishing
testable
hypotheses
on
competition
AOB,
The ISME Journal,
Journal Year:
2021,
Volume and Issue:
15(8), P. 2366 - 2378
Published: March 1, 2021
Abstract
In
marine
ecosystems,
viruses
exert
control
on
the
composition
and
metabolism
of
microbial
communities,
influencing
overall
biogeochemical
cycling.
Deep
sea
sediments
associated
with
cold
seeps
are
known
to
host
taxonomically
diverse
but
little
is
about
infecting
these
microorganisms.
Here,
we
probed
metagenomes
from
seven
geographically
across
global
oceans
assess
viral
diversity,
virus–host
interaction,
virus-encoded
auxiliary
metabolic
genes
(AMGs).
Gene-sharing
network
comparisons
inhabiting
other
ecosystems
reveal
that
seep
harbour
considerable
unexplored
diversity.
Most
display
high
degrees
endemism
fluid
flux
being
one
main
drivers
community
composition.
silico
predictions
linked
14.2%
populations
many
belonging
poorly
understood
candidate
bacterial
archaeal
phyla.
Lysis
was
predicted
be
a
predominant
lifestyle
based
lineage-specific
virus/host
abundance
ratios.
Metabolic
prokaryotic
genomes
AMGs
suggest
influence
hydrocarbon
biodegradation
at
seeps,
as
well
carbon,
sulfur
nitrogen
cycling
via
virus-induced
mortality
and/or
augmentation.
Overall,
findings
diversity
biogeography
indicate
how
may
manipulate
ecology
biogeochemistry.
Genome biology,
Journal Year:
2021,
Volume and Issue:
22(1)
Published: June 13, 2021
Abstract
Genomes
are
critical
units
in
microbiology,
yet
ascertaining
quality
prokaryotic
genome
assemblies
remains
a
formidable
challenge.
We
present
GUNC
(the
Genome
UNClutterer),
tool
that
accurately
detects
and
quantifies
chimerism
based
on
the
lineage
homogeneity
of
individual
contigs
using
genome’s
full
complement
genes.
complements
existing
approaches
by
targeting
previously
underdetected
types
contamination:
we
conservatively
estimate
5.7%
genomes
GenBank,
5.2%
RefSeq,
15–30%
pre-filtered
“high-quality”
metagenome-assembled
recent
studies
undetected
chimeras.
provides
fast
robust
to
substantially
improve
quality.
Nucleic Acids Research,
Journal Year:
2021,
Volume and Issue:
49(19), P. 10868 - 10878
Published: Sept. 18, 2021
Abstract
To
provide
protection
against
viral
infection
and
limit
the
uptake
of
mobile
genetic
elements,
bacteria
archaea
have
evolved
many
diverse
defence
systems.
The
discovery
application
CRISPR-Cas
adaptive
immune
systems
has
spurred
recent
interest
in
identification
classification
new
types
Many
recently
been
reported
but
there
is
a
lack
accessible
tools
available
to
identify
homologs
these
different
genomes.
Here,
we
report
Prokaryotic
Antiviral
Defence
LOCator
(PADLOC),
flexible
scalable
open-source
tool
for
system
identification.
With
PADLOC,
genes
are
identified
using
HMM-based
homologue
searches,
followed
by
validation
completeness
gene
presence/absence
synteny
criteria
specified
customisable
classifications.
We
show
that
PADLOC
identifies
with
high
accuracy
sensitivity.
Our
modular
approach
organising
HMMs
classifications
allows
additional
be
easily
integrated
into
database.
demonstrate
biological
questions,
used
six
subtypes
known
putative
novel
comprised
helicase,
methylase
ATPase.
as
standalone
package
(https://github.com/padlocbio/padloc)
webserver
(https://padloc.otago.ac.nz).
The ISME Journal,
Journal Year:
2021,
Volume and Issue:
16(1), P. 272 - 283
Published: July 27, 2021
Abstract
Nitrification,
the
oxidation
of
ammonia
to
nitrate,
is
an
essential
process
in
biogeochemical
nitrogen
cycle.
The
first
step
nitrification,
oxidation,
performed
by
three,
often
co-occurring
guilds
chemolithoautotrophs:
ammonia-oxidizing
bacteria
(AOB),
archaea
(AOA),
and
complete
oxidizers
(comammox).
Substrate
kinetics
are
considered
be
a
major
niche-differentiating
factor
between
these
guilds,
but
few
AOA
strains
have
been
kinetically
characterized.
Here,
kinetic
properties
12
representing
all
cultivated
phylogenetic
lineages
were
determined
using
microrespirometry.
Members
genus
Nitrosocosmicus
lowest
affinity
for
both
total
ammonium
any
characterized
AOA,
values
similar
previously
affinities
AOB.
This
contrasts
previous
assumptions
that
possess
much
higher
substrate
than
their
comammox
or
AOB
counterparts.
correlated
with
cell
surface
area
volume
ratios.
In
addition,
measurements
across
range
pH
supports
hypothesis
that—like
AOB—ammonia
not
monooxygenase
enzyme
comammox.
Together,
data
will
facilitate
predictions
interpretation
oxidizer
community
structures
provide
robust
basis
establishing
testable
hypotheses
on
competition
AOB,
