Microbiology Spectrum,
Journal Year:
2022,
Volume and Issue:
10(6)
Published: Oct. 26, 2022
The
Southwest
Indian
Ridge
(SWIR)
is
one
of
the
typical
representatives
deep-sea
ultraslow-spreading
ridges,
and
has
increasingly
become
a
hot
spot
studying
subsurface
geological
activities
mining
management.
However,
understanding
microbial
still
limited
on
active
hydrothermal
vent
chimneys
in
SWIR.
In
this
study,
samples
from
an
black
smoker
diffuse
located
Longqi
region
were
collected
for
deep
metagenomic
sequencing,
which
yielded
approximately
290
GB
clean
data
295
mid-to-high-quality
metagenome-assembled
genomes
(MAGs).
Sulfur
oxidation
conducted
by
variety
Gammaproteobacteria,
Alphaproteobacteria,
Campylobacterota
was
presumed
to
be
major
energy
source
chemosynthesis
vents.
Diverse
iron-related
microorganisms
recovered,
including
iron-oxidizing
Zetaproteobacteria,
iron-reducing
Environmental Microbiology,
Journal Year:
2020,
Volume and Issue:
23(6), P. 2834 - 2857
Published: Oct. 1, 2020
Dysoxic
marine
waters
(DMW,
<
1
μM
oxygen)
are
currently
expanding
in
volume
the
oceans,
which
has
biogeochemical,
ecological
and
societal
consequences
on
a
global
scale.
In
these
environments,
distinct
bacteria
drive
an
active
sulfur
cycle,
only
recently
been
recognized
for
open-ocean
DMW.
This
review
summarizes
current
knowledge
sulfur-cycling
bacteria.
Critical
bottlenecks
questions
future
research
specifically
addressed.
Sulfate-reducing
(SRB)
core
members
of
However,
their
roles
not
entirely
clear,
they
remain
largely
uncultured.
We
found
support
remarkable
diversity
taxonomic
novelty
by
mining
metagenome-assembled
genomes
from
Black
Sea
as
model
ecosystem.
highlight
recent
insights
into
metabolism
key
sulfur-oxidizing
SUP05
Sulfurimonas
bacteria,
discuss
probable
involvement
uncultivated
SAR324
BS-GSO2
oxidation.
Uncultivated
Marinimicrobia
with
presumed
organoheterotrophic
abundant
Like
SRB,
may
use
specific
molybdoenzymes
to
conserve
energy
oxidation,
reduction
or
disproportionation
cycle
intermediates
such
S
Limnology and Oceanography,
Journal Year:
2019,
Volume and Issue:
65(5), P. 1010 - 1027
Published: Nov. 12, 2019
Mercury
(Hg)
is
a
natural
and
widespread
trace
metal,
but
considered
priority
pollutant,
particularly
its
organic
form
methylmercury
(MMHg),
because
of
human's
exposure
to
MMHg
through
fish
consumption.
Pioneering
studies
showed
the
methylation
divalent
Hg
(HgII)
occur
under
oxygen-limited
conditions
depend
on
activity
anaerobic
microorganisms.
Recent
identified
hgcAB
gene
cluster
in
microorganisms
with
capacity
methylate
HgII
unveiled
much
wider
range
species
environmental
producing
than
previously
expected.
Here,
we
review
recent
knowledge
approaches
used
understand
HgII-methylation,
microbial
biodiversity
involved
these
processes,
highlight
current
limits
for
predicting
concentrations
environment.
The
available
data
unveil
fact
that
bio-physico-chemical
conundrum
which
efficiency
biological
appears
chiefly
nutrients
availability,
abundance
electron
acceptors
such
as
sulfate
or
iron,
composition
matter
well
structure
community.
An
increased
relationship
between
community
composition,
physico-chemical
conditions,
production,
demethylation
necessary
predict
variability
across
environments.
Microbiome,
Journal Year:
2020,
Volume and Issue:
8(1)
Published: June 30, 2020
Abstract
Background
Deep-sea
hydrothermal
vents
are
highly
productive
biodiversity
hotspots
in
the
deep
ocean
supported
by
chemosynthetic
microorganisms.
Prominent
features
of
these
systems
sulfide
chimneys
emanating
high-temperature
fluids.
While
several
studies
have
investigated
microbial
diversity
both
active
and
inactive
that
been
extinct
for
up
to
thousands
years,
little
is
known
about
ceased
activity
more
recently,
as
well
succession
occurring
during
transition
from
chimneys.
Results
Genome-resolved
metagenomics
was
applied
an
a
recently
(~
7
years)
chimney
9–10°
N
vent
field
on
East
Pacific
Rise.
Full-length
16S
rRNA
gene
total
173
high-quality
metagenome
assembled
genomes
(MAGs)
were
retrieved
comparative
analysis.
In
(L-vent),
sulfide-
and/or
hydrogen-oxidizing
Campylobacteria
Aquificae
with
potential
denitrification
identified
dominant
community
members
primary
producers,
fixing
carbon
through
reductive
tricarboxylic
acid
(rTCA)
cycle.
contrast,
microbiome
(M-vent)
largely
composed
heterotrophs
various
bacterial
phyla,
including
Delta
-/
Beta
Alphaproteobacteria
Bacteroidetes
.
Gammaproteobacteria
main
using
oxidation
metal
sulfides
iron
coupled
nitrate
reduction
fix
Calvin-Benson-Bassham
(CBB)
Further
analysis
revealed
phylogenetically
distinct
Nitrospirae
cluster
has
oxidize
minerals
oxygen
nitrite
reduction,
sulfate
might
serve
indicator
early
stages
after
venting
ceased.
Conclusions
This
study
sheds
light
composition,
metabolic
functions,
communities
inhabiting
deep-sea
Collectively,
life
span
could
be
described
proceed
“fluid-shaped”
newly
formed
actively
reductants
fluid
“mineral-shaped”
Remarkably,
appears
occur
within
first
few
which
stay
stable
years.
Frontiers in Microbiology,
Journal Year:
2021,
Volume and Issue:
12
Published: Aug. 2, 2021
Metagenomics
and
metatranscriptomics
are
powerful
methods
to
uncover
key
micro-organisms
processes
driving
biogeochemical
cycling
in
natural
ecosystems.
Databases
dedicated
depicting
pathways
(for
example,
metabolism
of
dimethylsulfoniopropionate
(DMSP),
which
is
an
abundant
organosulfur
compound)
from
metagenomic/metatranscriptomic
data
rarely
seen.
Additionally,
a
recognized
normalization
model
estimate
the
relative
abundance
environmental
importance
metagenomic
metatranscriptomic
has
not
been
organized
date.
These
limitations
impact
ability
accurately
relate
microbial-driven
differences
conditions.
Thus,
easy-to-use,
specialized
tool
that
infers
visually
compares
potential
for
processes,
including
DMSP
cycling,
urgently
required.
To
solve
these
issues,
we
developed
DiTing,
wrapper
infer
compare
among
set
given
or
reads
one
step,
based
on
Kyoto
Encyclopedia
Genes
Genomes
(KEGG)
manually
created
gene
database.
Accurate
specific
formulae
over
100
were
calculate
their
abundance.
Output
reports
detail
both
text
graphical
format.
DiTing
was
applied
simulated
resulted
consistent
genetic
features
benchmark
genomic
data.
Subsequently,
when
hydrothermal
vents
Tara
Ocean
project,
functional
profiles
predicted
by
correlated
with
condition
changes.
can
now
be
confidently
wider
datasets,
it
available
at
https://github.com/xuechunxu/DiTing
.
Frontiers in Marine Science,
Journal Year:
2019,
Volume and Issue:
6
Published: July 23, 2019
Polymetallic
seafloor
massive
sulfides
that
are
no
longer
hydrothermally
active
a
target
for
an
emergent
deep-sea
mining
industry,
but
the
paucity
of
ecological
studies
and
environmental
baselines
inactive
sulfide
ecosystems
makes
management
challenging.
The
current
state
knowledge
regarding
ecology
(microbiology
macrobiology)
is
reviewed
here
attention
given
to
considerations
where
lack
impedes
informed
policy
recommendations
decisions.
