bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Oct. 23, 2024
Abstract
Identification
of
both
prokaryotic
and
eukaryotic
microorganisms
in
environmental
samples
is
currently
challenged
by
either
the
burden
additional
sequencing
required
to
obtain
16S
18S
rRNA
sequences
or
introduction
multiple
biases
induced
use
“universal”
primers.
Organellar
are
automatically
amplified
sequenced
along
with
prokaryote
rRNA,
may
provide
an
alternative
method
identify
microorganisms.
CABO-16S
combines
bacterial
archaeal
from
SILVA
database
plastids
other
organelles
PR2
enable
identification
all
sequences.
Comparison
138.2
results
equivalent
taxonomic
classification
mock
communities
increased
diverse
samples.
In
particular,
phototrophic
eukaryotes
shallow
seagrass
environments,
marine
waters,
lake
waters
was
increased.
also
provides
framework
add
curated
datasets
specialized
for
further
clades
which
not
included
databases.
Addition
obtained
Sanger
methane
seep
sediments
polyphyletic
SEEP-SRB1
clade
resulted
differentiation
syntrophic
non-syntrophic
hydrothermal
vent
sediments.
Such
additions
simplify
analysis
contributing
anaerobic
oxidation
methane,
highlight
potential
benefit
amending
existing
training
sets
when
studying
extreme
unique
environments
underrepresented
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: March 20, 2024
Abstract
Extracellular
electron
transfer
(EET)
via
microbial
nanowires
drives
globally-important
environmental
processes
and
biotechnological
applications
for
bioenergy,
bioremediation,
bioelectronics.
Due
to
highly-redundant
complex
EET
pathways,
it
is
unclear
how
microbes
wire
electrons
rapidly
(>10
6
s
−1
)
from
the
inner-membrane
through
outer-surface
directly
an
external
environment
despite
a
crowded
periplasm
slow
(<10
5
diffusion
among
periplasmic
cytochromes.
Here,
we
show
that
Geobacter
sulfurreducens
cytochromes
PpcABCDE
inject
into
OmcS
by
binding
transiently
with
differing
efficiencies,
least-abundant
cytochrome
(PpcC)
showing
highest
efficiency.
Remarkably,
this
defined
nanowire-charging
pathway
evolutionarily
conserved
in
phylogenetically-diverse
bacteria
capable
of
EET.
heme
reduction
potentials
are
within
200
mV
each
other,
midpoint
82
mV-higher
than
reported
previously.
This
could
explain
efficient
over
micrometres
at
ultrafast
(<200
fs)
rates
negligible
energy
loss.
Engineering
minimal
may
yield
chassis
improved
performance.
Applied Microbiology and Biotechnology,
Journal Year:
2024,
Volume and Issue:
108(1)
Published: July 4, 2024
Abstract
Co-aggregation
of
anaerobic
microorganisms
into
suspended
microbial
biofilms
(aggregates)
serves
ecological
and
biotechnological
functions.
Tightly
packed
aggregates
metabolically
interdependent
bacteria
archaea
play
key
roles
in
cycling
carbon
nitrogen.
Additionally,
applications,
such
as
wastewater
treatment,
provide
a
complete
metabolic
network
to
convert
complex
organic
material.
Currently,
experimental
data
explaining
the
mechanisms
behind
co-aggregation
anoxic
environments
is
scarce
scattered
across
literature.
To
what
extent
does
this
process
resemble
aerobic
environments?
Does
limited
availability
terminal
electron
acceptors
drive
mutualistic
relationships,
contrary
commensal
relationships
observed
oxygen-rich
And
do
co-aggregating
archaea,
which
depend
on
each
other
harvest
bare
minimum
Gibbs
energy
from
energy-poor
substrates,
use
similar
cellular
those
used
by
pathogenic
that
form
biofilms?
Here,
we
an
overview
current
understanding
why
how
mixed
communities
co-aggregate
discuss
potential
future
scientific
advancements
could
improve
study
aggregates.
Key
points
•
Metabolic
dependency
promotes
aggregation
Flagella,
pili,
adhesins
role
formation
Cyclic
di-GMP/AMP
signaling
may
trigger
polysaccharides
production
anaerobes
Current Opinion in Microbiology,
Journal Year:
2024,
Volume and Issue:
79, P. 102486 - 102486
Published: May 10, 2024
This
review
synthesizes
recent
discoveries
of
novel
archaea
clades
capable
oxidizing
higher
alkanes,
from
volatile
ones
like
ethane
to
longer-chain
alkanes
hexadecane.
These
archaea,
termed
anaerobic
multicarbon
alkane-oxidizing
(ANKA),
initiate
alkane
oxidation
using
alkyl-coenzyme
M
reductases,
enzymes
similar
the
methyl-coenzyme
reductases
methanogenic
and
methanotrophic
(ANME).
The
polyphyletic
group
(ALOX),
encompassing
ANME
ANKA,
harbors
increasingly
complex
degradation
pathways,
correlated
with
chain
length.
We
discuss
evolutionary
trajectory
these
pathways
emphasizing
metabolic
innovations
acquisition
modules
via
lateral
gene
transfer.
Additionally,
we
explore
mechanisms
by
which
couple
reduction
electron
acceptors,
including
transfer
partner
sulfate-reducing
bacteria
(SRB).
phylogenetic
functional
constraints
that
shape
ALOX–SRB
associations
are
also
discussed.
conclude
highlighting
research
needs
in
this
emerging
field
its
potential
applications
biotechnology.
BMC Microbiology,
Journal Year:
2025,
Volume and Issue:
25(1)
Published: April 23, 2025
Sulfate-reducing
bacteria
(SRB)
are
a
major
cause
of
microbially-induced
corrosion
(MIC)
and
souring
(MIS),
leading
to
significant
challenges
in
industries
like
oil
recovery
wastewater
treatment.
Due
SRB's
resistance
antimicrobial
agents,
bacteriophage
(phage)
therapy
offers
promising
alternative
for
SRB
control.
In
this
study,
novel
lytic
phage,
SRB7757,
targeting
Desulfovibrio
vulgaris,
was
isolated
from
sewage.
SRB7757
inhibited
sulfide
production
by
92.3%
within
24
h
significantly
reduced
on
metal
specimens
after
28
days,
highlighting
its
potential
controlling
MIC
MIS.
Genome
analysis
revealed
has
genome
size
142,573
bp,
217
ORFs,
6
tRNAs,
belongs
the
Chaseviridae
family.
exhibits
latent
period
4
h,
burst
~
100
PFU/cell,
is
stable
between
°C
60
across
pH
range
2.0-12.0.
Two
predicted
enzymes
demonstrated
higher
inactivation
biofilm
removal
rates.
Journal of Molecular Chemistry.,
Journal Year:
2024,
Volume and Issue:
4(2)
Published: April 29, 2024
Coenzyme
F420
is
one
of
the
ancient
and
rare
coenzymes.
The
unique
electrochemical
properties
are
compared
with
ubiquitous
flavin
coenzymes
FMN
(flavin
mononucleotide),
FAD
adenine
dinucleotide),
nicotinamide
coenzyme
NADP+
(nicotinamide
dinucleotide
phosphate).
7,8-didemethyl-8-hydroxy-5-deazaflavin
core
structurally
biosynthetically
related
to
FAD,
but
chemical
reactions
similar
NADP+.
role
cofactors
in
methanogenesis
methanotrophic
methane
short
alkane
oxidations
widely
increasing
understand
mechanism
global
warming
climate
change.
URN:NBN:sciencein.jmc.2024.696
Frontiers in Microbiology,
Journal Year:
2025,
Volume and Issue:
16
Published: Feb. 12, 2025
Soil
microbial
communities
are
integral
to
almost
all
terrestrial
biogeochemical
cycles,
which
essential
coastal
wetland
functioning.
However,
how
soil
bacterial
community
assembly,
composition,
and
structure
respond
native
non-native
plant
invasions
in
wetlands
remains
unclear.
In
this
study
of
the
Yellow
River
Delta
China,
diversity
associated
with
four
species
(
Phragmites
australis
,
Spartina
alterniflora
Suaeda
salsa
Tamarix
chinensis
)
depths
(0–10
cm,
10–20
20–30
30–40
cm)
were
characterized
using
high-throughput
sequencing.
Plant
identity,
as
well
environmental
factors,
rather
than
depth,
was
found
play
predominant
roles
shaping
communities.
S.
invasion
altered
increased
diversity.
-associated
enriched
sulfate-reducing
bacteria
such
Desulfurivibrio
Desulfuromonas
.
comparison,
both
SEEP-SRB1
sulfate-oxidizing
Sulfurimonas
),
maintained
a
dynamic
balance
local
sulfur-cycle,
thereby
enhanced
growth.
addition,
stochastic
processes
dominated
assembly
species,
but
most
important
for
community.
The
also
showed
stronger
interactions
more
extensive
connections
among
taxa;
co-occurrence
network
had
greatest
average
clustering
coefficient,
degree,
modularity,
number
links
nodes,
lowest
path
length.
Altogether,
individual
distinct
effects
on
structure,
invasive
having
strongest
impact.
These
results
provide
insights
into
ecology
inform
management
strategies
restoration.
