The ISME Journal,
Год журнала:
2020,
Номер
15(3), С. 848 - 861
Опубликована: Ноя. 4, 2020
Abstract
Asgard
is
a
recently
discovered
archaeal
superphylum,
closely
linked
to
the
emergence
of
eukaryotes.
Among
archaea,
Lokiarchaeota
are
abundant
in
marine
sediments,
but
their
situ
activities
largely
unknown
except
for
Candidatus
‘Prometheoarchaeum
syntrophicum’.
Here,
we
tracked
activity
incubations
with
Helgoland
mud
area
sediments
(North
Sea)
by
stable
isotope
probing
(SIP)
organic
polymers,
13C-labelled
inorganic
carbon,
fermentation
intermediates
and
proteins.
Within
active
detected
members
class
Loki-3,
which
appeared
mixotrophically
participate
degradation
lignin
humic
acids
while
assimilating
CO2,
or
heterotrophically
used
lactate.
In
contrast,
Loki-2
utilized
protein
degraded
bacterial
biomass
formed
incubations.
Metagenomic
analysis
revealed
pathways
lactate
degradation,
involvement
aromatic
compound
less
globally
distributed
instead
rely
on
degradation.
We
conclude
that
Lokiarchaeotal
subgroups
vary
metabolic
capabilities
despite
overlaps
genomic
equipment,
suggest
these
occupy
different
ecologic
niches
sediments.
Nature,
Год журнала:
2022,
Номер
613(7943), С. 332 - 339
Опубликована: Дек. 21, 2022
Abstract
Asgard
archaea
are
considered
to
be
the
closest
known
relatives
of
eukaryotes.
Their
genomes
contain
hundreds
eukaryotic
signature
proteins
(ESPs),
which
inspired
hypotheses
on
evolution
cell
1–3
.
A
role
ESPs
in
formation
an
elaborate
cytoskeleton
and
complex
cellular
structures
has
been
postulated
4–6
,
but
never
visualized.
Here
we
describe
a
highly
enriched
culture
‘
Candidatus
Lokiarchaeum
ossiferum’,
member
phylum,
thrives
anaerobically
at
20
°C
organic
carbon
sources.
It
divides
every
7–14
days,
reaches
densities
up
5
×
10
7
cells
per
ml
significantly
larger
genome
compared
with
single
previously
cultivated
strain
represent
5%
its
protein-coding
genes,
including
four
actin
homologues.
We
imaged
enrichment
using
cryo-electron
tomography,
identifying
Ca
L.
ossiferum’
basis
characteristic
expansion
segments
their
ribosomes.
Cells
exhibited
coccoid
bodies
network
branched
protrusions
frequent
constrictions.
The
envelope
consists
membrane
surface
structures.
long-range
extends
throughout
bodies,
twisted
double-stranded
architecture
filaments
is
consistent
F-actin.
Immunostaining
indicates
that
comprise
Lokiactin—one
most
conserved
archaea.
propose
actin-based
predated
emergence
first
eukaryotes
was
crucial
feature
phylum
by
scaffolding
Methanogens
are
crucial
to
global
methane
budget
and
carbon
cycling.
from
the
phylum
Euryarchaeota
currently
classified
into
one
class
seven
orders,
including
two
novel
methanogen
taxa,
Methanofastidiosa
Methanomassiliicoccales.
The
relative
importance
of
methanogens
production
in
natural
environment
is
poorly
understood.Here,
we
used
a
combined
metagenomic
metatranscriptomic
approach
investigate
metabolic
activity
mangrove
sediments
Futian
Nature
Reserve,
Shenzhen.
We
obtained
13
metagenome-assembled
genomes
(MAGs)
representing
(Methanofastidiosa)
five
orders
(Methanomassiliicoccales,
Methanomicrobiales,
Methanobacteriales,
Methanocellales,
Methanosarcinales)
methanogens,
methanogens.
Comprehensive
annotation
indicated
presence
an
H2-dependent
methylotrophic
methanogenesis
pathway
Based
on
functional
gene
analysis,
hydrogenotrophic
dominant
pathways
sediments.
MAG
mapping
revealed
that
Methanomicrobiales
were
most
abundant
Methanomassiliicoccales
active
analyzed
sediment
profile,
suggesting
their
important
roles
production.Partial
or
near-complete
Methanomassiliicoccales,
environments
recovered
here
for
first
time.
presented
findings
highlight
ecological
complement
knowledge
how
produced
ecosystem.
This
study
implies
play
vital
role
cycle.
Video
Abstract.
Nature Microbiology,
Год журнала:
2022,
Номер
7(2), С. 200 - 212
Опубликована: Янв. 13, 2022
Eukaryotic
genomes
are
known
to
have
garnered
innovations
from
both
archaeal
and
bacterial
domains
but
the
sequence
of
events
that
led
complex
gene
repertoire
eukaryotes
is
largely
unresolved.
Here,
through
enrichment
hydrothermal
vent
microorganisms,
we
recovered
two
circularized
Heimdallarchaeum
species
belong
an
Asgard
archaea
clade
phylogenetically
closest
eukaryotes.
These
reveal
diverse
mobile
elements,
including
integrative
viral
genome
bidirectionally
replicates
in
a
circular
form
aloposons,
transposons
encode
5,000
amino
acid-sized
proteins
Otus
Ephialtes.
Heimdallaechaeal
elements
various
genes
bacteria
bacteriophages,
likely
playing
role
shuffling
functions
across
domains.
The
number
archaea-
bacteria-related
follow
strikingly
different
scaling
laws
archaea,
exhibiting
size-dependent
ratio
functional
division
resembling
bacteria-
archaea-derived
Bacterial
import
has
thus
been
continuous
process
unaltered
by
eukaryogenesis
scaled
up
expansion.
Our
data
further
highlight
importance
viewing
pan-Asgard
context,
which
proposal
conceptual
framework,
is,
Heimdall
nucleation-decentralized
innovation-hierarchical
model
accounts
for
emergence
eukaryotic
complexity.
The ISME Journal,
Год журнала:
2021,
Номер
15(6), С. 1826 - 1843
Опубликована: Янв. 15, 2021
Asgard
archaea
are
widely
distributed
in
anaerobic
environments.
Previous
studies
revealed
the
potential
capability
of
to
utilize
various
organic
substrates
including
proteins,
carbohydrates,
fatty
acids,
amino
acids
and
hydrocarbons,
suggesting
that
play
an
important
role
sediment
carbon
cycling.
Here,
we
describe
a
previously
unrecognized
archaeal
phylum,
Hermodarchaeota,
affiliated
with
superphylum.
The
genomes
these
were
recovered
from
metagenomes
generated
mangrove
sediments,
found
encode
alkyl/benzyl-succinate
synthases
their
activating
enzymes
similar
those
identified
alkane-degrading
sulfate-reducing
bacteria.
Hermodarchaeota
also
potentially
involved
alkyl-coenzyme
A
benzoyl-coenzyme
oxidation,
Wood-Ljungdahl
pathway
nitrate
reduction.
These
results
indicate
members
this
phylum
have
strictly
anaerobically
degrade
alkanes
aromatic
compounds,
coupling
reduction
nitrate.
By
screening
Sequence
Read
Archive,
additional
genes
encoding
16S
rRNA
analogous
metagenomic
datasets
wide
range
marine
freshwater
sediments.
findings
suggest
capable
degrading
aromatics
via
formation
alkyl/benzyl-substituted
succinates
ubiquitous
Annual Review of Microbiology,
Год журнала:
2021,
Номер
75(1), С. 359 - 381
Опубликована: Авг. 5, 2021
The
discovery
of
the
Archaea
is
a
major
scientific
hallmark
twentieth
century.
Since
then,
important
features
their
cell
biology,
physiology,
ecology,
and
diversity
have
been
revealed.
Over
course
some
40
years,
known
archaea
has
expanded
from
2
to
about
30
phyla
comprising
over
20,000
species.
Most
this
archaeal
revealed
by
environmental
16S
rRNA
gene
amplicon
sequencing
surveys
using
broad
range
universal
targeted
primers.
Of
few
primers
that
target
large
fraction
diversity,
all
display
bias
against
recently
discovered
lineages,
which
limits
studies
aiming
survey
overall
diversity.
Induced
genomic
exploration
improved
phylogenomics
approaches,
taxonomic
classification
frequently
revised.
Due
computational
limitations
continued
new
stable
phylogeny
not
yet
within
reach.
Obtaining
phylogenetic
consensus
should
be
high
priority
for
research
community.
Archaea
are
a
major
part
of
Earth's
life.
They
believed
to
play
important
roles
in
nutrient
biogeochemical
cycling
the
mangrove.
However,
only
few
studies
on
archaeal
community
mangroves
have
been
reported.
In
particular,
assembly
processes
and
interaction
patterns
that
impact
communities
not
investigated
date.
Here,
biogeography,
patterns,
driving
factors
seven
representative
across
southeastern
China
were
systematically
analyzed.
The
analysis
revealed
is
more
diverse
surface
sediments
than
subsurface
sediments,
at
low
latitudes
high
latitudes,
with