Heliyon,
Год журнала:
2024,
Номер
10(23), С. e40822 - e40822
Опубликована: Ноя. 30, 2024
The
annotated
and
predicted
genomes
of
five
archaeal
strains
(AS1,
AS2,
AS8,
AS11
AS19),
isolated
from
Sfax
solar
saltern
sediments
(Tunisia)
affiliated
with
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2024,
Номер
74(3)
Опубликована: Март 8, 2024
Halophilic
archaea
of
the
class
Halobacteria
are
most
salt-requiring
prokaryotes
within
domain
Archaea
.
In
1997,
minimal
standards
for
description
new
taxa
in
order
Halobacteriales
were
proposed.
From
then
on,
taxonomy
provides
an
excellent
example
how
changing
concepts
on
prokaryote
and
development
methods
implemented.
The
last
decades
have
witnessed
a
rapid
expansion
number
described
coinciding
with
era
genome
sequencing
development.
current
members
International
Committee
Systematics
Prokaryotes
Subcommittee
Taxonomy
propose
these
revisions
to
recommended
encourage
use
advanced
technologies
taxonomic
Most
previously
required
some
retained
present
revision,
but
changes
been
proposed
line
methodologies.
addition
16S
rRNA
gene,
rpoB′
gene
is
important
molecular
marker
identification
Phylogenomic
analysis
based
concatenated
conserved,
single-copy
genes
infer
status
taxa.
overall
relatedness
indexes
proven
be
determinative
classification
Average
nucleotide
identity,
digital
DNA–DNA
hybridization,
average
amino
acid
identity
values
should
calculated
rigorous
comparison
among
close
relatives.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2024,
Номер
74(1)
Опубликована: Янв. 5, 2024
The
naming
of
prokaryotes
is
governed
by
the
International
Code
Nomenclature
Prokaryotes
(ICNP)
and
partially
for
Algae,
Fungi
Plants
(ICN).
Such
codes
must
be
able
to
determine
names
taxa
in
a
universal
unambiguous
manner,
thus
serving
as
common
language
across
different
fields
activities.
This
unity
undermined
when
new
code
nomenclature
emerges
that
overlaps
scope
with
an
established,
time-tested
uses
same
format
but
assigns
nomenclatural
status
values
names.
resulting
confusion
not
beneficial
wider
scientific
community.
ambiguity
expected
result
from
establishment
‘Code
Described
DNA
Sequence
Data’
(‘SeqCode’),
which
general
specific
conflict
ICNP
ICN.
Shortcomings
interpretation
may
have
exacerbated
incompatibility
between
codes.
It
reiterated
why
proposals
accept
sequences
types
species
subspecies
validly
published
names,
now
implemented
SeqCode,
been
Committee
on
Systematics
(ICSP),
oversees
ICNP.
absence
certain
regulations
yet
uncultivated
acceptable
argument,
although
it
does
justify
separate
code.
Moreover,
rejected
ICSP
are
unnecessary
adequately
regulate
prokaryotes.
To
provide
better
service
community,
alternative
proposal
emend
presented,
would
Candidatus
being
regulated
analogously
fully
consistent
previous
decisions,
preserves
essential
avoids
confusion.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2023,
Номер
73(7)
Опубликована: Июль 24, 2023
Currently,
there
are
four
mainstream
taxonomic
opinions
on
the
classification
of
class
Halobacteria
at
family
and
order
levels.
The
International
Committee
Systematics
Prokaryotes
Subcommittee
Taxonomy
(ICSP),
List
Prokaryotic
names
with
Standing
in
Nomenclature
(LPSN)
National
Centre
for
Biotechnology
Information
(NCBI)
adopted
taxonomies
have
three
to
orders
up
eight
families,
while
Genome
Database
(GTDB)
taxonomy
proposes
only
one
nine
families.
To
resolve
inconsistency,
phylogenomic
analyses
based
concatenated
single-copy
orthologous
proteins
122
conserved
marker
were
conducted
infer
status
current
representatives
76
genera
validly
published
able
be
assigned
into
families
order.
On
basis
these
results,
it
is
proposed
that
species
should
remerged
Halobacteriales,
then
Haladaptataceae,
Haloarculaceae,
Halobacteriaceae,
Halococcaceae,
Haloferacaceae,
Natronoarchaeaceae,
Natrialbaceae
Halorubellaceae.
Thus,
Haladaptataceae
fam.
nov.
described
Haladaptatus,
Halomicrococcus
Halorussus
Halorubellaceae
incorporating
Haloarchaeobius
Halorubellus,
respectively.
Abstract
Our
understanding
of
the
microbial
diversity
inhabiting
hypersaline
environments,
here
defined
as
containing
>100–150
g/L
salts,
has
greatly
increased
in
past
five
years.
Halophiles
are
found
each
three
domains
life.
Many
novel
types
have
been
cultivated,
and
metagenomics
other
cultivation-independent
approaches
revealed
existence
many
previously
unrecognized
lineages.
Syntrophic
interactions
between
different
phylogenetic
lineages
discovered,
such
symbiosis
members
archaeal
class
Halobacteria
‘
Candidatus
Nanohalarchaeota’.
Metagenomics
techniques
also
shed
light
on
biogeography
halophiles,
especially
genera
Salinibacter
(
Bacteria
)
Haloquadratum
Halorubrum
Archaea
).
Exploration
microbiome
lakes
led
to
discovery
metabolism
unknown
occur
at
high
salt
concentrations.
Studies
environments
with
concentrations
chaotropic
ions
magnesium,
calcium,
lithium
refined
our
limits
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2023,
Номер
73(9)
Опубликована: Окт. 3, 2023
Microbiology
Society
journals
contain
high-quality
research
papers
and
topical
review
articles.
We
are
a
not-for-profit
publisher
we
support
invest
in
the
microbiology
community,
to
benefit
of
everyone.
This
supports
our
principal
goal
develop,
expand
strengthen
networks
available
members
so
that
they
can
generate
new
knowledge
about
microbes
ensure
it
is
shared
with
other
communities.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2024,
Номер
74(3)
Опубликована: Март 21, 2024
Eight
colonies
of
live
microbes
were
isolated
from
an
extensively
surface-sterilized
halite
sample
which
had
been
retrieved
a
depth
2000
m
salt
mine
in
the
Qianjiang
Depression,
Hubei
Province,
PR
China.
The
eight
colonies,
obtained
after
4
weeks
incubation,
named
JI20-1
T
–JI20-8
and
was
selected
as
type
strain.
strains
have
previously
described,
including
genomic
analysis
based
on
complete
genome
for
strain
draft
genomes
other
strains.
In
that
study,
name
Halobacterium
hubeiense
suggested,
location
drilling
site.
Previous
phylogenomic
showed
is
most
closely
related
to
Permian
isolate
noricense
Alpine
rock
salt.
orthologous
average
nucleotide
identity
(orthoANI)
digital
DNA–DNA
hybridization
(dDDH)
percentages
between
are
100–99.6
%
99.8–96.4
%,
respectively.
orthoANI
dDDH
values
these
with
respect
species
genus
89.9–78.2
37.3–21.6
respectively,
supporting
their
placement
novel
extremely
halophilic
archaeal
species.
tree
comparison
sequences
632
core-orthologous
proteins
confirmed
status
haloarchaea.
polar
lipid
profile
includes
phosphatidylglycerol,
phosphatidylglycerol
phosphate
methyl
ester,
sulfate,
sulfated
galactosyl
mannosyl
glucosyl
diether,
compatible
.
Based
genomic,
phenotypic,
chemotaxonomic
characterization,
we
propose
(=DSM
114402
=
HAMBI
3616
)
,
sp.
nov.
Frontiers in Plant Science,
Год журнала:
2025,
Номер
16
Опубликована: Фев. 7, 2025
The
denitrification
process
is
known
to
contribute
soil
nitrogen
(N)
loss,
which
strongly
affected
by
fertilization
strategies;
however,
the
effects
of
distinct
straw
retention
modes
on
activity
have
rarely
been
discriminated
and
underlying
mechanisms
remain
unclear.
This
study
coupled
field
incubation
experiments
explore
characteristics
activity,
standing
water
physicochemical
properties,
abundance,
community
diversity,
co-occurrence
network
nosZ
denitrifiers,
based
a
paddy
implementing
10-year
under
rice-wheat
rotation
system.
Four
treatments
with
equivalent
chemical
fertilizers
were
applied,
namely
no
(NS),
wheat
only
(WS),
rice
(RS),
(WRS).
Results
indicated
significant
increase
(by
41.93-45.80%
when
compared
that
NS)
in
RS
WRS.
Correspondingly,
resulted
development
similar
composition
(P
<
0.05),
structure
=
0.001),
more
positively
interconnected
network,
as
well
specific
keystone
taxa
relative
those
non-rice
mode.
Under
long-term
conditions,
core
nosZ-denitrifying
phylogroups
shifted
(r
0.83,
P
recruitment
from
phyla
Bacteroidetes
Euryarchaeota
playing
key
role
enhancing
stimulating
N
loss.
Accordingly,
field,
practice
single
season
recommended
because
it
will
not
markedly
sacrifice
availability
impaired
process.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 8, 2024
Abstract
Australian
isolates
of
Haloquadratum
walsbyi
,
a
square-shaped
haloarchaeon,
often
harbor
small
cryptic
plasmids
the
pL6-family,
approximately
6
kb
in
size.
These
exhibit
highly
conserved
gene
arrangement
and
encode
replicase
similar
to
those
betapleolipoviruses.
To
assess
their
global
distribution
recover
more
examples
for
analysis,
fifteen
additional
were
reconstructed
from
metagenomes
seven
hypersaline
sites
across
four
countries:
Argentina,
Australia,
Puerto
Rico,
Spain.
Including
five
previously
described
plasmids,
average
plasmid
size
is
6,002
bp,
with
an
G+C
content
52.5%.
The
tetramers
GGCC
CTAG
are
either
absent
or
significantly
under-represented,
except
two
highest
%G+C.
All
share
arrange-ment
genes
organized
as
outwardly
facing
replication
ATPase
modules,
but
variations
observed
some
core
genes,
such
F2,
had
acquired
accessory
genes.
Two
pCOLO-c1
pISLA-c6
shared
92.7%
nt
identity
despite
originating
Argentina
Spain,
respectively.
Numerous
metagenomic
CRISPR
spacers
matched
sequences
indicating
frequent
invasion
haloarchaea.
Spacers
could
be
assigned
haloarchaeal
genera
by
mapping
associated
direct
repeats
(DR),
half
these
matching
.
Finally,
strand-specific
metatranscriptome
(RNA-seq)
data
used
demonstrate
active
transcription
pL6-family
including
antisense
transcripts.