Science Advances,
Journal Year:
2024,
Volume and Issue:
10(51)
Published: Dec. 18, 2024
Subsurface
environments
are
among
Earth’s
largest
habitats
for
microbial
life.
Yet,
until
recently,
we
lacked
adequate
data
to
accurately
differentiate
between
globally
distributed
marine
and
terrestrial
surface
subsurface
microbiomes.
Here,
analyzed
478
archaeal
964
bacterial
metabarcoding
datasets
147
metagenomes
from
diverse
widely
environments.
Microbial
diversity
is
similar
in
microbiomes
at
local
global
scales.
However,
community
composition
greatly
differs
sea
land,
corroborating
a
phylogenetic
divide
that
mirrors
patterns
plant
animal
diversity.
In
contrast,
overlaps
supporting
continuum
rather
than
discrete
biosphere.
Differences
life
thus
seem
greater
land
subsurface.
Diversity
of
decreases
with
depth,
while
distance
cultured
isolates
rivals
or
exceeds
We
identify
distinct
compositions
but
PeerJ,
Journal Year:
2025,
Volume and Issue:
13, P. e18785 - e18785
Published: Jan. 14, 2025
The
virome,
composed
of
viruses
inhabiting
diverse
ecosystems,
significantly
influences
microbial
community
dynamics
and
host
health.
phenol-chloroform
DNA
extraction
protocol
for
viromes,
though
effective,
is
time-intensive
requires
the
use
multiple
toxic
chemicals.
This
study
introduces
a
streamlined,
scalable
using
commercially-available
kit
as
an
alternative,
assessing
its
performance
against
method
across
human
fecal,
mouse
soil
samples.
No
significant
differences
in
virome
diversity
or
composition
were
seen
between
methods.
Most
viral
operational
taxonomic
units
(vOTUs)
common
to
both
methods,
with
only
small
percentage
unique
either
approach.
Alpha-
beta-diversity
analyses
showed
no
impact
on
composition,
confirming
kit’s
efficacy
versatility
sample
types
beyond
those
officially
supported
by
manufacturer.
While
approach
offers
benefits
like
reduced
toxicity
increased
throughput,
it
has
limitations
such
higher
costs
potential
issues
reliably
capturing
low-abundance
taxa.
provides
viable
option
large-scale
studies,
although
may
still
be
preferable
specific
types.
ZooKeys,
Journal Year:
2025,
Volume and Issue:
1224, P. 283 - 316
Published: Feb. 3, 2025
More
than
a
decade
of
research
led
to
the
conclusion
in
2022
that
Soil
Biome
is
home
~
2.1
×
10
24
taxa
and
thus
supports
>
99.9%
global
species
biodiversity,
mostly
Bacteria
or
other
microbes,
based
upon
topographic
field
data.
A
subsequent
2023
report
tabulated
central
value
just
1.04
claiming
soils
had
59
±
15%,
i.e.,
44–74%
(or
truly
10–50%?)
total,
while
incidentally
confirming
upper
values
90%
for
soil
Bacteria.
Incompatibility
these
two
studies
reviewed,
supporting
prior
biodiversity
data
with
vast
majority
inhabiting
soils,
despite
excluding
viruses
(now
5
31
virions
26
most,
80%,
soils).
The
status
Oligochaeta
(earthworms)
marked
“?”
paper
are
clarified.
Although
biota
totals
increased
considerably,
inordinate
threats
topsoil
erosion
poisoning
yet
pertain
finality
extinction.
Species
affected
include
Keystone
taxa,
especially
earthworms
essential
healthy
foundation
sustain
Tree-of-Life
Earth.
Soil
moisture
is
a
fundamental
factor
affecting
terrestrial
ecosystem
functions.
In
this
study,
microscopic
enumeration
and
joint
metaviromic
metagenomic
sequencing
were
employed
together
to
investigate
the
impact
of
prolonged
drought
on
soil
phage
communities
their
interactions
with
prokaryotes
in
subtropical
evergreen
forest.
Our
findings
revealed
marked
reduction
abundances
prokaryotic
viral-like
particles,
by
73.1%
75.2%,
respectively,
significantly
altered
structure
under
drought.
Meanwhile,
substantially
increased
fraction
containing
lysogenic
phages
163%,
as
well
proportion
temperate
phages.
Nonetheless,
likely
amplified
negative
prokaryote-phage
given
nearly
doubled
links
co-occurrence
network,
higher
frequency
diversity
antiphage
defense
systems
found
genomes.
Under
drought,
exerted
greater
top-down
control
typical
k-strategists
including
Acidobacteria
Chloroflexi.
Moreover,
phage-encoded
auxiliary
metabolic
genes
may
host
metabolism
biosynthesis-related
Collectively,
study
underscore
profound
interactions.
These
results
also
emphasize
importance
managing
levels
during
amendment
microbiome
manipulation
account
for
influence
PLoS ONE,
Journal Year:
2025,
Volume and Issue:
20(2), P. e0313947 - e0313947
Published: Feb. 21, 2025
Bacteriophages
largely
impact
bacterial
communities
via
lysis,
gene
transfer,
and
metabolic
reprogramming
thus
are
increasingly
thought
to
alter
nutrient
energy
cycling
across
many
of
Earth's
ecosystems.
However,
there
few
model
systems
mechanistically
quantitatively
study
phage-bacteria
interactions,
especially
in
soil
systems.
Here,
we
isolated,
sequenced,
genomically
characterized
24
novel
phages
infecting
Klebsiella
sp.
M5al,
a
plant
growth-promoting,
nonencapsulated
rhizosphere-associated
bacterium,
compared
their
features
against
all
565
dsDNA
phage
genomes.
Taxonomic
analyses
revealed
that
these
belong
three
known
families
(Autographiviridae,
Drexlerviridae,
Straboviridae)
two
newly
proposed
(Candidatus
Mavericviridae
Ca.
Rivulusviridae).
At
the
family
level,
found
core
genes
were
often
phage-centric
proteins,
such
as
structural
proteins
for
head
tail
DNA
packaging
proteins.
In
contrast,
involved
transcription,
translation,
or
hypothetical
commonly
not
shared
flexible
genes.
Ecologically,
assessed
phages'
ubiquity
recent
large-scale
metagenomic
datasets,
which
they
widespread,
well
possible
direct
role
specific
metabolisms
during
infection
by
screening
genomes
phage-encoded
auxiliary
(AMGs).
Even
though
AMGs
common
environmental
literature,
only
one
our
families,
Straboviridae,
contained
AMGs,
types
correlated
at
genus
level.
Host
range
phenotyping
had
wide
infectivity,
between
1-14
22
strain
panel
included
pathogenic
Raoultella
strains.
This
indicates
capsule-independent
have
broad
host
ranges.
Together,
isolates,
with
corresponding
genome,
AMG,
analyses,
help
build
system
studying
phage-host
interactions
bacteria.
Microbiology and Molecular Biology Reviews,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 8, 2025
SUMMARY
Engineered
microbes
are
being
programmed
using
synthetic
DNA
for
applications
in
soil
to
overcome
global
challenges
related
climate
change,
energy,
food
security,
and
pollution.
However,
we
cannot
yet
predict
gene
transfer
processes
assess
the
frequency
of
unintentional
engineered
environmental
when
applying
biology
technologies
at
scale.
This
challenge
exists
because
complex
heterogeneous
characteristics
soils,
which
contribute
fitness
transport
cells
exchange
genetic
material
within
communities.
Here,
describe
knowledge
gaps
about
across
microbiomes.
We
propose
strategies
improve
our
understanding
communities,
highlight
need
benchmark
performance
biocontainment
measures
situ
,
discuss
responsibly
engaging
community
stakeholders.
opportunities
address
gaps,
such
as
creating
a
set
standards
studying
diverse
types
measuring
host
range
microbiomes
emerging
technologies.
By
comparing
rates,
range,
persistence
different
posit
that
community-scale,
environment-specific
models
can
be
built
anticipate
biotechnology
risks.
Such
studies
will
enable
design
safer
biotechnologies
allow
us
realize
benefits
mitigate
risks
associated
with
release
