International Journal of Environmental Research,
Год журнала:
2024,
Номер
19(2)
Опубликована: Дек. 23, 2024
Abstract
Increasing
levels
of
pervasive
harmful
chemicals
like
polycyclic
aromatic
hydrocarbons
(PAHs)
have
been
linked
to
unprecedentedly
high
cases
several
illnesses,
loss
biodiversity,
and
environmental
degradation,
posing
a
threat
the
sustainability
life.
Several
biodegradation
procedures
proposed
for
cleaning
up
contaminated
sites,
among
which
rhizoremediation,
type
phytoremediation,
is
perceived
be
one
most
cost-efficient
methods
has
good
public
acceptance.
To
enhance
effectiveness
use
transgenic
plants
deployed;
however,
many
studies
demonstrated
that
rhizosphere
microbial
communities
are
actively
involved
in
degradation
hydrocarbons.
The
plant
thus
facilitates
formidable
support
cross-communication
through
root
exudates,
rhizodeposition.
Unlike
conventional
microbiology
procedures,
throughput
metagenomic
approaches
unveil
both
individual
community
functional
capacities,
novel
species,
gene
molecular
composition,
allowing
alteration
growth
promotion,
resistance
PAHs,
metabolism
contaminant
compounds.
This
article
presents
an
updated
overview
modifying
soil
effective
enhanced
rhizoremediation
hydrocarbon-polluted
soil.
Graphical
abstract
International Journal of Molecular Sciences,
Год журнала:
2024,
Номер
25(23), С. 12603 - 12603
Опубликована: Ноя. 23, 2024
Oxford
Nanopore
Technology
(ONT)
allows
for
the
rapid
profiling
of
aquaculture
microbiomes.
However,
not
all
experimental
and
downstream
methodological
possibilities
have
been
benchmarked.
Here,
we
aimed
to
offer
novel
insights
into
use
different
library
preparation
methods
(standard-RAP
native
barcoding-LIG),
primers
(V3-V4,
V1-V3,
V1-V9),
basecalling
models
(fast-FAST,
high-HAC,
super-accuracy-SUP)
implemented
in
ONT
elucidate
microbiota
associated
with
aquatic
environment
farmed
fish,
including
faeces,
skin,
intestinal
mucus.
Microbial
DNA
from
water
faeces
samples
could
be
amplified
regardless
library-primer
strategy,
but
only
LIG
V1-V3/V1-V9
case
skin
intestine
Low
taxonomic
assignment
levels
were
favoured
by
full-length
V1-V9
primers,
though
silico
hybridisation
revealed
a
lower
number
potential
matching
sequences
SILVA
database,
especially
evident
increase
Actinobacteriota
real
datasets.
SUP
execution
allowed
higher
median
Phred
quality
(24)
than
FAST
(11)
HAC
(17),
its
time
(6-8
h)
was
comparison
other
(0.6-7
h).
Altogether,
optimised
water-
fish-related
microbial
analyses,
validating,
first
time,
strategy.
We
consider
that
LIG-V1-V9-HAC
is
optimal
time/cost-effective
option
amplify
environmental
samples.
V1-V3
help
maximise
dataset
microbiome
diversity,
representing
an
alternative
when
long
amplicon
become
compromised
and/or
high
host
loads
interfere
PCR
amplification/sequencing
procedures,
gut
International Journal of Environmental Research,
Год журнала:
2024,
Номер
19(2)
Опубликована: Дек. 23, 2024
Abstract
Increasing
levels
of
pervasive
harmful
chemicals
like
polycyclic
aromatic
hydrocarbons
(PAHs)
have
been
linked
to
unprecedentedly
high
cases
several
illnesses,
loss
biodiversity,
and
environmental
degradation,
posing
a
threat
the
sustainability
life.
Several
biodegradation
procedures
proposed
for
cleaning
up
contaminated
sites,
among
which
rhizoremediation,
type
phytoremediation,
is
perceived
be
one
most
cost-efficient
methods
has
good
public
acceptance.
To
enhance
effectiveness
use
transgenic
plants
deployed;
however,
many
studies
demonstrated
that
rhizosphere
microbial
communities
are
actively
involved
in
degradation
hydrocarbons.
The
plant
thus
facilitates
formidable
support
cross-communication
through
root
exudates,
rhizodeposition.
Unlike
conventional
microbiology
procedures,
throughput
metagenomic
approaches
unveil
both
individual
community
functional
capacities,
novel
species,
gene
molecular
composition,
allowing
alteration
growth
promotion,
resistance
PAHs,
metabolism
contaminant
compounds.
This
article
presents
an
updated
overview
modifying
soil
effective
enhanced
rhizoremediation
hydrocarbon-polluted
soil.
Graphical
abstract
