Data from: Controlled irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice

The rhizosphere microbiomes of rice plants under conventional flood
irrigation consist of highly complex consortia of microorganisms, and in
particular, methanogens purportedly associated with methane emissions
therein. Controlled irrigation has been proposed as a cultivation method
of choice over continuous flooding to reduce water and fertilizer usage in
an aerobic environment. However, a systemic understanding of the assembly
and function of microbiota in the rhizosphere under drip and flood
irrigation remains unclear. Using empirical analyses, we report a
significant reduction in methane emissions in controlled irrigation
compared to the flooded environment. Genotypic or varietal differences did
not influence such methane emissions under conventional flooded
cultivation of rice. Using metagenomic sequencing and computational
analyses, we provide a deeper understanding of how drip irrigation or
continuous flooding affects the root-associated microbiomes in rice.
Rhizosphere soil from two different rice varieties, Huanghuazhan and
Temasek rice, grown under drip or flood conditions in a greenhouse was
collected over 2 months post-transplantation for metagenomic analysis. Our
results reveal that drip irrigation favours microbes involved in the
nitrifying-denitrifying processes while continuous flooding enriches for
methanotrophs and methanogenic archaea. Syntrophic microbiomes associated
with methanogenesis were significantly reduced in drip irrigation. Several
keystone taxa were evident in the co-occurrence network model related to
methanogenic, methanotrophic, nitrifying, sulphur-oxidising and
sulphur-reducing activities. Lastly, oxygen availability and redox
potential were identified as key drivers that reshape rhizosphere
microbiota and the associated metabolic functional differences observed
between the two irrigation regimes leading up to the microbial mitigation
of climate impact.