Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes

Rice production is an important source of methane accounting for 11% of global anthropogenic emissions. Methane emissions can be effectively reduced by management practices and cultivar selection. However, whether cultivars lower methane emissions primarily through mediating whole microbial community shifts or through more targeted interactions with methane-cycling microbes is not understood. Here, we sequenced the soil metagenomes associated with two rice recombinant inbred lines (RILs) along with their parents, Francis and Rondo, displaying a range of low to high methane emitting phenotypes. Methane emissions and rhizosphere soil microbial communities were sampled at booting, heading, grain fill, and maturity growth stages to evaluate how plant development impacted rhizosphere communities. Methane emissions were low at booting and increased during heading and grain fill stages where peak methane emissions were observed and returned to basal levels at maturity. In response to genotype and plant developmental stage, we observed changes in rhizosphere microbial community structure in several methanogenic archaea as well as bacterial methane oxidizers and sulfur cyclers. Rice genotype played a larger role in influencing the soil microbial community structure during the reproductive phases of booting and heading as compared to the ripening phases (grain fill and maturity). Francis showed lower methane emissions and relative abundance of methanogen populations during the heading stage where methane emissions were highest for the other genotypes. This indicated that the reduced methane emissions trait was associated with small changes in the composition of methanogens rather than wholesale community shifts. This finding suggests future breeding efforts can focus on reducing methane emissions during high methane emitting phases (i.e., reproductive phases) by selecting genotypes that have lower methanogen populations and higher methanotroph populations during these developmental stages. • Rice genotype, ontogeny, and microbial communities affect methane emissions. • Methanogens and methanotrophs vary between low and high methane emission genotypes. • Heading is associated with higher methane emissions than later plant stages. • Selection of genotypes with low methanogen populations during reproducitve phase reduces methane.