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

Authors: FERNANDEZ-BACA, CRISTINA; Rivers, Adam; KIM, WOOJAE - RURAL DEVELOPMENT ADMINISTRATION - KOREA; MCCLUNG, ANNA; Roberts, Daniel; Reddy, Vangimalla; Barnaby, Jinyoung

Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2021
Publication Date: 3/26/2021
Citation: Fernandez-Baca, C.P., Rivers, A.R., Kim, W., McClung, A.M., Roberts, D.P., Reddy, V., Barnaby, J.Y. 2021. Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes. Soil Biology and Biochemistry. http://doi.org/10.1016/j.soilbio.2021.108233.
DOI: https://doi.org/10.1016/j.soilbio.2021.108233

Interpretive Summary: Rice has the highest global warming potential among the major cereals due to high methane emissions from flooded paddy soils. Methane is a potent greenhouse gas with a global warming potential 28 times that of carbon dioxide over a 100-year timespan. Thus, reducing methane emissions from rice production could significantly reduce anthropogenic greenhouse gas emissions overall. This study examined the interaction of rice genotypes and plant developmental stage with soil microbes that produce methane. Two cultivars differing in methane emission profiles, Rondo having high-methane emissions and Francis with low emissions, and two recombinant inbred line (RIL) offspring that display intermediate methane emissions were studied. Soil samples in the root zone were sampled at four developmental stages, booting, heading, grain fill, and maturity. Results revealed that rice genotype does influence the soil microbial community structure as does plant developmental stage. Additionally, rice genotype impacts the observed methane emissions particularly during the reproductive phases of booting and heading as compared to the ripening phases (i.e. grain fill and maturity). Our results suggest that future efforts to breed low methane cultivars should focus on mitigating methane emissions during the rice reproductive phase by selecting cultivars that modulate the methane-cycling community during this critical period.

Technical Abstract: Rice production is an important source of methane accounting for 11percent of global anthropogenic emissions. Work has been done to reduce methane emissions through modified cultural management practices and there is evidence that choice of cultivar can help in mitigation efforts. However, whether cultivars achieve lower methane emissions primarily through mediating large changes in the microbial community or through more targeted interactions with methane-cycling microbes that affect methane flux is not understood. To investigate this, 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 methane 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; returning to basal levels at maturity. We observed changes in rhizosphere microbial community structure in several archaea responsible for methanogenesis and bacteria involved in methane oxidation and sulfur cycling by genotype and plant developmental stage. We found that 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, having low methane emissions, showed lower relative abundance of methanogen populations during the critical heading stage where methane emissions were typically highest. 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.