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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #362091

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: Rice soil microbiome interactions with plant growth characteristics and methane emissions

item Fernandez-Baca, Cristina
item Rivers, Adam
item Maul, Jude
item KIM, WOOJAE - Rural Development Administration - Korea
item YARWOOD, STEPHANIE - University Of Maryland
item Roberts, Daniel
item McClung, Anna
item Barnaby, Jinyoung

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2019
Publication Date: 6/24/2019
Citation: Fernandez-Baca, C.P., Rivers, A.R., Maul, J.E., Kim, W., Yarwood, S.A., Roberts, D.P., McClung, A.M., Barnaby, J.Y. 2019. Rice soil microbiome interactions with plant growth characteristics and methane emissions. American Society for Microbiology.

Interpretive Summary:

Technical Abstract: Agriculture is recognized as a significant contributor to greenhouse gas emissions (GHGE) globally. Methane (CH4) is an important greenhouse gas (GHG) and is 25 x more potent than carbon dioxide (CO2) and is the primary GHGE from flooded rice fields, ideal conditions for methanogens, the anaerobic archaea that produce methane. Because of the extensive global rice acreage, reducing CH4 emissions from rice production would have a significant impact on global warming. Research has shown that the amount of CH4 emitted from paddy rice can vary by cultivar indicating that genetics has the potential for mitigating the effects of GHGE. Our recent study confirmed genotypic variation in methane emissions, and further indicated positive correlation of root/shoot biomass with CH4 emissions. Previously it was reported that there was a positive correlation of root/shoot biomass (RB/SB) with microbial diversity. However, how genetic variation in root-soil-microbe interactions is linked to CH4 emissions and biomass is largely unknown. To understand temporal relationships between soil microbial composition and rice cultivar-specific traits, two parent lines, a high CH4 emitter (Rondo) with high root/shoot biomass (RB/SB) and a low CH4 emitter (Francis) with low RB/SB, were selected for this study. Methane emissions differ by developmental stage; therefore, nine recombinant inbred lines (RILs) from a Francis/Rondo (FR) mapping population were selected based on their heading dates (within 10 days apart) as well as RB/SB. CH4 gas samples were collected weekly to capture the seasonal CH4 profile. Soil and plant samples for microbial analysis and agronomic traits such as RB, SB, plant height (HT) and yield were collected at four developmental stages, i.e. booting, heading, grain fill, and harvest, throughout the reproductive stage, when CH4 emissions are most significant. Libraries were constructed with DNA extracted from rhizosphere soil samples for shotgun metagenomic sequencing on the NextSeq platform. Additionally, mcrA gene abundances, involved in the final step of methanogenesis, were quantified via qPCR. Rice genotype and developmental stage appeared to be the strongest influencers of the microbial community structure and diversity. Shannon diversity index trends follow biomass trends which showed an initial increase during heading and grain fill stages, with a slight decrease in biomass (RB and SB) at harvest. Soil microbial communities shifted throughout plant growth stages, which was supported by mcrA gene abundance which likewise varied between developmental stages.