Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication
Tian, Lei; Chang, Jingjing; Shi, Shaohua; Ji, Li; Zhang, Jianfeng; Sun, Yu; Li, Xiaojie; Li, Xiujun; Xie, Hongwei; Cai, Yaohui; Chen, Dazhou; Wang, Jilin; van Veen, Johannes A.; Kuramae, Eiko E.; Tran, Lam Son Phan; Tian, Chunjie
(2022) Science of the Total Environment, volume 803
(Article)
Abstract
Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in
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the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.
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Keywords: Cultivated rice, Domestication, Methane production, Microbial functional potential, Root-inhabited microbiomes, Wild rice, Environmental Engineering, Environmental Chemistry, Waste Management and Disposal, Pollution
ISSN: 0048-9697
Publisher: Elsevier bedrijfsinformatie b.v.
Note: Funding Information: This work is financially supported by the National Natural Science Foundation of China (41920104008, 42007043), Science and Technology Project for Black Soil Granary (XDA28020400, XDA28080200), Special Foundation for Basic Research Program in Wild China of CAS (XDA23070501), Key Laboratory Foundation of Mollisols Agroecology (2020ZKHT-02). Publication number 7269 of the Netherlands Institute of Ecology (NIOO-KNAW). Funding Information: This work is financially supported by the National Natural Science Foundation of China ( 41920104008 , 42007043 ), Science and Technology Project for Black Soil Granary ( XDA28020400 , XDA28080200 ), Special Foundation for Basic Research Program in Wild China of CAS ( XDA23070501 ), Key Laboratory Foundation of Mollisols Agroecology ( 2020ZKHT-02 ). Publication number 7269 of the Netherlands Institute of Ecology (NIOO-KNAW). Publisher Copyright: © 2021
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