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 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.
Highlights
Rice (Oryza spp.) is one of the major food crops produced in the world; especially Oryza sativa that is the major contributor to the food requirement of more than half of the world's population (Khush, 2005)
Seeds of African wild and cultivated rice accessions were kindly provided by the International Rice Research Institute (IRRI), while those of the Asian cultivated rice accessions were obtained from the Jiangxi Academy of Agricultural Sciences (Table 1)
A significant linear relationship was observed between the transcripts per million reads (TPM) of K00402, K11781 and K00200 and the relative abundance of Methanomicrobia (Fig. 5a, b and c)
Summary
Rice (Oryza spp.) is one of the major food crops produced in the world; especially Oryza sativa that is the major contributor to the food requirement of more than half of the world's population (Khush, 2005). There are many wild and cultivated Oryza species that are distributed worldwide. Genomes of Oryza species were classified based on the chromosomes in pairing correctly during meiosis in interspecies F1 hybrids (Kurata, 2008). All cultivated species of rice and their wild progenitors are diploid and represent species possessing the AA genome (Vaughan et al, 2008). African and Asian cultivated rice species were independently domesticated (Chang, 1976; Nayar, 2012; Waters et al, 2012). O. glaberrima, was domesticated from African wild rice, O. barthii, while Asian cultivated rice, O. sativa, was domesticated from common wild rice (O. rufipogon) or nivara wild rice (O. nivara) (Yamanaka et al, 2003; Li et al, 2006; Bessho-Uehara et al, 2017). Oryza sativa has been continuously subjected to breeding efforts, which resulted in the establishment of two main varieties indica and japonica (Cheng et al, 2019)
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