Impact Of Rice Domestication On The Assembly Of Rhizosphere Bacterial And Fungal Communities Associated With Strains Of Rice

Rice domestication is a biological evolution process under the influence of the human activities,which is closely related to human survival trajectory.To clarify the changes of rhizosphere microbiome driven by rice domestication,recombination and construction of rhizosphere microbiome of cultivated rice are important growth points of agricultural development.There are two branches of cultivated rice in the world:African cultivated rice and Asian cultivated rice which are thought to have been domesticated by different primitive relatives,and the origin of them was from Africa and Asia.Modern molecular techniques such as 16S r RNA,ITS amplification and shotgun metagenomics sequencing were used to analyze microbial communities and functions in the samples.Totally,12 wild and cultivated rice accessions have been cultivated in a field experiment.Firstly,we identify the core microbiome in the rhizosphere of wild rice,particularly of the same genotype but in different soil condition for long time.And if the core microbiome would be their potential functions related to plant growth.After we found the microbiomes really benefit the wild rice against the strict environmental stress of wild rice,then we investigate the impact of rice domestication exclude soil conditions influence on the structure and function of the rhizomicrobiome including fungal and bacterial community and to determine the link with nutrients metabolism,which is the most important ecosystem function from rice domestication;if we use wild rice for genome cultivation,how does the influence of wild rice on the rhizomicrobial assembly in their generations.The preliminary conclusions are as follows:（1）We sampled three natural reserves of wild rice named‘in-situ’and the transplanted wild rice of‘in-situ’grown in‘ex-situ’for more than 40 years to determine the core wild rice microbiome.By using generalized joint attribute model（GJAM）analysis we identify a total of 44 amplicon sequence variants（ASVs）as the core of wild rice rhizosphere,35 bacteria and 9 fungi.The bacterial ASVs belonged to the phyla Actinobacteria,Chloroflexi,Firmicutes,and Nitrospirae,while 9 fungal ASVs belonged to Ascomycota,Basidiomycota and Rozellomycota.Nine ASVs core bacteria of genera Haliangium,Anaeromyxobacter,Bradyrhizobium and Bacillus were more abundant in the rhizosphere of wild rice of ex-situ than that of in-situ.The different abundance of the core microbiome Bradyrhizobium is positively or negatively related to soil properties like available phosphorus.The ecological functions of the core microbiome were nitrogen fixation,manganese oxidation,aerobic chemoheterotrophy,chemoheterotrophy and iron respiration,suggesting that the core microbiome in the rhizosphere of wild rice have the potential to improve nutrient resources acquisition for rice growth.（2）Internal transcribed spacer amplicon sequencing（ITS amplicon sequencing）was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice.The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community.The changes of alpha diversity index may be associated with the enrichment of Acremonium,Lecythophora,and other specific rare taxa in the rhizosphere of domesticated rice.The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community.Arbuscular mycorrhizal fungi and soil-born fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere,respectively.For restructuring the rhizomicrobial community of domesticated crops,we hypothesize that microbes which hold positive connections with arbuscular mycorrhizal fungi and negative connections with soil-born fungi can be used as potential sources for bio-inoculation.（3）Microbial functional potential in the rhizospheres of wild and domesticated rice accessions originating from Asia and Africa were comparatively assessed under field conditions by conducting shotgun metagenomic sequencing of rhizomicrobiomes.This approach could provide information on the impact of rice domestication on the structure and the potential functional traits in the rhizomicrobiomes of domesticated rice accessions.Specific genes,such as those related to carbon metabolism and amino acid metabolism,were primarily enriched in wild rice,while others,such as those related to nitrogen metabolism,amino acid metabolism,lipid metabolism,metabolism of factors and vitamins,biodegradation of obiotics,and metabolism and biosynthesis of secondary metabolites,were enriched in cultivated rice,relative to wild rice.Notably,the methane metabolism pathway was significantly and consistently enriched in the rhizomicrobiomes of all wild accessions relative to the accessions and varieties of cultivated rice.This was true for genes involved in methane production and those related to methane oxidation.（4）The genes that participated in N₂O production and reduction were over represented in cultivated rice species in comparison with wild rice.Combining the abundance of amo A,amo B and amo C genes that were a bit higher in the rhizosphere of cultivated rice,suggests that rice domestication improves the N₂O emission.Notably,the nitrogen fixation genes were significantly higher in the rhizosphere of wild rice than in those cultivated rice accessions,suggesting that wild rice has a clever nutrient acquisition strategy to utilize nitrogen-fixing microbes.The metagenomes of microbiome in the rhizosphere of wild and cultivated rice produced 7 high-quality MAGs,belong to taxonomic families Bradyrhizobiaceae,Bukholderiaceae,Oxalobacteraceae,Comanonadaceae,Geobacteraceae,Gallionellaceae,Syntrophaceae and Nitrospiraceae within bacteria.All these MAGs contained genes involved in N-cycling including dissimilatory nitrate reduction,nitrification and denitrification.（5）We compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice;male parent Oryza sativa cultivated rice;their F1 progeny;and the F2,F3,and F4 self-crossing generations.Our results showed that the bacterial and fungal-diversities of the hybrid F1 and self-crossing generations（F2,F3,F4）were closer to one of the two parental lines,which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly.Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes.In the parental and self-crossing progenies,the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.In summary,rice domestication has gradually lost the microbial community and functions of the wild rice rhizosphere that are conducive to resource acquisition like methane oxidation and nitrogen fixation.When developing novel systems for restructuring the rhizomicrobial community of cultivated crops,we suggest using these beneficial rhizomicrobiomes to help to improve rice growth and production.Therefore,our research provides a scientific basis for reshaping the structure of the rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.