| The rhizosphere microbiome is recognized as the plants secondary genome playing important roles in increasing nutrients availability,suppressing soil-borne diseases and enhancing plant resistance.Exploring the biological potential of rhizosphere microbiome is of great importance for reducing fertilizer applications and sustaining the green development of agriculture.However,the mechanisms of the structural and functional assembly of rhizosphere microbiome remain unclear.In this research,Illumina high-throughput sequencing technology and PICRUSt metagenome functional prediction methods were used to explore the characteristics and mechanisms of rhizosphere microbiome structural and functional assembly in maize.First,we analyzed the microbiome composition of rhizosphere and root samples at successive intervals at maize seedling stage.Then,transplanting was conducted among different soils to investigate the structural and functional assembly characteristics of maize rhizosphere microbiome,and to construct a functional assembly concept model for maize rhizosphere microbiome.Finally,the concept model was validated and optimized using maize rhizosphere microbiome data in large scale.The main results are as follows:1.The succession characteristics of root-associated microbiome(rhizosphere microbiome and endosphere microbiome)were investigated by sampling at successive interval(0,6th,9th,12th,16th and 20th day)in maize seedling stage.We found that the ecological niche and growing time were the main driving factors of root-associated microbiome.Driven by ecological niche,the Shannon diversity of rhizosphere bacterial community was significantly lower than that of soil bacterial community,but was significantly higher than that of endosphere bacterial community.In addition,the composition of bacterial community of maize roots is also influenced by ecological niche.Actinobacteria is significantly enriched in endosphere with an average relative abundance of 14.0%,while the average relative abundance in rhizosphere is 2.2%.By contrast,Acidobacteria is significantly enriched in rhizosphere with an average relative abundance of 4.0%,whereas the average relative abundance in endosphere is 0.8%.Meanwhile,the rootassociated microbiome was also affected by different growing time.The Shannon diversity of root microbiome increased with the growth of maize and tended to be stable after 12 days.The relative abundance of Gammaproteobacteria decreased while Bacteroidetes increased with the growth of maize and tended to be stable after 12 days.The weighted UniFrac-based community similarity analysis was performed between rhizosphere microbiome at 20th day and the other time points.The results showed that the root microbiome structure was significantly different at the early stage,while was relatively stable after 12 days.2.The characteristics and mechanisms of maize rhizosphere microbiome structural assembly were studied by transplanting maize seedlings among different types of soil(black soil,paddy soil and red soil).We found that soil microbiome is an important seed bank in rhizosphere microbiome assembly.Besides,the endosphere microbiome of maize roots was also an important source of rhizosphere microbiome assembly.The maize root-associated microbiomes were diverse in different soils.The Shannon diversity of maize root-associated microbiomes were not significantly differed in black and paddy soils,but both were significantly higher than in red soil.Before transplanting,Gammaproteobacteria was the dominant taxon(relative abundance was 5.3%-20.7%)in root microbiome from black and paddy soils,while Betaproteobacteria was the dominant taxon(relative abundance was 49.3%-79.3%)in root microbiome from red soil.After transplanting,Gammaproteobacteria was still the dominant taxon(relative abundance was 34.2%-53.7%)in rhizosphere microbiome after transplanting from black soil to black and paddy soils,and Betaproteobacteria was still the dominant taxon(relative abundance was 15.9%-32.8%)in rhizosphere microbiome after transplanting from black soil to red soil.Interestingly,Gammaproteobacteria,which is the dominant taxon in black soil,had become the most dominant taxon in rhizosphere microbiome(relative abundance was 35.5%-71.6%)after transplanting from black soil to red soil.Moreover,we found that the rhizosphere microbiome shared 50.8%,28.2%and 50.1%microorganisms with the endosphere microbiomes after transplanting from black soil to black,paddy and red soils,respectively.The results indicated that rhizosphere microbiome is mainly originated from soil microbiome and also be affected by endosphere microbiome.Therefore,the rhizosphere microbiome assembly is a two-way process both of from "outside to inside" and from "inside to outside".3.The characteristics and mechanisms of maize rhizosphere microbiome functional assembly were investigated by ecological network analysis and PICRUSt function prediction.We found that transplanting had significant effects on the ecological network structure of maize rhizosphere microbiome.The number of network nodes of rhizosphere microbiomes transplanting from black soil to black,paddy and red soils was 349,393 and 176,respectively,while the number of links was 993,883 and 706,respectively.The importance of OTU(Operational Taxonomic Unit)in rhizosphere microbiomes were accessed according to node degree in network.The functional characteristics were predicted using PICRUSt software.We found that Actinobacteria.Proteobacteria.Bacteroidetes and Acidobacteria were the most critical taxa(5%OTU with the highest degree)in rhizosphere microbiome.These critical taxa were keystone species and were mainly originated from soil microbiome.Functional prediction results demonstrated that these taxa were mainly contributed to the functions related to assisting plant stress tolerance in rhizosphere,such as Glycosphingolipid biosynthesis,Flavonoid biosynthesis,Streptomycin biosynthesis,etc.Further analysis of the taxa at different importance levels in ecological network revealed that the functional genes associated with assisting host plant stress tolerance were more abundant in the top 30%taxa of importance in maize rhizosphere microbiome from black soil,while the functional genes associated with soil nitrogen and phosphorus nutrient conversion were more abundant in 30%-60%taxa of importance.After transplanting from black soil to paddy soil,the functional genes associated with assisting host plant stress tolerance were still abundant in top 30%taxa of importance.However,due to the high content of available nitrogen and phosphorus in paddy soil,the functional genes associated with soil nitrogen and phosphorus nutrient conversion were abundant in the last 50%taxa of importance.After transplanting from black soil to red soil,due to the poor content of available nitrogen and phosphorus in red soil,the functional genes associated with assisting host plant stress tolerance were abundant in top 10%taxa of importance and the functional genes associated with soil nitrogen and phosphorus nutrient conversion were abundant in 10%-30%taxa of importance.Furthermore,we found that the root-derived Gammaproteobacterial species Klebsiella(average relative abundance was 19.7%)and Pseudomonas(average relative abundance was 13.3%),which are related to improving soil nitrogen and phosphorus nutrient availability,was significantly higher in maize rhizosphere microbiome after transplanting from black soil to red soil.According to these results,a functional assembly concept model of rhizosphere microbiome was constructed.The functional compensation of rhizosphere microbiome assembly via regulating the rhizosphere microbiome structure to maintain the healthy growth of maize.4.A large-scale maize rhizosphere microbiome data were collected to validate and optimize the functional assembly concept model.In the nutrient balanced soils,the rhizosphere microbiome preferentially performed functions related to improving host stress tolerance to ensure plant survival,and followed by functions related to nutrient conversion to ensure nutrient demand during plant growth.Besides,in the soils with excess available nutrients,the rhizosphere microbiome still prioritizes functions related to improving host stress tolerance while functions of nutrient conversion and the related taxa are marginalized.However,in the available nutrient deficient soils,plants may sacrifice part of the functions related to stress tolerance to satisfy the functions related to nutrient conversion.Moreover,in the available nutrient extremely deficient soils,the importance of functions related to nutrient conversion were further improved,and followed by functions improving host stress tolerance.In this research,the succession characteristics of maize root-associated microbiome were evaluated by analyzing the structure of maize root microbiome at successive interval.Then,the characteristics of maize root microbiome assembly were investigated by transplanting among different soils.The "Soil microbiome determines while plant root selects"assembly of rhizosphere microbiome,was proposed.Next,a new functional assembly concept model of rhizosphere microbiome based on soil nutrient availability was constructed by rhizosphere microbiome ecological network analysis and PICRUSt function prediction.Finally,the model was validated and optimized by large-scale maize rhizosphere microbiome data.This study analyzed the structural and functional assembly characteristics of maize rhizosphere microbiome,and proposed the functional compensation of rhizosphere microbiome.The structural and functional assembly processes were driven by the functional requirements of plants.This study could lay a theoretical foundation for excavating and exerting the ecological function of rhizosphere microbiome in green agriculture development. |
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