The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere ...The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.展开更多
Modern breeding primarily targets crop yield traits and is likely to influence root-associated microbiomes, which play significant roles in plant growth and health. The relative importance of soil and cultivar factors...Modern breeding primarily targets crop yield traits and is likely to influence root-associated microbiomes, which play significant roles in plant growth and health. The relative importance of soil and cultivar factors in shaping root-associated microbiomes of modern maize (Zea mays L.) remains uncertain. We conducted a pot experiment in a controlled environment using three soils (Mollisol, Inceptisol, and Ultisol) and four contrasting cultivars, Denghai 605, Nonghua 816, Qiaoyu 8, and Zhengdan 958, which are widely planted in China. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities in the bulk soil, rhizosphere, and endosphere. Our results showed that the four cultivars had different shoot biomass and root exudate total organic carbon and organic acid contents. The microbiomes in the bulk soil, rhizosphere, and endosphere were different. We observed apparent community divergence between soils rather than cultivars, within which edaphic factors substantially contributed to microbiome variation. Moreover, permutational multivariate analysis of variance corroborated significant contributions of soil type but not cultivar on the root-associated microbiome structure. Differential abundance analysis confirmed that each soil presented a distinct root microbiome, while network analysis indicated different co-occurrence patterns of the root microbiome among the three soils. The core root microbiome members are implicated in plant growth promotion and nutrient acquisition in the roots. In conclusion, root-associated microbiomes of modern maize are much more controlled by soil characteristics than by cultivar root exudation. Our study is anticipated to help improve breeding strategies through integrative interactions of soils, cultivars, and their associated microbiomes.展开更多
The root microdomain represents a“hot spot”where microorganisms play a pivotal role in driving ecological processes and interact intimately with the host plants.In this study,we investigated 11 indica and 4 japonica...The root microdomain represents a“hot spot”where microorganisms play a pivotal role in driving ecological processes and interact intimately with the host plants.In this study,we investigated 11 indica and 4 japonica rice varieties as test crops and analyzed the structural and functional characteristics of the microbial communities in the rhizosphere,rhizoplane and root endosphere ofindica and japonica rice using high-throughput sequencing technology.Our findings reveal that,during the assembly process within the root microdomain,community diversity gradually decreases,while the filtering effect of the rice root intensifies from the rhizosphere to the root endosphere.Gammaproteobacteria tended to be recruited by both indica and japonica rice,while Clostridia and Betaproteobacteria were specifically recruited by japonica rice to colonize the rhizoplane and root endosphere.In contrast,Bacteroidia were depleted in the root microdomain of both indica and japonica rice,whereas Deltaproteobacteria and Nitrospira were specifically depleted in the root microdomain of indica rice.Compared to japonica rice,the bacteria enriched in the root microdomain of indica rice were primarily affiliated with Bacillales,Pseudomonadales,and Nitrospirales.Moreover,the indica rice had a lower number of instances of co-occurrence(edge/node ratio),network density and degree,while displayed a higher number of modularity,among-module connectivities,average path length and closeness centrality compared with japonica rice.These findings provide detailed insights into the assembly process of the microbiome in the root microdomain of different rice cultivars,as well as host genotype-regulated changes in microbial communities.展开更多
Soil microbiomes play a crucial role in maintaining ecological functions and are of great importance for soil health.Some of them could bring benefits to plants for growth promotion.Despite numerous studies have focus...Soil microbiomes play a crucial role in maintaining ecological functions and are of great importance for soil health.Some of them could bring benefits to plants for growth promotion.Despite numerous studies have focused on specific beneficial bacteria and their interactions with soils and plants,we still lack a comprehensive understanding of beneficial communities in plant–soil continuums and their responses to agricultural activities.To address this gap,we carried out a microcosm experiment using 16S rRNA amplicon sequencing to explore the effects of organic fertilization on beneficial communities in plant–soil continuums and assess their potential multifunctionality.Our findings reveal that organic fertilization had a positive impact on the beneficial functionality of bacterial communities in plant–soil continuums.This improvement was primarily attributed to the optimized soil physicochemical conditions resulting from organic fertilization.Additionally,organic fertilization increased the complexity of bacterial co-occurrence networks in both soils and the endosphere.Keystone taxa in the endosphere undergone a shift of functions toward pathogen suppression as the result of organic fertilization.Furthermore,this study revealed that plants exhibited a preference for internalizing beneficial bacteria over other type of bacteria.We also provided new insights for evaluating the multifunctionality of microbiomes,and found that the functionality of beneficial communities in plant–soil continuums is enhanced by organic fertilization.All these findings suggested that organic fertilization can be an effective strategy for maintaining plant and soil health.展开更多
基金supported by the National Natural Science Foundation of China (Nos. 41907212 , 42007224 and 41907285 )GDAS' Project of Science and Technology Development (Nos. 2020GDASYL-20200103082 , 2020GDASYL-20200102015 , 2020GDASYL-20200102014 , 2019GDASYL-0301002 and 2018GDASCX-0106 )+2 种基金the Science and Technology Planning Project of Guangzhou (No. 202002020072 )China Postdoctoral Science Foundation funded Project (No. 2020T130127 )the High-Level Talents Project of the Pearl River Talents Recruitment Program (No. 2017GC010570 )。
文摘The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.
基金financially supported by the National Key Research and Development Program of China (Nos. 2016YFD0200107 and 2016YFD0300802)the Key Deployment Program of Chinese Academy of Sciences (No. KFZD-SW-108)+4 种基金the Science and Technology Services Program of Chinese Academy of Sciences (No. KFJ-STS-ZDTP-054)the Earmarked Fund for China Agriculture Research System (No. CARS-03)the National Natural Science Foundation of China (No. 41807017)the Natural Science Foundation of Jiangsu Province, China (No. BK20171106)the Open Foundation of State Key Laboratory of Soil and Sustainable Agriculture of China (No. Y20160014)
文摘Modern breeding primarily targets crop yield traits and is likely to influence root-associated microbiomes, which play significant roles in plant growth and health. The relative importance of soil and cultivar factors in shaping root-associated microbiomes of modern maize (Zea mays L.) remains uncertain. We conducted a pot experiment in a controlled environment using three soils (Mollisol, Inceptisol, and Ultisol) and four contrasting cultivars, Denghai 605, Nonghua 816, Qiaoyu 8, and Zhengdan 958, which are widely planted in China. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities in the bulk soil, rhizosphere, and endosphere. Our results showed that the four cultivars had different shoot biomass and root exudate total organic carbon and organic acid contents. The microbiomes in the bulk soil, rhizosphere, and endosphere were different. We observed apparent community divergence between soils rather than cultivars, within which edaphic factors substantially contributed to microbiome variation. Moreover, permutational multivariate analysis of variance corroborated significant contributions of soil type but not cultivar on the root-associated microbiome structure. Differential abundance analysis confirmed that each soil presented a distinct root microbiome, while network analysis indicated different co-occurrence patterns of the root microbiome among the three soils. The core root microbiome members are implicated in plant growth promotion and nutrient acquisition in the roots. In conclusion, root-associated microbiomes of modern maize are much more controlled by soil characteristics than by cultivar root exudation. Our study is anticipated to help improve breeding strategies through integrative interactions of soils, cultivars, and their associated microbiomes.
基金supported by the National Key R&D Program of China(Grant No.2023YFD2301400)the National Natural Science Foundation of China(Grant Nos.42207343,42307387).
文摘The root microdomain represents a“hot spot”where microorganisms play a pivotal role in driving ecological processes and interact intimately with the host plants.In this study,we investigated 11 indica and 4 japonica rice varieties as test crops and analyzed the structural and functional characteristics of the microbial communities in the rhizosphere,rhizoplane and root endosphere ofindica and japonica rice using high-throughput sequencing technology.Our findings reveal that,during the assembly process within the root microdomain,community diversity gradually decreases,while the filtering effect of the rice root intensifies from the rhizosphere to the root endosphere.Gammaproteobacteria tended to be recruited by both indica and japonica rice,while Clostridia and Betaproteobacteria were specifically recruited by japonica rice to colonize the rhizoplane and root endosphere.In contrast,Bacteroidia were depleted in the root microdomain of both indica and japonica rice,whereas Deltaproteobacteria and Nitrospira were specifically depleted in the root microdomain of indica rice.Compared to japonica rice,the bacteria enriched in the root microdomain of indica rice were primarily affiliated with Bacillales,Pseudomonadales,and Nitrospirales.Moreover,the indica rice had a lower number of instances of co-occurrence(edge/node ratio),network density and degree,while displayed a higher number of modularity,among-module connectivities,average path length and closeness centrality compared with japonica rice.These findings provide detailed insights into the assembly process of the microbiome in the root microdomain of different rice cultivars,as well as host genotype-regulated changes in microbial communities.
基金supported by the State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products(No.2021DG700024-KF202307).
文摘Soil microbiomes play a crucial role in maintaining ecological functions and are of great importance for soil health.Some of them could bring benefits to plants for growth promotion.Despite numerous studies have focused on specific beneficial bacteria and their interactions with soils and plants,we still lack a comprehensive understanding of beneficial communities in plant–soil continuums and their responses to agricultural activities.To address this gap,we carried out a microcosm experiment using 16S rRNA amplicon sequencing to explore the effects of organic fertilization on beneficial communities in plant–soil continuums and assess their potential multifunctionality.Our findings reveal that organic fertilization had a positive impact on the beneficial functionality of bacterial communities in plant–soil continuums.This improvement was primarily attributed to the optimized soil physicochemical conditions resulting from organic fertilization.Additionally,organic fertilization increased the complexity of bacterial co-occurrence networks in both soils and the endosphere.Keystone taxa in the endosphere undergone a shift of functions toward pathogen suppression as the result of organic fertilization.Furthermore,this study revealed that plants exhibited a preference for internalizing beneficial bacteria over other type of bacteria.We also provided new insights for evaluating the multifunctionality of microbiomes,and found that the functionality of beneficial communities in plant–soil continuums is enhanced by organic fertilization.All these findings suggested that organic fertilization can be an effective strategy for maintaining plant and soil health.
