The root microbiome refers to the community of microbes living in association with a plant's roots,and includes mutualists,pathogens,and commensals.Here we focus on recent advances in the study of root commensal c...The root microbiome refers to the community of microbes living in association with a plant's roots,and includes mutualists,pathogens,and commensals.Here we focus on recent advances in the study of root commensal community which is the major research object of microbiomerelated researches.With the rapid development of new technologies,plant-commensal interactions can be explored with unprecedented breadth and depth.Both the soil environment and the host plant drive commensal community assembly.The bulk soil is the seed bank of potential commensals,and plants use root exudates and immune responses to build healthy microbial communities from the available microbes.The plant microbiome extends the functional system of plants by participating in a variety of processes,including nutrient absorption,growth promotion,and resistance to biotic and abiotic stresses.Plants and their microbiomes have evolved adaptation strategies over time.However,there is still a huge gap in our understanding of the regulatory mechanisms of plant-commensal interactions.In this review,we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development,and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome.展开更多
Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relat...Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa.However,this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues.Here,we report the development of a host-associated quantitative abundance profiling(HA-QAP)method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome.We validate the HAQAP method using mock experiments,perturbation experiments,and metagenomic sequencing.The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance,and reveals the load of root microbiome to host plants.Using the HA-QAP method,we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat.Furthermore,using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease,which significantly influences patterns of differential taxa and species interaction networks.Given its accuracy and technical feasibility,HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.展开更多
Assisted natural remediation(ANR)has been highlighted as a promising,less expensive,and environmentally friendly solution to remediate soil contaminated with heavy metals.We tested the effects of three amendments(10%c...Assisted natural remediation(ANR)has been highlighted as a promising,less expensive,and environmentally friendly solution to remediate soil contaminated with heavy metals.We tested the effects of three amendments(10%compost,C;5 or 15%phosphate sludge,PS5 and PS15;and 5 or 15%marble waste,MW5 and MW15)in combination with microorganism inoculation(rhizobacteria consortium alone,mycorrhizae alone,and the two incombination)on alfalfa in contaminated soil.Plant concentrations of Zn,Cu,and Pb were measured,along with proline and malondialdehyde production.The microbiological and physicochemical properties of the mining soil were evaluated.Application of the amendments allowed germination and promoted growth.Inoculation with the rhizobacteria consortium and/or mycorrhizae stimulated plant growth.PS and MW stimulated the production of proline.Inoculation of alfalfa with the rhizobacteria-mycorrhizae mixture and the application of MW allowed the safe cultivation of the legume,as shown by the low concentrations of metals in plant shoots.Zn and Pb concentrations were below the limits recommended for animal grazing and accumulated essentially in roots.Soil analyses showed the positive effect of the amendments on the soil physicochemical properties.All treatments increased soil p H(around 7),total organic carbon,and assimilable phosphorus content.Notably,an important decrease in soluble heavy metals concentrations was observed.Overall,our findings revealed that the applied treatments reduced the risk of metal-polluted soils limiting plant growth.The ANR has great potential for success in the restoration of polymetallic and acidic mining soils using the interaction between alfalfa,microorganisms,and organomineral amendments.展开更多
Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil type...Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil types and fertilization regimes affect both soil and root microbiome is still lacking,such as how fertilization regimes affect the root microbiome's stability,and whether it follows the same patterns as the soil microbiome.In this study,we carried out a longterm experiment to see how different soil types,plant varieties,and fertilizer regimens affected the soil and root bacterial communities.Our results revealed higher stability of microbial networks under combined organic-inorganic fertilization than those relied solely on inorganic or organic fertilization.The root microbiome variation was predominantly caused by total nitrogen,while the soil microbiome variation was primarily caused by pH and soil organic matter.Bacteroidetes and Firmicutes were major drivers when the soil was amended with organic fertilizer,but Actinobacteria was found to be enriched in the soil when the soil was treated with inorganic fertilizer.Our findings demonstrate how the soil and root microbiome respond to diverse fertilizing regimes,and hence contribute to a better understanding of smart fertilizer as a strategy for sustainable agriculture.展开更多
Salicylic acid(SA)is widely recognized as the active ingredient in the commonly used medication aspirin.In plants,SA is best known for its crucial role in plant defense against biotrophic and hemibiotrophic pathogens(...Salicylic acid(SA)is widely recognized as the active ingredient in the commonly used medication aspirin.In plants,SA is best known for its crucial role in plant defense against biotrophic and hemibiotrophic pathogens(Fu and Dong,2013;Peng et al.,2021).In addition,SA has been documented to play important roles in plant adaptation to abiotic stresses,plant growth and development,stomatal closure,thermogenesis,and structuring root microbiome(Vlot et al.,2009;Wang et al.,2025).展开更多
The objective of this study was to investigate the combined effect of soil amendments and pest attack on plant-induced defense and their impact on a biological control agent’s behavior.The effects of olive mill waste...The objective of this study was to investigate the combined effect of soil amendments and pest attack on plant-induced defense and their impact on a biological control agent’s behavior.The effects of olive mill wastes revalorized through vermicomposting on the aboveground tri-trophic interactions among olive trees(Olea europaea),the olive seed-feeder,Prays oleae,and its natural predator,Chrysoperla carnea,were evaluated.The findings demonstrate that soil nitrogen and organic carbon levels,in conjunction with fungal diversity and functionality within olive roots,exert a significant influence on the volatile compounds emitted by the plant under attack that are most appealing to C.carnea.Moreover,the attractiveness of aerial volatiles was found to correlate with soil organic carbon content and the taxonomic and functional diversity of both bacteria and fungi in the olive root system.It is worthy of note that three particular volatile compounds,namely 5-hepten-2-one-6-methyl,acetic acid and nonanal,were consistently observed to attract C.carnea.These findings highlight the potential of soil amendments to enhance biological control strategies.Future research should prioritise the validation the greenhouse findings through large-scale field trials and the assessment of the practical applications of soil amendments in pest management programmes.展开更多
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24020104,XDA28030202)the National Natural Science Foundation of China(31772400,31801945)+3 种基金the Hainan Yazhou Bay Seed Laboratory(B21HJ0102)the Team of precise rice breedingthe Innovation Program of SAAS(CXGC2016C06)the Chinese Academy of Sciences Youth Innovation Promotion Association(2020101)。
文摘The root microbiome refers to the community of microbes living in association with a plant's roots,and includes mutualists,pathogens,and commensals.Here we focus on recent advances in the study of root commensal community which is the major research object of microbiomerelated researches.With the rapid development of new technologies,plant-commensal interactions can be explored with unprecedented breadth and depth.Both the soil environment and the host plant drive commensal community assembly.The bulk soil is the seed bank of potential commensals,and plants use root exudates and immune responses to build healthy microbial communities from the available microbes.The plant microbiome extends the functional system of plants by participating in a variety of processes,including nutrient absorption,growth promotion,and resistance to biotic and abiotic stresses.Plants and their microbiomes have evolved adaptation strategies over time.However,there is still a huge gap in our understanding of the regulatory mechanisms of plant-commensal interactions.In this review,we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development,and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome.
基金This work is financially supported by the National Natural Science Foundation of China(grant nos.31772400,31761143017)the National Natural Science Foundation for Young Scientists of China(grant no.31701997)+1 种基金the Key Research Program of the Chinese Academy of Sciences(grant nos.KFZD-SW-112-02-02 and KFZD-SW-219)the Key Research Program of Frontier Sciences,CAS(grant no.QYZDB-SSW-SMC021).
文摘Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa.However,this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues.Here,we report the development of a host-associated quantitative abundance profiling(HA-QAP)method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome.We validate the HAQAP method using mock experiments,perturbation experiments,and metagenomic sequencing.The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance,and reveals the load of root microbiome to host plants.Using the HA-QAP method,we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat.Furthermore,using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease,which significantly influences patterns of differential taxa and species interaction networks.Given its accuracy and technical feasibility,HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.
基金supported by PPR2/2016/42 project(CNRST Morocco)KAKENHI Grants-in-Aid for Scientific Research(A)(15H02486)from Japan Society for the Promotion of Sciences+1 种基金Strategic International Collaborative Research Program by the Japan Science and Technology Agency(JPMJSC16C5)Grant for Promotion of KAAB Projects(Niigata University)from the Ministry of Education,Culture,Sports,Science,and Technology,Japan。
文摘Assisted natural remediation(ANR)has been highlighted as a promising,less expensive,and environmentally friendly solution to remediate soil contaminated with heavy metals.We tested the effects of three amendments(10%compost,C;5 or 15%phosphate sludge,PS5 and PS15;and 5 or 15%marble waste,MW5 and MW15)in combination with microorganism inoculation(rhizobacteria consortium alone,mycorrhizae alone,and the two incombination)on alfalfa in contaminated soil.Plant concentrations of Zn,Cu,and Pb were measured,along with proline and malondialdehyde production.The microbiological and physicochemical properties of the mining soil were evaluated.Application of the amendments allowed germination and promoted growth.Inoculation with the rhizobacteria consortium and/or mycorrhizae stimulated plant growth.PS and MW stimulated the production of proline.Inoculation of alfalfa with the rhizobacteria-mycorrhizae mixture and the application of MW allowed the safe cultivation of the legume,as shown by the low concentrations of metals in plant shoots.Zn and Pb concentrations were below the limits recommended for animal grazing and accumulated essentially in roots.Soil analyses showed the positive effect of the amendments on the soil physicochemical properties.All treatments increased soil p H(around 7),total organic carbon,and assimilable phosphorus content.Notably,an important decrease in soluble heavy metals concentrations was observed.Overall,our findings revealed that the applied treatments reduced the risk of metal-polluted soils limiting plant growth.The ANR has great potential for success in the restoration of polymetallic and acidic mining soils using the interaction between alfalfa,microorganisms,and organomineral amendments.
基金supported by the National Key Research and Development Program of China(Grant No.2021YFD1700900)the National Natural Science Foundation of China(Grant No.31972519)the Taishan Industry Leading Talents HighEfficiency Agriculture Innovation Project(Grant No.LJNY202125).
文摘Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil types and fertilization regimes affect both soil and root microbiome is still lacking,such as how fertilization regimes affect the root microbiome's stability,and whether it follows the same patterns as the soil microbiome.In this study,we carried out a longterm experiment to see how different soil types,plant varieties,and fertilizer regimens affected the soil and root bacterial communities.Our results revealed higher stability of microbial networks under combined organic-inorganic fertilization than those relied solely on inorganic or organic fertilization.The root microbiome variation was predominantly caused by total nitrogen,while the soil microbiome variation was primarily caused by pH and soil organic matter.Bacteroidetes and Firmicutes were major drivers when the soil was amended with organic fertilizer,but Actinobacteria was found to be enriched in the soil when the soil was treated with inorganic fertilizer.Our findings demonstrate how the soil and root microbiome respond to diverse fertilizing regimes,and hence contribute to a better understanding of smart fertilizer as a strategy for sustainable agriculture.
基金supported by the National Science Foundation(IOS-2207677 to Z.Q.F.)the National Natural Science Foundation of China(32472527 to F.L.and 32300164 and 32460045 to K.L.)the Guizhou Provincial Basic Research Program(Natural Science)(Qian Ke He Ji Chu-ZK[2023]General 095 to K.L.).
文摘Salicylic acid(SA)is widely recognized as the active ingredient in the commonly used medication aspirin.In plants,SA is best known for its crucial role in plant defense against biotrophic and hemibiotrophic pathogens(Fu and Dong,2013;Peng et al.,2021).In addition,SA has been documented to play important roles in plant adaptation to abiotic stresses,plant growth and development,stomatal closure,thermogenesis,and structuring root microbiome(Vlot et al.,2009;Wang et al.,2025).
基金supported by grant P20-00139 funded by Consejería de Transformación Económica,Industria,Conocimiento y Universidades,Junta de Andalucía,and by“ERDF A way of making EuropeOpen Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature.
文摘The objective of this study was to investigate the combined effect of soil amendments and pest attack on plant-induced defense and their impact on a biological control agent’s behavior.The effects of olive mill wastes revalorized through vermicomposting on the aboveground tri-trophic interactions among olive trees(Olea europaea),the olive seed-feeder,Prays oleae,and its natural predator,Chrysoperla carnea,were evaluated.The findings demonstrate that soil nitrogen and organic carbon levels,in conjunction with fungal diversity and functionality within olive roots,exert a significant influence on the volatile compounds emitted by the plant under attack that are most appealing to C.carnea.Moreover,the attractiveness of aerial volatiles was found to correlate with soil organic carbon content and the taxonomic and functional diversity of both bacteria and fungi in the olive root system.It is worthy of note that three particular volatile compounds,namely 5-hepten-2-one-6-methyl,acetic acid and nonanal,were consistently observed to attract C.carnea.These findings highlight the potential of soil amendments to enhance biological control strategies.Future research should prioritise the validation the greenhouse findings through large-scale field trials and the assessment of the practical applications of soil amendments in pest management programmes.
