| Plant disease,which is responsible for around 10-20%losses of global food every year,can have severe threat to the sustainable development of world agriculture.Fusarium wilt,which is caused by the soil-borne fungus Fusarium oxysporum,is one of the most serious and destructive plant diseases,causing great economic losses to susceptible crops at the global level.Natural plants interact closely with a diverse community of soil microorganisms that form a shield against pathogens infection.Before causing disease,pathogens must break this first line of defense.Unbalanced emergence and proliferation of soil harmful microbes cause plant diseases,and in turn,rehabilitate and deploy the microbiomes can control pathogen populations and prevent plant diseases to maintain plant health.In this research,we used Fusarium wilt of banana as disease model.We used the traditional plate cultivation method,functional microbiome screening method,Biolog method,real time PCR method,and high-throughput sequencing method to explore 1)the effects of bio-organic fertilizer continuous application on banana plant health and soil microbial community composition,2)the effects of soil microbial community composition on the rhizosphere and endosphere microbiome assembly,3)the effects of bacterial inoculants,microbial populations naturally resident to the organic fertilizer and the physicalchemical properties of the compost substrate on banana plant health and soil bacterial community composition,4)the effects of fungal inoculants and sterile organic fertilizer on banana plant health and soil fungal community composition.This study aims to decipher the microbial ecological mechanisms of soil microbiome manipulation to induce soil suppressiveness and maintain plant health.Our main results are listed as followed:1.We conducted a long-term field experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over 9 crop years in response to the bio-organic fertilizer treatment.Effective suppression of banana Fusarium wilt by bio-organic fertilizer application were realized in recent five crop seasons,and significant lower F.oxysporum and higher Bacillus abundance was also observed.Significant different soil microbiome composition was observed during different crop seasons.By contrast,biofertilizer treatments significantly enhance the microbial community diversity and stability,as well as enrich the relative abundance of subgroup of Actinobacteria and Firmicutes.Random forest model results showed that microbial community diversity and structure,as well as Proteobacteria,Actinobacteria,Firmicutes,Chloroflexi and Gemmatimonadetes relative abundance variation were the most important variables for predicting Fusarium wilt disease incidence.At OTU level,most of the "legacy effects" bacterial OTUs which were associated with disease suppression were enriched in the bio-organic fertilizer treatment during further microbiome development across 5 crop years.Additionally,"legacy effects" OTUs showed synergy effects in suppressing pathogen in co-occurred network.2.By investigating the banana rhizosphere soil and root samples at the ninth crop year,we demonstrated modulate soil microbiome can significantly affect the rhizosphere and endosphere microbiome assembly.In bio-organic fertilizer treatment,significant lower pathogen abundance were observed in soil,rhizosphere and endosphere microbiome,with higher Bacillus abundance were observed in bulk and rhizosphere soil.Higher soil microbial community diversity decrease the diversity of rhizosphere fungal community in bio-organic fertilizer treated soil.The "legacy effects" of bulk soil on rhizosphere soil was prominent in bio-organic fertilizer treatment,which caused higher microbial community similarity between bulk and rhizosphere soil.Both rhizosphere and endosphere microbiome are significantly correlated with banana Fusarium wilt disease incidence,which are significantly affected by bulk soil.Random forest model results showed that soil bacterial community structure,rhizosphere bacterial and fungal community structures,rhizosphere fungal community diversity,endosphere bacterial and fungal community structures were the most important variables for predicting Fusarium wilt disease incidence.Furthermore,Gp1,Skermanella,Povalibacter,Bacillus,Bradyrhizobium,Geodermatophilus,Trichoderma,Penicilliopsis,Acremonium,Humicola,Purpureocillium and Aphanoascus were the potentially disease suppression microbial groups with soil-rhizosphere-endosphere "legacy effects".Therefore,a healthy microbiome in bulk soil is the basic for disease suppressive rhizosphere.3.To disentangle the mechanism of bio-organic fertilizer action,we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to bio-organic fertilizer,organic fertilizer,sterilized organic fertilizer and sterilized organic fertilizer supplemented with B.amyloliquefaciens treatments.We found that both of the two biofertilizer treatments could decrease the Fusarium wilt disease incidence during every crop seasons,and significantly decrease and increase the abundance of rhizosphere F.oxysporum and Bacillus,respectively.Fertilizers application significantly impact the resident soil microbial communities,in which the two biofertilizer treatments have more similar bacterial community.Structural equation modeling revealed that the rhizosphere bacterial community could directly and indirectly affect the incidence of Fusarium wilt disease with the important responsible of the increases in specific Pseudomonas spp..The link between Bacillus amendment and indigenous Pseudomonas spp.was further examined using pot experiments and biofilm assays.Bacillus and Pseudomonas were found to interact synergistically in biofilm formation and together they could be a plant-beneficial consortium to against FOC growth and its root colonization.Together we demonstrate that the action of bio-organic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome.4.Based on the results of long-term field experiment,we conducted a 3-season consecutive pot experiment with organic matter either containing a plant fungal probiotic(Trichoderma)or lacking this inoculum and subsequently tracked disease suppression and the soil fungal community.High-throughput sequencing of fungal ITS regions was complemented with cultivation-dependent methods for providing detailed insights into changes in environmental fungal communities and potential links with plant performance.Trichoderma application increased banana plant biomass by decreasing disease incidence,and this effect was attributed to changes in the fungal community composition including a reduction in Fusarium pathogen density and an increase in a Fusarium-suppressing fungal consortia comprised of Trichoderma and Humicola taxa.Trichoderma application also induced an increase in the fraction of saprotrophic fungi and range of microbial carbon resource utilization,features that may contribute to the disease suppression.The suppressive actions of Trichoderma and Humicola species against Fusarium were confirmed using lab and pot experiments,and results suggest that niche overlap would be a driving mechanism explaining the observed biocontrol efficacy for against pathogen infection.Together,we demonstrate that fungal inoculants can modify the composition and functioning of the resident soil fungal microbiome to become pathogen suppressive.In conclusion,we show that bio-organic fertilizer application can positively modulate soil microbiome,and the beneficial "legacy effects" of soil microbes on rhizosphere and endosphere microbiome was associated with disease suppression.The action of bio-organic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impacts on the resident soil microbiome,in particular the synergistic effects among introduced biocontrol agents with soil native beneficial microbial groups enhance the disease suppression effects. |
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