Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

Lee, Sang Moo; Kong, Hyun Gi; Song, Geun Cheol; Ryu, Choong‐Min

doi:10.1038/s41396-020-00785-x

Cited by 260 publications

(217 citation statements)

References 93 publications

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“…Importantly, we further found that isolates presumably related to keystone taxa have inhibitory effects on the pathogen and reduction of bacterial wilt disease incidence, highlighting the importance of keystone taxa in suppressing disease. Large numbers of previous studies have analyzed the soil microbial community, abundance, and diversity when bacterial wilt disease outbreak (Wang et al, 2017b;Qi et al, 2019;Wei et al, 2019;Lee et al, 2020). As they reported, we also found that the relative abundance of Firmicutes was higher in the suppressive soil compared to that in the conducive soil ( Figure 3A).…”

Section: Discussionsupporting

confidence: 75%

Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy

et al. 2021

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Recent studies have observed differing microbiomes between disease-suppressive and disease-conducive soils. However, it remains unclear whether the microbial keystone taxa in suppressive soil are critical for the suppression of diseases. Bacterial wilt is a common soil-borne disease caused by Ralstonia solanacearum that affects tobacco plants. In this study, two contrasting tobacco fields with bacterial wilt disease incidences of 0% (disease suppressive) and 100% (disease conducive) were observed. Through amplicon sequencing, as expected, a high abundance of Ralstonia was found in the disease-conducive soil, while large amounts of potential beneficial bacteria were found in the disease-suppressive soil. In the fungal community, an abundance of the Fusarium genus, which contains species that cause Fusarium wilt, showed a positive correlation (p < 0.001) with the abundance of Ralstonia. Network analysis revealed that the healthy plants had more complex bacterial networks than the diseased plants. A total of 9 and 13 bacterial keystone taxa were identified from the disease-suppressive soil and healthy root, respectively. Accumulated abundance of these bacterial keystones showed a negative correlation (p < 0.001) with the abundance of Ralstonia. To complement network analysis, culturable strains were isolated, and three species belonging to Pseudomonas showed high 16S rRNA gene similarity (98.4–100%) with keystone taxa. These strains displayed strong inhibition on pathogens and reduced the incidence of bacterial wilt disease in greenhouse condition. This study highlighted the importance of keystone species in the protection of crops against pathogen infection and proposed an approach to obtain beneficial bacteria through identifying keystone species, avoiding large-scale bacterial isolation and cultivation.

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Section: Discussionsupporting

confidence: 75%

Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy

et al. 2021

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“…This is consistent with the finding that Proteobacteria, Actinobacteria and Ascomycota are the most abundant phyla in plants and soil (24, 64). Actinobacteria is one of the bacteria whose dysbiosis in abundance in tomato rhizosphere causes the incidence of bacterial wilt disease (12).…”

Section: Discussionmentioning

confidence: 99%

“…Actinobacteria is one of the bacteria whose dysbiosis in abundance in tomato rhizosphere causes the incidence of bacterial wilt disease (12).…”

Section: Hub Microbesmentioning

confidence: 99%

“…Many studies have characterized strong associations between the microbiota and a variety of human disorders (1)(2)(3)(4), but research on how the microbiota impacts plant growth has not been conducted until recently (5,6). Increasing evidence shows that the microbiota plays a pivotal role in promoting plants' stress tolerance, determining plant productivity, improving the bioavailability of nutrients, and preventing invasion by bacterial pathogens (5,(7)(8)(9)(10)(11)(12). Some bacteria can fix and preserve nitrogen in root nodules for plants (13,14), whereas others even can modulate the timing of flowering of plants (15,16) and save hosts from extinction (17).…”

Section: Introductionmentioning

confidence: 99%

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Network mapping of root-microbe interactions inArabidopsis thaliana

Zhang

Jin

et al. 2020

Preprint

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Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are based on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic architecture of microbial interactions that are thought to a determinant of microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs and find 91 hub QTLs. Gene annotation shows that a number of the hub genes detected are biologically relevant, playing roles in plant growth and development, resilience against pathogens, root development, and improving resistance against abiotic stress conditions. The new model allows us to better understand the underlying mechanisms that govern the relationships between plants and their entire microbiota and harness soil microbes for plant production.

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“…There is an established concept of soil disease suppressiveness, which implies that natural soils can suppress the pathogens; however, this phenomenon varies and depends, among others, on cropping years, crop species, and soil types [3,4]. Generally, the soil is considered the disease-suppressive when it keeps most plants healthy, while the converse is true for the disease-conducive soil [5,6]. The adoption of some farm management and soil conservation practices such as using organic fertilizers, amendments, and crop rotation can enhance the soil disease suppressiveness [7,8].…”

Section: Introductionmentioning

confidence: 99%

Soil Phosphorus Availability Determines the Invasion of Rhizospheric Microbial Networks and Peanut Infection by Ralstonia

Li¹,

Liu²,

Li³

et al. 2020

Preprint

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Background The soil disease-suppressiveness may depend on complex interactions between pathogens and microbiome in response to limiting nutrients. However, these interactions remain poorly understood. Thus, we investigated the significance of soil available phosphorus (AP) in modulating pathogen-microbiome interactions for the emergence or suppression of peanut wilt using receiver operating characteristic curve (ROC) analysis and structural equation modeling (SEM) approaches. Results We observed significant differences in the relative abundance of pathogenic and beneficial microbes, alpha- and beta-diversity indices between disease-conducive and -suppressive soils. The pathogenic ( Ralstonia) and beneficial ( Burkholderia and Bacillus ) taxa dominated the rhizosphere of wilted and healthy peanut plants. The rhizosphere of healthy rather than wilted plants showed significantly higher microbial biodiversity. Moreover, co-occurrences between Ralstonia and microbiome species were highly positive and negative in the disease-conducive and -suppressive soil, respectively, thus predicting facilitative ( Rudaea ) and suppressive ( Burkholderia , Enterobacter , Bacillus ) role of indigenous microbes in Ralstonia invasion in soil. Moreover, both ROC and SEM analyses revealed that Ralstonia invaded rhizospheric microbial networks and caused peanut wilt, very likely by competently utilizing soil phosphorus under copiotrophic (high AP) than oligotrophic (low AP) conditions. Conclusion Our results suggest the importance of soil phosphorus availability in altering the interactions between pathobiome and beneficial microbiome. Our study concludes that feeding soil with labile nutrients could deplete microbial biodiversity and interactions while paving the way for pathogen invasion.

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Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

Cited by 260 publications

References 93 publications

Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy

Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy

Network mapping of root-microbe interactions inArabidopsis thaliana

Soil Phosphorus Availability Determines the Invasion of Rhizospheric Microbial Networks and Peanut Infection by Ralstonia

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