Growing Interest in Microbiome Research Unraveling Disease Suppressive Soils against Plant Pathogens

Toyota, Koki; Shirai, Sayo

doi:10.1264/jsme2.me3304rh

Cited by 16 publications

(15 citation statements)

References 32 publications

(37 reference statements)

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“…However, there is accumulating evidence showing the suppressive functions to be of the entire resident soil microbial community, instead of individual, beneficial microbial components (Toyota and Shira, 2018), and that the diversity of microbial taxonomic diversity is not linked to suppressiveness (Bonanomi et al, 2018). In fact, van Agtmaal et al (2018) showed that only a small portion of natural disease suppression (caused by volatile organic compounds) was explained by microbial community attributes.…”

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confidence: 99%

Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate

et al. 2020

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The soil-borne plant pathogens cause serious yield losses and are difficult to control. In suppressive soils, disease incidence remains low regardless of the presence of the pathogen, the host plant, and favorable environmental conditions. The potential to improve natural soil disease suppressiveness through agricultural management practices would enable sustainable and resilient crop production systems. Our aim was to study the impact of autumn tillage methods and crop sequence on the soil carbon status, fungistasis and yield in boreal climate. The disease suppression was improved by the long-term reduced and no tillage management practices with and without crop rotation. Compared to the conventional plowing, the non-inversion tillage systems were shown to change the vertical distribution of soil carbon fractions and the amount of microbial biomass by concentrating them on the soil surface. Crop sequence and the choice of tillage method had a combined effect on soil organic carbon (SOC) sequestration. The improved general disease suppression had a positive correlation with the labile carbon status and microbial biomass. From the most common Fusarium species, the predominantly saprophytic F. avenaceum was more abundant under noninversion practice, whereas the opposite was true for the pathogenic ones. Our findings furthermore demonstrated the correlation of the soil fungistasis laboratory assay results and the prevalence of the pathogenic test fungus Fusarium culmorum on the crop cereals in the field. Our results indicate that optimized management strategies have potential to improve microbial related soil fungistasis in boreal climate.

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confidence: 99%

Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate

et al. 2020

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“…Such disease-suppressive soils have been described for various soil-borne pathogens, including fungi, bacteria, oomycetes, and nematodes ( Mazzola, 2007 ; Kwak et al, 2018 ). To date, several microbial genera have been proposed as key players in disease suppressiveness of soils, but the complexity of the microbiome, as well as the underlying mechanisms and microbial traits, remain elusive for most disease suppressive soils ( Toyota and Shirai, 2018 ).…”

Section: Principles and Management Of Rhizosphere Microbiomes For Susmentioning

confidence: 99%

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

et al. 2020

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Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

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“…Elucidation of which methodologies may help with the assessment of effectiveness indicators of soil disease suppressiveness is needed. In this regard, sequencing, transcriptomics, quantitative PCR, metabolomics, and proteomics techniques are promising [132] . However, the link between potential antagonistic activity of the microbial community assessed by molecular methods (e.g., presence of genes coding for antagonistic properties) and the actual soil suppressiveness measured with bioassays as well as the predictive value for field conditions need to be established.…”

Section: General Remarks and Suggestions For Future Researchmentioning

confidence: 99%

Novel soil quality indicators for the evaluation of agricultural management practices: a biological perspective

Bongiorno¹

2020

Front. Agr. Sci. Eng.

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Developments in soil biology and in methods to characterize soil organic carbon can potentially deliver novel soil quality indicators that can help identify management practices able to sustain soil productivity and environmental resilience. This work aimed at synthesizing results regarding the suitability of a range of soil biological and biochemical properties as novel soil quality indicators for agricultural management. The soil properties, selected through a published literature review, comprised different labile organic carbon fractions [hydrophilic dissolved organic carbon, dissolved organic carbon, permanganate oxidizable carbon (POXC), hot water extractable carbon and particulate organic matter carbon], soil disease suppressiveness measured using a Pythium-Lepidium bioassay, nematode communities characterized by amplicon sequencing and qPCR, and microbial community level physiological profiling measured with MicroResp TM. Prior studies tested the sensitivity of each of the novel indicators to tillage and organic matter addition in ten European long-term field experiments (LTEs) and assessed their relationships with pre-existing soil quality indicators of soil functioning. Here, the results of these previous studies are brought together and interpreted relative to each other and to the broader body of literature on soil quality assessment. Reduced tillage increased carbon availability, disease suppressiveness, nematode richness and diversity, the stability and maturity of the food web, and microbial activity and functional diversity. Organic matter addition played a weaker role in enhancing soil quality, possibly due to the range of composition of the organic matter inputs used in the LTEs. POXC was the indicator that discriminated best between soil management practices, followed by nematode indices based on functional characteristics. Structural equation modeling shows that POXC has a central role in nutrient retention/supply, carbon sequestration, biodiversity conservation, erosion control and disease regulation/suppression. The novel indicators proposed here have great potential to improve existing soil quality assessment schemes. Their feasibility of application is discussed and needs for future research are outlined.

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Growing Interest in Microbiome Research Unraveling Disease Suppressive Soils against Plant Pathogens

Cited by 16 publications

References 32 publications

Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate

Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Novel soil quality indicators for the evaluation of agricultural management practices: a biological perspective

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