Legacy of land use history determines reprogramming of plant physiology by soil microbiome

Li, Yong; Jousset, Alexandre; Boer, Wietse de; Carrión, Víctor J.; Zhang, Taolin; Wang, Xingxiang; Kuramae, Eiko E.

doi:10.1038/s41396-018-0300-0

Cited by 194 publications

(151 citation statements)

References 90 publications

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“…P -value adjustments for multiple comparisons were performed using the false discovery rate (FDR) correction [ 63 ]. Fold change of each OTU in treatments with the biocontrol agent (OF+W19 and SOF+W19) relative those without the biocontrol agent (OF and SOF) was calculated using the following formula: (B-N)/N, B is the relative abundance of a given OTU in Bacillus positive (OF+W19 and SOF+W19) samples and N represents the relative abundance of that OTU in Bacillus negative (OF and SOF) samples [ 64 ]. Structural equation modelling (SEM) was applied to evaluate the direct and indirect contributions of soil microbial community (bulk and rhizosphere soil) and F. oxysporum pathogen density to disease incidence [ 65 ].…”

Section: Methodsmentioning

confidence: 99%

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

et al. 2020

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Background Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. Results 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 the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. Conclusion Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.

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Section: Methodsmentioning

confidence: 99%

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

et al. 2020

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“…P-value adjustments for multiple comparisons were performed using the false discovery rate (FDR) correction [63]. Fold change of each OTU in treatments with the biocontrol agent (OF+W19 and SOF+W19) relative those without the biocontrol agent (OF and SOF) was calculated using the following formula: (B-N)/N, B is the relative abundance of a given OTU in Bacillus positive samples (OF+W19 and SOF+W19) samples and N represents the relative abundance of that OTU in Bacillus negative (OF and SOF) samples [64]. Structural equation modelling (SEM) was applied to evaluate the direct and indirect contributions of soil microbial community (bulk and rhizosphere soil) and F. oxysporum pathogen density to disease incidence [65].…”

Section: Statistical Analysesmentioning

confidence: 99%

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Tao

Xiong

et al. 2020

Preprint

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Background: Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers.Results: 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 the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer. We further observed that disease suppression in these treatments could be linked to impacts on the resident soil microbial communities, with noted increases in specific Pseudomonas spp.. The link between Bacillus amendment and indigenous Pseudomonas spp. was further examined using pot experiments and biofilm assays. Conclusion: Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.

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“…Moreover, most of such studies have been conducted on different vineyards or soils located in different areas, thus providing severe limitations for the assignment of any soil microbial taxa/groups associated to a specific vine plant. In fact, it is well-known that microbial community structure and biogeography change with environmental variations and are primarily controlled by edaphic features (Fierer and Jackson, 2006;Kuramae et al, 2012;Burns et al, 2015;Li et al, 2019). Thus, in order to assess the role of soil microbial diversity and functions in determining grape and wine quality, it is essential to minimize the environmental variability and conduct the research at a within-vineyard scale, in the same soil or among similar soils.…”

Section: Introductionmentioning

confidence: 99%

Microbial Functional Diversity in Vineyard Soils: Sulfur Metabolism and Links With Grapevine Plants and Wine Quality

Mocali

Kuramae

Kowalchuk

et al. 2020

Front. Environ. Sci.

Self Cite

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The quality of the vineyard soils has a direct impact on grapes and wine quality and represents a key component of the "Terroir concept." However, information on the impact of soil microbiota on grapevine plants and wine quality are generally lacking. In fact, over the last few years most of the attempts made to correlate soil microbial communities and wine quality were limited by overlooking both the functional traits of soil microbiota and the spatial variability of vineyards soils. In this work, we used a functional gene microarray approach (GeoChip) and soil enzymatic analyses to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a "within-vineyard" scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar (BRO12 exhibited the higher quality). Our results showed an enrichment of Actinobacteria in BRO12, whereas Alfa-and Gamma-Proteobacteria were more abundant in BRO11, where an enrichment of bacteria involved in N fixation and denitrification occurred. Overall, the GeoChip output revealed a greater biological activity in BRO11 but a significant enrichment of sulfur-oxidation genes in BRO12 compared to BRO11 soil, where a higher level of arylsulfatase activity was also detected. Moreover, the low content of sulfates and available nitrogen found in BRO12 suggested that the reduced availability of sulfates for vine plants might limit the reduced glutathione (GSH) synthesis, which plays an important role in aroma protection in musts and wines. In conclusion, in addition to nitrogen availability, we propose that soil microbial sulfur metabolism may also play a key role in shaping plant physiology, grapes and wine quality. Overall, these results support the existence of a "microbial functional terroir" effect as a determining factor in vineyard-scale variation among wine grapes.

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Legacy of land use history determines reprogramming of plant physiology by soil microbiome

Cited by 194 publications

References 90 publications

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Microbial Functional Diversity in Vineyard Soils: Sulfur Metabolism and Links With Grapevine Plants and Wine Quality

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