Soil-plant compartments affect fungal microbiome diversity and composition in grapevine

Martínez-Diz, María del Pilar; Andrés-Sodupe, Marcos; Bujanda, Rebeca; Losada, Emilia Díaz; Eichmeier, Aleš; Gramaje, David

doi:10.1016/j.funeco.2019.07.003

Cited by 75 publications

(75 citation statements)

References 65 publications

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“…The remarkable differences between soil and root-associated fungal and oomycete communities described here have been already reported for multiple microbial groups and plant lineages. Studies on several plant species have found compartments, ranging from root-associated soil to the root endosphere, to be the strongest determinants of community variation, following patterns similar to those found here, both in fungi (Almario et al, 2017;Coleman-Derr et al, 2016;Durán et al, 2018;Martínez-Diz et al, 2019;Thiergart et al, 2019) and oomycetes Thiergart et al, 2019), but also in other microbial groups like protists (Sapp et al, 2018) and bacteria (Bulgarelli et al, 2012;Coleman-Derr et al, 2016;Durán et al, 2018;Edwards et al, 2015;Lundberg et al, 2012;Thiergart et al, 2019). Altogether, there is strong evidence that the root surface exerts a control on the entry of soil microorganisms into the root tissues.…”

Section: Discussionsupporting

confidence: 80%

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae

Thines

2020

Preprint

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AbstractThe plant family Brassicaceae includes some of the most studied hosts of plant microbiomes, targeting microbial diversity, community assembly rules, and effects on host performance. Compared to bacteria, eukaryotes in the brassicaceous microbiome remain understudied, especially under natural settings. Here, we assessed the impact of host identity and age on the assembly of fungal and oomycete root communities, using DNA metabarcoding of roots and associated soil of three annual co-habiting Brassicaceae collected at two time points. Our results showed that fungal communities are more diverse and structured than those of oomycetes. In both cases, plant identity and sampling time had little influence on community variation, whereas root/soil compartment had a strong effect by exerting control on the entry of soil microorganisms into the roots. The enrichment in roots of specific fungi suggests a specialization towards the asymptomatic colonization of plant tissues, which could be relevant to host’s fitness and health.

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Section: Discussionsupporting

confidence: 80%

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae

Thines

2020

Preprint

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“…For example, geographic distance had more influence over community structure of bacteria known to be poor dispersers/colonizers than good dispersers/colonizers ( Bissett et al, 2010 ). Furthermore, previous work on a more detailed analysis on the effect of soil-plant compartment, as previously done for grapevine fungal microbiomes ( Martínez-Diz et al, 2019 ), is adamant to fully understand the diversity and composition of grapevine microbiomes.…”

Section: Discussionmentioning

confidence: 99%

“…Plant genotypes exert an influence on the structural and functional diversity of soil microbiomes by varying root exudates and rhizodeposition ( Broeckling et al, 2008 ; Dias et al, 2013 ; Philippot et al, 2013 ). Additionally, soil-plant compartments (bulk soil, rhizosphere and endorhizosphere) have been found more dominant in shaping fungal communities diversity and composition than spatial variability ( Martínez-Diz et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing–Based Assessment of the Barossa Valley and Its Sub-Regions

et al. 2021

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A wines’ terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

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“…The presence of Cadophora spp. in soils has been recently confirmed using ITS high‐throughput amplicon sequencing (HTAS) approach 17 . Therefore, the main hypothesis is that these fungi could gain entry into the xylem of young plants at the nursery or newly established vineyards through root and/or basal end of the rootstock infections.…”

Section: Introductionmentioning

confidence: 99%

Field evaluation of biocontrol agents against black‐foot and Petri diseases of grapevine

Martínez-Diz

Losada

Andrés-Sodupe

et al. 2020

Pest Management Science

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BACKGROUND Black‐foot and Petri diseases are the main fungal diseases associated with young grapevine decline. Two field experiments were established to evaluate the preventive effect of two potential biocontrol agents (BCAs), that is Streptomyces sp. E1 + R4 and Pythium oligandrum Po37, and three BCA‐commercial products containing Trichoderma atroviride SC1, Trichoderma koningii TK7 and Pseudomonas fluorescens + Bacillus atrophaeus on fungal infection in grafted plants and plant growth parameters. RESULTS The effectiveness of some BCA in reducing the incidence and severity of both diseases was dependent on the plant part analyzed and the plant age. No single BCA application was able to control both diseases. Streptomyces sp. E1 + R4 were able to reduce significantly the infection of the most prevalent black‐foot disease fungi while P. oligandrum Po37 and Trichoderma spp. were able to reduce significantly Phaeomoniella chlamydospora and Phaeoacremonium minimum (Petri disease) infection. BCA treatments had no effect on the shoot weight, and root weight was significantly lower in all BCA treatments with respect to the control. CONCLUSIONS The combination of the disease‐suppressive activity of two or more beneficial microbes in a biocontrol preparation is required to prevent infection by black‐foot and Petri disease fungi in vineyards.

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Soil-plant compartments affect fungal microbiome diversity and composition in grapevine

Cited by 75 publications

References 65 publications

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing–Based Assessment of the Barossa Valley and Its Sub-Regions

Field evaluation of biocontrol agents against black‐foot and Petri diseases of grapevine

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