Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes

Cureau, Natacha; Threlfall, Renee T.; Savin, Mary C.; Marasini, Daya; Lavefve, Laura; Carbonero, Franck

doi:10.1007/s00248-021-01698-8

Cited by 12 publications

(9 citation statements)

References 55 publications

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“…Our results showed that Mortierella was one of the most abundant genera found in the rhizosphere and bulk soil, accounting for 9 to 17% and 14 to 20% of the relative abundance of all genera, respectively. Similar results were found in previous grapevine studies, in which Mortierellaceae was the most abundant family in the bulk soil and rhizosphere, and Mortierella was the most dominant genus in the root-zone soil and showed lower abundances in the plant-compartments (root, leaf, flower, and grape) [ 27 , 30 , 63 ]. The genus Mortierella is a phosphate solubilizing fungus which plays an important role in the phosphorus cycling in the rhizosphere [ 64 ].…”

Section: Discussionsupporting

confidence: 90%

“…On the other hand, in a previous research conducted in Spain, Berlanas et al [ 29 ] observed a non-clear pattern of fluctuation of fungal diversity in the rhizosphere of vines grown in two vineyards of different geographical location, age, climate, and soil management practices. Year of sampling has also been pointed out as a major factor that can influence the diversity and composition of the microbiota in grapevine [ 29 , 63 ]. This phenomenon can be attributed to distinct root responses to different environmental factors, such as precipitation or temperature [ 29 , 67 ].…”

Section: Discussionmentioning

confidence: 99%

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Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

Carbone

Alaniz

Mondino

et al. 2021

JoF

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Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO4 when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

Carbone

Alaniz

Mondino

et al. 2021

JoF

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“…Illumina short reads technology with optimized and universal primers targeting both ITS1 and ITS2 rDNA regions, confirmed the presence of the most representative species of each syndrome, but also allowed the discovery of species not-yet assigned to this complex [ 43 , 44 ]. As compared to diseases of wood, diagnosis of Vitis phylloplane diseases by NGS received less interest but it is foreseeable its use in the next future [ 45 , 46 ]. NGS was used to study the effect of elicitors or biocontrol agents on the leaf epiphytic populations [ 47 , 48 ].…”

Section: Metabarcodingmentioning

confidence: 99%

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

Aragona

Haegi

Valente

et al. 2022

JoF

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The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as “What’s in my soil?”, to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.

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“…In recent years, high-throughput sequencing and multi-omics technologies have been widely applied in many microbial-related research fields, such as gut flora, fermentation foods and ecological environments (Cureau et al, 2021;Guo et al, 2022;Tigrero-Vaca et al, 2022). Previous studies have preliminarily analyzed the microbial community structure in tobacco fermentation products based on pure culture, denaturing gradient gel electrophoresis (PCR-DGGE) and high-throughput sequencing (Liu et al, 2021;Zheng et al, 2022b).…”

Section: Introductionmentioning

confidence: 99%

Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome

Jia

Liu

et al. 2023

Front. Microbiol.

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IntroductionThe main goal of tobacco fermentation technology is to minimize the alkaloid content while improving flavor substance content.MethodsThis study revealed the microbial community structure and their metabolic functions during cigar leaf fermentation by high-throughput sequencing and correlation analysis, and evaluated the fermentation performance of functional microbes based on in vitro isolation and bioaugmentation fermentation.ResultsThe relative abundance of Staphylococcus and Aspergillus increased first but then decreased during the fermentation, and would occupy the dominant position of bacterial and fungal communities, respectively, on the 21st day. Correlation analysis predicted that Aspergillus, Staphylococcus and Filobasidium could contribute to the formation of saccharide compounds, Bacillus might have degradation effects on nitrogenous substances. In particular, Candida, as a co-occurring taxa and biomarker in the later stage of fermentation, could not only degrade nitrogenous substrates and synthesize flavor substances, but also contribute to maintaining the stability of microbial community. Moreover, based on in vitro isolation and bioaugmentation inoculation, it was found that Candida parapsilosis and Candida metapsilosis could significantly reduce the alkaloids content and increase the content of flavor components in tobacco leaves.DiscussionThis study found and validated the critical role of Candida in the fermentation of cigar tobacco leaves through high-throughput sequencing and bioaugmentation inoculation, which would help guide the development of microbial starters and directional regulation of cigar tobacco quality.

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Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes

Cited by 12 publications

References 55 publications

Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome

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