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Evaluation of Different Phyllosphere Sample Types for Parallel Metabarcoding of Fungi and Oomycetes in Vitis vinifera

Behrens, Falk and Fischer, Michael (2022) Evaluation of Different Phyllosphere Sample Types for Parallel Metabarcoding of Fungi and Oomycetes in Vitis vinifera. Phytobiomes Journal, 6 (3), pp. 207-213.

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Document available online at: https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-11-21-0072-SC


Summary

Metabarcoding is an effective and cost-efficient approach to study environmental microbiomes and has become a standard
method in studying microbial community structures and relative species abundance. In grapevine research on leaf microbial communities, two kinds of sample types, either leaf wash sediments representing the phyllosphere microbiome from leaf surfaces or leaf tissue samples, e.g., leaf disks, including phyllosphere and endosphere microorganisms, are used to characterize leaf microbiomes. The goal of this study was to analyze the advantages and disadvantages of these sample preparation methods for the characterization of the phyllosphere microbiome by fungal metabarcoding with both sample types being processed from the exact same set of leaves. We used a metabarcoding strategy, which can detect Fungi and Oomycetes, facilitating the parallel analysis of these communities. At each sampling time point, species richness was shown to be higher in leaf wash samples, and differences in the community structure between samples was smaller for this sample type as well. Furthermore, by comparing read count abundance to qPCR measured relative proportions of selected amplicon sequence variants, a higher congruence was observed for leaf wash samples. Therefore, metabarcoding analyses of leaf samples using leaf wash sediments outperform analyses using leaf disks and should be applied to characterize phyllosphere fungal communities. As a second goal, we show that the direct comparison of metabarcoding libraries of both sample types prepared from the exact same set of leaves also provides a new strategy to identify endophytes that may not be culturable.


EPrint Type:Journal paper
Keywords:metabarcoding, phyllosphere, Vitis vinifera, VITIFIT, Plasmopara, viticola, Weinbau, Praxisforschungsnetzwerk, Pflanzenschutz, BÖL, BOEL, FKZ 18OE033
Agrovoc keywords:
Language
Value
URI
English
metabarcoding
http://aims.fao.org/aos/agrovoc/c_dd1560b3
English
phyllosphere
http://aims.fao.org/aos/agrovoc/c_36822
English
Vitis vinifera
http://aims.fao.org/aos/agrovoc/c_8283
Subjects: Crop husbandry > Crop health, quality, protection
Crop husbandry > Production systems > Fruit and berries > Viticulture
Research affiliation: Germany > Federal Organic Farming Scheme - BOEL > Plants > Pflanzenschutz
Germany > Federal Research Centre for Cultivated Plants - JKI > Institute for Plant Protection in Fruit Crops and Viticulture
DOI:10.1094/PBIOMES-11-21-0072-SC
Related Links:https://www.bundesprogramm.de/
Deposited By: Zug, Dr. Katharina
ID Code:55797
Deposited On:05 Jun 2025 07:33
Last Modified:05 Jun 2025 07:33
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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