Evaluation of different phyllosphere sample types for parallel metabarcoding of Fungi and Oomycetes in Vitis vinifera

IF 3.3 3区 生物学 Q2 MICROBIOLOGY Phytobiomes Journal Pub Date : 2022-02-11 DOI:10.1094/pbiomes-11-21-0072-sc
F. H. Behrens, M. Fischer
{"title":"Evaluation of different phyllosphere sample types for parallel metabarcoding of Fungi and Oomycetes in Vitis vinifera","authors":"F. H. Behrens, M. Fischer","doi":"10.1094/pbiomes-11-21-0072-sc","DOIUrl":null,"url":null,"abstract":"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 is capable of detecting 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 (ASVs), a higher congruence was observed for leaf wash samples. Therefore, metabarcoding analyses of leaf samples using leaf wash sediments outperforms 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 potentially not culturable endophytes.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":3.3000,"publicationDate":"2022-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"3","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Phytobiomes Journal","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1094/pbiomes-11-21-0072-sc","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 3

Abstract

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 is capable of detecting 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 (ASVs), a higher congruence was observed for leaf wash samples. Therefore, metabarcoding analyses of leaf samples using leaf wash sediments outperforms 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 potentially not culturable endophytes.
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
葡萄不同层球样品类型对真菌和卵菌平行元条形码的评价
代谢编码是研究环境微生物组的一种有效且成本效益高的方法,已成为研究微生物群落结构和相对物种丰度的标准方法。在葡萄藤对叶片微生物群落的研究中,使用两种样品类型来表征叶片微生物组,即代表叶片表面叶层微生物组的叶洗沉积物,或叶组织样品,如叶盘,包括叶层和内层微生物。本研究的目的是分析这些样品制备方法的优缺点,通过真菌代谢条形码对叶层微生物组进行表征,两种样品类型都是从完全相同的叶片中加工而成。我们使用了一种代谢编码策略,该策略能够检测真菌和卵菌,促进对这些群落的平行分析。在每个采样时间点,洗叶样本的物种丰富度较高,该样本类型样本之间的群落结构差异也较小。此外,通过将读取计数丰度与qPCR测量的所选扩增子序列变体(ASV)的相对比例进行比较,观察到洗叶样品的一致性更高。因此,使用叶洗沉积物对叶片样本进行的代谢条形码分析优于使用叶盘进行的分析,应用于表征叶层真菌群落。作为第二个目标,我们表明,直接比较由完全相同的一组叶子制备的两种样品类型的代谢条形码文库也为鉴定潜在的不可培养的内生菌提供了一种新的策略。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
CiteScore
7.40
自引率
6.80%
发文量
42
审稿时长
4 weeks
期刊最新文献
The Tomato’s Tale: Exploring taxonomy, biogeography, domestication and microbiome for enhanced resilience Disentangling shifts in the soil microbiome of potatoes infected with Rhizoctonia solani AG 3-PT in search of potential biocontrol agents Linnemannia elongata: a key species in chitin-based plant growth promotion High diversity of Curtobacterium flaccumfaciens in poinsettia and detection of three pathogenicity plasmids for identification of C. f. pv. poinsettiae Deciphering the key players within the bacterial microbiota associated with aerial crown gall tumors on rhododendron: Insights into the gallobiome
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1