高通量元条形码表征大麦作物叶根圈真菌内生菌多样性

IF 3.3 3区 生物学 Q2 MICROBIOLOGY
Carla Bridget Milazzo, Katherine G. Zulak, M. J. Muria-Gonzalez, Darcy A. B. Jones, M. Power, K. Bransgrove, M. Bunce, F. López-Ruiz
{"title":"高通量元条形码表征大麦作物叶根圈真菌内生菌多样性","authors":"Carla Bridget Milazzo, Katherine G. Zulak, M. J. Muria-Gonzalez, Darcy A. B. Jones, M. Power, K. Bransgrove, M. Bunce, F. López-Ruiz","doi":"10.1094/PBIOMES-09-20-0066-R","DOIUrl":null,"url":null,"abstract":"Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis and permutational analysis of variance, ASV diversity did not change in response to barley cultivar or fungicide treatment; however, the community structure of unsprayed plants did change between two collection times 8 days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":"1 1","pages":""},"PeriodicalIF":3.3000,"publicationDate":"2021-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"8","resultStr":"{\"title\":\"High-Throughput Metabarcoding Characterizes Fungal Endophyte Diversity in the Phyllosphere of a Barley Crop\",\"authors\":\"Carla Bridget Milazzo, Katherine G. Zulak, M. J. Muria-Gonzalez, Darcy A. B. Jones, M. Power, K. Bransgrove, M. Bunce, F. López-Ruiz\",\"doi\":\"10.1094/PBIOMES-09-20-0066-R\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis and permutational analysis of variance, ASV diversity did not change in response to barley cultivar or fungicide treatment; however, the community structure of unsprayed plants did change between two collection times 8 days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.\",\"PeriodicalId\":48504,\"journal\":{\"name\":\"Phytobiomes Journal\",\"volume\":\"1 1\",\"pages\":\"\"},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2021-02-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"8\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Phytobiomes Journal\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1094/PBIOMES-09-20-0066-R\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Phytobiomes Journal","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1094/PBIOMES-09-20-0066-R","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: 8

摘要

在过去的十年里,微生物组作为宏观有机体适应性的关键因素受到了越来越多的关注。可持续的害虫管理需要了解植物内共生的复杂微生物内生菌群落,以及合成杀虫剂与它们相互作用的方式。众所周知,真菌内生菌有利于植物生长和健康,并可能阻止病虫害。高通量测序(HTS)的最新进展使微生物组的综合研究成为可能,尤其是在农业领域。在这里,我们使用代谢条形码(一种从环境DNA构建群落图谱的HTS工具),对暴露于两种系统性叶面杀菌剂的两个大麦(Hordeum vulgare)品种的叶际真菌内生菌群落进行了分析。我们通过生物信息学管道研究了真菌核核糖体大亚基D2和内部转录间隔区2(ITS2)DNA标记。我们使用D2和ITS2代谢编码分析分别发现了88个和128个独特的扩增子序列变体(ASV)。通过主配位分析和方差排列分析,ASV多样性不随大麦品种或杀菌剂处理的变化而变化;然而,未播种植物的群落结构在间隔8天的两次采集之间确实发生了变化。这里描述的工作流程可以应用于农业中的其他微生物组研究,我们希望它能鼓励对作物微生物组的进一步研究,以改善农业生态系统管理。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
High-Throughput Metabarcoding Characterizes Fungal Endophyte Diversity in the Phyllosphere of a Barley Crop
Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis and permutational analysis of variance, ASV diversity did not change in response to barley cultivar or fungicide treatment; however, the community structure of unsprayed plants did change between two collection times 8 days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 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
×
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
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
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 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信