Yau Payton To, Taketani Rodrigo G, Bonnin J Miguel, Stewart Helen, Thompson Catriona M A, Clark Ian M, Mauchline Tim H, Malone Jacob G, Ryan Matthew J, Jones Susan, Holden Nicola
Department of Rural Land Use, Scotland's Rural College, Aberdeen, AB21 9YA, UK.
Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK.
Environ Microbiome. 2025 Aug 21;20(1):108. doi: 10.1186/s40793-025-00768-5.
Here, we describe AgMicrobiomeBase as an output of the UK Crop Microbiome Cryobank (UKCMCB) project, including details of the underlying meta-barcode sequence-based methods and three microbiome analysis case studies. The UKCMCB links genomic datasets and associated soil metadata with a cryobank collection of samples, for six economically significant crops: fava bean (Vicia faba), oil seed rape (Brassica napus), spring barley (Hordeum vulgare), spring oats (Avena sativa), spring wheat (Triticum aestivum) and sugar beet (Beta vulgaris). The crops were grown in nine agricultural soils from the UK, representing three major soil texture classes. The UKCMCB is a scalable sequence-based data catalogue linked to a cryo-preserved sample collection.
The focus of this paper is the amplicon sequencing, associated bioinformatics workflows, and development of the project data catalogue. Short-read amplicon sequencing (16 S rRNA gene and ITS region) was implemented to describe the rhizosphere and bulk soil communities, for the multiple crop-soil combinations. Three case studies illustrate how different biological questions in phytobiome research can be addressed using this data resource. The three case studies illustrate how to (1) determine the impact of soil texture and location on microbiome composition, (2) determine a core microbiome for a single crop across different soil types, and (3) analyse a single genus, Fusarium within a single crop microbiome. The UKCMCB data catalogue AgMicroBiomeBase ( https://agmicrobiomebase.org/data ) links the sequence-based data with soil metadata and to cryopreserved samples.
The UKCMCB provides baseline data and resources to enable researchers to assess the impact of soil type, location and crop type variables on crop soil microbiomes. The resource can be used to address biological questions and cross-study comparisons. Development of the UKCMCB will continue with the addition of metagenome and bacterial isolate genomic sequence data and has the potential to integrate additional data types including microbial phenotypes and synthetic microbial communities.
在此，我们将AgMicrobiomeBase描述为英国作物微生物组冷冻库（UKCMCB）项目的成果，包括基于元条形码序列的基础方法细节以及三个微生物组分析案例研究。UKCMCB将基因组数据集和相关土壤元数据与六个具有经济重要性的作物的冷冻样本库相联系，这六种作物分别是：蚕豆（Vicia faba）、油菜（Brassica napus）、春大麦（Hordeum vulgare）、春燕麦（Avena sativa）、春小麦（Triticum aestivum）和甜菜（Beta vulgaris）。这些作物种植于英国的九种农业土壤中，代表了三种主要的土壤质地类别。UKCMCB是一个可扩展的基于序列的数据目录，与冷冻保存的样本库相关联。
本文重点关注扩增子测序、相关生物信息学工作流程以及项目数据目录的开发。实施了短读长扩增子测序（16S rRNA基因和ITS区域）来描述多种作物 - 土壤组合的根际和土壤整体群落。三个案例研究说明了如何利用这一数据资源解决植物微生物组研究中不同的生物学问题。这三个案例研究展示了如何：（1）确定土壤质地和位置对微生物组组成的影响；（2）确定单一作物在不同土壤类型中的核心微生物组；（3）分析单一作物微生物组中的单一属——镰刀菌属。UKCMCB数据目录AgMicroBiomeBase（https://agmicrobiomebase.org/data）将基于序列的数据与土壤元数据以及冷冻保存的样本相联系。
UKCMCB提供了基线数据和资源，使研究人员能够评估土壤类型、位置和作物类型变量对作物土壤微生物组的影响。该资源可用于解决生物学问题和进行跨研究比较。UKCMCB的开发将继续，增加宏基因组和细菌分离株基因组序列数据，并有可能整合包括微生物表型和合成微生物群落在内的其他数据类型。
