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Title:

ZeaMiC 玉米根际微生物分离菌株数据库：助力植物-微生物互作研究

Take home message:

little is known about their individual functions and even less is known about their emergent community-level traits

Main:

ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria

摘要

（1）Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits 植物相关微生物群由数百种微生物组成。对他们中的许多人来说，对他们的个体功能知之甚少，对他们出现的群体水平特征更是知之甚少 . 

（2）While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. 虽然不依赖培养的方法为植物相关微生物群的组成、多样性和功能潜力提供了有价值的见解，但依赖培养的方法对于研究单个物种的作用及其在群落中的相互作用的简化方法是必不可少的。

（3）  Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). 在这里，我们提出了ZeaMiC，一个公开可得的来自玉蜀黍(玉米)的根相关细菌的培养物集合。该资源包括从不同土壤和几种玉米基因型中获得的88个分离物，活培养物可通过DSMZ(德国微生物和细胞培养物保藏中心)以单一储备获得 

（4）To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. 为了最大限度地提高相关性，根据以前发表的根系微生物组数据的丰度-占有率模式、系统发育多样性和基于文献的功能重要性证据，选择分离株作为美国玉米带玉米根系相关微生物组的代表。  

（5）Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes. 全基因组测序和注释揭示了与根部定殖、植物生长促进和营养循环相关的基因，包括趋化性、生物膜形成、分泌系统、激素调节和磷酸盐溶解等功能。该集合作为未来植物-微生物和微生物-微生物相互作用的机制研究的社区资源，填补了我们对植物微生物组中生态相互作用理解的空白。

（6）Result

图片

玉米根际细菌培养物库（ZeaMiC）构建流程图。

A 美国玉米带地图（展示玉米产量分布），土壤来源：草原土、农业土、后农业土操作，用这些土壤接种玉米幼苗，分离玉米根系定植的细菌

                                                                                B 两种分离方法：微生物阵列（高通量）+ 平板涂布
                                                                                C. 培养物库的精炼 两个筛选标准：① 核心菌属（基于丰度-占据率）② 最大化多样性（基于系统发育树）
                                                                                D 从其他全球玉米培养物库中引入菌株 + 针对性培养（如Telluria）
                                                                                E 菌落PCR（确认纯度和属水平鉴定）+ 全基因组测序
                                                                                F 在10项已发表的玉米微生物组数据中验证这些菌株的存在
方法
For high-throughput microbial isolations, three replicates (whole root systems) from the same soil source were pooled and then cut into ≤1 cm fragments using a flame sterilized razor blade. Between 2-2.5 g of root fragments for each sample were placed into separate 15 mL conical tubes. Tubes were then filled with sterile 25% glycerol, incubated at room temperature for 20 mins, and then placed at −20°C until they were shipped to General Automation Lab Technologies (GALT; now Isolation Bio, Inc., San Carlos, CA, USA) for isolation in 50% strength R2A media using their Prospector microbial isolation array technology. Bacterial cultures were received from GALT as glycerol stocks in multiple 96-well plates, with each well presumably containing a single bacterial strain.

用于高通量微生物分离时，将来自同一土壤来源的三个重复样本（整个根系）合并，用火焰灭菌的刀片切成 ≤1 cm 的片段。每个样本取 2–2.5 g 根片段，放入单独的 15 mL 锥形管中。向管中加入无菌 25% 甘油，室温孵育 20 分钟，然后置于 −20°C 保存，直至送至 General Automation Lab Technologies（GALT，现为 Isolation Bio, Inc.），使用其 Prospector 微生物阵列分离技术在 50% 浓度的 R2A 培养基中进行分离。从 GALT 获得的细菌培养物以甘油冻存形式保存在多个 96 孔板中，每个孔中假定含有单一的细菌菌株。

Words:

While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community