McClure Ryan, Naylor Dan, Farris Yuliya, Davison Michelle, Fansler Sarah J, Hofmockel Kirsten S, Jansson Janet K
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States.
Front Microbiol. 2020 Aug 26;11:1987. doi: 10.3389/fmicb.2020.01987. eCollection 2020.
The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30-50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at -80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.
土壤微生物群落在碳和其他养分循环以及促进植物生长方面起着核心作用。尽管其很重要，但由于土壤微生物群落极其复杂，包含数千种相互作用的物种，对其进行分析颇具难度。在此，我们通过构建模型土壤微生物联合体降低了这种复杂性，这些联合体更简单且更便于进行实验分析，但仍能代表原生土壤生态系统的重要微生物功能。从干旱草原土壤中采集样本，在以几丁质作为主要碳源的琼脂平板上富集微生物群落（主要由细菌物种组成）。选择几丁质是因为它是土壤中一种丰富的碳氮聚合物，通常需要多种微生物协同作用才能完全代谢降解。由此获得了几个土壤联合体，其具有易于处理的丰富度（30 - 50个操作分类单元），包含了代表原生土壤的不同门类，如放线菌门、拟杆菌门、厚壁菌门、变形菌门和疣微菌门。所得联合体可作为甘油或冻干菌液保存在 -80°C，并在复苏时保持群落组成，极大地增加了其作为广大研究群体工具的用途。选择其中一个特别稳定的联合体作为模型土壤联合体（MSC - 1）进行进一步分析。使用液体培养基中的成对共培养以及在几种扰动条件下土壤生长过程对MSC - 1的物种相互作用进行了研究。共丰度分析突出了种间相互作用，并有助于确定关键物种，包括分枝杆菌属、红球菌属和根瘤菌目分类群。这些实验证明了基于自然富集可储存、复苏和共享的相互作用物种群落的方法的成功。通过研究这些群落及其相互作用所获得的知识将有助于更好地理解土壤微生物群落以及这些相互作用在该环境中所起的作用。
