Collaborative Research: Direction and Mechanisms of Seasonal Change in Arctic Microbial Communities

合作研究：北极微生物群落季节变化的方向和机制

• 批准号: 1203857
• 负责人: Slava Epstein
• 金额: $ 66万
• 依托单位: Northeastern University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1203857&HistoricalAwards=false
• 关键词: Collaborative; Research; Direction; Mechanisms; Seasonal

This research focuses on the characteristics and mechanisms of microbial succession in the high Arctic. Empirical observations suggest that seasonal change could be viewed as consisting of two phases, with simpler communities gradually replaced by more complex assemblages. The researchers hypothesize that life histories of the early colonizers include metabolic versatility and ability to expand quickly, which leads to communities characterized more by interspecies chemical warfare than intricate species integration. They also hypothesize that at later stages, species develop multiple synergies, their communities become more complex, and integrated by a signaling and regulatory network. A corollary of these traits is that the first phase is populated with species that are relatively easy to cultivate in pure culture, whereas species dominating at later stages may appear ?uncultivable? in pure culture due to their dependencies on other species. They will test these hypotheses in a study of a microbial community in the Thule Area in Northern Greenland. This environment offers a range of communities from simple to more complex with tractable (short) seasonal succession and constitutes a pristine and endangered community.Methodological challenges are one of the principal reasons that many aspects of microbial seasonal succession remain unresolved. Instead of applying either culture-dependent or culture-independent methodologies, this group will combine the two so that they compensate synergistically for their respective weaknesses. They will interrogate the microbial richness and identify a model assemblage, followed by seasonal studies of the metagenome and metatranscriptome, with a particular focus on two hallmarks of microbial activities: production of antimicrobials and signaling compounds. They will cultivate 50% of the microbial species present using an arsenal of new cultivation platforms that depart radically from conventional cultivation and enable them to isolate previously uncultivated species. The ability to do so is one of the keys to the success of this project, because it will enable them to connect microbial function to microbial species, and vice versa. For that, they will sequence genomes of at least 150 novel previously uncultivated strains, and identify species whose antimicrobial, signaling activities were detected by their meta-omics approach. They will integrate the data, test the hypotheses, and infer how to artificially manipulate the trajectory of successional change. The inferences will be tested in direct in situ experimentation.Intellectual merit of this study is two-fold. The first is about bringing together in one study the culture- dependent and culture-independent approaches, enabling us to relate microbial diversity and function in the most general sense. The enabling technology is important for general microbial ecology because it identifies functions expressed by the community with specific microbial players, and deciphers the roles of individual species, spatially and temporally. It has the potential to transform the study of arctic and other environmental microorganisms by informing us what key species are present, what functions they perform, and how the structure-function relationship changes over time. Second is the application of this platform to the ecology of arctic microorganisms, whereby they will test specific hypotheses related to the direction and aspects of microbial seasonal succession, aiming at their mechanistic explanation. Regardless of whether the hypotheses stand, they will assess the importance of community-level microbial interactions that are based on production of bioactive compounds, how these interactions change over the course of seasonal succession, and whether trajectory of the microbial seasonal succession can be manipulated in a predictable fashion.This approach may become useful in human and animal microbiome research helping establish roles of species implicated in a range of diseases; in bioremediation efforts by explaining roles of individual species in biotransformation of pollutants; and drug discovery since bioactive compounds are often produced in a community setting but not in isolation. These cultivation approaches are already used in biotechnology efforts, and are licensed to a biotech startup company. The project will provide opportunities for undergraduate and graduate training in a multidisciplinary setting.

本研究的重点是高北极地区微生物演替的特点和机制。经验观察表明，季节性变化可以被视为由两个阶段组成，简单的社区逐渐取代更复杂的组合。研究人员假设，早期殖民者的生活史包括代谢的多样性和快速扩张的能力，这导致社区的特征更多地是物种间的化学战争，而不是复杂的物种整合。他们还假设，在后期阶段，物种发展出多种协同作用，它们的群落变得更加复杂，并通过信号和调控网络进行整合。这些特征的一个必然结果是，第一阶段是由相对容易在纯培养中培养的物种组成的，而在后期阶段占主导地位的物种可能会出现？不可培养的？由于它们对其他物种的依赖性，他们将在对格陵兰岛北方图勒地区微生物群落的研究中检验这些假设。这种环境提供了一系列从简单到更复杂的群落，具有易处理的（短）季节性演替，构成了一个原始的和濒危的community.Methodological挑战是微生物季节性演替的许多方面尚未解决的主要原因之一。该小组将联合收割机与文化依赖或文化独立的方法结合起来，以协同方式弥补各自的弱点，而不是采用这两种方法。他们将询问微生物的丰富程度并确定模型组合，然后对宏基因组和元转录组进行季节性研究，特别关注微生物活动的两个标志：抗菌剂和信号化合物的生产。他们将使用一系列新的培养平台培养50%的微生物物种，这些平台从根本上不同于传统的培养，并使他们能够分离出以前未培养的物种。这样做的能力是这个项目成功的关键之一，因为它将使他们能够将微生物功能与微生物物种联系起来，反之亦然。为此，他们将对至少150种以前未培养的新型菌株的基因组进行测序，并通过元组学方法检测其抗菌信号活性的物种。他们将整合数据，测试假设，并推断如何人为地操纵演替变化的轨迹。这些推论将在直接的现场实验中得到验证。本研究的智力价值是双重的。第一个是关于在一项研究中将依赖培养和不依赖培养的方法结合起来，使我们能够在最普遍的意义上将微生物多样性和功能联系起来。使能技术对于一般微生物生态学是重要的，因为它识别由具有特定微生物参与者的群落表达的功能，并在空间和时间上破译单个物种的作用。它有可能改变北极和其他环境微生物的研究，告诉我们哪些关键物种存在，它们执行什么功能，以及结构-功能关系如何随时间变化。第二个是这个平台的北极微生物生态学的应用，他们将测试有关微生物季节性演替的方向和方面的具体假设，旨在对它们进行机械解释。无论假设是否成立，他们将评估基于生物活性化合物生产的社区水平微生物相互作用的重要性，这些相互作用如何在季节更替过程中变化，以及是否可以以可预测的方式操纵微生物季节性演替的轨迹。这种方法可能在人类和动物微生物组研究中变得有用，有助于确定与微生物季节性演替有关的物种的作用。疾病种类;在生物补救工作中，通过解释单个物种在污染物生物转化中的作用;以及药物发现，因为生物活性化合物通常是在社区环境中产生的，而不是孤立的。这些培养方法已经用于生物技术工作，并被授权给一家生物技术初创公司。该项目将为本科生和研究生提供多学科培训机会。