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

研究了高北极地区微生物演替的特征和机制。经验观察表明，季节变化可被视为由两个阶段组成，较简单的群落逐渐被较复杂的组合所取代。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，这导致了更多以物种间化学战为特征的社区，而不是复杂的物种整合。他们还假设，在后期，物种发展出多种协同作用，它们的群落变得更加复杂，并通过信号和调节网络整合在一起。这些特征的一个必然结果是，第一阶段的物种在纯培养中相对容易培养，而在后期阶段占主导地位的物种可能显得“不可培养”。在纯培养中，由于它们对其他物种的依赖。他们将在格陵兰岛北部图勒地区的微生物群落研究中验证这些假设。这种环境提供了一系列从简单到复杂的群落，具有可处理的（短）季节性演替，构成了一个原始的濒危群落。方法上的挑战是微生物季节演替的许多方面仍未解决的主要原因之一。这个小组将结合两者，而不是应用文化依赖或文化独立的方法，以便它们协同补偿各自的弱点。他们将调查微生物丰富度并确定模型组合，随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产生。他们将利用一系列新的培养平台培养50%的微生物物种，这些平台与传统的培养方式截然不同，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的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进行基因组测序，并鉴定出通过他们的元组学方法检测到其抗菌信号活性的物种。他们将整合数据，检验假设，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检验。这项研究的智力价值是双重的。第一个是将依赖培养和不依赖培养的方法结合在一起，使我们能够在最一般的意义上把微生物的多样性和功能联系起来。使能技术对一般微生物生态学很重要，因为它识别了特定微生物参与者的群落表达的功能，并破译了单个物种在空间和时间上的作用。它有可能改变北极和其他环境微生物的研究，告诉我们存在哪些关键物种，它们发挥什么功能，以及结构-功能关系如何随时间变化。二是将该平台应用于北极微生物生态学，他们将测试与微生物季节演替方向和方面相关的特定假设，旨在对其进行机制解释。无论这些假设是否成立，他们都将评估基于生物活性化合物生产的群落水平微生物相互作用的重要性，这些相互作用在季节演替过程中如何变化，以及微生物季节演替的轨迹是否可以以可预测的方式进行操纵。这种方法可能在人类和动物微生物组研究中有用，有助于确定与一系列疾病有关的物种的作用；通过解释单个物种在污染物生物转化中的作用来进行生物修复工作；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。这些培育方法已经在生物技术工作中使用，并被授权给一家生物技术初创公司。该项目将在多学科环境下为本科生和研究生提供培训机会。

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.