Ecology and genomics of extremophilic bacteria

极端细菌的生态学和基因组学

• 批准号: RGPIN-2014-05067
• 负责人: Dunfield, Peter
• 金额: $ 4.44万
• 依托单位: University of Calgary
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=649776
• 关键词: Ecology; genomics; extremophilic; bacteria

Microbiologists estimate that there are over ten million species of bacteria on Earth. However, fewer than 0.1% of them have been cultured in a laboratory. A major goal of microbial ecology is to understand the full genetic and ecological diversity of this uncultured bacterial majority. This goal can be achieved in two ways: by developing improved methods to culture bacteria, or by using DNA-based methods that deliver information about their lifestyles without the need for cultivation. One such molecular technique is metagenomics, in which DNA is extracted from an environment and sequenced on a large scale in an attempt to piece together the the genetic makeup of uncultured bacteria. My research program will employ metagenomics and other techniques in two main studies. **Firstly, we will grow and characterize new bacteria from extreme environments such as geothermal springs. We have already studied many thermal springs in Canada and identified unusual bacteria to study in more depth. The most interesting of these belong to unknown branches of the tree of life called "candidate divisions", which diverged from known bacteria billions of years before any plant or animal species existed. There are an estimated 100 main evolutionary lineages of bacteria (Phyla or Kingdoms), and those that have no cultured representatives are the candidate divisions. My laboratory has recently found a bacterium belonging to one candidate division (OP11) in a hot spring in Lakelse, BC and one belonging to another candidate division (WPS2) in the Paint Pots Spring in Kootenay, BC. In both sites these bacteria were very abundant, making up nearly half of all cells present. We will extract and sequence DNA from these samples, and assemble the genomes of the two organisms. The genome data will provide evolutionary and metabolic information about what they are doing in their respective environments, and will also provide clues to culturing them, which is our ultimate goal. **Secondly, we will take a fundamental theoretical approach to bacterial diversity. One of the only universal laws of ecology is the latitude-diversity or temperature-diversity gradient, first observed by the naturalist Alexander von Humboldt in 1808. He noted that species diversity of plants and animals peaks at warm tropical latitudes and decreases towards the poles. In a recent study of geothermal springs we demonstrated for the first time that a strong temperature-diversity relationship exists for bacteria as well. We postulated that this is caused by stress: as stress increases, fewer metabolic pathways can provide enough energy for an organism to survive, and therefore diversity declines. We will test this theory via metagenomics. Hot springs spanning a range of temperature will be used for metagenomic DNA sequencing, and bioinformatic tools will assess the diversity of metabolic pathways in each community. In addition we will examine another set of environments where we expect to see a stress-diversity effect: a group of hypersaline springs in Wood Buffalo National Park. **This work is of fundamental academic interest in understanding the full scope of Earth's biodiversity. It is also of potential biotechnological interest, as uncultured microbes may be sources of new enzymes and processes with medical or industrial value. For example, our target OP11 bacterium grows by fermenting cellulose, a process that is the basis of second-generation biofuel production. Finally, the work will deliver fundamental data about unique ecosystems in Canada's North. The saline springs of Wood Buffalo National Park are one reason the park was declared a UNESCO World Heritage Site. Studying the spring communities will contribute to Canada's mandate to understand and preserve these unique ecosystems.

微生物学家估计地球上有超过一千万种细菌。但是，其中不到0.1％在实验室中进行了培养。微生物生态学的主要目标是了解这种未培养的细菌多数的全部遗传和生态多样性。可以通过两种方式实现此目标：通过开发改进的方法来培养细菌，或者使用基于DNA的方法来提供有关其生活方式的信息而无需培养的信息。一种这样的分子技术是宏基因组学，其中从环境中提取DNA并进行了大规模测序，以试图将未培养细菌的遗传组成组合在一起。我的研究计划将在两项主要研究中采用宏基因组学和其他技术。 **首先，我们将从地热弹簧等极端环境中成长并表征新细菌。我们已经研究了加拿大的许多热弹簧，并确定了异常细菌以更深入研究。其中最有趣的是生命树的未知分支，称为“候选师”，这与已知细菌存在数十亿年的植物或动物物种存在。估计有100个细菌（门或王国）的主要进化谱系，而没有文化代表的人是候选人的。我的实验室最近在不列颠哥伦比亚省Lakelse的一个温泉中发现了一个属于一个候选师（OP11）的细菌，一个属于卑诗省Kootenay的油漆锅弹簧中的另一个属于另一个候选人师（WPS2）。在两个部位，这些细菌都非常丰富，构成了所有细胞的一半。我们将从这些样品中提取和序列DNA，并组装两个生物的基因组。基因组数据将提供有关它们在各自环境中所做的事情的进化和代谢信息，还将提供培养它们的线索，这是我们的最终目标。 **其次，我们将采取一种基本的理论方法来实现细菌多样性。生态学的唯一普遍定律之一是自然主义者亚历山大·冯·洪堡（Alexander von Humboldt）在1808年首次观察到的纬度多样性或温度多样性梯度。在最近对地热弹簧的研究中，我们首次证明了细菌也存在较强的温度多样性关系。我们假设这是由压力引起的：随着压力的增加，较少的代谢途径可以为生物生存提供足够的能量，因此多样性下降。我们将通过宏基因组学检验该理论。横跨一系列温度的温泉将用于宏基因组DNA测序，生物信息学工具将评估每个社区中代谢途径的多样性。此外，我们将研究另一组环境，我们希望看到压力多样性效应：伍德布法罗国家公园中的一组催眠springs。 **这项工作对理解地球生物多样性的全部范围具有根本的学术兴趣。它也具有潜在的生物技术兴趣，因为未培养的微生物可能是具有医疗或工业价值的新酶和过程的来源。例如，我们的靶标OP11细菌通过发酵纤维素而生长，这是第二代生物燃料生产的基础。最后，这项工作将提供有关加拿大北部独特生态系统的基本数据。伍德布法罗国家公园的盐泉是该公园被宣布为联合国教科文组织世界遗产的原因之一。研究春季社区将有助于加拿大理解和保留这些独特的生态系统的任务。