Ecology and genomics of extremophilic bacteria

微生物学家估计，地球上有超过一千万种细菌。然而，只有不到0.1%的人在实验室中培养。微生物生态学的一个主要目标是了解这种未培养细菌大多数的完整遗传和生态多样性。这一目标可以通过两种方式实现：通过开发改进的方法来培养细菌，或者通过使用基于DNA的方法来提供有关其生活方式的信息，而无需培养。其中一种分子技术是宏基因组学，从环境中提取DNA并进行大规模测序，试图将未培养细菌的基因组成拼凑在一起。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，我们将培养和表征来自极端环境（如地热泉）的新细菌。我们已经研究了加拿大的许多温泉，并确定了不寻常的细菌进行更深入的研究。其中最有趣的属于生命之树的未知分支，称为“候选分支”，它在任何植物或动物物种存在之前数十亿年就从已知细菌中分离出来。估计有100个主要的细菌进化谱系（门或界），那些没有培养的代表是候选部门。我的实验室最近在Lakelse的一个温泉中发现了一种属于一个候选部门（OP11）的细菌，BC和一种属于另一个候选部门（WPS2）的细菌在Kootenay的Paint Pots Spring，BC。在这两个地点，这些细菌非常丰富，占所有细胞的近一半。我们将从这些样本中提取DNA并进行测序，然后组装这两种生物的基因组。基因组数据将提供它们在各自环境中所做的进化和代谢信息，也将为培养它们提供线索，这是我们的最终目标。其次，我们将采取基本的理论方法来研究细菌多样性。生态学唯一的普遍规律之一是纬度多样性或温度多样性梯度，这是博物学家亚历山大·冯·洪堡在1808年首次观察到的。他指出，植物和动物的物种多样性在温暖的热带纬度达到高峰，向两极逐渐减少。在最近一项关于地热泉的研究中，我们首次证明了细菌也存在强烈的温度多样性关系。我们假设这是由压力引起的：随着压力的增加，更少的代谢途径可以为生物体提供足够的生存能量，因此多样性下降。我们将通过宏基因组学来验证这一理论。温度范围内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，我们希望看到一个压力多样性的影响：一组高盐泉在伍德布法罗国家公园。这项工作对于了解地球生物多样性的全部范围具有根本的学术意义。它也具有潜在的生物技术意义，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工艺的来源。例如，我们的目标OP11细菌通过发酵纤维素生长，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水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。研究春季群落将有助于加拿大理解和保护这些独特的生态系统。

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.