Ecology and genomics of extremophilic bacteria

微生物学家估计地球上有超过1000万种细菌。然而，只有不到0.1%的人在实验室培养。微生物生态学的一个主要目标是了解这些未培养细菌的全部遗传和生态多样性。这一目标可以通过两种方式实现：开发改进的细菌培养方法，或者使用基于dna的方法，在不需要培养的情况下传递有关细菌生活方式的信息。其中一种分子技术是宏基因组学，即从环境中提取DNA，并对其进行大规模测序，试图拼凑出未培养细菌的基因组成。我的研究计划将在两个主要研究中使用宏基因组学和其他技术。首先，我们将在地热泉等极端环境中培养和鉴定新的细菌。我们已经研究了加拿大的许多温泉，并发现了不寻常的细菌，以进行更深入的研究。其中最有趣的是属于生命之树的未知分支，称为“候选分支”，在任何植物或动物物种存在之前的数十亿年，这些分支就从已知的细菌中分化出来了。估计有100个主要的细菌进化谱系（门或王国），那些没有培养代表的是候选分支。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分部（OP11）的细菌，在不列颠哥伦比亚省Kootenay的油漆罐泉中发现了一个属于另一个候选分部（WPS2）的细菌。在这两个地点，这些细菌都非常丰富，几乎占所有细胞的一半。我们将从这些样本中提取和测序DNA，并组装两种生物的基因组。基因组数据将提供它们在各自环境下的进化和代谢信息，也将为培养它们提供线索，这是我们的最终目标。其次，我们将对细菌多样性采取基本的理论方法。自然学家亚历山大·冯·洪堡（Alexander von Humboldt）于1808年首次发现了纬度多样性或温度多样性梯度，这是生态学中唯一的普遍规律之一。他指出，植物和动物的物种多样性在温暖的热带纬度地区达到顶峰，向两极地区下降。在最近对地热泉的一项研究中，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能量来生存，因此多样性下降。我们将通过宏基因组学来验证这一理论。不同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群落代谢途径的多样性。此外，我们还将研究另一组环境，在那里我们预计会看到压力多样性效应：伍德布法罗国家公园的一组高盐泉。这项工作对于全面了解地球生物多样性具有重要的学术意义。它还具有潜在的生物技术价值，因为未经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，这一过程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咸水泉是该公园被联合国教科文组织列为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.