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%的细菌是在实验室培养的。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：通过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提供关于它们生活方式的信息。其中一项这样的分子技术是元基因组学，即从环境中提取DNA，并进行大规模测序，试图拼凑出未培养细菌的基因构成。我的研究计划将在两个主要研究中使用元基因组学和其他技术。首先，我们将从地热温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，并发现了一些特殊的细菌，可以进行更深入的研究。其中最有趣的是生命树中未知的分支，称为“候选分支”，它们是在动植物物种存在前数十亿年从已知细菌中分离出来的。据估计，细菌有100个主要的进化谱系(Phyla或王国)，而那些没有培养代表的细菌是候选的分支。我的实验室最近在不列颠哥伦比亚省莱克瑟斯的一个温泉中发现了一种属于一个候选科(OP11)的细菌，在BC库特奈的油漆罐泉中发现了另一种候选科(WPS2)。在这两个地点，这些细菌都非常丰富，几乎占到所有细胞的一半。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。基因组数据将提供有关它们在各自环境中所做工作的进化和新陈代谢信息，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·洪堡于1808年首次观察到纬度-多样性或温度-多样性梯度，这是唯一的普遍生态学定律之一。他指出，植物和动物的物种多样性在热带温暖的纬度达到顶峰，并向两极下降。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着强烈的温度-多样性关系。我们推测这是由压力引起的：随着压力的增加，能够为有机体提供足够能量的代谢途径更少，因此多样性下降。我们将通过元基因组学来检验这一理论。跨越一定温度范围的温泉将被用于元基因组DNA测序，生物信息学工具将评估每个群落中代谢途径的多样性。此外，我们将研究另一组我们预计会看到压力-多样性效应的环境：伍德布法罗国家公园的一组高盐度泉水。这项工作对全面了解地球生物多样性具有重要的学术意义。这也是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盐泉是该公园被联合国教科文组织宣布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.