Ecology and genomics of extremophilic bacteria

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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.