- CIFAR Scholar and Associate Professor, University of British Columbia
- Department of Microbiology & Immunology, Life Sciences Institute
I have collaborated with the JGI since 2002 before the CSP program came online. These collaborations have spanned my postdoctoral years with Ed DeLong [now at the University of Hawai’i, Mānoa] and my time as an independent investigator at the University of British Columbia. In 2002, the JGI was doing several pilot projects to explore environmental sequencing that included acid mines, eel river basin sediments and marine sponges. I worked with Nik Putnam closely on the sediment and sponge projects with some coding support from Jarrod Chapman and Sam Pitluck. (Hallam, S. J., Putnam, N. Preston, C.M., Detter, J.C., Richardson, P. M., Rokhsar, D., and E. F. DeLong. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics, Science, 305: 1457-1462. http://www.sciencemag.org/content/305/5689/1457.full)
Over the years I have worked on projects that explored the genomic potential of anaerobic methane oxidizing Archaea and the symbiotic thaumarchaeota Cenarchaeum symbiosum as well as more community based studies focused on microbial community structure and function in expanding marine oxygen minimum zones and long term soil productivity sites across north American ecozones. I have also participated in single-cell genomic studies exploring microbial dark matter from both metabolic reconstruction and technology development perspectives.
Understanding the ecological and biogeochemical roles played by microorganisms alone and in community is a fundamental research problem with important implications for modeling the earth system and developing new technologies for sustainable economic growth. This is not abstract science but empirical and object oriented exploration of nature with real world implications for human societies trying to make a balance living on a dynamic planet. My JGI projects have tended to focus on metabolic reconstruction of uncultivated microorganisms that play important roles in carbon, nitrogen and sulfur transformations in aquatic ecosystems. Several of these projects have resulted in foundational advances related to biochemical pathways mediating methane oxidation along continental margins, autotrophic carbon assimilation by marine thaumarchaeota (http://www.plosbiology.org/ and http://www.pnas.org/) and more recently coupled carbon, nitrogen and sulfur cycling in expanding marine oxygen minimum zones (OMZs).
The OMZ work highlights the promise and the power of monitoring microbial communities in natural and human engineered ecosystems as sensitive indicators of change. Indeed, dissolved oxygen concentration is a critical organizing principle in the ocean. As oxygen levels decline, energy is diverted away from plants and animals into microbial community metabolism. Over the past 50 years oxygen minimum zones have expanded due to climate change and increased waste run-off from our farms and cities. At present 8% of the ocean is considered oxygen-starved. In certain coastal areas extreme oxygen-starvation produces “dead zones” decimating marine fisheries and destroying food web structure. Although inhospitable to many plants and animals, oxygen minimum zones support thriving microbial communities.
OMZ research in my laboratory has focused on the northeast subarctic Pacific Ocean and Saanich Inlet as model ecosystems for understanding microbial community responses to OMZ expansion. Using DNA and RNA extracted directly from the environment, we observed that oxygen-starvation produces alternative niches that organize and direct microbial community metabolism. Changes in microbial community metabolism in turn control marine nutrient and energy recycling, including the production and consumption of the greenhouse gases carbon dioxide, methane and nitrous oxide. We identified one specific group of microorganisms, called SUP05 related to gill symbionts of deep-sea clams and mussels that dominate the most oxygen-starved regions of the water column. SUP05 breathes-in nitrate and exhales nitrous oxide. This respiratory process is coupled to carbon dioxide fixation and the removal of toxic hydrogen sulphide. The presence of SUP05 in non-sulfidic oxygen minimum zones prompted the description of a cryptic sulphur cycle linking the metabolic activities of SUP05 with other microorganisms involved in nitrogen and sulphur cycling.
Thus, knowing how microorganisms interact with and respond to ocean oxygen starvation teaches us about the organizing principles that shape ocean food webs and define how these species work with each other and their environment in a time of climate change.
I have effectively grown up as scientist with support from the JGI. I have been exposed to cutting edge technologies and incredibly talented people that have pushed my research into unexpected and impactful places through the Community Science Program. There is no way that I could have reached this level of scientific engagement without the community sequencing program and collaborative interactions with JGI staff and the extended network of people that results from programmatic initiatives like the GEBA uncultivated project. The JGI is truly a unique human resource and an engine for innovation and discovery in genome science and systems biology.
Check out Steven presenting in TEDxRenfrewCollingwood in Vancouver, British Columbia on October 25th, 2014.