Microbial Dormancy and the Rare Biosphere

Microbial evolution and diversity are determined by the potential for widespread dispersal among microorganisms. This is consistent with observations of enormous natural microbial diversity in the ocean and elsewhere being comprised of many low-abundance taxa. This ‘rare biosphere’ points to the importance of cell dormancy in shaping and maintaining biodiversity. Hand in hand with this biodiversity is a breadth of metabolic traits that may not necessarily be immediately relevant under prevailing environmental conditions, but that could become important if conditions change. In this regard the rare biosphere has been referred to as a microbial ‘seed bank’ with the potential to respond rapidly to environmental perturbation.

Our group is particularly interested in thermophilic spores found in cold environments such as marine sediments in the Arctic. These dormant thermophiles cannot grow and divide in these permanently cold settings, thus allowing passive dispersal to be disentangled from other determinants of microbial biogeography and assessed via sediment heating experiments. Spores of anaerobic thermophilic, and halophilic Clostridia must be coming from environments that reflect these preferences (anoxic, hot, saline) and that offer a fluid flow dispersal vector. Ongoing investigations of mid ocean ridge crustal fluids and hydrocarbon seepage from petroleum-bearing deep sediments allow our projects to intersect questions about the rare biosphere, the deep biosphere, and geofluids as vectors for cell dispersal.



Another group of rare organisms are hydrocarbon-degrading bacteria in pristine parts of the ocean. In the event of an oil spill in the marine environment, these microbes find a purpose and become rapidly enriched in the process of biodegradation of newly added pollutants. In this way, the rare biosphere is a seed bank of metabolic potential that can offer ecosystem services in the form of spill mitigation. Reasons for the presence of these bacteria in the ocean in the first place may be related to natural hydrocarbon seepage, or the synthesis of alkanes for membrane lipids by marine cyanobacteria. These processes may be ‘priming’ the ocean to respond to inputs of hydrocarbons.
In polar seas water begins to freeze when seawater temperatures drop below –2°C. During sea ice formation salts are expelled into brine channels that form amidst the solid ice, and salinities can reach 10x that of seawater. Liquid brines are suitable habitats for certain microorganisms, and sea ice has been shown to contain surprisingly high numbers of bacteria – sometimes more than in surrounding seawater. Brine channel microbial community assembly is poorly understood, and likely involves environmental selection of seawater bacteria that are dormant or otherwise marginalized in that unfrozen setting, but that gain an advantage when they encounter colder and saltier conditions in winter sea ice brine channels.
The Geomicrobiology Group’s research on dormant spores and the rare biosphere is and has been funded by NSERC, the Campus Alberta Innovates Program (CAIP), and Genome Canada.