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Microbiology of Extreme Environments

Studying the microbiology of extreme environments can provide important insights into the limits of life, microbial diversity, evolution, and biotechnological applications of microorganisms that have evolved to thrive in extreme conditions. The relatively low diversity of organisms able to survive in such environments allows for complete or near-complete genome assembly from the dominant populations, which can be used to unravel population heterogeneity and characterize changes in population and community structure over time.

Lake Tyrrell is an Archaea-dominated hypersaline lake in Victoria, Australia, with highly dynamic virus and host assemblage structures [1]. Hypersaline systems are near the limit of salt concentration, harboring organisms that exhibit extraordinary adaptive mechanisms for survival. In comparison to marine environments, hypersaline aquatic systems have lower species richness and exhibit clear spatial boundaries, making them an excellent model system for diel cycle analysis [2]. As the solubility of oxygen in hypersaline environments is low, square archaeal Haloquadratum species often do well owing to their gas vesicles and high surface area-to-volume ratio, positioning them near the surface to maximize available oxygen and phototrophic growth. Detailed genomic comparisons between planktonic samples and publically available Haloquadratum genomes have provided insight into how these organisms thrive [3]. 


Metagenomic analysis has demonstrated that even historically well-studied environments can unveil surprising diversity, significantly enhancing our knowledge of the ecology of hypersaline environments and the evolutionary history of archaea. De novo metagenomic assembly of multiple, deeply sequenced libraries from the surface waters of Lake Tyrrell uncovered a new archaeal class named nanohaloarchaea, belonging to a new major euryarchaeal lineage [4].

The sources of carbon sources in this environment remain a mystery as no eukaryotic algae or other photosynthetic primary producers have been identified yet. Current work is investigating the microbial mats at the sediment-water interface for an explanation, aiming to elucidate the underlying mechanisms able to support life in such extreme conditions.

For more information, visit our Lake Tyrrell research page here


Additionally, the Banfield lab is investigating the effects of wildfires on the soil microbiome across scales of time and severity in the coniferous forests of California. Although many of California’s diverse ecosystems are fire-dependent or fire-adapted, the increasing severity of wildfires can reduce carbon stocks, increase erosion and runoff, destroy seedbanks, and catalyze the transformation of forests to non-forest lands, all of which can exacerbate impacts on biodiversity and carbon-cycle feedbacks. Studying the dynamics of microbial succession in soils following severe wildfires in California will not only elucidate the succession of the soil microbiome following wildfire but may also provide critical insight into possible solutions, including the potential for the development of probiotic amendments to aid in the conversion of charred forest soils to a relatively “un-burnt” state. Using metagenome-assembled genomes to inform the selection of native microorganisms to include in a probiotic mixture, a successful amendment would catalyze the conversion of pyrogenic carbon in surface soils to more broadly bioavailable forms, allowing for the recovery of a diversity of native microbes within the microbiome, improved soil quality, and the reintroduction of seed banks.

Relevant publications

[1] Emerson, Joanne B et al. “Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia.” Archaea (Vancouver, B.C.) vol. 2013 (2013): 370871. doi:10.1155/2013/370871
[2] Andrade, Karen et al. “Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem.” The ISME journal vol. 9,12 (2015): 2697-711. doi:10.1038/ismej.2015.66
[3]Tully, Benjamin J et al. “De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.” Archaea (Vancouver, B.C.) vol. 2015 875784. 1 Feb. 2015, doi:10.1155/2015/875784
[3]Narasingarao, Priya et al. “De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.” The ISME journal vol. 6,1 (2012): 81-93. doi:10.1038/ismej.2011.78

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