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Research Laboratories
Extremophiles - Research Projects
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A cold biosphere
We live on a cold planet where more than 80% of the biosphere is permanently below 5°C, yet comparatively little is known about the genetics and physiology of the microorganisms inhabiting these environments. In cold habitats, such as the ocean, Archaea are prevalent, yet surprisingly little is known about the molecular mechanisms that facilitate low temperature survival. |
Archaea
Archaea are one of the three domains of life, phylogenetically distinct from Bacteria and Eucarya. Biochemical and genomic analyses reveal that Archaea possess a number of unique molecular traits (e.g. methanogenesis, ether-linked lipids), as well as mechanisms common to Bacteria (e.g. energy generation, metabolism, biosynthesis, transport and nitrogen fixation) and Eucarya (e.g. transcription, translation, replication and protein folding). Our current picture is of a mosaic evolution, with Archaea resembling Eucaryotes with respect to macromolecule-handling machinery, and resembling Bacteria with respect to metabolic systems and genome organisation.
As a group, Archaea may best be described as adaptable and ubiquitous, and many Archaea thrive under extreme conditions of temperature, pH, pressure or salinity.
Cold-adapted archaea
Even though Archaea contribute significantly to biomass in the predominantly cold biosphere (e.g. ~1028 cells in the world's oceans), the only free living isolates that have been formally characterized are a handful of methanogens. Consequently, our understanding of cold adaptation in this domain of life is limited. The methanogen with the lowest known optimum growth temperature (OGT) is Methanogenium frigidum (15°C) which is unable to grow above 18°C. It was isolated from Ace Lake in the Vestfold Hills region of Antarctica where the bottom waters are saturated in methane and permanently 1-2°C. Ace Lake was also the source of Methanococcoides burtonii. Its ability to grow on methyl-substrates and tolerate a broader range of growth temperatures (<4°C to 29°C) has led to its use for studies on protein and RNA adaptation and gene regulation.
Methanogen thermal extremes
The methanogens stand out as the only group of organisms that have species capable of growth at 0°C (M. frigidum and M. burtonii) and 110°C (Methanopyrus kandleri). Moreover, there are complete genome sequences for M. kandleri (OGT 98°C), Methanocaldococcus jannaschii (85°C), Methanothermobacter thermautotrophicus (65°C), Methanosarcina acetivorans (37°C), Methanosarcina mazei (37°C,) and high quality draft sequences for Methanococcus maripaludis (37°C) and Methanosarcina barkeri (35°C).
Genomic analysis
The analysis of thermal adaptation across the full spectrum of known growth temperatures has been hampered by the lack of genome sequences for cold-adapted organisms. The majority of complete archaeal genome sequences are for thermophiles or hyperthermophiles and the remainder are for mesophiles. We recently reported the draft sequencing of M. frigidum and M. burtonii. These data provide the missing link for enabling a rigorous assessment of thermal adaptation at the genomic level and highlight the use of comparative genomics for identifying genome-wide characteristics of cold adaptation. These include trends in amino acid and tRNA composition, and structural and compositional features of protein homology models, that distinguish the genomes of the cold-adapted Archaea from other Archaea. It also highlights the value of the genome sequence data for rationalising research efforts from gene specific to global phenomic.
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