Metaproteomic and genomic analyses of Antarctic haloarchaea

• Main Author: Tschitschko, Bernhard
• Format: Doctoral or Postdoctoral Thesis
• Language: unknown
• Published: UNSW Sydney 2017
• Subjects: Hypersaline; Metaproteomics; haloarchaea; Antarctica; Genomics; Antarctic; Vestfold; Vestfold Hills; Antarc*
• Online Access: https://dx.doi.org/10.26190/unsworks/3118; http://hdl.handle.net/1959.4/57305

Deep Lake is a hypersaline lake in the Vestfold Hills, Antarctica. Because of its high salinity (around ten times seawater), Deep Lake does not freeze during winter and the water temperature drops to -20°C. Environmental sequencing of Deep Lake biomass revealed that the lake harbours a low-complexity microbial community that is dominated by haloarchaea. Genomic analyses of four isolated haloarchaeal species, including the three most abundant species (Halohasta litchfieldiae, DL31 and Halorubrum lacusprofundi), revealed differences in nutrient utilization and a high level of gene exchange between them. In this thesis, the Deep Lake microbial community was studied using metaproteomics. Through analyses of proteins that were present in lake samples, inferences were made about population structures and the functioning of the dominant members of the haloarchaeal community. The metaproteomics was complemented by metagenomic and genomic analyses, allowing an assessment of the viral community present in Deep Lake and interactions of viruses with haloarchaeal hosts. Strain variation was also assessed for Hrr. lacusprofundi by comparing the genome sequence of the Deep Lake type strain with a new strain isolated from a lake 30 km away. The metaproteomics revealed differences in targeted substrates that were linked to the distinct physiologies of the dominant haloarchaea. Proteins derived from viruses indicated a diverse viral population in Deep Lake. Cell surface proteins with a high degree of sequence variation were detected for the haloarchaea. These proteins were derived from phylotypes that exist in the lake and represent a defence strategy of the haloarchaea to escape virus infection. Other anti-viral defence systems such as CRISPR and BREX were also determined to be active, and CRISPR-spacer analysis revealed host-virus relationships, including the identification of broad host-range viruses. The genomic comparison between the two Hrr. lacusprofundi strains revealed distinct types of strain variation, with the primary replicons highly conserved between the strains in comparison to the secondary replicons, which contained high levels of variation. The findings from this thesis significantly extend understanding of haloarchaeal community functioning in hypersaline environments, and provide unprecedented insight into the ecophysiology of Antarctic archaea.