Metagenomic analysis of the biodiversity and seasonal variation in the meromictic Antarctic lake, Ace Lake

• Main Author: Panwar, Pratibha
• Format: Doctoral or Postdoctoral Thesis
• Language: unknown
• Published: UNSW Sydney 2021
• Subjects: meromictic lake; Antarctic microbiology; Bioinformatics; FOS Computer and information sciences; metagenome time series; generalist virus; metagenome assembled genomes; polar light cycle; phototroph; green sulfur bacteria; cyanobacteria; phylotype; ecotype; host-virus interactions; Ace Lake; Antarctic; Ellis Fjord; Rauer Islands; Taynaya Bay; Vestfold; Vestfold Hills; Antarc*; Antarctica
• Online Access: https://dx.doi.org/10.26190/unsworks/22609; http://hdl.handle.net/1959.4/70961

Ace lake is a stratified lake in the Vestfold Hills, Antarctica. The presence of a thick ice-cover for ~11 months of the year and a strong salinity gradient are responsible for its permanent stratification. Taxonomy analyses showed depth-based segregation of its microbial community, including viruses. Functional potential analyses of the lake taxa highlighted their roles in nutrient cycling. In this thesis, the seasonal changes in Ace Lake microbial community were studied using a time-series of metagenomes utilizing the Cavlab metagenome analysis pipeline. Statistical analyses of taxa abundance and environmental factors revealed the effects of the polar light cycle, with 24 hours of daylight in summer and no sunlight in winter, on the phototrophs identified in the lake, indicating the importance of light-based primary production in summer to prevail through the dark winter. Analysis of viral data generated from the metagenomes showed the presence of viruses, including a ‘huge phage’, throughout the lake, with a diverse population existing in the oxic zone. Analysis of virus-host associations of phototrophic bacteria revealed that the availability of light, rather than viral predation, was probably responsible for seasonal variations in host abundances. Genomic variation in Synechococcus and Chlorobium populations, analysed using metagenome-assembled genomes (MAGs) from Ace Lake, revealed phylotypes that highlighted their adaptation to the lake environment. Synechococcus phylotypes were linked to complex interaction with viruses, whereas some Chlorobium phylotypes were inferred to interact with Synechococcus. Some Chlorobium phylotypes were also inferred to have improved photosynthetic capacity, which might contribute to the very high abundance of this species in Ace Lake. Comparative genomic analysis of Chlorobium was performed using MAGs from Ace Lake, Ellis Fjord, and Taynaya Bay and the genome of a non-Antarctic Chlorobium phaeovibrioides. A single Chlorobium species, distinct from the non-Antarctic species, was prevalent in the oxycline of all three stratified systems, highlighting its endemicity to the Vestfold Hills. Potential Chlorobium viruses, representing generalist viruses, were identified in aquatic systems from the Vestfold Hills and the Rauer Islands, indicating a widespread geographic distribution. Seasonal variation in the Chlorobium population appeared to be caused by reliance on sunlight rather than the impact of viral predation, and was inferred to benefit the host by restricting the ability of specialist viruses to establish effective lifecycles. The findings in this thesis highlight the seasonal influence on Ace Lake biodiversity, the adaptations and potential interactions of the two key species Synechococcus and Chlorobium, and the endemicity of Ace Lake Chlorobium to the Vestfold Hills.