A metaproteomic analysis of microbial communities of Ace Lake, Antarctica

Abstract

The Vestfold Hills is an ice free oasis in East Antarctica with possibly the highest distribution of stratified lakes and marine basins in the world. Ace Lake is a meromictic lake located on the Long Peninsula in the Vestfold Hills region, and is one of the most intensively studied stratified lakes in Antarctica. Since its isolation from the Southern Ocean over 10,000 years ago, the marine derived community of Ace Lake have evolved with changes in the physical and chemical structure of the lake. Metaproteomics (environmental proteomics) was used to investigate the interactions and functional activity of microbial populations within the layers of Ace Lake. To achieve this, a protein extraction procedure was developed using test samples of filtered biomass from coastal marine waters (Botany Bay). The performance of two mass spectrometry analysis softwares, Mascot (spectral searching) and Peaks (de novo sequencing) were also evaluated using the metaproteomic datasets generated from Botany Bay. Although it was concluded that Mascot was a more rapid and reliable method for processing large metaproteomic datasets, the de novo sequencing capability of Peaks hold much promise for identification of proteins with novel sequences. The simulated mixed community study of Sphingopyxis alaskensis and Escherichia coli indicated that well represented organisms in terms of cell abundance resulted in higher levels of protein detection by mass spectrometry. The simulated community study provided metaproteomic datasets, which enabled the performance of Mascot database searching and protein identification validation techniques to be tested.

Cross-species matching (NR database) of proteomic data derived from microbial populations at different depths of Ace Lake provided insights to th e microbial composition and functional activity of members within the lake. A SAR11 community in the surface waters of Ace Lake likely adapts to oligotrophic conditions of the lake by expressing transport proteins associated with nutrient uptake. The detection of Phycodnaviridae capsid proteins in the aerobic zone suggests that these algal viruses may be active in the Antarctic summer during periods of algal bloom. Proteins involved in processes such as methanogenesis, sulfur and carbon cycling were also identified.

Through metagenomics, an almost complete genome sequence of a single, dominant ass (C-Ace) was assembled from shotgun sequencing data taken from the oxycline (12.7 m) of the lake. Approximately 34 Mb of D A sequence data was assembled into nine scaffolds totalling 1.79 Mb, representing a 19-fold coverage for the C-Ace composite genome. Using a metaproteogenomic approach, metaproteomic data obtained from biomass at the chemocline was mapped back to the refe rence C-Ace genome sequence data, which resulted in high levels (~ 31 %) of metaproteomic coverage. The findings of this study revealed the physiological traits that promote the ass to compete very effectively to gain dominance under cold, nutrient-, oxygen-limited and extremely varied annual light cycles.

Metaproteomics is a relatively new and rapidly emerging area of study in the field of environmental microbiology. An increasing number of community proteogenomic analyses over the past few years have successfully unravelled the structure, function, and microbial diversity of a range of different ecosystems (e.g. aquatic, soil biospheres, biofilms). Ace Lake is one of the most studied meromictic lakes in Antarctic, however few studies have attempted to provide a comprehensive analysis of the identity and functional activity of the microbial populations within the stratified layers of the lake. The metaproteomic analysis presented in this thesis has provided a broad survey of the microbial community structure and a glimpse into the biochemical processes occurring at the various depths throughout the water column. The role of the dominant ass (C-Ace) as a major player in nutrient cycling and primary productivity was established through a detailed analysis of the metaproteogenomic data, which also provided insights into microbial interact ions and adaptive responses for survival in the Antarctic environment. Studying microbial communities ill situ is challenging hence the successful application of methods developed in this metaproteomic study of microbial communities from Ace Lake is valuable as it demonstrates the potential of applying the same approach to other Antarctic aquatic environments.