Dissertation Abstract
Dimensions of Antarctic microbial life revealed through microscopic, cultivation-based, molecular phylogenetic and environmental genomic characterization
Kuhn, Emanuele 2014 http://www.dri.edu/ema-kuhn
Division of Earth and Ecosystem Sciences, DRI, University of Nevada, Reno and Desert Research Institute (United States), 208 pp.
This dissertation focused on the investigation of the microbial assemblage in two Antarctic environments: Lake Vida (McMurdo Dry Valleys) and the surface seawater from the Antarctic Peninsula.
Lake Vida has a thick (27+ m) ice cover which seals a cryogenic brine reservoir within the lake ice below 16 m. This brine’s environment challenges the conditions for the existence of life. Despite the perceived challenges of aphotic, anoxic and freezing conditions, the brine contained an abundant assemblage (6.13 × 107 cells mL-1) of ultra-small cells 0.192 ± 0.065 μm in diameter and a less abundant assemblage (1.47 × 105 cells mL-1) of microbial cells ranging from > 0.2 to 1.5 μm in length. Electron microscopy provided supporting evidence for cell membranes associated with the ~ 0.2 μm cells and helped discern a second smaller size class of particles (0.084 ± 0.063 μm). 16S rRNA clone library analyses indicated that the ultra-small cell-size assemblage was dominated by the Proteobacteria-affiliated genera. Cultivation efforts of the 0.1 – 0.2 μm size fraction led to the isolation of Actinobacteria-affiliated genera. Based on our results, we hypothesize that the ultra-small cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life-cycle related conditions.
The deeper ice of Lake Vida (from 18 to 27 m) revealed an ice column banded by sediment layers and a diverse and cell-rich microbial assemblage (3.73 × 104 to 8.58 × 106 cells mL-1). Illumina tag sequencing indicated that the microbial assemblage from the lake ice and sediment layers below 21 m was dominated by organisms capable of the reduction and oxidation of sulfur compounds. The distribution of the microbial assemblage was correlated with the presence of sediment particles, total dissolved solids, total carbon, SO42-, and Na+ concentration. Chemolithoautotrophic and heterotrophic genera dominated the ice segments and heterotrophic genera dominated the sediment layers. Therefore, the detection of abundant and considerably diverse microbial assemblages in Lake Vida brine, ice and sediment layers indicates that life is likely sustained in isolated deep, icy and dark anoxic environments. This also suggests that if similar conditions are found elsewhere beyond Earth, there is the possibility to find life.
The second subject was to conduct an in-depth assessment of the environmental genomics of the archaeal phylum Thaumarchaeota within Antarctic surface seawaters during the wintertime. Thaumarchaeota (Marine Group I.1a) composes 10-30% of the bacterioplankton during the winter in Antarctic surface seawaters playing a noteworthy role in carbon fixation coupled to ammonia oxidation. By comparative genomic analyses, we found that the Antarctic Group I.1a genome fragments represent a unique low diversity Group I.1a cluster affiliated with a “Ca. Nitrosopumilus” that has not yet been cultivated. Antarctic Group I.1a exhibited highly conserved genes in a rearranged genomic structure when compared to the genome of N. maritimus SCM1 indicating a high frequency of recombination (30% of the Antarctic Group I.1a open reading frames). The results provided insights into the genomic variability of a thaumarchaeal Antarctic assemblage indicating very low diversity that motivates the importance of acquiring the Antarctic strain in pure culture for further analysis of its physiological capacities and evolutionary history.
Lake Vida has a thick (27+ m) ice cover which seals a cryogenic brine reservoir within the lake ice below 16 m. This brine’s environment challenges the conditions for the existence of life. Despite the perceived challenges of aphotic, anoxic and freezing conditions, the brine contained an abundant assemblage (6.13 × 107 cells mL-1) of ultra-small cells 0.192 ± 0.065 μm in diameter and a less abundant assemblage (1.47 × 105 cells mL-1) of microbial cells ranging from > 0.2 to 1.5 μm in length. Electron microscopy provided supporting evidence for cell membranes associated with the ~ 0.2 μm cells and helped discern a second smaller size class of particles (0.084 ± 0.063 μm). 16S rRNA clone library analyses indicated that the ultra-small cell-size assemblage was dominated by the Proteobacteria-affiliated genera. Cultivation efforts of the 0.1 – 0.2 μm size fraction led to the isolation of Actinobacteria-affiliated genera. Based on our results, we hypothesize that the ultra-small cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life-cycle related conditions.
The deeper ice of Lake Vida (from 18 to 27 m) revealed an ice column banded by sediment layers and a diverse and cell-rich microbial assemblage (3.73 × 104 to 8.58 × 106 cells mL-1). Illumina tag sequencing indicated that the microbial assemblage from the lake ice and sediment layers below 21 m was dominated by organisms capable of the reduction and oxidation of sulfur compounds. The distribution of the microbial assemblage was correlated with the presence of sediment particles, total dissolved solids, total carbon, SO42-, and Na+ concentration. Chemolithoautotrophic and heterotrophic genera dominated the ice segments and heterotrophic genera dominated the sediment layers. Therefore, the detection of abundant and considerably diverse microbial assemblages in Lake Vida brine, ice and sediment layers indicates that life is likely sustained in isolated deep, icy and dark anoxic environments. This also suggests that if similar conditions are found elsewhere beyond Earth, there is the possibility to find life.
The second subject was to conduct an in-depth assessment of the environmental genomics of the archaeal phylum Thaumarchaeota within Antarctic surface seawaters during the wintertime. Thaumarchaeota (Marine Group I.1a) composes 10-30% of the bacterioplankton during the winter in Antarctic surface seawaters playing a noteworthy role in carbon fixation coupled to ammonia oxidation. By comparative genomic analyses, we found that the Antarctic Group I.1a genome fragments represent a unique low diversity Group I.1a cluster affiliated with a “Ca. Nitrosopumilus” that has not yet been cultivated. Antarctic Group I.1a exhibited highly conserved genes in a rearranged genomic structure when compared to the genome of N. maritimus SCM1 indicating a high frequency of recombination (30% of the Antarctic Group I.1a open reading frames). The results provided insights into the genomic variability of a thaumarchaeal Antarctic assemblage indicating very low diversity that motivates the importance of acquiring the Antarctic strain in pure culture for further analysis of its physiological capacities and evolutionary history.