Bacterial Diversity of the Atacama Desert, Chile: The Challenges of Characterizing the Community Dynamics of Extreme Oligotrophic Ecosystems

Abstract

This dissertation examines the bacterial diversity of hyperarid and arid regions of the Atacama Desert, Chile, as a first step towards understanding the global biogeochemical significance of arid-land microbial communities. The specific objectives were to characterize bacterial diversity and infer the possible metabolic potential of these bacterial communities, and to evaluate the influence of moisture exposure on community structure. In addition, the strengths and limitations of available tools for probing microbial diversity and activity in terrestrial ecosystems were characterized for their application to extreme oligotrophic communities. Preliminary PCR-DGGE analysis of a west-east elevational transect from the Pacific Ocean near Antofagasta to the western slopes of the central Andes indicated that bacterial communities along this transect belonged to two distinct community types: 1) hyperarid (700 - 2000 m) and 2) arid (2500 - 4500 m) communities that included both vegetated and unvegetated regions. Subsequent diversity analysis of these two regions revealed novel but distinct communities in both regions. A greater diversity was observed in the unvegetated arid regions than in the unvegetated hyperarid areas. The unvegetated arid sites were characterized by a bacterial community harboring a combination of radiotolerant and halotolerant heterotrophs as wells as diverse phylotypes closely related to chemolithoautotrophs. These rare phylotypes may be uniquely adapted to arid ecosystems. Molecular tools evaluated for community diversity analysis included PCR-DGGE, Sanger-clone and 454-pyrosequencing analysis of 16S rRNA gene libraries, and the use of reverse transcriptase quantitative PCR (RT-qPCR) for quantifying the impact of environmental variables on the metabolic activity of a specific organism. These techniques were evaluated using the ecosystems of the Atacama Desert as well as model ecosystems designed to address specific questions. Molecular tools are invaluable to the study of microbial ecology because they facilitate the study of fastidious organisms that are difficult or impossible to culture, but the analysis presented in this dissertation demonstrates that each of these methods has limitations and biases which must be acknowledged to avoid inaccurate conclusions from skewed results. The most complete picture of the taxonomic and functional profile of a microbial community is obtained by employing a combination of molecular techniques.