Development of a Genome-Proxy Microarray for Profiling Marine Microbial Communities and its Application to a Time Series in Monterey Bay, California
MASSACHUSETTS INST OF TECH CAMBRIDGE JOINT PROGRAM IN APPLIED OCEAN SCIENCE AND ENGINEERING
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This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the genome proxy microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance R2 of 1.0, with a dynamic range from 10-10 cellsmI. Genotypes with --80 average nucleotide identity to those targeted cross-hybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods R20.85-0.91. Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions.
- Biological Oceanography