(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2008-09)
Rich, Virginia I.
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 102-106 cells/ml.
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 (R2=0.85-
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.