Each liter of ocean water they collect contains up to a billion bacterial cells. For several years, researchers have been sequencing the DNA found in those bacteria, creating large databases of prevalent marine microbial genes found in the environment.
However, those DNA sequences alone cannot reveal which genes the bacteria are actually using in their day-to-day activities, or when they are expressing them.
Its a lot of information, and its hard to know where to start, said DeLong. How do you know which genes are actually important in any given environmental context?
To figure out which genes are expressed, DeLong and colleagues sequenced the messenger RNA (mRNA) produced by the cells living in complex microbial communities. mRNA carries instructions to the protein-building machinery of the cell, so if there is a lot of mRNA corresponding to a particular gene, it means that gene is highly expressed.
The new technique requires the researchers to convert bacterial mRNA to eukaryotic (non-bacterial) DNA, which can be more easily amplified and sequenced. They then use sequencing technology that is fast enough to analyze hundreds of millions of DNA base pairs in a day.
Once the sequences of highly expressed mRNA are known, the researchers can compare them with DNA sequences in the database of bacterial genes and try to figure out which genes are key players and what their functions are.
The team found some surprising patterns of gene expression, DeLong said. For example, about half of the mRNA sequences found are not similar to any previously known bacterial genes.
|Contact: Elizabeth Thomson|
Massachusetts Institute of Technology