Developed by a team of MIT researchers led by Professors Edward De Long and Penny Chisholm, this method was achieved by borrowing gene-sequencing tools developed for sequencing the human genome.
This project can help us get a better handle on the specific details of how microbes affect the flux of energy and matter on Earth, and how microbes respond to environmental change," said De Long.
"The new approach also has other potential applications, for example, one can now realistically consider using indigenous microbes as in situ biosensors, as well as monitor the activities of human-associated microbial communities much more comprehensively," he added.
For the research, the MIT team gathers microbe samples from the waters off Hawaii, in a part of the ocean known as the North Pacific Gyre. 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.
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," said De Long. "For example, about half of the mRNA sequences found are not similar to any previously known bacterial genes," he added.