Wee creatures are key to Earth's environment

Microbes living in the oceans play a critical role inregulating Earth's environment, but very little is known about theiractivities and how they work together to help control natural cycles ofwater, carbon and energy. A team of MIT researchers led by ProfessorsEdward DeLong and Penny Chisholm is trying to change that.Borrowing gene sequencing tools developed for sequencing the humangenome, the researchers have devised a new method to analyze geneexpression in complex microbial populations. The work could helpscientists better understand how oceans respond to climate change."This project can help us get a better handle on the specific details ofhow microbes affect the flux of energy and matter on Earth, and howmicrobes respond to environmental change," said DeLong, a professor ofbiological engineering and civil and environmental engineering."The new approach also has other potential applications, for example,one can now realistically consider using indigenous microbes as in situbiosensors, as well as monitor the activities of human-associatedmicrobial communities much more comprehensively, " DeLong said.Their technique, which has already yielded a few surprising discoveries,is reported in the March 3 issue of the Proceedings of the NationalAcademy of Sciences.The work was facilitated by the Center for Microbial Oceanography:Research and Education (C-MORE), a National Science Foundation Scienceand Technology Center established in 2006 to explore microbial oceanlife, most of which is not well understood.The traditional way to study bacteria is to grow them in Petri dishes ina laboratory, but that yields limited information, and not all strainsare suited to life in the lab. "The cast of characters we can grow inthe lab is a really small percentage of what's out there," said DeLong,who is research coordinator for C-MORE.The MIT team gathers microbe samples from the waters off Hawaii, in apart of the ocean known as the North Pacific Gyre.Each liter of ocean water they collect contains up to a billionbacterial cells. For several years, researchers have been sequencing theDNA found in those bacteria, creating large databases of prevalentmarine microbial genes found in the environment.However, those DNA sequences alone cannot reveal which genes thebacteria are actually using in their day-to-day activities, or when theyare expressing them."It's a lot of information, and it's hard to know where to start," saidDeLong. "How do you know which genes are actually important in any givenenvironmental context?"To figure out which genes are expressed, DeLong and colleagues sequencedthe messenger RNA (mRNA) produced by the cells living in complexmicrobial communities. mRNA carries instructions to the protein-buildingmachinery of the cell, so if there is a lot of mRNA corresponding to aparticular gene, it means that gene is highly expressed.The new technique requires the researchers to convert bacterial mRNA toeukaryotic (non-bacterial) DNA, which can be more easily amplified andsequenced. They then use sequencing technology that is fast enough toanalyze hundreds of millions of DNA base pairs in a day.Once the sequences of highly expressed mRNA are known, the researcherscan compare them with DNA sequences in the database of bacterial genesand try to figure out which genes are key players and what theirfunctions are.The team found some surprising patterns of gene expression, DeLong said.For example, about half of the mRNA sequences found are not similar toany previously known bacterial genes.Massachusetts Institute of Technology