The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist

One of the most comprehensive and most important contemporary surveys has been the recently completed Census of Marine Life (Census; http://www.coml.org webcite). This ten-year initiative involved 2,700 scientists from more than 80 countries and cost in excess of US$650 million. The Census was driven by a fundamental hypothesis, that 'there exist fundamental gaps in our knowledge and understanding of the biology of the oceans and the subsequent functioning of this system'. It has often been said that the absence of knowledge should be enough justification for exploration. The fact that the Census identified more than 6000 potentially new species and resulted in more than 2600 scientific publications validates the hypothesis. The Census community observed a potential gap in knowledge about biodiversity on our planet and wanted to fill it. Indeed this was driven not just by the scientific community, but also by public pressure for discovery. People are very responsive to new discovery, as indicated by the media response to new species found in the Census, and the questions asked of the Census by the public, e.g. 'how much biodiversity is there?'; 'why is there so much?'; 'how did it get there?'; and how much biodiversity is enough?' [1]. What has been striking has been the reinforcement of our original theory - that these voluminous observations have generated innumerable new hypotheses. This no more true than in the microbial component of the census, the International Census of Marine Microbes (ICoMM; http://icomm.mbl.edu/ webcite), which has been one of the most comprehensive studies of microbial diversity ever accomplished.Were Darwin or his financiers around today, they would surely be deeply interested in the possibilities of exploring microbial life. Undoubtedly they would achieve this using metagenomics. In metagenomics, we isolate DNA directly from the environment and use it to characterize the taxonomy and function of the biological community in that ecosyste