tional disciplines, such as environmental and clinical microbiology, biogeochemistry, biological oceanography, soil sciences, and theoretical ecology. It will indeed be the systems biology of the most inclusive biological system we know about: the biosphere of the planet. These disciplines will in the process be transformed and many questions redefined and refocused, most often at a level below (genes and genomes) or above (communities and ecosystems) the organism and species levels at which microbial ecologists have traditionally concentrated their efforts. Although individual microbial cells will always be suitable units of study, the “species,” because we have just begun to uncover the enormous genomic diversity within it, may no longer be a reliable or useful ecological unit. Instead, we will understand ecosystems in terms of the collective activities and interactions of the genes they contain, how these are distributed and expressed in space and time, and how they function together.

We can expect, in 20 years, enormous advances on three fronts— technical, computational, and biological—as well as a host of specific applications.


Sequencing technology will have reduced the per-base price of finished sequence to fractions of a cent, and the cost of sequence-data acquisition will no longer by a serious consideration in studies of specific ecosystems. Sequencing methods now in use will have increased run lengths substantially but will themselves probably have been replaced with even more direct, and often also cloning-independent, approaches, perhaps single-molecule technologies now under development or others yet to be imagined. Single cell genome sequencing will be routine, and cell-sorting methods that readily permit recovery of even unique individual cells will be well advanced. Complete genome sequences, some produced by “traditional” methods based on isolates (or single cells) but others acquired metagenomically, will number in the thousands, perhaps even tens of thousands. There will be many “species” for which hundreds of individual isolates will have been sequenced.

Transcriptomic and proteomic applications to community samples will be comparable in their reliability and efficiency with such methods as are used in human genomics today. Incremental improvements in microarray sensitivity, specificity, and reproducibility will make it possible to assess community membership and abundance down to the “species” level, however that concept is then understood. New normalization protocols will allow a census of even the rarest members of a community, and whole-community RNA amplification will access their transcriptomes. We will be able routinely to classify or type ecosystems and monitor changes in

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