Fuhrman.indd MH

and fungi, are vital to the function of all ecosystems. This is largely because they exist in enormous numbers (there are roughly 5 × 10 bacteria alone worldwide) and so have immense cumulative mass and activity. They are also probably more diverse than any other organisms, so it is easy to see why the structure of microbial communities, that is, the different kinds of organisms and their abundances, is so important to the way in which ecosystems function. But even with modern tools, it is not easy to determine microbial community structure and map its variations in space and time; we have only recently begun to learn about the scales of variation (Box 1). Understanding ecosystem function, and predicting Earth’s response to global changes such as warming and ocean acidification, calls for much better knowledge than we have today about microbial processes and interactions. In the past couple of decades, the use of genome sequences and related approaches has overcome the need for cultivation to characterize and identify microorganisms in nature (Box 2). It still seems almost hopeless to sort out the identities and interrelationships among the trillions of microorganisms in a cubic metre of sea water, let alone a few hectares of ocean, but high-throughput sequencing and whole-community fingerprinting techniques have enabled researchers to make considerable progress (Box 2). This review summarizes our knowledge of microbial community structure, with a focus on planktonic marine bacteria, and discusses what we can learn about microbial systems and their functions from this information (Box 3).