How many species of prokaryotes are there?

The microorganisms classified in the two prokaryotic domains of the tree of life, Bacteria and Archaea, possess immense metabolic diversity, and their activities are critical in processes ranging from sewage treatment to regulating the composition of the atmosphere. Especially in light of the rate of modern climate change, it is essential to understand how microbial communities affect ecosystem functioning and how human activities, such as agriculture, waste management, and climate modification, affect microbial communities. Thus discovering and understanding the diversity of microbial communities (the number of species and their relative abundances) is a high priority in ecology. In this issue of PNAS, Curtis et al. (1) address what is therefore one of the most fundamental questions in microbial ecology—how many species of prokaryotes are there in nature? Only in the last 10–15 years has it even been possible to pose the question and hope realistically for an answer in the case of prokaryotes. Less than 30 years ago, the answer to the even more fundamental question “How many individuals are there?” was revised in such a way as to change the entire focus of environmental microbiology. So to appreciate the significance of the question and answer provided by Curtis et al. (1), it is useful to review that recent history briefly. Before the mid-1970s, microbial ecologists assessed the population size of bacteria in soils, sediments, and natural waters by culturing the microbes and counting the number of colonies that grew on nutrient agar plates. For seawater, the cultivable prokaryotic population size was a few hundred cells per milliliter (2, 3). That was an almost inconsequential number relative to the thousands or tens of thousands of planktonic algal cells that could be seen (literally, with a microscope) in the same milliliter of water. The primary importance then ascribed to environmental …