Most prokaryotes have defied all attempts to grow them in pure culture, causing biologists to wonder how many species, and possibly even major clades, we might be missing. A window onto this problem was opened with the introduction of a new way of examining nucleic acid sequences. When biologists are unable to work with the whole genome of a single prokaryote species, they can instead examine genomes collected from an environmental sample (such as a scoop of sediment from the sea floor). This technique is known as environmental genomics.

Biologists now routinely isolate gene sequences, or even whole genomes, from environmental samples such as soil and seawater. Comparing such sequences with previously known ones has revealed that an extraordinary number of the sequences represent new, previously unrecognized species. Biologists have described only about 10,000 species of bacteria and only a few hundred species of prokaryotic archaea (see Figure 1.9). The results of some environmental genomic studies suggest that there may be millions—perhaps hundreds of millions—of prokaryote species. Other biologists put the estimate much lower, arguing that the high dispersal ability of many bacterial species greatly reduces endemism (i.e., the number of species restricted to a small geographic area). Only the magnitude of these estimates differs, however; all sides agree that we have just begun to uncover Earth’s prokaryotic diversity.