Chapter 26. Bacteria and Archaea

26.4 The Diversity of Bacteria

Traditionally, bacterial taxonomy was a laborious process. Microbiologists grew bacteria in beakers or on petri dishes, carefully separating and enriching individual populations until only one type of bacterium—that is, a pure culture—was present. Species were identified on the basis of details of cell structure and division observed under the microscope, and metabolic capabilities established through experiments and reactions to chemical stains or antibiotics. By the 1980s, a few thousand species had been described in this way.

With molecular sequencing technologies, however, bacterial species are now characterized by their DNA sequences, especially the genes for the small subunit of ribosomal RNA (rRNA). A novel application of sequencing technology paved the way for modern studies of bacterial diversity and ecology. Microbiologists reasoned that the same procedures used to extract, amplify, and sequence genes from pure cultures in the lab could be used to study bacteria in nature. That is, extracting and reading gene sequences directly from soil or seawater could reveal the diversity of the microbial communities in these environments.

The results were stunning. Most bacteria in nature—perhaps 99% or more—are species that have not been cultured in the lab. Indeed, species well characterized by studies of pure cultures commonly represent only minor components of natural communities. To give just one illustration, a bacterium called SAR11 was originally identified on the basis of gene sequences amplified from seawater. SAR11 caught the attention of microbiologists because it makes up about a third of all sequences identified in the samples from the surface ocean. How could we be ignorant of a bacterium that must be among the most abundant organisms on Earth? The answer is simple: No one had cultured it. Recently, SAR11 has been cultured. Formally described as Pelagibacter ubique (ubique is Latin for “everywhere”), this bacterium is now known to be a heterotroph that plays an important role in recycling organic molecules dissolved in the sea.

More recently, the application of shotgun sequencing techniques (Chapter 13) to the environmental sampling of genomes has allowed microbiologists to begin matching uncultured populations with specific metabolisms. That is, we need no longer be content to know from molecular sequences what is living in a given environment. Now we can begin to understand what the different microorganisms are doing there. For this reason, another revolution in our understanding of the microbial world lies just around the corner (Fig. 26.13).

HOW DO WE KNOW?

FIG. 26.13

How many kinds of bacterium live in the oceans?

BACKGROUND The oceans are full of bacteria—by some estimates, the sea harbors more than 10²⁹ bacterial cells. How diverse are these bacterial communities?

METHOD 1 Different types of bacterium can be recognized by the unique nucleotide sequences of their genes. In fact, individual types of bacterium can be identified on the basis of nucleotide sequence in a relatively small region of the gene for the small subunit of ribosomal RNA (rRNA). This molecular “barcode” can be sequenced quickly and accurately for samples of DNA drawn from the environment.

FIG. 26.13 Relative abundance of different bacterial groups in samples from the Sargasso Sea, based on percent representation of small subunit rRNA sequences. Note the abundance of SAR11, only recently characterized.

Using this strategy, scientists associated with the International Census of Marine Life obtained samples of seawater and seafloor sediment from deep-ocean environments. In the laboratory, the rRNA sequences were amplified by PCR, separated by gel electrophoresis, and sequenced, thus providing a library of tags that document bacterial diversity.

METHOD 2 In another set of experiments, scientists collected samples of seawater from the Sargasso Sea, and from these they amplified whole genomes—more than a billion nucleotides’ worth. They used small-subunit rRNA and other genes to characterize species richness, and also characterized a large assortment of additional sequence data to understand genetic and physiological diversity.

Computer-aided comparison of sequences from the world’s oceans shows that about 75% of all sequences collected are similar to other sequences in the library of sequence tags. However, 25% are distinctive, forming a rare but enormously diverse pool of bacterial types.

RESULTS Both surveys found that the bacterial diversity of marine environments is much higher than had been thought. The barcode survey (method 1) found as many as 20,000 distinct types of bacteria in a single liter of seawater and estimated that as many as 5–10 million different microbes may live in the world’s oceans. Some of these bacteria are abundant and widespread, but most are rare. The genomic survey (method 2) of the Sargasso Sea found more than 1800 distinct bacteria in sea-surface samples and, remarkably, identified more than 1.2 million previously unknown genes within these genomes.

CONCLUSION The bacterial diversity of the oceans is huge and still largely unexplored. Both barcode and genomic surveys are continuing, and promise a more nearly complete accounting of marine diversity. Together, these surveys will help us understand how marine bacteria function and how they sort into communities.

SOURCES Venter, J. C., et al. 2004. “Environmental Genome Shotgun Sequencing of the Sargasso Sea.” Science 304:66–74; Sogin, M. L., et al. 2006. “Microbial Diversity in the Deep Sea and the Underexplored ‘Rare Biosphere’” Proceedings of the National Academy of Sciences USA 103:12115–12120.