Some Carolina bays are wet and others are dry, and all seem to support an unusual profusion of plants and animals, including more than 30 endangered and unusual species such as the Venus flytrap. Now, researchers from the University of Georgia have found that the bacteria in the bays include of species heretofore unknown to science.
"People tend to think that biodiversity is tied up in plants and animals, but in truth much of the world's biodiversity is found in the microbial world," said Lawrence Shimkets, professor and head of the department of microbiology at the University of Georgia.
Shimkets, along with graduate student Mark Wise and J. Vaun McArthur of UGA's Savannah River Ecology Laboratory (SREL) in Aiken, S.C., are co-authors of the study, which was just published in the April issue of Applied and Environmental Microbiology.
In one sense, the novel bacteria discovered from samples taken in Rainbow Bay at SREL are not unexpected. Scientists estimate that at best 10 percent of the bacteria on Earth have been classified and catalogued, and the percentage may actually be far less. Still, the fact that so many of the bacteria in the samples were previously unknown gives a good idea about biodiversity in both Carolina bays generally and the microbial world as a whole.
For years, even discovering and classifying species of bacteria was daunting because of inherent problems in growing them in the lab. Traditional culturing techniques more often than not failed, and researchers were sometimes left with nothing more than educated guesses. That all changed, however, with the advent of two new analytical tools. Polymerase chain reaction (PCR) is a method of taking small sections of genetic material and amplifying it millions of times. It has dramatically changed how microbiologists study the natural world.
Another method vital in classifying bacteria is the use of certain molecular markers, especially a common and conserved gene called 16S ribosomal RNA, which acts as a kind of genetic" fingerprint" for species. Using a combination of the two techniques, the UGA researchers were able to determine that some of the samples were similar to known bacteria, but most diverged in unusual ways in the phylogenetic tree.
"What we found were a number of new species that have been undescribed before," said Shimkets. "As with all such novel species, however, we don't yet know how to culture them in the lab."
Researchers have carried out this kind of research in a variety of habitats and have found that most natural ecosystems have novel species unknown to microbiologists. But the observed diversity is not equally spread throughout the natural world, and scientists have discovered that most genetic sequences tend to cluster in distinct groups. These clusters, sometimes called "phylotypes," may be related to a bacterium's habitat.
The team determined the DNA sequences of some 35 clones from the Carolina bay samples, which were taken in the mud beneath a shallow layer of water. Of these 35, some 32 were affiliated with five bacterial groups, Proteobacteria (11); Acidobacterium-like bacteria (8); Verrucomicrobium-like bacteria (7); gram-positive bacteria (3) and green nonsulfur bacteria (3).
One sequence did not seem to be associated with any major division. The most interesting fact, howver, is that none of the clones exhibited an exact match to any of the 16S rDNA sequences deposited in numerous databases.
"This suggests that most of the bacteria in Rainbow Bay are novel species," said Shimkets.
Sediments and soils may represent the most complex microbial habitat on Earth, with several thousand species of bacteria in a single gram of soil.
Indeed, the understanding of how to classify bacteria and lower species has changed dramatically in the past two decades. For eukaryotes (organisms of one or more cells that contain well-defined nuclei), a species is a group whose members can reproduce but who cannot reproduce with others. Chimpanzees cannot reproduce with humans, for example, so they are separate species.
For prokaryotes (cellular organisms whose nuclear material lacks a limiting membrane), however, the term "species" can also be defined by genetic sequence similarities or homology. Two bacteria are generally classified as different species if their 16S sequences differ by 2-3 percent. If this same type of classification system were applied to higher organisms, the number of currently recognized species would dramatically increase.
"An interesting example," said Wise, "is the classification of rats and humans. These two rather different mammals differ by less than 1 percent and would likely be classified in the same species if they were bacteria."
It is clear that the bacteria discovered in Rainbow Bay are unlike any ever catalogued before and lend credence to the theory that bacterial biodiversity may be the richest in the natural world.