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Carl R. Woese Institute for Genomic Biology

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Using Genomics to Look at Microbial Evolution

Most microbiologists sequence genes in order to determine what a given gene does. Rachel Whitaker, a member of the biocomplexity theme at IGB and assistant professor of microbiology, studies gene sequences to answer other kinds of questions. She would like to know, for example, "How do microbes, specifically Archaea, evolve? Is the system by which they evolve different or similar to eukaryotes or to bacteria?" Ultimately the answers to some of these questions may give researchers insight into what Whitaker calls "deep, open questions about microbial evolution, the most fundamental of which is, how did all of this diversity come to be?"

The trick is, instead of comparing, for example, the shape of finch beaks, like Darwin did, Whitaker is looking at Archaea, which do not have distinctive physical characteristics.

"Those studying the evolution of ?charismatic macrofauna' have the theory, statistical methods and tools," says Whitaker. "We're trying to adapt those tools to microbial systems."

This involves comparing sequences across a particular microbe. In Whitaker's case that microbe is Sulfolobus islandicus, which was one of the relatively few Archaea that had been cultured and sequenced when she was in graduate school at University of California, Berkeley. This Archaea thrives in volcanic hot springs of Yellowstone National Park and the Kamchatka Peninsula.

Scientists had assumed that microbes, in part because they are so small and abundant, did not fit the conventional model of evolution in which physical barriers led to distinct species. The discovery that some microbes in far corners of the world have identical 16S rRNA sequences supported this "everything is everywhere" model. Scientists interpreted this as all microbes exist in every location but thrive only in certain environmental conditions.

Whitaker set out to test this assumption by looking at whether there were, in fact, physical barriers that resulted in distinct Sulfolobus populations. In order to gather more data, she collected strains from three geographically distinct areas ? Yellowstone National Park, Kamchatka Peninsula and Lassen National Park (in northeastern California) and sequenced their entire genomes before they could mutate in the lab.

"With more data, like with a microscope, you can zoom in and see more detail," says Whitaker.

With complete sequences of eight Sulfolobus islandicus strains from three sites Whitaker was able to determine whether the populations were genetically the same or different. If they were the same that would support the "everything is everywhere" model; if they were different that would support the idea that microbes evolve and provide evidence for allopatric speciation, à la finch beaks. Whitaker's findings indicate that the Kamchatka Peninsula strain is, indeed, different from the Yellowstone Sulfolobus. In addition, all the strains from Yellowstone are more closely related to each other than to the Kamchatka strains. These findings, which have been published in both Science and in the Proceedings of the National Academy of Sciences, suggest that the Archaea are, in fact, distinct by geographic location and that geographical isolation plays a significant role in the evolution of Archaea.

Whitaker first became interested in Archaea and microbial diversity in 1997 after reading an article in Science by Norman Pace, titled A Molecular View of Microbial Diversity and the Biosphere. In that paper Pace advocated for the kind of "microbial naturalism" approach Whitaker is taking. Few other microbiologists have pursued this direction, in part because the questions it poses are complex, the experiments are difficult to design and the results can be difficult to interpret.

Nevertheless, Whitaker perseveres. Her most recent projects have focused on the discovery that, while Sulfolobus is rapidly changing genetic material, that material is coming, not from other Archaea or even Bacteria, but from viruses and plasmids.

"Viruses and plasmids are clearly what is important, they are what is driving Archaea to evolve," says Whitaker. "Studying viruses and plasmids is difficult and frustrating but very exciting." Whitaker has recently noticed that the greatest variation among Sulfolobus islandicus strains is in a section of the genome called CRISPR, a recently discovered microbial immune system. Understanding the CRISPR is a new and emerging field.

Whitaker's lab is now looking at how the CRISPR evolves in Sulfolobus islandicus and how that evolution affects both the host and the virus or plasmid. Whitaker's lab is seeking to determine the extent that the biogeographic distribution of elements like viruses and plasmids is determined by the biogeography of its hosts.

Having spent the summer at Yellowstone collecting samples, Whitaker and her students have hundreds of strains to be purified, amplified and sequenced. With more samples, Whitaker will be better able to pursue her line of questioning.

In another project, Whitaker is looking at the microbial population ecology of temperate lakes in northern Wisconsin to see how water disturbances affect archaeal diversity. She has found that each lake has a slightly different set of Archaea, specifically methanogens, each on its own evolutionary trajectory. Lake mixing, says Whitaker, does not seem to be the driver of that evolution or of the diversity, so there is much more to be learned about how and why Archaea evolve. Whitaker is passionate about helping to lead the charge.

The other members of the biocomplexity theme and of IGB as a whole are an enormous boost to her efforts, says Whitaker. "Every time I go to the IGB I get excited about new ideas," she says. "By asking questions across lines of research it stimulates people to have new ideas, and those ideas are big and interdisciplinary. It's the informal, in-the-hallway kind of exchanges that are the most exciting."