Investigating the Basis of Life through Archaea

This cluster of Sulfolobus spindle-shaped viruses was captured using the transmission electron microscope (TEM) in the Microscopy Suite at Beckman. These viruses are unique in the fact that they only infect members of the order Sulfolobales, a type of hyperthermophilic archaea that resides in the acidic hot springs in Yellowstone National Park and the Kamchatka Peninsula in Russia.
This cluster of Sulfolobus spindle-shaped viruses was captured using the transmission electron microscope (TEM) in the Microscopy Suite at Beckman. These viruses are unique in the fact that they only infect members of the order Sulfolobales, a type of hyperthermophilic archaea that resides in the acidic hot springs in Yellowstone National Park and the Kamchatka Peninsula in Russia.

Maria A. Bautista, a microbiology graduate student, studies archaea and their viruses, and tries to find connections between the two in order to explain their evolutionary histories.

“Viruses are pretty awesome,” said Maria A. Bautista. Not the most common thing people say when talking about viruses, types of microbes responsible for the common cold, measles, mumps, influenza, and, more recently, Ebola.

Yet Bautista, a graduate student working in Illinois microbiology professor Rachel Whitaker’s lab, eagerly investigates the role viruses play in the very basis of life, and how they can sometimes help instead of harm.

“It has been found that 8 percent of the human genome is of retroviral origin: somewhere along the evolutionary history, viruses integrated into the chromosome of the host cell, and stayed there to bring novel functions to the cells, which gives them an immediate advantage,” said Bautista.

“People overlook viruses as if they’re just disease, but they’re not just diseases. That 8 percent of the human genome is pretty important.”

Bautista, who’s working toward her Ph.D. in microbiology, has been studying viruses for the past several years, especially how they interact with archaea, one of the three domains of life.

Prior to the 1970s, scientists had lumped all living organisms into two main branches in the tree of life: bacteria and everything else that did not have a nucleus (prokaryotes) and plants and animals (eukaryotes). In 1977, however, Carl Woese, a professor at the University of Illinois, upended this assumption when he reported on archaea, single-cell microbes genetically distinct from bacteria and eukaryotes. 

Woese had set out to map the evolutionary history of life by comparing the genetic sequences of protein-building structures in cells, known as ribosomes and ribosomal RNA. Along the way, he found that archaea, which had originally been grouped with bacteria as a prokaryote, had evolved separately from the other two groups. 

The new discovery added archaea as a third main branch of the evolutionary family tree.

He argued that understanding the evolution of microbes, which includes archaea, is central to understanding evolutionary biology. The secrets of the complexity of life today, he said, are written in the genomic sequences of microbes.

“So these two populations (of archaea from Yellowstone and Kamchatka) have evolved differently and we’re trying to understand why. Because even though they’re the same hosts and the same types of viruses, their evolutionary history is different. Understanding this will help unlock some answers in evolutionary biology.” - Maria Bautista

Woese, who died in 2012, advised Whitaker, who has devoted her research to understanding the biodiversity of microbes and how they impact ecological and evolutionary processes. 

As Whitaker’s student, Bautista investigates the evolutionary history of a specific type of archaeon, Sulfolobus islandicus, and how viruses infect it. This archaeon lives in acidic hot springs found in Yellowstone National Park and the Kamchatka Peninsula in Russia. 

“The cool thing about Sulfolobus islandicus is that it lives in these acidic hot springs that are low complexity and completely isolated. The hot springs are removed from other influences or new species. So you can actually look at evolution in nature, which is really hard to do nowadays because people tend to tamper with natural evolution,” Bautista said.

The archaea that Bautista works on not only live in a unique environment, but they also host unique viruses.

Sulfolobus islandicus has the weirdest-looking viruses ever discovered, like spindle-shaped ones or some with claws. We’re comparing the same type of viruses from the different locations to see how they’ve evolved,” Bautista said. “The springs are so separate from one other that they’ve evolved very differently. The viruses have the same shape, and, if you look at their genetic information, they are related, but they have a lot of variations in how they infect Sulfolobus islandicus.”

Bautista, with the help of undergraduate microbiology student Jesse Black, is finding that the Yellowstone archaeon’s reactions to the spindle-shaped virus are very mild, even beneficial to the cells. To the archaeon from Kamchatka, the reaction is deadly.

“We infect the culture from Yellowstone, and nothing happens. The cells don’t die, don’t start growing slower, even though the virus is super abundant. And then you look at the samples from Kamchatka, and these viruses kill them,” Bautista said. “So these two populations have evolved differently and we’re trying to understand why. Because even though they’re the same hosts and the same types of viruses, their evolutionary history is different. Understanding this will help unlock some answers in evolutionary biology.”

One of the ways to understand the nature of these viruses is to visualize them. To do this, Bautista uses the transmission electron microscope (TEM) housed in the Microscopy Suite of the Beckman Institute. Scott Robinson, the lab manager, assists in identifying and imaging the viruses.

“Scott has been instrumental in helping us visualize these viruses under the TEM. We call him the virus whisperer—no matter what, he can always find the virus and get an amazing image,” Bautista said. “These archaeal viruses have unique morphologies only found in viruses that infect the archaea, so we’re discovering something new. They are just so cool.”

With the TEM, they have identified around 20 viruses. They then extract each virus’ DNA and sequence it. With this genomic sequence, they can start to find connections that could explain the differences between the Yellowstone and Kamchatka samples. 

This project is one of hundreds, at any given time, that benefits from the capabilities of the Microscopy Suite, which is open to all users across campus. Robinson feels privileged to be able to work with these scientists and assist them in conducting this leading research. 

“It truly is an absolute privilege and a huge thrill to be involved in this work,” Robinson said. “In some cases I’m the first person, if only by a few seconds, to get to see these viruses.”  

This article is part of the Fall 2014 Synergy Issue, a publication of the Communications Office of the Beckman Institute.