Tag Archives: bacteria

Microbiology can be dirty

Students are starting to repopulate the campus and the relaxed pace of the summer is being quickly replaced by frenzied preparation for the start of the semester. This semester, I will be teaching the intro to microbiology course that I have taught every year. In the lab, we do some bioinformatics analysis of metagenomic data from a Winogradsky column. A Winogradsky column is a clear cylinder full of pond mud that is used as an enrichment culture to grow bacteria that cant be grown under normal laboratory conditions. To make a Winogradsky column, you collect mud from a pond or riverbank. (For those of us that are used to the cleanliness of working in a sterile hood, that means you have to take off your lab coat, get down on your hands and knees, and scoop up handfuls of goopy stinky slimy stuff from the the edge of a pond. I wear latex gloves.) You then add it to a plexiglass cylinder along with a source of cellulose (I use leaf litter) and additional sulfate to promote enrichment for microorganisms involved in the sulfur cycle. Over a period of months, layers of microorganisms requiring a range of environmental conditions develop in distinct niches with distinct populations participating in diverse metabolic activities. As various metabolites in the column are used, byproducts are produced, and the environment in the column changes. As a result of changing concentrations of oxygen, hydrogen sulfide, and variations in metabolites, different microbes will thrive and create their own niche.

Although you can see some changes occurring in the first few days, it takes several weeks or months for it to develop so I always set it up before the semester starts. This year, I had the help of my daughter (age 5) who was eager to get her hands into the gooey muck. We took the mud from the edge of Vassar Lake, a pond on campus. In the pictures you can see the changes that take place over time. The column starts out as grey silt, while the column on the left is 1 year old. The patches of colours are the different communities of bacteria.

(OK, so there is no virology in this post but it sure would be interesting to analyze the viral population of the column in addition to the bacterial population. What is the role of bacteriophages in the community dynamics and nutrient cycling in the Winogradsky column?)


Of Aliens and Arsenic

Or How to Screw up an Interesting Discovery with Mediocrity and Media Hype

NASA annonced an “astrobiology discovery”….Aliens! No, sorry, bacteria…in California! WOW! OK, this is no ordinary bacteria as it can grow in astonishing concentrations of arsenic, a highly toxic compound. It’s nothing new that bacteria can grow in all kinds of extreme environments, but this is growth in a lot more arsenic than we’ve seen before. The claim however is that this bacterium actually replaces phosphorus with arsenic. Phosphorus is used as part of the structure of DNA, as well as proteins and many important small metabolites, most notably ATP, used as an energy source. Arsenic is much like phosphorus but arsenic containing compounds are quite unstable in water (which is why arsenic is toxic). This would be novel in cellular life as we know it; DNA containing arsenic! I was initially very interested in this discovery…and then I read the paper.
When you make a claim as big as replacing one of the most import elements in a cell, it seems to me your data better be rock solid. The paper is quite underwhelming. Although it seems there might be arsenic associated with the DNA it certainly doesn’t provide good evidence that it’s a part of its structure. In fact, others have argued more convincingly that the trace amount of phosphorus contaminating the preparation is sufficient for the cells to use to make everything they would need to.
It seems to me this is a case of the researchers jumping ahead of themselves and interpreting something from the data that is just not there, a failure of the peer review system, and an overly enthusiastic media running with a thrilling but incorrect story about alternative branches of life and our need to re-write biology textbooks. Whats sad is that there actually is something interesting here that has been missed and would be a more reasonable interpretation of the data. This bacteria can grow at extreme concentrations of arsenic, in the near absence of phosphorus, but can still somehow scavenge those few available atoms of phosporus and use them, where probably all other organisms would have long since died of arsenic poisoning. How does it do that? This is still a fascinating bacterium…it just wont redefine life.
FInally, why am I writing about bacteria on a virology blog? I learned some time ago never to underestimate viruses. After being surprised about the existence of viruses infecting organisms in places like bubbling geothermal acid pools, I realized that where there are cells, there are viruses. I wonder if this arsenic loving bacteria is host to some interesting viruses? I bet Mono Lake, where this discovery was made, is full of interesting viruses.


Distant Evolutionary Relationships

We’ve been talking about protein structure and folding in my Biol 105 class.  Proteins are made of chains of amino acids and the sequence of amino acids, or primary structure, dictates the way the protein will fold into its final 3D or tertiary structure.  We may assume that two proteins with similar sequences would have a similar structure, and that two proteins with very different sequences would have different structures.  However, this is not true.  Proteins with very different sequences can end up with similar 3D structures.

A great example of this is the structure of capsid proteins from three very different viruses.  Adenoviruses infect animals (eukaryotes), and is one of many viruses that cause colds.  PRD1 is a bacteriphage, a virus that infects bacteria.  STIV (Sulfolobus turreted icosahedral virus) infects Sulfolobus, an archaea that lives in geothermal hotsprings in Yellowstone National Park.  STIV and its host love the 80 degree celsius, pH 3 environment of the hotsprings.  The fact that there are viruses that infect archaea in those extreme environments is cool enough.  But it turns out that the capsid proteins of these three viruses are actually quite similar.  Their sequence differs significantly, but their tertiary structures are highly similar, meaning these very different polypeptides fold into essentially the same shape.

What is the basis of this similarity?  Do all theses viruses share a common ancestor, which would have existed before the three domains of cellular life (eukarya, bacteria, archaea) diverged over 3 billion years ago? Is it convergent evolution?  Was there a horizontal gene transfer event in which a gene moved among all three domains?  The authors of the paper argue for a common ancestor but the other possibilities have not been formally excluded.  We still don’t really know, and it raises interesting questions about the origin of viruses.