Tuesday, December 14, 2010

CATP Seminar Series, Dr. Gordon Southam

Astrobiology is a big, big field and so many of its aspects remain a bit of a learning experience for me. One of the fun parts of being a fellow of the Canadian Astrobiology Training Program (CATP or "Cat-Pee" to us in the program, part of NSERC/NRCAN's CREATE program) is that we hold seminars every two weeks that are broadcast across the country. The seminars give those of us working in one part of the field a chance to see what is happening in other parts, and to learn about potential synergies with our own work. My area of focus is habitability and water cycles, and so last week's talk, given by Dr. Gordon Southam of the University of Western Ontario, a hard-core microbiologist, was quite a departure.

While I'll be the first to admit that some of the material was over my head, there were a number of interesting aspects which were a little surprising for me. I plan on using this space to discuss those aspects from this talk and from future talks. So hopefully the "CATP Seminar Series" will become a regular feature here. Don't think of it so much as a review, but instead look at it as an exploration or a discovery journal. The full list of upcomming talks can be found on the CREATE website, located here.

Dr. Southam's talk, delivered last Friday, was entitled "Biogeochemical Processes from the perspective of a Bacteria." His main take-home point was that conditions that are extreme (high temperature, pressure, salinity, pH) to you and me are normal to certain strains of bacteria. At first that statement seems a bit simplistic. After all, if bacteria have evolved to take advantage of so-called extreme conditions, then naturally those would be the environments under which they would be most "comfortable" (by which I mean their biological processes would be optimized). Thus even the term for these organisms, extremophiles, is a bit misleading.

But when you dig deeper, you find that you need to be cautious for several reasons. The first of these has to do with human interpretation. For instance, the simple act of removing an extremophile from its natural environment by sampling may cause changes in the sample environment. One SEM image (which I have unfortunately been unable to find) showed a forrest-like filligree of curving lines studded with small round tips. Within the lines there were rod-shaped structures and spheres. Since there was complicated structure shown all around, how were we to know which objects are abiotic and which represent organisms? In fact, everything but the rods are abiotic, precipitated out as the sample was taken into the laboratory. This is just another reminder of the dangers of making a biotic/abiotic determination based on morphology alone (ALH84001 anyone?)

Secondly, as life is a process in which disequilibrium conditions are maintained though abundant energy (in some cases harvested directly as electrons from the outside environment!), it should come as no surprise that bacteria are able to modify their local environments to suit their needs. Thus, the pH values of the bulk environment may not be characteristic of conditions surrounding the bacteria, or between the bacteria and a substrate. These "nano-environments" make sense when you consider the scale - when millions of bacteria are easily able to fit on the tip of a pH measuring stick, that measurement will be no more than an average, as Dr. Southam mentioned.

[ The two images above show conductive "nanowires" extruded by bacteria to directly harvest electrons from metal surfaces (helping to corrode them) and from other species. The second shows a crafty experiment to measure the current-carrying capacity of the wires. I must apologize for not being able to find primary sources for these images - if you know their origin, make a note in the comments and I will update here]

Many bacteria can use these nano-environments to do surprising things, such as precipitate unexpected mineral phases that would not have been otherwise produced. The presence of such mineral phases can in turn be used as a "biomarker," something that indicates the past presence of life, but this is only useful if the broader context is known. If the biotic products are overwhelming, they can trick a researcher into believing that the specific conditions of the microbe's nano-environment are in fact bulk constraints on the general environment in which it can live. Worse, one could interpret the presence of such minerals as evidence for an extreme environment that never existed except just beyond the cell wall.

This is complicated by the tendency of bacteria to form "biofilms" in which an entire chain of life may be present. Within these chains, organisms will be present that do nothing but feed off the waste products of other organisms. The example given in the talk was of "mine slime" in which colourful films bursting with life are observed when water heavy in nutrients, leaching subsurface sources, hits oxygenated air:

[ Mine Slime containing brightly coloured biofilm. From Wanger et al, retrieved from Astrobiology Magazine]

If you thought the colourful bacteria must be aerobic ("oxygen eaters"), you would be wrong. In fact they are methanogens, an archaean organism for which oxygen is toxic. However, it happily lives underneath the surface of the living biofilm, consuming the waste products of the aerobic bacteria on the outside. Thus, while the presence of such an organism usually indicates anoxic ("oxygen starved") conditions, in this case you couldn't be more wrong!

As a fun side note, I was impressed to learn that we can actually take advantage of these sorts of processes for economic advantage. Have you ever heard of Biological mining (sometimes called "bioleaching")? Neither had I until last Friday. However, this is the way that 20% of the world's copper is produced today. In ore deposits too poor to extract economically, bacteria which extract and mobilize the copper through their metabolism can be used. All you need is water to activate the bacteria and to draw off the metal-rich water for processing. Literally, through the action of biology, the metals leach straight from the rock!

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