2: Microbial Diversity

Ok, this entry's bound to be more entertaining, and reflects some of what we've been talking about in my Microbiology class.

Molecular identification by ‘‘suicide PCR’’ of Yersinia pestis as the agent of Medieval Black Death
Raoult, et al. 2000

This paper confirmed that the Black Death was caused by Yersinia pestis. They did this, by exhuming a few bodies, and removing the pulp from their teeth (apparently, when we die, the pulp gets sealed off from the external environment, and allows pristine preservation of whatever is inside. They used a special technique called "Suicide PCR" that supposedly only uses the primers once (I don't really understand how it works) to prevent contamination.
Detection of a bioluminescent milky sea from space
Miller, et al. 2005

So, apparently, it's a common myth to see the ocean glowing at night. Well, apparently, in January of 1995, this naval ship came across this phenomenon, and it was co-documented by a satellite that took a picture of the area - basically, a spot as big as the state of Connecticut, in the Indian Ocean, glowing. Pretty crazy. They confirmed it was bioluminescent bacteria.

Biomineralization of Gold: Biofilms on Bacterioform Gold
Reith, et al. 2006

Apparently, bacteria can spit out gold. Good job, them.

Coevolved Crypts and Exocrine Glands Support Mutualistic Bacteria in Fungus-Growing Ants Currie, et al. 2006

So, this type of thing I've seen in several classes, because one of the guys I'm interested in working with here (Jon Clardy) encounters this in his chemical ecology research.

Anyway, in case you haven't figured it out yet from this entry, bacteria are pretty amazing. Without them, we wouldn't be here - They're responsible for making the Earth hospitable for other forms of life (cyanobacteria created all the oxygen from...the nitrogen and carbon dioxide that was there before), they help everyone with nutrition (plants absorb nutrients from the soil, us digest food and absorb nutrients, cows and termites digest cellulose), they help break down detritus and cycle chemicals, and provide us with resources like natural gas.

Anyway, it's pretty common for mutualistic bacteria and their hosts to have coevolved together for millions of years:
The illustrated example is somewhat complicated, with about 5 players: 1) the Southern pine beetle likes to bore into trees and lay eggs, killing our forests. It has special compartments that 2) store a "good" fungus that grows in the tree with the eggs, and then serves as a food source.
But, there's a 3) "bad" fungus that kills off the good fungus and takes over. Fortunately, the beetle also carries a 4) bacterium that kills off the bad fungus with an antifungal compound it produces. Not shown is a 5) "poser" bacterium that hitches along for the ride sometimes, but doesn't actually produce the antifungal.

There's a very similar situation with leaf-cutter ants, which is what the cited article is actually about. People travel to Costa Rica to research this, and I believe Cornell owns a fully functional, big, reconstructed leaf-cutter ant farm.
A Molecular View of Microbial Diversity and the Biosphere
Pace Science 1997

It's hard to categorize bacteria - if you think about it, they all look very similar to us (well, it's pretty hard to see them), and unlike animals, we wouldn't be able to effectively categorize them by morphological differences. Also, because of all the genetic swapping they did over long periods of evolutionary time, it's hard to see lineage. Nevertheless, Woese came up with the brilliant idea of sequencing their 16S rRNA to construct a phylogenetic tree, that after years of harsh disbelief by the scientific community, displaced the five kingdom model, and replaced it with the three domain model.
This has been expanded through various expeditions to the ends of the Earth. In the image, plants, humans, and fungi represent the smallest 3 fingers in Eucarya. Isn't it crazy how much more diverse the monocellular organisms are?

These things can be found everywhere. I won't post the details, but, there are several efforts right now to sequence all the bacteria found in the human intestinal system. The article I have in front of me found 395 different phylotypes of bacteria. I think this works out to something like 100x the number of genes that we actually have. Crazy.

I also learned that bacteria may be responsible for clouds. In the CLAW hypothesis (you can wikipedia this), phytoplankton are responsible for releasing sulfates that nucleate clouds.

Finally, an important idea that has special relevance to me: We still don't understand anything about the majority of bacteria out there because scientists can't figure out how to grow them. The estimate is that we can only grow 1% of the stuff we find in dirt. While eDNA cloning techniques enable us to at least harness and see the DNA of these organisms, and use that to predict what they make and how they're structured, this isn't usually a substitute for the real thing. I've seen a couple of people working on "co-culturing", where it's believed that one bacteria will grow only if it senses the presence of another one nearby (using small molecule signals that probably evolved between the two species over the course of evolution)