Thursday, March 8, 2007

run, microbe, run!

The field of microbiology is incredibly exciting and has way too many words for the things it professes to study. More on those words in a moment! Let us first attempt to describe microbiology in the most general terms. "Micro" just means "small" (or, if you want to be precise, 10-6), but microbiology is not merely the study of small things. It is the study of microscopic things, things too small to be seen with the unclothed eye. Of course, individual human cells are (mostly) microscopic, but studying them is cell biology, not microbiology. So, let us qualify further: microbiology is the study of whole organisms that are microscopic. That still leaves us a mind-boggling array of study organisms:

animals
plants
fungi
bacteria
archaea
viruses

Heck, that's just about every kind of life you've ever heard of (and maybe one kind you haven't, unless you've been reading). Wait a sec--are viruses organisms? Well, most viruses are bacteriophages (yum, yum, bacteria!) and they have a pretty notable impact on bacterial populations, so just from that perspective, it seems like folks that study bacteria ought to care about them.

Now let's get back to those "too many words," because they get thrown around all the time. Some of this terminology is taxonomically outdated, but it sticks around due to a combination of practicality and linguistic inertia.

Microbe is the most general term, and it includes--you guessed it--all microscopic organisms. Eukaryotic microbes are all called protists although they have very little in common with each other; they include the protozoa (similar to animals), algae (similar to plants) and (similar to fungi)*. Prokaryotic microbes include the domains Bacteria and Archaea, which, like protists, are only superficially similar to one another.

I really wanted to sort all that out, but actually the only microbes I'm going to talk about are bacteria. Marine bacteria, to be specific, because the coolest stuff is always in the ocean.

However, as cool as the ocean is, it is also a very difficult environment to study, and thus the field of marine microbiology is only a few decades old. We've only just begun to characterize the diverse** microbial fauna of the seas. So, most of our knowledge of detailed bacterial behavior comes from the bacterial poster child: Escherichia coli. It's big, it's easy to culture, and it's everywhere. It uses flagella (powered by nature's only true rotary motor) to swim around. Different species of bacteria can have any number and distribution of flagella.

E. coli have peritrichous flagella, which they use to swim with a strategy called "run and tumble". The bacterium wraps all of its flagella up into one propeller, swims in one direction for a little while, then suddenly flings the flagella apart, which halts its progress and reorients it in a random direction. Rinse and repeat. If you want to explore a given area for tasty things, this is a pretty decent way to do it; it's more or less a random walk.

Marine bacteria, on the other hand, exhibit a different behavior, called "run and reverse". It's just what it sounds like: swim in one direction, then turn around and swim back. This sounds like a great way to get nowhere fast, but wait! Marine bacteria are tiny. Much tinier than our friend Escherichia. They are so tiny that the Brownian motion of water molecules becomes relevant to them, and they end up constantly bombarded with H2O. So whatever direction they think they're going in, they'll almost certainly be headed off in another direction. In this context, the run and reverse strategy is totally reasonable.

To conclude, I present a mindblowing calculation from Fuhrman (Nature, 10 June 1999). Quick background: He's talking about two weird ways that microorganisms could pick up genes their parents didn't give them. Viral nonspecific horizontal gene transfer is when a virus picks up DNA from one host and transfers it to another, totally unrelated host. Natural transformation is when organisms pick up "loose" DNA dissolved in seawater and incorporate it into their own DNA.

Now. Take a second to let your mind recover from contemplating these bizarre possibilities, then read on . . .

"Although transfers of these sorts may be extremely rare, the typical bacterial abundance of 109 per litre in the euphotic zone and the huge volume of the sea (3.6 X 107 km3 in the top 100 m), coupled with generation times on the order of a day, implies that an event with a probability of only 10-20 per generation would be occurring about a million times per day."

Wow.




* I've always been kind of annoyed that there isn't a separate word for the fungus-like protists. But they make up for it by including the ultra-sci-fi slime molds in this group.

** How diverse can it be? you ask. They're tiny! They're single cells!

But ah!
I respond. The many faces of diversity! What microbes lack in morphological diversity, they make up in metabolic diversity.

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