Forget cockroaches.  Bacteria will be the only organisms left if we manage to launch a warhead too many or if any doomsday scenarios actually occur.  It's a good thing - without bacteria we wouldn't be alive.  Bacteria control nutrient cycles and help us make cheese, but they can also kill us (it should be noted that pathogenic bacteria make up a minuscule portion of the known bacteria).  Their astounding diversity has allowed them to become the earth's dominant life form.

Even our bodies are not our own.  The average person has five pounds of bacteria (1.2 kg) in their intestinal tracts and on their skin - and bacterial cells outnumber our own cells by a factor of 10 to 1.  This difference is more pronounced on the genetic level.  While the human genome encodes approximately 25,000 unique genes, the bacterial community in our intestines alone produces an astounding 9 million.  Some scientists have even proposed that the human is a "super-organism" and these bacteria play a major role in our health.  Scientists have postulated that bacteria may cause syndromes as diverse as irritable bowel syndrome, colon cancer, and yes, even autism. 

One major misconception is that bacteria are inferior or unevolved when compared to higher animals.  Although they may be simpler (in the context of size and structural complexity), bacteria have also spent the last 3.5 billion years evolving to inhabit niche habitats.  So a better way to think of bacteria is how we think of humans - perfectly adapted and at the pinnacle of evolution.  And they can survive conditions that we can't even imagine - I've isolated bacteria from hot springs so acidic that they can dissolve a cow within two weeks, and I've worked with bacteria that can eat methane and breathe sulfur.  If we find bacteria on other planets, it will probably be because we sent them there - even NASA clean rooms are not sterilized enough to kill every bacteria.

Even more astounding than the diversity we've discovered is the diversity that we can't discover - it is estimated that up to 99.99% of all bacterial species cannot be isolated in a pure culture using current technologies.  Imagine if 99.99% of birds were invisible, and you begin to see the problems that microbiologists face trying to catalog life's dominant form.  In a gram of soil there are as many as 10 billion bacterial cells - more than the Earth's human population.  Go to deep salt mines, oxygen-free caves filled with sulfuric acid, and the bottom of the ocean; look inside rocks, trees, your mouth, and nuclear waste dumps; in all of these places you'll find bacterial life.

While here at the MPI, we've tried to discover more information about a small subset of these soil bacteria, those that consume methane.  Although this order of bacteria was discovered in 1904, we still don't know very much about them.  For example, we know that they can consume atmospheric methane (23 times more potent as a greenhouse gas than carbon dioxide) but we're still not sure exactly how - the leading theory is that some bacteria contain an isozyme which allows them to consume methane at a lower concentration than cultured species, but we still have not detected this isozyme in nature.  On a more general note, we're not even sure what percentage of soil bacteria can consume methane, nor do we know how many types of methanotrophs there are.

As we discover more about microbial ecology, we realize how little we know - but also that these organisms determine many more aspects of our lives than we thought possible.  In the 18th and 19th centuries, scientists began to catalog life's macroscopic diversity, providing us with a good overview of how the environment is structured.  We are now beginning to discover life's microscopic diversity, and while bacteria may be less exciting than, say, tigers or lions, this knowledge will deepen our understanding of earth's fundamental ecological processes.  We will probably discover unexpected benefits along the way (how many pharmaceuticals were developed from plants?), but the most exciting aspect is its audacity.  At it's most basic level, we're extracting information from dirt and using it to understand the world around us.  How cool is that?

New research from Mitchell et al. (Nature, July 2009) seems to indicate that higher animals (i.e., those of us lucky enough to have a central nervous system) aren't the only ones able to prepare for the future based on current environmental conditions - bacteria (E. coli) and yeast (S. cerevisiae) can do it too.  While it seems odd, the basic principle has been recognized for years.  Indeed, the lac operon in E. coli activates the genes needed to digest the sugar lactose, but the lac operon is activated only by lactose.  This mechanism makes good sense from an evolutionary perspective - proteins are expensive to produce, and if the cell does not need them (i.e. there is no lactose to digest) then producing them is wasteful.  While direct links like this one are easy to uncover, more subtle ones have remained a mystery - until now.

The biggest misconception that we need to get rid as higher mammals is the concept of memory - bacteria are unicellular organisms, so there is quite literally no way for them to develop a nervous system (or even a single neuron!), so any response and regulation has to be encoded directly into their genome.  That's where the second misconception comes in - individual bacteria don't really matter, and since their doubling time is about one hour, the number of offspring that can be produced in a short amount of time is high - as is the corresponding number of mutations and selection pressure. 

Here's where we come to the experiment.  Imagine that every time an E. coli culture is exposed to lactose, exposure to glucose follows.  Over time, the bacteria whose genes encode for the appropriate regulatory response (every time you see lactose, make the enzymes needed to digest glucose) will have a significant survival advantage over those that don't.  Think Pavlov's dog - every time the bell rings, it was conditioned to salivate.  With E. coli, lactose is the bell and glucose enzyme production is the salivation. 

Why might this be useful?  E. coli and Homo sapiens (that's us!) have a long history (not just related to contaminated beef).  In fact, most E. coli strains are helpful and make it easier to digest food.  But they have to get into our intestines somehow, and that environment is variable.  The sugars present in the stomach (where the bacteria enter) are different from those present in the large intestine (where the bacteria spend a lot of time), so if the stomach sugars can prime the bacterial cells to digest the sugars found in the large intestine, they'll have an easier time surviving in the new environment. 

The most fascinating implication of this study is how old the conditioning pathway is.  Eukaryotes (everything ranging from amoebas to humans) split from the bacteria (and archaea!) about three billion years ago, and since this genetic conditioning response is found in both bacteria (E. coli) and yeast (eukaryote), it is likely that the age of the pathway predates both - so "planning" for the future (anthropomorphism is a bad idea at the unicellular level) may actually be one of the oldest complex processes that there is.

For the scientifically-minded, here's a link to the original article.  Sadly, it is not open-access.

Bacteria are everywhere.  It's estimated that there are over 100 trillion (with a t) individual bacteria living in the average humans digestive tract.  While it sounds fairly disgusting (unless, of course, you're a microbiologist), their presence is actually a Good Thing - these bacteria help us to break down and digest foods that we would normally not be able to eat on our own.  However, sometimes this symbiosis has some unintended consequences, as this wonderful paper in PLoS ONE shows. 

Normally, our immune systems are used to the presence of our gut microbiota, but sometimes (fairly rarely) they provoke a spontaneous immune response.  Since it's not the body itself which causes the heightened immune response, it's not an autoimmune disorder, but the symptoms are very similar - in both cases, the body's immune system ends up attacking itself, which in the intestinal tract leads to Crohn's Disease and/or inflammatory bowel disease.  These conditions then increase the risk of colon cancer.  What this paper demonstrates is that modulation of the gut microbiota is enough to provoke this heightened immune response - and possibly lead to colon cancer.  Should you have time, it's a good read (it does get a bit technical though) but the real highlight (for me at least) is that it underscores the major role that bacteria play in just about everything.