Save the Wild e-coli

by John on July 3, 2010

The poor old microbes have been taking a beating in the popular press.  Current articles reported on ravening hoards of Mycobacterium leaping from our shower heads, drug resistant Staphylococcus lurking in our beach sands, and great pandemics threatening to sweep away big chunks of the human population.  And many of those who live along the Russian River and other California coastal areas seem certain that the e-coli in septic tanks are just waiting for the opportunity to rise up against us. One might wonder if we exist above a seething froth of angry microorganisms only by the grace of God…or if it’s all just part of the natural scheme of things.

Hopefully, all this bad PR is about to change and it’s a really exciting time to be involved in microbial ecology.  Modern DNA techniques are letting us look at complex microbiomes in a way not possible only a couple of years ago, and at the other end of the spectrum, the NASA’s  SEAWiFS satellite sensor lets us look at the concentration of phytoplankton in the oceans around the globe. They’ve animated several years of the data,  and it’s fascinating to watch the swirls and flow of microscopic life in the oceans and the snow on the continents retreating and advancing as the seasons drive a dance of the microbes that has gone on for 3.5 billion years.  Not only are we looking at the very base of the ocean food chain, but the very nature of that which makes possible life as we know it.

One result of all this new science is downright humbling, underscoring just how little we know of the microbial world.  The best example is Dr. Penny Chisholm’s discovery, in 1985, of prochlorococcus, a tiny photosynthetic microorganism.  After years of subsequent study, it turns out to account for ten percent of the world’s oxygen production and is a vital component of the ocean system that regulates our atmosphere, and probably the most plentiful organism on earth. There are over 100,000 prochlorococci in a single millilitre of surface seawater.  Like so many scientific discoveries, Dr. Chisholm made her discovery when looking for a much larger phytoplankton called Synechococcus and the instrument gave readings that was at first dismissed as electronic noise, but after some tinkering, revealed the tiny oxygen producer.

Every science teacher and responsible environmentalist should watch Dr Chisholm’s MIT “SoapBox Series”video, Invisible Forest:Microbes in the Sea, especially with respect to global warming.  Consider: the tiny prochlorococcus takes 5 gigatons (5,000,000,000 tons) of CO2 out of the atmosphere every year.  So why are the microbes getting such bad press? In embarrassing number of very serious research labs, you can find the plush toys of various really nasty microbes like bubonic plague and a flesh eating bacteria (complete with knife and fork) produced by GiantMicrobes Inc.  However, the general population seems to suffer from extreme microbiophobia, and it’s true that there are a few really bad actors that don’t really like us at all.  They are only a tiny fraction of a percent of the entire microbial population which, by weight, is greater than all the rest of the living matter on earth.

Consider the relationship of humans and bacteria.  A newborn’s gut is essentially sterile, but it rapidly becomes colonized with a complex bacterial microflora, including e-coli, which is really a useful microorganism, except for a few nasty strains like O157/H7 that causes many of the illness outbreaks from processed meats and leafy crops.  Infants probably pick up many of the gut microflora from the birth process, and indeed, children borne by c-section tend to take much longer establish a stable gut ecology than natural birth.  By the time we’re adults, there are ten times as many microbial cells that have established themselves in our gut as there are in the whole human body.  The do all sorts of useful things, like helping digest food, producing vitamins, and keeping out unwanted microbial visitors.

Microbes have evolved right along with us, though we’re really johnny-come-lately’s on the geologic time scale.  They have this incredible mechanism of swapping genes between bacteria, virus and phages that enables them to rapidly fill any available ecological niche and they’ve been doing it for 3.5 billion years.  For a while we were probably just another place for their ongoing dance.  As long as we stayed in small groups of hunter gatherer, say 50,000 years ago, if a pathogenic bacterial gained a foothold, it could be bad for the group, but probably would not spread to other humans.  Then we developed agriculture and cities, and microbes moved into the new niches created by humans and a few of the microorganisms got out of hand, like the black plague, cholera and others.  In fact many of our childhood diseases like mumps and measles seemed to have evolved as population densities increased.

What do humans bring to this never ending dance, as we don’t have the incredibly rapid and diverse gene swapping capabilities of the microbes?  While we do develop resistance after an infection or immunization, most important of what we bring is our curiosity and imagination, embodied in science.  Within the last two hundred years, we made our first discovery of microbes, Pasteur developed immunization, Florence Nightingale, Oliver Wendell Holmes and others discovered the importance of sanitation, cities developed sewers, Darwin came up with the theory of evolution, we discovered antibiotics and the dance goes on, and it’s not going to stop.   Bacteria evolve drug resistance, we discover cell biology and DNA, opening the way to controlling newly emerging diseases, and just as surely, the microbes will continue to change and adapt.

And this is where we humans do some spectacularly stupid things.  It is really, really dumb to allow people to live in filth and poverty along with their pigs and birds, where it is easy for microbes to swap genes and jump species.  It’s equally stupid to use antibiotics irresponsibly in a way that will guarantee promoting resistant strains, like not fully treating pneumonia in homeless patients. And dumbest of all is raising the temperature of the earth, as each microbe has its own optimum temperature, and heating things up is just like playing a fast number at the microbe’s gene swapping dance, as they all seek the best way to adapt to the change in temperature, and in the process, they may do some things we really don’t like.

We’ve spent a ton of money on human health, and now, as Dr. Chisholm says, we need to spend some on planetary health…”It’s preventive medicine for the earth”.  In the meantime, lets see if we can persuade GiantMicrobes to come up with a plush prochlorococcus, with a nice thank-you tag for all the oxygen, and until we fund the research to understand the microbial world a lot better, lets “Save the wild e-coli”.

Photo:  A coccolithophore, Gephyrocapsa oceanica Kamptner from Mie Prefecture, Japan by NEON Ja, a scanning electron microscope image with color added by Richard Bartz.  They are distinguished by calcium carbonate plates, which allowed them to be preserved as index fossils, acting as sensitive indicators of changes in temperature and salinity.  They are also important in the CLAW hypothesis, first proposed by Lovelock, wherein the coccolithophorids release dimethyl sulfate into the atmosphere, promoting cloud formation and decreasing the amount of solar energy reaching the surface, providing negative feedback maintaining planetary homeostasis consistent with the Gaia Hypothesis.  However, there is an anti-CLAW hypothesis that holds that future global warming will stratify the oceans, limiting nutrient supply, in which case the feedback loop becomes positive.  There is some evidence supporting both mechanisms…hardly a comfort.

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