Leading a bacterium to culture

(Graphic from http://www.compostinfo.com/tutorial/microbes.htm)

This past weekend we were once again honored to have a radio broadcast conversation with host Boyd Matson on National Geographic Weekend, this time about our work exploring how to harness Alaska's psychrophilic bacteria to produce biofuels around the world in areas where it is too cold for the typcial mesophiles that we get from animal manure (our last interview was about building solar hot water systems in Cairo with the Zabaleen and Darb Al Ahmar communities).

One of the excellent questions that Boyd asked at the end of the show spoke to a concern that many people have, and one that is impeding our ability here in Germany to replicate the experiments we are conducting at Cordova High School with the students of science instructor Adam Low: should we be concerned about bringing Alaskan bacteria (an "exotic species" -- actually a consortium of different species) to Europe and Africa?

Psychrophilic bacteria are found all over the world with the hardiest of the extremophiles, like the ones pictured above, found at the Poles. These are Antarctic bacteria featured on "The Worlds of David Darling". We use the ones from the Arctic circle. They can survive and metabolize at temperatures as low as -17 C because they have polyunsaturated fatty acids in their cell membranes, something very unusual for prokaryotic cells. For more information on the Nutrition and Growth of these Bacteria see Lessons In Microbiology by Kenneth Todar, Ph.D..

In fact the German High School that has supported our solar and biogas work in Cairo, a very forward thinking school that has its own renewable energy association, is now thinking of canceling the biogas program we were going to start there because they are afraid that the German health authorities will not give permission to work with "alien microbes".

So just how big a concern is this issue?

The standard answer I gave on-air to Boyd Matson and his listeners, and the one that Dr. Katey Walter, our colleague from the University of Alaska at Fairbanks, repeats when she and her scientific team are shipping bacteria-laden lake mud to the Max Plank institute in Germany and elsewhere, is that during the millions and millions of years that these bacteria have been freezing and thawing in the lakes of the Artic Circle, migrating birds that play in the mud have been carrying them on their feet and feathers all over the globe as part of their normal migratory fly-way. Thus they would have been introduced to other lakes in the temperate and tropical zones repeatedly for millenia, but, because they are optimized to metabolize at low temperatures, any that might survive the journey would perish or be outcompeted by the other methanogens already present. As Zakhia et al. write in "Psychrophiles: From Biodiversity to Biotechnology" (Springer 2008, p. 130),

"A long standing theory of microbial distribution is that 'everything is everywhere, but the environment selects' and that local habitats select for specific microbial flora that is globally distributed (Baas Becking 1934)"

The question of endemism and distribution of bacteria is a topic of much debate (see "Poles apart: biodiversity and biogeography of sea ice bacteria by Staley, James T. in Annual Review of Microbiology v. 53 (1999)), but there is no question that psychrophilic methanogens occur all over the earth, varying in their cold tolerance by region according to the selection pressures they endured (much of the permafrost of the Arctic circle is about 3 million years old while the permanent Antarctic ice sheets originated some 15 million years ago; what we see in these regions today are presumably ordinary psychrophiles that adapted to the relatively recent temperature extremes). So it is extremely unlikely that one could "contaminate" other regions with bacteria that have recently evolved abilities to handle even colder weather.
Furthermore, because they are strict anaerobes and cannot tolerate any oxygen, exposure to air inevitably kills the methanogens we are harnessing. So unless they make to it an anoxic area of the right temperature, they perish.

Are they dangerous to humans or any other animal, or to plants? There is no evidence of any pathogenicity whatsoever, and as if to prove it, our entire team of explorers, scientists, teachers and students spent several weeks "playing in the mud" as we scooped buckets of the microbe carrying Alaskan lake mud into the 8 digestors that we built in the town of Cordova and drew off the bacteria saturated effluent for testing and starting new reactors. We got it on our hands and faces. We spilled it on our clothes. As one of the Alaskan officers of Fish and Wildlife said when I went to ask him about exporting the psychrophiles "it's lake mud. It contains lots of different organisms. We've never heard of any toxicity -- in fact the lake muds here in Alaska are getting famous and being sold as mud for expensive facial masks. I suppose it could be good for you!"

Bacteria good for you?

Well yes, of course! Despite a terrible smear campaign against the smallest of living things, most bacteria are good for you, and if not you directly then they are good for the planet itself. According to Scientific American's article "Stopping Infections: The Art of Bacterial Warfare",

Most bacteria are well-behaved companions. Indeed, if you are ever feeling lonely, remember that the trillions of microbes living in and on the average human body outnumber the human cells by a ratio of 10 to one. Of all the tens of thousands of known bacterial species, only about 100 are renegades that break the rules of peaceful coexistence and make us sick.

Methanogens and other members of the archaic Archaea, psychrophiles among them, are some of the most important and yet misunderstood beneficial microbes.

But should we be transporting them knowingly across state lines, across national boundaries?

What I should have answered Boyd on National Geographic radio for all the listeners, and what I'll be responding with from now on, was another question: "Should we worry about bringing sourdough starters or the starter cultures of yoghurt or the microbes that allow us to ferment cheese, beer and wine and sake and tempe and kafir and kombucha and komchi and sauerkraut and pickles etc. around the world?" Because that is basically what we are talking about -- harnessing the good bacteria from one place to do their good in another place.

If the bacterial and fungal cultures that have so improved nutrition around the world were considered invasive species and were prohibited from being spread beyond their centers of origin our civilization would be much much poorer .

Of course the beauty of most microbial species is that they are easily confined, particularly fermentative microbes, which cannot normally survive outside the narrow conditions they are used in; outside of their watery fermentation tank most dry up and die; exposed to the air, all the obligate anaerobes perish. Hardly the recipe for an invasion. The same cannot be said for arguably much more invasive species that we have not only allowed but encouraged to spread around the globe: weedy grasses like wheat (once confined to Eurasia), corn (once confined to the Americas), rice (once confined to Africa and Asia) and sugar cane (once confined to the Indian subcontinent), roots and tubers like potatoes (once confined to South American highlands) and fruits like tomatoes (once found only in the new world), domestic animals like cows and pigs and horses and goats and sheep (once confined to Eurasia) and chickens (once confined to Asia) to name just a few invasive species whose pandemic spread we not only take for granted but consider beneficial (for more on this topic see Green Imperialism: Colonial Expansion, Tropical Island Edens and the Origins of Environmentalism 1600 to 1860 by Richard Grove, Ecological Imperialism: the Biological Expansion of Europe 900 to 1900 and The Columbian Exchange: Biological and Cultural Consequences of 1492 by Alfred Crosby; also A Green History of the World: The Environment and the Collapse of Great Civilizations by Clive Ponting and The Botany of Desire: A Plants Eye View of the World and Second Nature: A Gardener's Education by Michael Pollan to name just a few!)

The idea of harnessing newly discovered bacteria to do good is hardly news. This entry from the book "Defining Moments in Science" (page 54) tells the story of the discovery of Lactobacillus bulgaricus in 1905:

Key Discovery
Friendly Bacteria (by David Hall)

"Yoghurt, in its original form, could only be produced in Bulgaria and some isolated surrounding areas. It was a mystery as to why and unlocking the mystery opened new avenues of microbiological research.
Born in Bulgaria in 1878, Stamen Grigorov was well placed to solve this mystery. At the age of just twenty-seven, whilst working in an institute of microbiology in Geneva, he made his most important discovery -- a certain strain of bacillus (rod-shaped) bacteria which we now know to be central to the production of natural yoghurt. It was a microbe which would only grow in the climatic conditions peculiar to the Balkan regions.
The bacterial strain, named Lactobacillus bulgaricus, produces the chemical acetaldehyde while it ferments, which helps to give yoghurt its characteristic smell. But it has a more important role than just supplying a pleasant niff. The bacterium feeds on the lactic acid found in milk. This not only helps to preserve the white stuff but also breaks down lactose into more simple sugars. People who suffer from lactose intolerance often find that such yoghurts can help their digestion.
Isolating the bacteria meant that, for the first time, yoghurt could be manufactured on a large scale, which was handy, since Grigorov had also found that yoghurt could help in the treatment of diseases such as tuberculosis, ulcers, and various gynaecological conditions. It was one of the first instances that scientists had realized bacteria has a beneficial role to play in maintaining health."
Why it's key: Bacteria aren't just dirty germs. And Yoghurt can be made all over the world.

Now scientists realize that methanogenic bacteria have beneficial roles to play in maintaining both community and planetary health, cleaning water, reducing pathogens in waste and turning those wastes into clean burning methane gas and into valuable fertilizers and value added products.

Somehow, though, when it comes to trying to set the planet aright, to free us from the damaging spread of the toxins and social instability that are the result of dependency on fossil fuels or the spread of cancer causing radioactive isotopes and the proliferation of nuclear weapons that result from dependency on atomic fuels, the old prejudices and xenophobic fears are raised -- shouldn't we worry about what might happen if we commingle with foreign microbes?

I would say rather, shouldn't we worry about what is going to happen if we don't start putting our planets microbes to work to solve our energy and food and water problems?

Anyway, we know what we are going to do here in Germany until we can convince the authorities to let us bring in Alaskan psychrophilic bacteria: We will simply go into the local German lakes and core out some mud and use German psychrophilic bacteria. Yes they exist -- they are everywhere, and they hurt no-one and they can be harnessed to make methane and other beneficial products. Why then, the need to bring bacteria down from the arctic circle? Only because they do all those good things about 4 times as efficiently as the local species and in temperature ranges far lower, the result of spending so many generations in the harshest conditions.

But as we learned from visiting Blue Marble Energy in Seattle (a cutting edge company working with anaerobic bacterial cultures), one can train bacterial populations and breed them using artificial selection techniques to increase their outputs and tolerances. Assumedly German psychrophiles and African psychrophiles (which must exist in the colder regions) can be selected to be ever more beneficial in the struggle to solve human induced problems. The question is, do we really need to go to all that effort when creatures that natural selection has honed to the task already exist and can be put into service immediately?

Well, you can lead a bacterium to culture, but it may be hard to get human beings to think. For now, here in Germany, we'll work with what the local environment provides until we see what the health ministry decides...


(For comprehensive information on the psychrophilic bacteria and their new applications in industry see Psychrophiles: from biodiversity to biotechnology edited by Von Rosa Margesin et al., Springer 2008.)