How a Bacteria Almost Destroyed All Life on Earth

Life is infinitely complex in ways even our most sophisticated science is still struggling to understand. Until we recognize that — we continue to put ourselves and future generations at risk.

Image by Douglas from Pixabay

Too many people don’t know that when they harm the earth they harm themselves, nor do they realize when they harm themselves, they harm the earth
—Rolling Thunder

I just finished reading the new Michael Crichton/James Patterson novel Eruption. In it, scientists had buried a pathogen that kills pretty much everything it comes in contact with — from trees to plants to people — deep into the mountainside of the largest volcano on the Big Island of Hawaii. And now that volcano is on the verge of erupting, possibly blasting this stuff into the upper atmosphere where it could kill all life on Earth.

It’s a great novel, if you like light summer reading (I do) that takes your mind away from day-to-day politics, etc., but reading it I kept wondering if Crichton (who wrote most of the manuscript before he died and Patterson finished it) knew about a real-life experiment that could have ended up with the same all-life-on-Earth destroying consequences.

Here’s the true story:

It seemed like an ordinary day and an ordinary science project. Little did Dr. Elaine Ingham and her Ph.D. student Michael Holmes know that the simple project they were doing could have caused the end of most complex life on earth.

But it may well have.

A tree is a living organism—it’s a complex entity that requires continual interaction with billions of other entities to survive. Trees can bring nutrients in only through their roots; bacterial and fungal colonies on those roots predigest the minerals in the soil and then make available to the tree the resulting nutrient soup.

Some of these colonies are so complex in their interaction with the soil that there is as much growing under the ground—separate from the tree but necessary for its life—as there is above the ground.

Your body contains trillions of bacteria, fungi, and viruses, most benign, many absolutely necessary for life (we know best of the intestinal bacteria), as does the body of every other mammal. We’re mind-bogglingly complex, with more than a trillion cellular interactions happening in our bodies every second of every day.

And, of course, we depend on the food we eat, which all begins in the soil (even the animals we eat have to eat plants, which are grown in the soil).

As Dr. Ingham noted in a paper she wrote about hers and Holmes’s experiment:

“Agricultural soil should have 600 million bacteria in a teaspoon. There should be approximately three miles of fungal hyphae in a teaspoon of soil. There should be 10,000 protozoa and 20 to 30 beneficial nematodes in a teaspoon of soil.”

Soil is complex stuff. And one of the bacteria found in soil all over the planet, and on the roots of most plants all over the planet, is a common and ubiquitous little organism named Klebsiella planticola.

It’s everywhere—every plant ever tested for it, anywhere on earth, has been found to carry Klebsiella on its roots.

Thus, a small company based out of Europe had come to Oregon—where there are not the strict laws Europe has in place regarding the dispersal of genetically modified organisms into the environment—with a really neat idea.

The world has a lot of plant waste. Sugarcane and wheat stalks, for example, are often burned after the sugar and wheat berries, respectively, have been removed. This burning throws carbon, soot, and all sorts of pollutants into the air.

But what if all that cellulose, those leftover canes and stalks, could be converted into alcohol? If it could be done cheaply and easily, it would take care of a waste problem and provide a great new fuel source.

So this company came to Oregon and purified a common local strand of Klebsiella bacteria they found in the soil. Using the tools of genetic engineering, they modified the DNA of this Klebsiella to produce alcohol, inserting into its DNA the gene fragment in yeast that causes it to “ferment” things.

Because Klebsiella grows on cellulose (unlike fermenting yeast, which grows on sugars), it could be tossed straight into a vat with a few tons of plant waste and, poof, within a few days you’d have hundreds of gallons of alcohol.

The company’s founders had visions of dollars in their eyes, and were preparing to field-test their newly modified organism within a matter of months (since at that time the George H. W. Bush administration was actively working against any sort of regulation of genetically modified organisms through Vice President Dan Quayle’s “Competitiveness Council”).

Dr. Ingham’s student needed a project to work on as part of his doctoral thesis, so he decided to test the toxicity of this newly minted Klebsiella bacterium. In an article she wrote in 1999, Dr. Ingham described what happened next:

“One of the experiments that Michael Holmes did for his Ph.D. work was to bring typical agricultural soil into the lab, sieve it so it was nice and uniform, and place it in small containers. We tested it to make sure it had not lost any of the typical soil organisms, and indeed, we found a very typical soil food web present in the soil.

“We divided up the soil into pint-size Mason jars, added a sterile wheat seedling in every jar, and made certain that each jar was the same as all the jars. Into a third of the jars we just added water. Into another third of the jars, the not-engineered Klebsiella planticola, the parent organism, was added. Into a final third of the jars, the genetically engineered microorganism was added.

“The wheat plants grew quite well in the Mason jars in the laboratory incubator, until about a week after we started the experiment. We came into the laboratory one morning, opened up the incubator and went, ‘Oh my God, some of the plants are dead. What’s gone wrong? What did we do wrong?’

“We started removing the Mason jars from the incubator. When we were done splitting up the Mason jars, we found that every one of the genetically engineered plants in the Mason jars was dead. Wheat with the parent bacterium, the normal bacterium, was alive and growing well. Wheat plants in the water-only treatment were alive and growing well.”

It turns out that the beneficial contribution Klebsiella makes to plants’ roots is similar to that of intestinal bacteria in humans—it produces a slime layer that protects the roots while also helping the bacteria adhere to the roots and move nutrients into the root systems.

But when the Klebsiella on the wheat in the lab began producing alcohol (as it had been genetically modified to do), Dr. Ingram and Mr. Holmes found it was doing so at a level of around seventeen parts per million—almost twenty times more alcohol than a plant could withstand on its roots without dying. As Dr. Ingham wrote, “The engineered bacterium makes the plants drunk, and kills them.”

Needless to say, when these results were communicated to the company, it pulled the experiment. But consider the possible outcome if they’d gone ahead and created a fermentation vat, fermented a bunch of agricultural waste, and then tossed the sludge out as fertilizer for a field (as is normally done with yeast fermentation to produce alcohol).

“Think about a wine barrel or beer barrel after the wine or beer has been produced,” Dr. Ingham wrote. “There is a good thick layer of sludge left at the bottom. After Klebsiella planticola has decomposed plant material, the sludge left at the bottom would be high in nitrogen and phosphorus and sulfur and magnesium and calcium—all of those materials that make a perfectly wonderful fertilizer. This material could be spread as a fertilizer then, and there wouldn’t be a waste product in this system at all. A win-win-win situation.

“But my colleagues and I asked the question: What is the effect of the sludge when put on fields? Would it contain live Klebsiella planticola engineered to produce alcohol? Yes, it would. Once the sludge was spread onto fields in the form of fertilizer, would the Klebsiella planticola get into root systems? Would it have an effect on ecological balance; on the biological integrity of the ecosystem; or on the agricultural soil that the fertilizer would be spread on?”

As her experiment demonstrated, it would and it did. And if that organism, or one like it, had gotten out into the wild, and if it turned out to be (or mutated into) a highly “contagious” bacterium, in the most extreme (albeit unlikely) possibility, it could have infected and then killed every root-based life form on the planet.

As Dr. Ingham wrote:

“From that experiment, we might suspect that there’s a problem with this genetically engineered microorganism. The logical extrapolation from this experiment is to suggest that it is possible to make a genetically engineered microorganism that would kill all terrestrial plants. Since Klebsiella planticola is in the root system of all terrestrial plants, presumably all terrestrial plants would be at risk.”

Michael Crichton was famous for writing about the greed and hubris of scientists and businesspeople who think they’re smarter than mother nature (Jurrasic Park, among others), highlighting the dangerous thinking of modern society that every problem we create we can also solve with just a little more engineering expertise.

As people across the world are discovering this summer, though, there are some problems created by that same greed and hubris that don’t have easy solutions. Global warming is killing thousands of humans every day across the planet, while fossil fuel barons and Republican politicians continue to deny the role of carbon pollution in what is already a crisis and may one day even become a life-on-Earth-ending event, as Leonardo DiCaprio, a dozen scientists, and I documented here:

The simple reality is that our planet is a single living organism, as much as our bodies are. And we’re rapidly poisoning the very biosphere that sustains us, and continue to do so in large part because greedy rightwing fossil fuel billionaires have prevented political action for over 50 years.

The Cartesian worldview that holds that our planet and all the life on it are simply a giant machine that we can manipulate to our benefit ad infinitum is deadly wrong. While I can take apart my car in my driveway and put it back together and turn the switch and have the engine roar to life, there’s no way I can do the same with a cow.

Life is infinitely complex in ways even our most sophisticated science is still struggling to understand. Until we recognize that — at the level of our politics, religion, and overall culture — we continue to put ourselves and future generations at risk.