The Three Microb-eteers: Methanogens, methanotrophs, acetogens and knallgas bacteria

July 30, 2015 |

Which microbes achieve a better, faster, cheaper transformation of the world around us?

OK, so you’ve just counted “one, methanogens, two, methanotrophs, three, acetogens, four, knallgas bacteria.” Three Microbeteers?! Lookee, Mom, at those morons at The Digest! They can’t even count to four!

So, grasshopper, explain to me Athos, Porthos, Aramis and D’Artagnan as the Three Musketeers.

Besides, throwing three balls in the air and counting four coming down is a well-accepted financial strategy (generally referred to as ”quantitative easing” by the US Federal Reserve, though you might call it Dumas math, after the author of the Three Musketeers).

Three inputs resulting in four returns. That’s elsewhere described as 33% ROI, also known as “the sunny side of the corporate hurdle rate” and is the kind of math you’ll be demonstrating if ever you need money from a venture capitalist, amigo.

So, if you inform me that D’Artagnan wasn’t really one of the Three Musketeers, he joined the Three Musketeers, I’ll send you to Federal Reserve chairman Janet Yellen for a whoopin’ behind the woodshed.

Today, we have The Three Microbeteers and there are four of them, you can figure for yourself which one is the outlying D’Artagnan, and I hope that’s as clear as mud.

Transmitting ourselves into a world of mud

Because mud is what we’re going to look at today. And not just good, clean, ordinary mud. We’re delving into the sticky, oozy, smelly kind that you find in marshes. The filthy mud that wants to make you take a shower and escape these mortal coils.

Because therein, my friend, and not in the halls of the Federal Reserve, lies the true math that may well save this beleaguered world.

Down there in the mud, too small to be seen with the naked eye, are some of your new best friends. Some of the most colorful and transformative little varmints that, tiny as they are, can do astonishing things when it comes to turning basic molecules like hydrogen, oxygen and carbon into the building blocks and consumables of our civilization.

As the title of this column suggests, we’ll be looking methanogens, methanotrophs, acetogens, and knallgas bacteria. Four groups of microbial dudes that, if the human brain was better tuned for survival and advancement, would be better known than Athos, Porthos, Aramis and D’Artagnan. Or even Justin Bieber or the Kardashians.

Now, let’s do the polite thing and make introductions.


These guys consume hydrogen and carbon dioxide and produce methane. You’ll find them described in many cases as “gut bacteria” and just about any animal producing methane through rumination or digestion has a boat-load of them.

Yes, kemosabe, we’re supposed to be reducing methane production — after all, it’s a potent greenhouse gas and we’re awash these days in low-cost natural gas. So, where’s the gold rush?

The Joy of Stress

Turns out, methanogens can produce, under the right stress conditions, a whole bunch of useful bioproducts in addition to methane. Take, for instance, salt stress. We’re all aware that too much salt or too little is dangerous for our health, that drinking seawater is capable of dehydrating a person to the point of death. That’s a complex world, salt stress — but let’s focus in on one effect just for a moment.

At the cellular level, when a whole bunch of salt is swimming around inside you, the water inside your living cells tends to want to leach out of the cell, to equalize the solute concentration. Because your cells have semi-permeable walls, or membranes, they permit this flow of water in and out of the cell — it’s a natural process called osmosis, but when salt levels are dramatically high, the water transfer is so dramatic that it inhibits other natural and vital processes in and around the cell. It’s called osmotic shock, and it can be a real dangerous thing to life.

If the science feels daunting at this stage, just think, when organisms get stressed, they do all sorts of weird things.

schimpf-losConsider the German telephone service Schimpf-los, where operators are standing by 24/7/365 and when you feel stress you call in and shout filthy oaths and raging abuse, with trained professionals egging you on, until the rage is expended, the stress relieved, the mood passes and you feel better.

Ah, yes, we live in a world stranger than fiction. We are a species grounded in stress, abuse and mud-slinging. And not always the good, clean ordinary mud, either. I mention this in case you haven’t visited Washington, DC in the past two years. So, it’s good to know that even bacteria get stressed.

However, microbes can’t speak German and don’t make telephone calls.

Accordingly, over the eons, they have developed their own coping strategies. One way of doing so is to accumulate some small, soluble organic molecules inside the cell. Defenders of the realm, you might call them.

One group just happens to be the alpha amino acids— such as lysine, methionine and threonine. Which just happen to be essential to healthy people, and also healthy cows and chickens. And just happen to be something that animal protein is relatively replete with, but vegetable protein is not.

Meaning that, if you feed a steady diet of veggie protein instead of animal protein to someone you love or a farm animal, it comes in handy to have an amino acid supplement if growth or milk production is on your agenda. And you may have heard that farmers supplement dairy feed with lysine.

Opportunity knocks, and are you there at the door?

At this point, you may be miles ahead of me.

Yes! you have cried. What if we could train up some friendly archaea methanogens to make industrially feasible concentrations of amino acids, as a byproduct along with the methane we usually get from them?

Yes! Then feed that to farm animals to improve their diet, thereby making it possible to use lower-cost veggie rations such as corn grain.

Yes! Because it takes 8 pounds of corn to raise a pound of beef, stretch our agricultural resources in a meaningful way, and do a better job of feeding China as the Chinese shift diets to eating more meat, which they are doing.

Yes! What if we feed that methane back to a facility, which is reforming natural gas into hydrogen? That way, I get a hydrogen source for my archaea and they get a methane source for their reformation process?

Yes! Isn’t industrial hydrogen a big business, at 55 million tons a year? Aren’t we entering the Hydrogen Economy? Do we not have the biological tools to tune up the right Archaea? Is this a billion-dollar idea or what?

Yes! you cry, Yes! Sounding perhaps like Meg Ryan slapping the delicatessen table in When Harry Met Sally. Yes! Yes! Right before Estelle Reiner playing a snappy nearby patron says, “I’ll have what she’s having.”

The good news is that you’ve got one whale of an idea.

The bad news is that you are, ahem, “having what someone else is having”. Because Jay Kouba and his team at Trelys already had the same idea, and are busy getting down the road with it. They’ve picked up early-stage investment from Arch Venture Partners and First Green Partners — with amino acids in early focus, and a whole bunch of products in the potential mix. Food, polymers, feed, chemical intermediates, lubricants and fuels. Much more on Trelys here.


So, if a methanogen eats hydrogen and CO2 and produces methane along with other things, a methanotroph eats methane and oxygen.

And we sure have a lot of methane lying around — think cheap natural gas piling up at Oklahoma’s Henry Hub. Or, if your tastes run more to “waste makes haste”, think all the methane being flared in the Bakken oil field, too expensive to transport out. Or, if you are a diehard biohead like most of us here in Digestville, just think about all that landfill or other biogenic sources of methane, some of which we covered last week in Biogas!

Turns out, you can do a lot more with methane than make compressed natural gas as a trucking fuel, or generate power with a natgas steam turbine.

Yes, my friends, and I do mean my friends! With this little microbe you can take methane and make it right back into the very food that the cows ate to produce waste sludge in the first place. My friends, step right up, it’s food!

Yes, food. The oft-praised star of the “Food vs Fuel” debate, and that staple of the kitchen table. Specifically, in this case, protein.

The Finicky Fish of Fishville

And we live in a protein-short world, and that a product of a fast-rising world population and a growing affluence in the developing world. Which leads to more meat consumption, or fish. And fish are getting to be in short supply, and one of the reasons for that is the soaring cost of fishmeal. As in $1500 per ton, or double the cost of fuel.

Turns out, fish are finicky. Big fish, as it turns out, not only do they eat little fish, they only want to eat little fish. They don’t like soymeal all that much. Not as many vegetarians down there in the Deep Blue Sea, as we would like. So, at best you can use soymeal or other vegetable protein as a fishmeal supplement, but rarely have we found a fish who has a “Mikey Likes It!” moment when it comes to veggie protein.

So, what happens when we find a methanotroph that eats methane, adds oxygen, and produces a whole bunch of potentially useful proteins and possibly pharma, fuel or chemical products. Some of us start clapping…while some make a beeline for the United States Patent Office in one of the biggest intellectual property land grabs since Boomers and Sooners ride westwards into Oklahoma.

Why not? Here, we’ve found something to do with something we have in abundance, that turns it into something we are short of.

Now, before you can say “medieval alchemy”, let’s declare affirmatively that only a few companies are getting materially down the road with methanotrophic technology. Calysta, Mango Materials and Industrial Microbes among them — all of them are early-stage, no one has built a plant yet. And the drive to make single-celled protein from fossil methane is possible The Idea That Sunk The Soviet Union. See our reporting from the front lines of the Cold War, and the aftermath, for more on that one.

But that was then, this is now. We are in a completely different world when it comes to the synthetic opportunities in biology. Training up a microbe is not as dang hard or as durn expensive as it used to be. But it’s still pretty dang hard and durn expensive, dadgummit.


If you can say “LanzaTech” and ring a bell somewhere in your mind, then you already know something about acetogens. What does an acetogen eat? Unlike methanogens that eat hydrogen and carbon dioxide, these critters naturally gravitate towards a diet of hydrogen and carbon monoxide.

Now, that’s a useful trick, because you can vent carbon dioxide pretty much all day of the week, and more on Sundays, and all you get is the ire of toothless organizations like the Intergovernmental Panel on Climate Change, while winning friends in the far more important and transformative galactic center of the Tragedy of the Commons, the Planet Houston.

Yes, Houston is a planet, as was revealed in the early scenes of Superman II.

It’s somewhat smaller than Pluto, but Houston has definitively fulfilled the three conditions for planetary status as set by the International Astronomical Union. It is in orbit around the sun, also known as the oil industry. It has sufficient mass to have established hydrostatic equilibrium (if you’ve noticed on any travels you made on the Space Shuttle, the metro area is pretty much round in shape). And, it has cleared the orbit around it — which you can tell from the dearth of investment in anything resembling a biofuel.

The 4 Universal Rules of Greenhouse Gas Emissions

Now, Houston has established the four universal rules of greenhouse gas emissions:

Rule #1. Carbon dioxide and methane emissions are harmless or might as well be harmless because we’re not going to do anything about them, and in fact will actively seek to prevent anyone else doing anything about them, until someone figures out a way that remediation becomes an industry valuable to Houston. Until then, venting is fine.

Rule #2. Unfortunately, carbon monoxide is poisonous to residents of Houston and can’t be vented. So it can and should be flared into carbon dioxide. Thence, refer to Rule #1.

Rule #3. All other greenhouse gas emissions don’t count because no one in Houston can pronounce them.

Rule #4. We have in Houston some otherwise intelligent and valuable citizens who don’t agree with the universal rules of greenhouse gas emissions. They are permitted to dwell amongst us so long as they don’t bring up the subject at parties, subject to a fine of one cow.

Now, acetogens are a perfectly good way to attack the 1st Universal Law of Greenhouse Gas Emissions, because they use carbon monoxide, which can be captured from, say, steel mill off-gas prior to flaring. That’s the basic vanilla LanzaTech strategy for Taking Over the Known World. Acetogens were names for their ability to produce acetic acid, and can be trained to produce ethanol.

In the new bioeconomy, where there’s smoke, there’s spandex

Acetogens, as it happens, can make some amazing things beside the dread alcohol fuel. Especially a chemical known as BDO, which is basically is, or could be, in just about anything you wear. That is, depending on how much Spandex your fashion sensibility will tolerate. Here’s a nifty diagram from LanzaTech on everything this vitamin-shaped little micro-critter can be tuned to produce, one day.


There are other companies using acetogens with that interesting property of being able to ferment a carbon monoxide gas. ZeaChem is one, INEOS Bio is another. And if steel mill off-gases sounds like a teensy market to you, there is enough CO in that source to make more than 30 billion gallons of fuel per year. But, wait, there’s more. You see, you can gasify biomass and make — you guessed it, a synthesis gas composed of hydrogen and carbon monoxide.

Perfect for our friend the acetogen, and one of the reasons that INEOS Bio is gasifying landfill and agricultural waste while ZeaChem looks to gasify wood residues and fast-growing poplar.

They drag CO2 from the atmosphere, which is then converted into fuels and chemicals, some of that volume becomes CO2 when you burn the fuel (but not all, it can also be sequestered in chemicals), and that CO2 is reabsorbed by the trees. The carbon-neutral cycle, in a nutshell, which is why these technologies can have extravagant 70-90 greenhouse gas emission savings compared to baseline gasoline.

knallgas-microbeteerKnallgas bacteria

So, if methanotrophs use methane and oxygen, acetogens use hydrogen and carbon monoxide and methanogens use hydrogen and carbon dioxide, what are knallgas bacteria and what do they eat?

Unlike four-year old children, turns out there’s a varied diet. There’s the hydrogen and oxygen type, and then there’s the hydrogen and CO2 type (similar to methanogens). And they make a valuable gas, which contains energy.

Yes! I hear you cry. Hydrogen and oxygen? They eat water! Water that can be converted into energy! We’ll make fuels from seawater! World problem solved!

Not quite. They use oxygen and hydrogen, yes, and you can obtain both by splitting water, and yes you could propel a car that way. So far, so good.

But the electric energy needed to split water is more than the energy in knallgas. So, there’s no point to it. You might as well drive an electric car. Now, there are some super-combustive purposes where the energy density of knallgas is useful. After all, it literally means in German, “bang-gas”.  Think welding, for one.

So, what’s the deal with knallgas bacteria? For one, they are not photosynthetic. They are chemolithoautotrophs. And you thought that pronouncing greenhouse gases like difluoromonochloromethane was hard.

Also, they are basically the toughest little critters ever, in terms of surviving in hot environments. In about 4 billion years when the sun expands and the world heats up, maybe the last organism left on earth will be this one. So, don’t think of them as bacteria, but as the last interested audience for programs like Life on Earth.

Usefully, it has a little of that magic found in methanogens — they can produce fatty acids of interest. But what about electrofuels?

As a note from the Berkeley Lab mentions, “R. eutropha and other Knallgas bacteria oxidize hydrogen under aerobic conditions and are ideal candidates for production of Electrofuels, the focus of a Department of Energy ARPA-E program for research on microorganisms that can produce liquid fuels without using petroleum or biomass. ARPA-E estimates that that electrofuels technology has the potential to be ten times more efficient than methods that rely on biomass.

A Berkeley Lab team led by Steven Singer and funded by ARPA-E has developed a method to blend hydrogen-producing electrocatalytic materials with genetically modified Ralstonia eutropha, a common soil bacterium, to produce hydrocarbons in a reactor — requiring only CO2 and electricity. This Microbial-Electrocatalytic system is a living inorganic-organic hybrid that can be tailored for the production of a broad range of useful hydrocarbon products, including biodiesel, jet fuel, and specialty chemicals.

R. eutropha is a model organism that can naturally produce hydrocarbons by metabolizing hydrogen (H2) and carbon dioxide (CO2). It has a natural metabolic pathway that already supports significant carbon flux, producing polyhydroxybutyrate (PHB) in granules. The Berkeley Lab team is using synthetic biology tools to optimize the bacterium for production of hydrocarbons such as methyl ketones, isoprenoids, and alkanes. In addition, the genetics of R. eutropha can be programmed to integrate onto the cellular surface inorganic electrocatalysts, which will generate hydrogen in the presence of an electric current.

Where are they on this? Bench-stage prototype, according to the Microbial-Electrocatalytic System for Hydrocarbon Production project summary, here.

Bringing it all together

So, who’s the champ? In the long-term, any of the above, most likely. Here’s a chart from Trelys on the whyfore of preferring methanogens.


In terms of getting towards commercial-scale, acetogens are well ahead right now based on LanzaTech and ZeaChem already at demo scale, and INEOS Bio at commercial scale (albeit with a unit that, for reasons we are not quite sure of, is not producing registered gallons of ethanol at the moment).

Next, probably the methanotrophs. There’s been a wave of investment interest as a result of the transformative science advances in the lab, especially with the genetics of these organisms, and the collapse of natgas prices.

After that, companies like Trelys are at the forefront of the wave of methanogens. Knallgas bacteria are still at the ARPA-E moonshot phase in terms of development.

But every one of them is worth keeping an eye on. Powerful in the transformation of the world via an advanced bioeconomy is the Coalition of the Willing, but even more powerful is the Coalition of the Able — and able indeed are these organisms and the teams working on them.

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