by Jennifer Frazer

Your floor – particularly if you own a dog – is covered with bacteria that, oddly enough, look and act just like fungi. They are called Frankia, and they were named after a scientist who understandably thought they were fungi, except for around the time they were named after him, during which he didn’t believe they were alive at all. Obviously, Frankia are peculiar bacteria. What on Earth are they doing on your floor?

You have seen fungi if you have ever seen fuzzy molds on bread or fruit. Frankia resemble these fungi in several ways. Fungi are built of long, branched filaments. Though most people think of bacteria as single cells, Frankia belongs to a group of bacteria that grow in long branched filaments like fungi.

Fungi also grow spores, or reproductive cells, by the dozens or hundreds on or in structures called sporangia. Frankia make spores, too, inside lumpy, potato-shaped sporangia.

Finally, like some fungi called mycorrhizae (a term that Dr. Frank, after whom Frankia are named, coined), Frankia can grow inside the roots of some woody shrubs and trees for their mutual benefit.

But there is one thing Frankia can do that fungi cannot. Frankia can “fix” nitrogen. And this is a rare Earth superpower indeed.

Every day, we swim in a sea of nitrogen. Nearly 80 percent of the air you are breathing right now is composed of the stuff. Yet for most of their lives, plants are probing the soil for every scrap of nitrogen they can get their root hairs on, and they often have a hard time finding enough. They desperately need nitrogen to make protein. Plant proteins are the ultimate source of all the proteins in you, so getting nitrogen out of the air and into plants is obviously very important to all of us.

But the two atoms in nitrogen gas are joined by triple bonds, so prying them apart requires lots of energy. Scads of energy. Humans did not discover a way to do it until 1909, and it requires 500 degrees C and 300 atmospheres of pressure to get the job done.

But humans were late to the game by several billion years. Bacteria began fixing nitrogen soon after life evolved by lucking into one of the most important enzymes on earth: nitrogenase. Nitrogenase splits nitrogen gas into its pieces and reincorporates the nitrogen atoms into ammonia. Plants can easily use ammonia to make protein.

But nitrogenase is quirky. While it requires lots of energy to do its job, it cannot tolerate oxygen, the usual source of the power to do it. Scientists call this quandry the “oxygen dilemma of nitrogen fixation.” Plants and microbes would presumably call it a bummer.

But some of them have evolved their way out of this dilemma. One group of free-living bacteria – the blue-green algae – stuff their nitrogenase into a special swollen, fortified cells that serve as anti-oxygen chambers. Another solution arose from a cooperative agreement between plants called legumes (like beans or peas) and root-dwelling bacteria called Rhizobia. In this case, the plant provides both the power for nitrogenase and protection from oxygen. Instead of hiding nitrogenase in an oxygen-free cell, legumes make an enzyme that mops up any oxygen that gets too close to nitrogenase.

Frankia has taken a best-of-both-worlds approach. Like blue-green algae, it builds thick-walled spherical or club-shaped anti-oxygen chambers at the ends of some of its filaments. Unlike blue-green algae, at some point starting about 100 million years ago, it began to crawl inside the roots of certain woody trees and shrubs. There, it sponges the energy to run nitrogenase in return for a providing a cut of the goods.

When Frankia enters plant roots for this purpose, the roots swell into knobby clusters called nodules. They confused the heck out of the first scientists to notice them. An Italian named Marcello Malphigi first mentioned them in 1675, but he thought they were insect-induced plant tumors called galls. Over the next 250 years, the nodules were variously thought to be caused by parasitic plants, parasitic fungi, insect bites, bacteria, giant crawling amoebas called slime molds, or, as briefly espoused by Dr. Frank, by no living thing at all. It was only with the invention of the high-powered electron microscope that Frankia were definitely ID’d as bacteria.

And they turned out to be bacteria with unexpected kin. Frankia’s closest relative lives in a hot spring and is called Acidothermus, which should give you a clue about the radically different life it leads. Frankia’s next closest relatives live a plant-free life in dry soil. Scientists think Frankia parted ways with these relatives about 350 million years ago, about the same time land plants evolved.

Then, starting about 100 million years ago, when the plant families that now host Frankia in their roots were evolving, the bacteria underwent a second burst of evolution into many different strains we see today. Their new hosts were all flowering trees or shrubs in eight loosely-related plant families. The most famous host is probably the alder tree, but Frankia also reside in the roots of the colorfully named bayberry, sea buckthorn, autumn olive, and beefwood.

But there seems to be much more to the story than the tale about Team Frankia. Because Frankia, it appears, are also capable of living quite happily on their own, with nary a host plant nearby. Soil that has never hosted the plants Frankia is known to shack up with has yielded the bacteria. On the flip side, sometimes plants that are known to host Frankia are not nodulated, even though they’re living in soil filled with the bacteria. Scientists have also noticed they find more Frankia under birch trees, which don’t host Frankia, than under alder, which do. In short, Frankia seem to have no problem living independently, eating whatever plant or insect leftovers they can scavenge and fixing nitrogen inside vesicles just fine on their own, thank you very much.

So what are Frankia doing on our floors? And why do floors sporting dogs have more? Because these bacteria live in soil, we probably track them in on our shoes. Or they may blow inside in dusty breezes. As for dogs, the abundance of Frankia in their homes is probably due to some well-known dog passions: loping through the woods, burying bones in the Frankia-filled yard, and obliviously tracking it all inside on their paws. Whether Frankia treated to this unexpected one-way trip thrive in the new world of house dust and dog dander that they enter is anyone’s guess.


Brock Biology of Microorganisms (2009)
San Francisco, CA : Pearson/Benjamin Cummings, c2009. 12th ed.

“The Biology of Frankia and Actinorhizal Plants”
Christa R. Schwintzer and John D. Tjepkema (1990)
San Diego, CA: Academic Press, Inc. p. 1-19

“Frankia taxonomy and diversity”
Microbiol Monogr (2009) Vol. 8: 103–125
K. Pawlowski: Prokaryotic Symbionts in Plants
DOI 10.1007/7171_2008_121/Published online: 28 November 2008

About the Author

Jennifer Frazer is a freelance science writer fascinated by lifeforms without vertebrae. She blogs at The Artful Amoeba for Scientific American and has written for Scientific American online, Nature, Grist, High Country News, and the Wyoming Tribune-Eagle, where she worked as a health and environment reporter for three years, competed in the Chugwater Chili Cookoff, and wrote the stories on a mysterious elk die-off that earned her a 2007 AAAS Science Journalism award. You can find her on twitter @JenniferFrazer.