An excerpt from Jeff Lowenfels’ Teaming with Bacteria
The following is an excerpt from Teaming with Bacteria, author Jeff Lowenfels’ new book that describes the fascinating rhizophagy cycle: the process whereby bacteria actually enter into and out of living plants to provide nutrients, in the process triggering root hair development.
Learn more on this subject by listening to Acres U.S.A.’s Tractor Time podcast, which recently featured a discussion between Jeff Lowenfels, Dr. James White of Rutgers University and Laura Decker of MicroBiometer.
Pretend You Are a Bacterium
All gardeners know there is a big difference between reading about a great garden and actually visiting it. The same applies to bacteria. It is one thing to read about them and another to see one in the flesh, at the right size, living among its fellows. For just a moment, become a rhizophagy bacterium. This will help you understand what you have learned.
Say you are rod-shaped, and there are rod-shaped bacteria all around you. (A human might take you for a colorful Cheetos.) There are other-shaped bacteria too, and archaeans, with their distinctive cell walls (but who complains when there is plenty of space and lots to eat?). Oddly, you can’t just do your usual crawl. The liquid you are in is thick, and movement feels more like wading through chest-high mud than swimming. You can feel the Jell-O-like viscosity, and it is strange how you have to wave your arms in circles to move about, how flipping and twisting are suddenly effective ways to progress through your surroundings. There is a feeling of weightlessness as you tumble about, doing somersaults, flips, and corkscrew twists.
You are alone at first but are quickly surrounded by others. You stick to some. Some trade genes with you. You can act as a loner, but sometimes your body fills with molecules that tell you to do something and you do. Your friends do as well. You light up. You move as a group. You sense your neighbors and communicate.
The protective features of your new biofilm home, constructed when you all pooled your stickiness, make it possible to move through tunnels, find food, and live without much fear of those paramecia and nematodes you keep hearing about. Unimaginably big, relatively speaking, they have a difficult time getting through the biofilm, thank goodness, so you won’t be one of the 10,000 bacteria that will be lost that day to every single paramecium. Stay away from edges and anaerobic pockets and watch out for smelly acids, and things should be fine.
If you leave the colony, you might stumble into any number of neighboring colonies of different bacteria. You might find yourself attracted to metals. You might get eaten by other bacteria or protozoa or nematodes or—if you don’t watch where you are going—a root. There sure are some neat things to eat in the soil, and you turn out to be one of them.
Your ancestors were brought to this patch of soil in the coat of an ancient seed. Some forebears who were on that seed went through huge tubes filled with water and sugars inside a plant; others swam through the cell wall lattice and made it into aboveground parts of the plant. Either way, they established themselves—finally winding up in a flower, which folded in on itself—and became entrapped in another seed.
Some of your ancestors disappeared in these seeds, not to be heard from other than an occasional notice that you have a distant relative in the soil of a nearby field. Meanwhile, you and your cousins grow up, living off the ample exudates that are delivered like clockwork. Food just appears. You would be suspicious if your parent hadn’t signaled what was going on. (Where is Mom? She was here 20 minutes ago.) As long as you stick to the exudates, all is well. Stay away from those E. coli metabolites and anaerobic pockets. They might make you sick, and the latter can kill.
You learn the protocols and processes of biosynthesis. You find materials, hammer out a few with bonds, and use them to build whatever you need. Some you use to regulate your metabolic functions. You might even saddle up to a neighbor, put out a tube, and trade little bits of DNA. Fun. You never know what you will get and how you can use it to better your situation.
Ah, to grow. This is how you make your contribution to the colony. You grow, and that leads to duplication. A sustainable population that can pass on traits is the goal of bacterial life (the peaceful ones), and you are meeting it. Over and over, every 20 minutes, this is made clear. You realize that somewhere along the way you picked up a trait that is now shared by others. You created a strain. Way to go!
Then one day while minding your own business, moving lazily through the biofilm of your colony, hungrier than normal due to too much competition for food, you detect the delicious smell of buttery popcorn. (I know the lure of fresh butter: Hotel Bar Butter, a New York favorite, was sold by generations of my family.) You have only unbuttered popcorn, so you attach yourself to the wall of the plant root cell from which the tantalizing odor is originating.
You are leaning right up against the root, drooling enzymes, when the wall develops breaks and that smell intensifies! You drool more enzymes and follow the trail, swimming through the cracks in the wall and finally finding yourself inside a plant cell. You are exhaling ethylene, and you note this place is different from soil, a gel-like liquid with a bunch of your siblings moving around against the inner wall in a big circle. The current is strong, and you are swept into it as it circulates around the cell.
Some instinctive urge to repay the cell for the great circular ride (or perhaps to lighten your load, so the ride is more fun) causes you to convert one of the amino acids you picked up out in the soil, from the plant’s exudates, into more ethylene. It is a gas, and you can’t hold it in, so you release it into the eddies. The ethylene coats the cell wall.
The plant that lured you in now treats you like you are in a car wash. It sprays a mist from nozzles in its membrane, and you notice your cell wall disappearing. It doesn’t hurt; you can still fully function, but now you leak from your exposed, embedded membrane proteins. It would be embarrassing if the same thing wasn’t happening to your friends.
You fix nitrogen into nitric oxide and combine it with superoxide to make nitrates to stop the wall disintegration. This it does, but the plant takes the nitrates and uses them to grow.
Where does the wall go? What happens to leaked electrolytes? Why are you feeling like you have been to a plastic surgeon and had your membrane tightened? You look at your siblings forming smaller forms and quads, and instead of the familiar rod shape, they are now all round bubbles. You realize your own body has become positively spherical.
You are being cycled around, completely naked, inside the plant root cell wall. Everything still works, though, so you enjoy the ride. You bump into a plasma membrane, but it only pushes you back into the current. Still, you can see holes where the components of your wall are disappearing.
You now throw all inhibitions to the protoplasmic forces and multiply right there in front of the others. No wall, so you can easily and quickly form a bleb—and another, and another. The next thing you know there are four of you in a bubble, like four adult humans in a Volkswagen bug. When it gets too crowded, you line the others up and use ethylene to soften and then push a portion of the plant cell wall outward, forming a tube, to make more room.
Then, the most amazing thing happens—something that makes the whole two-day journey worth repeating: a tidal wave blasts into the tube that you helped form and pushes you out through the tip. When you catch your aerobic breath, you find yourself and your close friends back in soil. What a short, strange trip it’s been! Was that only two days? How many new clones are out there in the soil with you? Power is in numbers.
Famished, you find nutrients in this fresh soil to rebuild your wall. At the same time, you fill your pantries with arginine and other components from the plant’s exudates. You divide and divide again. Life returns to normal.
Ah, but there is that butter smell again and you remember the great wave ride. Popcorn and butter! The spinning around, all that budding! Fixing nitrogen. The heck with just eating exudates, you just have to return to the inside of a new cell and experience the great ride over again. And this time you will take that curl standing up. And so you do.
Pretend You Are a Plant
Your feet, er, roots are in rich, well-aerated soil. There is a wonderfully warm film of water around each soil particle and your roots. You are surrounded by 50 or so different kinds of bacteria, fungi, nematodes, and protozoa that your ancestors coded you to recognized and, in some instances, domesticate. This is a great place to live. All you have to do is develop new roots, get nutrients to grow a few leaves, and the next thing you know, you are photosynthesizing away.
You make carbon from the sun to biosynthesize organic compounds to serve as soil exudates. You cook up some great dishes, which you leave in the soil to attract bacteria and fungi. You combine lots of nutrients with your carbon, and once microbes discover a cache like this, they call their friends. An orgy of molecular decay ensues. All manner of essential nutrients are flowing toward your roots.
You are patient. For a few days you can live off the microbes and starch that were cached in the seed from which you sprouted. Those leaves really help jump start things, however. The next thing you know, the nutrients in the soil are converted by all those microbes you attracted into a form you can eat. This is too good to be true. The microbes think you are foolish to produce exudates for them, but they don’t know you are setting up a system to take advantage of them. The bacteria and fungi attract nematodes and protozoa; they in turn eat some of your bacteria and fungi. It happens every time.
The waste products that result from all this activity are in the form of nutrient ions, just the kind of food you like and need. You use your knowledge of chemistry to diffuse them into your root cells, where they are used or transported to other places in you.
This is great food, but you are still hungry. You need more. Fortunately, you remember you are a plant, and you are in control. You remember a plant friend, Seymour, who could never get enough because he was not kept organically. Always screaming “Feed me!” Let that be a lesson: no one else is going to help you—especially not humans who try to foist that artificial junk on you.
You concoct a special exudate and attract special fungi. In return for the special mix and a place to live, in between root cells, these go out and get you water and additional nutrients. They always bring pets, too—bacteria all along their hyphae that help solubilize phosphates, which was hard to get on your own but is suddenly plentiful.
You discover you have a legume plant friend who can attract bacteria that fix nitrogen. You try and duplicate the act, but the nitrogen you get is mere spillage from her nodes. (Later, as some of her leaves decay on the ground, you might get some nitrogen newly put into the soil.) You are still hungry, and you need more.
Then you realize you are not using your exudates efficiently. They are growing a great population of microbes in the soil, but how do you get at their nutrients more directly? Why support nematodes and protozoa? Experience (and plant business school) taught you to cut out the middlemen. And, wonders of Nature, you find a group of bacteria in the mix willing to work with you. These agree to become temporary endophytes. All it takes is popcorn and a bit of butter. Once you get them inside, you entertain them and make sure they want to keep coming back.
As they eat their buttered popcorn, the bacteria open the wall of one of your new cells. Once these bacteria enter your roots, they let you gently shear off their walls, freeing them of that weight and constraint. The constituent parts of these bacterial walls are moved from your periplasmic space to inside your protective membrane. You are no longer hungry. And dessert: you get to enjoy leaking nutrients from the now wall-less bacterial forms.
Realizing you want them to come back again and again, you push them onto the best amusement park ride ever conceived (sorry, Mr. Disney)—the Cyclosis Coaster and Hairy Catapult. Bacteria get to ride the Cyclosis Coaster, and they get to bud in a nice safe place where they don’t have to worry about parents, predators, or competing relatives. You give them some sugars from your own supply, and they seem trapped by this. Plus, they must realize that if they stopped feeding you nitrogen, they would die: their nitrogen fixation stops their own wall deterioration.
The euphoria caused by strength in numbers takes over. The bacteria are having a great time. The bonus is your promise to put them back into the soil in a location where they can rebuild walls and live a better life. You let them help you build a long tubular wave pool, and they immediately gather for the fun. And fun it is. Welcome to Hawaiian surfing conditions, right here inside your root meristem cells.
To distinguish these bacteria from bad bacteria, you learn to recognize the signals they send. You might not trust bacteria, but you have evolved to tolerate the ones that can feed you, especially when that food is nitrates. Tolerance makes you strong in lots of ways. It is like working out and building muscle. That spray you put on the entering walled bacteria requires that you toughen up too, to avoid collateral damage, as you can’t help but get some on your own walls.
Hey! You become a better plant because you are amped up by the presence of these bacteria. All your root hairs are full of them. You experiment and discover other bacteria like different parts of your body. It isn’t so bad having them there, either. You let more bacteria in where branches form on your roots. Suddenly it isn’t so cold, and you find you can handle a change in pH or whatever amount of water is available. Salt? No longer a problem (up to a point). Life becomes a bit more carefree, and you feel so much stronger. Oh, and the food from rhizophagy! Tastes fantastic. Everyone wins.
It is a wonderful thing to be able to build populations of bacteria internally as well as in the soil. They both feed you. They both protect you. You recognize that some bacteria really are your best friends, not enemies at all. From now on, you promise to give them more respect and treat them better—or get your humans to do so by at least trying to visualize them from time to time.
A Lot of Work to Do
Research on the rhizophagy cycle is just beginning. We can take in what researchers have discovered thus far, but the very newness of the concept heavily hints that our understanding of it is only at the pioneering stage. There is much more to come and a lot more to learn. But that doesn’t mean that it isn’t time to educate ourselves and others about what is known to date. Armed with knowledge about endophytic bacteria, particularly those that engage in the rhizophagy cycle, we and our fellow gardeners, farmers, and growers of all kinds can adjust our cultivation practices, now, so as not to interfere with—and better yet, to assist—these tremendously beneficial bacterial helpers.
The rhizophagy cycle is new. It is revolutionary. It is happening now. It is time to acknowledge it. It’s the start of a new chapter, not the end of this one.
Taken from Teaming with Bacteria, copyright 2022 by Jeff Lowenfels. Published by Timber Press, Portland, OR. Used by permission of the publisher. All rights reserved.
