Explaining Rhizophagy

How bacteria enter plants cyclically to deliver nutrients

Editor’s note: This article is an edited version of part of an interview with Dr. James White of Rutgers University, who along with his colleagues has been at the forefront of the discovery of the phenomenon of rhizophagy. We feel that this is incredibly important information for growers and agronomists, and we plan to include more from this interview in the coming months. 

We typically think of plants as these organisms that need our chemical fertilizers, but they actually don’t depend on them. That’s what the work we’re doing suggests — plants have to develop their own methods for getting nutrients, and they involve microbes. 

Plants have this character that people didn’t know about: they are internalizing microbes and degrading them and getting nutrients from them. They maintain them as endosymbionts in the plant cells for a period of time. 

Plants are basically eating microbes and internalizing them. The idea of endosymbionts giving rise evolutionarily to organelles, mitochondria and chloroplasts has been called endosymbiotic theory — basically that eukaryotic cells evolved by internalizing other microbes. 

I’m trying to say that, actually, this process is ongoing; it’s not just evolutionary. It is happening today — this is an active way that plants get nutrients out of microbes — by internalizing them into their cells. It’s not just something that happened long ago. 

This takes a fundamental change in how we think of plants. Plants are cultivators of microbes. They are not just growing in the soil, waiting for us to apply nutrients to them. The degradation of microbes, or the consumption of microbes to get nutrients, is called microbivory. It’s like herbivory — but the eating of microbes. 

The evidence we have is that bacteria are fixing nitrogen inside plant cells. 

Plant-Bacteria Interactions

Here’s one of the chemical reactions that’s happening inside plant cells — between the bacteria and the plant cell:

The bacteria produce ethylene (C₂H₄). The plant detects the production of ethylene and secretes superoxide (O^–) onto the microbe. The ethylene and the superoxide combine and form hydrogen peroxide (H₂O₂). We know this happens because we can use different stains under the microscope to detect ethylene, superoxide, hydrogen peroxide, proteins or nitrate. 

Figure 1 shows caulonemata — non-photosynthetic filaments that are produced by a moss. The slide is stained for ethylene. It’s a blue color. The black arrows show bacteria that are inside the plant — the blue around it is the ethylene the bacteria are producing. 

The bacteria are in the pariplasmic space of those cells. They’re probably not in the cytoplasm; they’re probably just pressing down on the membrane. They’re really outside the membrane. The bacteria actually get lodged into that area.

The plant is producing superoxide, which is highly potent. It will degrade the microbe unless the microbe can protect against it. But the microbe is protecting itself is by secreting antioxidant forms of nitrogen, like nitric oxide. We also think it can also secrete ammonia. We can actually see all forms of nitrogen in the tissue. We’re certain nitrate is there because we can stain for nitrate. The nitric oxide from the bacteria combines with the superoxide from the plant in a second interaction to form this nitrate inside the plant:

So superoxide will combine with the nitric oxide, which is in antioxidant produced by the bacteria. We think nitrogen fixers would be producing nitric oxide to protect themselves from this superoxide. Then those combine and you get nitrate. The nitrate can be absorbed into the plant cells as a fertilizer. 

Some of the bacteria die as soon as they get internalized, and they’re broken down with superoxide. These bacteria that can do this reaction — this second reaction — survive. They survive because they are secreting nitrogen. That enables them to detoxify superoxide. They detoxify it, and nitrate gets formed and the plant absorbs it. Then the bacteria are ejected from the tips of the plant’s root hairs. 

As far as we know, all plants can do this. Even the simplest of plants have been doing this since they came on planet Earth. If you want to put it into a creation scenario, as soon as God created them. Or, put another way, the earliest adaptation plants got for living on land was probably how to milk microbes for nutrients. 

We see variations of this in our advanced plants and our crops. In our crops, there are some variations of these reactions between the plant and the microbe, but you see it in all plants. Some of the microbes are truly, 100 percent, broken down. We can see them breaking down all the way, so the plant gets everything out of those microbes. Other microbes can survive in the symbiosis; this prolonged nutrient exchange between the microbe and the plant that can go on for days. 

Microbes in Seeds

We did some work 10 or 11 years ago with big cacti on the desert island of Bonaire. We got the seeds out of the cactus and germinated them and grew little seedlings. We discovered bacteria in the roots that had to have come from the seed.

Plants have good bacteria inside them. They put it on their seeds, so the bacteria will then be for their seedlings — so the seedlings can grow and get nutrients. All the plants that we study are healthy, so this is not an internal parasitism. 

The plant is producing superoxide, which is highly potent and oxidative and prevents these microbes from producing enzymes — at least, they certainly can’t secrete the enzymes. The superoxide will oxidize those enzymes and denature them. 

In fact, these bacteria are without cell walls. They’re spherical when we look at them, but they are actually not spherical bacteria. If you isolate them and grow them, they’ll be rod-shaped. When they lose their walls, they become spherical. 

So, the microbes aren’t able to do anything when they’re inside the plant, because the plant is controlling them with, among other things, superoxide. 

All plants have endophytes; they have whole communities of endophytes in them. You think of a tomato as a sterile entity inside, but, in fact, it isn’t. There are bacteria all over the surfaces of seeds and inside the seed, too. 

These microbes come from two places. They come from the soil — they’re all soil microbes — but they also get into seeds; the plant will put them on its seed so the seedlings have them. If the plant loses them on the seeds, it can reacquire microbes from the soil. And if the plant is in a soil where the microbes are better, then the microbes that are in the seed can be replaced with those better microbes. 

Rhizophagy — Plants “Eating” Bacteria, Triggering Root Hair Growth

There is a cyclic process for some types of bacteria called “rhizophagy:” rhizo (root) and phagy (eating). It denotes the idea that these plants are “eating” bacteria as a source of nutrients. 

The microbes are attracted to the plant from the soil by exudates — the plant is secreting sugars out to attract these microbes. These microbes are finding the root tips and then they’re being cultivated there and then internalized into the root cells. We don’t exactly know how they internalize them, although we have some theories. The whole question is really interesting. 

The bacteria enter the plant where these exudates are going out. The exudates are sugars, carbohydrates, organic acids — in some cases, amino acids — and other small molecules that the plant is secreting to attract bacteria and also to feed bacteria in the soil. The bacteria go into the root cells. They get hit with superoxide that strips off the cell walls. They form protoplasts — wall-less bacterial stages — and they continue to be bombarded and they interact chemically in the two interactions discussed earlier. 

Then the surviving microbes will trigger root hair elongation. We know they trigger root hair elongation because if we remove the bacteria, we have no hair elongation. 

As these hairs elongate, the bacteria then are ejected back out into the soil, where they reform their cell walls and then go back out into the soil and reform flagella (if they have them) to swim. They live in the soil like happy microbes in their little microbial lifestyle in the soil, until they get attracted back again to the tips through those exudates. 

These exudates are cheap for plants because they photosynthesize, so they’ve got tons of sugars. It costs them almost nothing to feed these microbes. It’s been estimated that 40 percent of the photosynthate that plants produce doesn’t go into the plant, but rather into the soil to manage these microbes. 

Some of the exchange of nutrients between plants and microbes may be happening outside the plant. We know that plants can acquire nutrients solubilized in liquid from the soil water, so they’re definitely taking in those nutrients that way. They can also get nutrients from mycorrhizae. The rhizophagy cycle is the piece that was missing. Plants also are internalizing these microbes and forcibly extracting nutrients from them. That was the piece that was missing.