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Even More Roles for Microbes

Roles include root hair formation, seedling growth and nitrogen fixation

By Dr. James White

Editor’s note: This article from the June 2022 Issue of the AcresUSA magazine 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. The first part of this interview — which explains how bacteria enter plants to provide them with nutrients and to enable root-hair growth — was published in the May 2022 Issue of this magazine. 

Microbes Article

Without microbes, you don’t get root hairs forming at all. You have to have microbes in the roots to get root hairs forming.

Plants that use rhizophagy are hardier. They’re tougher. They’re going to be more resilient — better for climate change, heatwaves or droughts. If we could have our crop plants getting most of their nutrients through this process, plants would become stronger. When you apply nitrogen — say, some liquid form of nitrate — what happens is that the plants stop using the rhizophagy cycle. They stop secreting exudates, and they stop taking in microbes.

Why is root hair growth linked to the presence of bacteria in the roots? This is a really important question. The bottom line is that bacteria are producing plant hormones. They’re SOIL SCIENCE producing ethylene and nitric oxide. Ethylene is a growth hormone in plants. The bacteria are also producing nitric oxide, which is also a growth hormone. Because they produce it in bulk, that causes root hairs to grow a little bit. When it grows, it will just continue to grow in spurts. Each time it grows, some of these bacteria are ejected out into the soil.

The more root hairs a plant has, the more nutrients it can extract from soil and from water. Rhizophagy is an active extraction process, but the increased growth of root hairs increases the surface area of the root and spreads it way out into the soil, further enabling nutrient absorption from soil water. So, these microphagic bacteria are not only directly giving the plant nutrients; they’re also making it more possible for plants to receive nutrients through other absorption methods — via expanded root hairs.

Microbes on Seed

A visiting scientist we work with developed an experiment to demonstrate the nutrient absorption function of the rhizophagy cycle. He identified native microbes on wheat seedlings, and then he sterilized some wheat seeds so there weren’t any bacteria left on them. He put the native microbes back on the wheat seeds one at a time, and then he measured the nutrients in the grown wheat.

Figure 1 Seeds

The figure (above) shows some of the plants he grew. On the left are the plants grown from the sterile seeds. You can see that the roots are small. The plants with one of the bacteria added back in are several times larger.

The plants with bacteria added back in — for any of the individual bacteria — also contained at least 20 to 30 percent more nitrogen and phosphorus and several times more potassium than the plants grown from sterile seed. This would be an argument for vegetable growers to just use good seed. The microbes are already on the seed.

But we often pick seed early — as soon as possible — and then we take the seed into a dry, cool place for storage before planting. The problem with this is that these microbiomes on seed take some time to mature.

In nature — if you think about how wild plants do it — they’ll make their seeds, they’ll shatter, they’ll drop their seeds to the soil, and frequently the seeds will lie on the soil until it’s time to germinate. They’re on the ground attracting microbes to the seed surface, and they’re maturing there in nature — they’re maturing that microbiome that’s on the seed.

In our agricultural processes, we don’t mimic mother nature very well. We might have to do something to reacquire the natural systems in plants. Some seeds in nature are quite good at it. In fact, some of these microbes are already inside the seed itself — around the embryo. You get microbes that are on the seed, microbes that are inside the seed, and microbes that are from the soil.

Nitrogen Fixation on Leaves

It turns out that all plants have microbes — even on their leaves. Plants internalize microbes into their leaves and their flowers. These same processes that are happening in the roots for nitrogen acquisition are happening on plant leaves.

Microbes in plants produce ethylene, the plant produces superoxide, and hydrogen peroxide is produced. Microbes are also producing antioxidant forms of nitrogen.

We did an experiment looking at over 30 different vascular plants. We looked specifically at all the cells in the leaves and the flowers — especially the non-photosynthetic cells, because we were looking for nitrogen fixation. The nodules on the roots of legumes are filled with bacteria-fixing nitrogen, but they also produce hemoglobin and other chemicals to reduce the oxygen around those microbes so that they can fix nitrogen.

We looked at non-photosynthetic cells, with the idea that the photosynthetic cells are going to be inhibiting nitrogen fixation. We saw that there are microbes going in both photosynthetic and non-photosynthetic cells, but they’re really accumulating in these non-photosynthetic cells, and they appear to be fixing nitrogen.

Hosta leaves are variegated — they have green and non-green areas. If you look at epidermal cells in the non-green areas (or light green) — where there aren’t chloroplasts — you’ll see a nucleus in the center and little vesicles filled with bacteria. The vesicles actually come out of that nucleus, and they’re going over to the paraplasmic space on the edges of the cells. The hosta plants cultivate bacteria in the nuclei. They’ll put sugars in there. Then they will release the bacteria into the cytoplasm, where they then begin to hit them with superoxide. The ethylene that the microbes produce triggers the superoxide. This leads to the production of nitrogen that the plant can use.

This raises a lot of questions. These epidermal cells — these particular cells that have these bacteria — are not active in photosynthesis, so maybe they’re not doing anything else but fixing nitrogen.

These cells have two compartments: the main cell compartment and the nuclear compartment. Why would the plant put microbes in the nuclear compartment? Well, they probably do that because it’s a part of the cell where there’s not a lot of oxygen, which would inhibit nitrogen fixation by the microbe. The microbes are shielded from oxygen. We think that what happens is that the plant fixes nitrogen in the nucleus, where there’s low oxygen and where there are high sugars, and then it sends the microbes out to the cytoplasm, where the nitrogen is extracted from the microbes.

Some kind of foliar feeding — food for microbes — might give some benefits to these associations in leaves. We’re working to discover the specific nutrients that bacteria need to fix nitrogen from the air, and that’s what we want to use for foliar fertilization.

Foliar fertilization is something that’s been around a long time and it is controversial, but because we now know that there are microbes in the leaves, it now makes sense. Instead of putting all our inputs in the soil, where it’s going down and running off, maybe we want to put some on the leaves.

Dr. James White is a professor of plant biology at Rutgers University. He will speak at the Acres U.S.A. Healthy Soil Summit in Sacramento this August.