Sleeping Beauty, Underground

Sleeping Beauty, Underground

Will the leguminous Prince find her? And what root will he take?

This story can also be read on Medium.

Once  upon a time, there was a Sleeping Beauty. She had waited for years,  floating in a thin layer of water and surrounded by giant rocky  aggregates.

This  Sleeping Beauty is not a princess imprisoned in a castle and surrounded  by a moat full of water. She is a soil bacterium, a bacterium of the  soil. She swims in the soil water, and moves between soil clusters.

Sleeping Beauty comes from a noble family, the Rhizobia. A family of bacteria whose special skill is fixing nitrogen.


Nitrogen  is the most important element for plants. Nitrogen atoms are used an  ingredients for many parts of the plant body — including DNA, RNA and  the many hard-working proteins. But nitrogen is not easy to find in the  ground. It’s water-soluble, which means it gets “leached” — that is,  dissolved and carried away by the rain.

That’s why rhizobia don’t search for nitrogen in the soil. Instead, they take it from the air.

Nitrogen  atoms are very common in the sky. That’s where they stay, in the form  of ‘dinitrogen’. Dinitrogen — what we know as N₂ or “nitrogen gas” — is  one of the easiest things to find in the sky. In fact, it makes up 78%  of the Earth’s atmosphere. So it must be very frustrating for plants,  who have this great source of nourishment floating everywhere but can’t  get to any of it.


Plants  can’t eat nitrogen through their leaves. They’re not built for it. The  only way for plants to get nitrogen is through their roots, which can  suck up ammonium (NH₄) or nitrate (NO₃) through their leaves. Which  means they have to wait for it to get into the soil, either through  natural processes or when someone pours in nitrogen-filled fertilisers.

That’s  also why lots of plants grow near a lightning-strike. As the lightning  slices through the air, it breaks apart the dinitrogen into separate  nitrogen atoms. Some of these atoms then fall down with the rain, mixing  with oxygen to form nitrates in the ground that the plant can use. So a  bolt of lightning may injure a tree, but it also fertilises the soil  for the next generation of plants to grow.

What  about the rhizobia? They’re not plants. They’re bacteria, and they have  just the right enzymes to digest bacteria from the sky. Enzymes are  little workers inside the cell that do stuff: in this case, they take in  dinitrogen, transform it into ammonium, and release it into the soil  for plants to eat. This is what is known — with a term plants will  certainly relate to — as “fixing” nitrogen.

But  our own rhizobium, the Sleeping Beauty, is not fixing anything. She is  still fast asleep, waiting and waiting for her Prince Charming to come  to her.


Prince  Charming is not actually a prince. He is a root hair, a hair of root. A  long, thin, woody string, winding its way out from the root of a plant.  He feels his way through the soil, probing the ground and deciding  which direction to grow in. One day, he arrives under a dark forest,  and, being adventurous, decides to explore it. And then, a strange  signal attracts his attention.

The sweet scent — or is it feel? — of fat and sugar molecules.

Fat  and sugar. These are the molecules that Sleeping Beauty sends out in  her sleep, tiny strings of atoms which her Prince can recognise and grow  towards. Not everyone can understand this message and create a  relationship with Sleeping Rhizobia Beauty. Only a  certain select family can do that: the Legumes. They’re diverse family  of plants, but you probably already know some legumes, such as alfalfa,  clover, pea, and bean.

Legume  Prince Charming is charmed by the signal. He grows rapidly towards it,  until he and the princess are practically touching. Does he kiss her?  Well, not quite. But what happens next is, in some way, quite similar.


Not all humans kiss the same way or for the same reasons. It differs from culture to culture. But when people do kiss, in a romantic way, scientists think there’s also a biological reason behind it.

When  two humans kiss, it’s also a chance for their bodies to exchange  pheromones. These chemical signals contain information about the people  behind them, such as their health or genetic make-up. For example, women  have been found to prefer partners with immune-system genes that are  different from their own. Probably because that’d help her children get a  wider range of immune-system protection.

For the legume and the Sleeping Beauty, it’s not so much about finding the right person, but about finding the right species.

As  soon as the root hair is in contact with her, a chemical conversation  is started with her future plant host. The plant, on the other hand,  checks the identity of the bacterium by emitting flavonoids.


Flavonoids are a kind of carbon-based molecules made by plants. Their name comes from the Latin flavus,  meaning “yellow”, because that’s their natural colour. But they’re not  just about yellow: flavonoids are responsible for colour in plants, and  they can make flowers in any shade from red to purple. Other kinds of  flavonoid have other jobs, including blocking harmful radiation,  controlling the cell cycle, or acting as chemical messengers.

In this case, chemical messengers is exactly what these flavonoids are. And they’re designed specially to attract Rhizobia bacteria. Because Sleeping Beauty is from the Rhizobia family, the plant will consider her as a potential mutualistic partner.

On  receiving the princely plant’s flavonoids, Sleeping Beauty replies with  signals of her own. Known as “Nod factors”, these molecules help the  root to be sure of her identity. As for why it’s called a “Nod factor”,  I’ll tell you about that in a bit.


When  he receives her signals, the root hair curls around Sleeping Beauty,  holding her in an embrace. The bacterium is then taken up, through the  root, and into a special room where she can multiply. This room is  called the “cellular infection compartment”. Yes, the bacteria is  technically “infecting” the plant’s root, although in this case it’s an  infection that’s loved and welcomed.

As  the princess and her progeny live and multiply in this room, the root  grows an extra protective structure around them. This is the nodule.  It’s a sort of ball you can see, attached to the outside of the root.

Inside the nodule is the Rhizobia bacteria’s own little world. The plant works to create the optimum  environment, with the perfect temperature, nutrients, and chemical  make-up, for the bacteria to live comfortably and fix nitrogen. Apart  from protection them, the nodule also regulates the bacteria’s oxygen  supply.

And now, can you guess the reason behind the name “Nod factor”?

Yes  — “Nod” is short for “Nodulation”. The nodulation factor, in other  words, tells the plant went to nodulate — that is, create a nodule for  the bacteria to live in.


You  know haemoglobin? The oxygen-carrying protein that gives blood its  colour? The nodules of leguminous plants have something similar.

Leghaemoglobin,  as it is called, carries plants just like haemoglobin in blood. By  controlling leghaemoglobin levels, the plant can give just the right  amount of oxygen to the bacteria. And, it can keep oxygen away from the  nitrogen-fixing enzymes, which find oxygen toxic.

Thanks to this mutualism, the Rhizobia bacteria gets protection, oxygen and sugars, while the legume plant  gets its precious nitrogen. It’s an exchange where both parties are  winning.

Sometimes,  a group of rhizobia try to cheat and steal all the services from the  plant, without giving nitrogen back. In this case, the plant has a  mechanism to detect and punish bad partners. It can stop the nutrient  supply to those bacteria, and let the nodule die.


Today,  humankind needs these nitrogen-fixing plants and bacteria. They’re  needed to reduce pollution of the environment. Most of the nitrogen  fertilizer we use are made in industrial, energy-consuming, ways.  Getting help from legumes and rhizobia would make us less dependent on  these polluting industries.

Thousand  of legume plants are able to fix nitrogen thanks to this cooperation  with bacteria. Most of the bacteria who can do this are still to be  discovered. Many Sleeping Beauties are waiting, waiting for scientists  to find them underground.

Hold on. Are they really waiting for scientists? Probably not.

All  they want are safe, comfortable nodules to live in. Whatever happens in  the human world above ground, it is not their concern. They simply wait  for their Prince Charming root hairs to take them home.

And then, they live happily ever after.


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Sources and references for this article can be found here.