Amazing Nature

"Probiotics" in the Plant Kingdom

Originally published in Green Country, Issue 119 (Apr 2016)
Author: Green Power
Rhizobia of root nodules
The pale red of the root nodules indicates that there are active rhizobia.
"nitrogen fixating nodules" by Foxy Tigre is licensed under CC BY 2.0

To humans, probiotics are beneficial microbes. From long ago, people have learned to acquire probiotics from food to improve gastrointestinal functions and the immune system. There are "probiotics" in the plant kingdom too: microbes in the soil. In the long evolutionary history, these microbes have even built up symbiotic relationships with many plants.


Rhizobia are nitrogen fixing microbes such as actinobacteria and cyanobacteria. Generally hosted in legumes, these microbes can transform nitrogen in the air into nitrogen compounds that can be utilised by plants. These nitrogen compounds are essential nutrients for plants in making protein, DNA and chlorophyll. Although there is abundant nitrogen in the air, it cannot be used directly by plants. When the soil lacks nitrogen, legumes secrete betaine, flavonoids and isoflavonoids, which attract rhizobia. Once the microbes grow in the roots of the legumes, they become "nitrogen fixing factories". At the same time, the plant provides food for the microbes. This is a typical symbiotic relationship in nature.

Phosphate solubilising microbes

Phosphorus is another essential nutrient for plants in photosynthesis, nutrient transport and making new cells. There are a few phosphate compounds in the soil, broadly classified into inorganic and organic forms. They are both insoluble in water, and can hardly be utilised by plants. To obtain this essential nutrient, the plants need the help of phosphate solubilising microbes. These secrete enzymes or acids by different mechanisms, and dissolve inorganic and organic phosphate in water so it can be taken up by plants. Known phosphate solubilising microbes include bacteria, actinobacteria and fungi.

A piece of arable land with plants
Phosphate solubilising microbes are used as biological fertiliser that can substitute for chemical fertiliser.

Mycorrhizal microbes

Most mycorrhizal microbes are fungi. According to the penetration level of hyphae in the root cells of the plant, they can be classified into endomycorrhizal fungi, ectomycorrhizal fungi, and ectendomycorrhiza fungi. Endomycorrhizal fungi enter the root cells and develop a huge hyphal network around the root, which delivers nutrients to the plant. Ectomycorrhizal fungi form a fungal sheath outside the fine roots of the plant to stabilise the roots as well as protect the roots against diseases and pests, so that the plant may survive in poor environments (such as lacking water or with high salinity). Ectendomycorrhiza fungi act in both ways.

Wild matsutake
Wild matsutake
"tricholoma_magnivelare" by Peter Pearsall/U.S. Fish and Wildlife Service, USFWS - Pacific Region" is licensed under CC BY-NC 2.0

Mycorrhizal microbes can be seen sometimes, particularly under pines and oaks which host the microbes. Truffles, matsutake and bolete mushrooms are the fruiting bodies of mycorrhizal microbes that are used for propagating spores, as the microbes enter reproductive periods. These microbes not only help trees but are fine food for people. However, fruiting bodies of many fungi are poisonous and may be fatal. Many species look closely alike, and it is very difficult for us to distinguish between them. Therefore, it is best to not eat these wild "probiotics"!

A pine tree
There are pine trees in Hong Kong. But their mycorrhizal microbes do not grow into truffles and matsutake.