Core Concept Biodiversity Published: February 24, 2023

Underground Heroes: Plants and Microbes Partner to Shape Our World


Did you know that microbes and plants can help each other survive? Microbes—like bacteria and fungi, for example—can help plants find food and water and can even make them healthier during stressful times. In return, plants give microbes food and a place to live. The world as we know it would not exist without plants, microbes, and their partnerships. Unfortunately, changes to climate will also change our environments. Therefore, studying how plants and microbes partner will help us predict environmental changes to our planet and its inhabitants. In this article, we discuss how microbes and plants partner to support life on Earth.

The Plant Microbiome

Every plant on Earth has trillions of microbes that live closely with it. Together, all these microbes are called the plant microbiome (Figure 1). What are these microbes doing, exactly? Are they helping or hurting plants? Most microbes that we know of help their plant hosts by increasing the amounts of nutrients, like sugars, proteins, and water, that are available to plants. Microbes can also strengthen a plant’s ability to fight off infections. Without a microbiome, plant health suffers.

Figure 1 - The below-ground compartment around the roots is called the rhizosphere.
  • Figure 1 - The below-ground compartment around the roots is called the rhizosphere.
  • Research has shown that the rhizosphere facilitates close interactions between and among microbes and mycorrhizal fungi, allowing them to exchange nutrients. Although fungi can often be seen by the human eye, powerful microscopes are needed to see the billions of bacteria and other microbes in the rhizosphere.

Although research on plants and microbes has come a long way since its start in the late 1800s, we still have plenty to learn. Researchers are currently working on ways to use microbes to produce larger crops, more food for our growing population, and healthier forests for future generations [1]. Learning more about how microbes interact with each other and with plants brings us one step closer to accomplishing these goals.

Where exactly do plants and microbes interact? One main area of research focuses on the underground space around the plant root, called the rhizosphere. The rhizosphere is home for many types of microbes, and it is a hotspot for plant-microbe interactions. We still do not completely understand how microbes communicate with each other or share food, so these are important questions to answer. If we understand the rules that plant microbiomes play by, then we will be better at predicting the ways that climate change may affect plants and their microbes.

Research has already helped us engineer plants that can withstand drought and increased temperatures, and that can grow larger and faster. But we are still unsure how microbes will interact with plants as Earth’s climate changes. Will some microbes lose their ability to help plants grow? Will plants be overtaken by pathogens, becoming sick and stunted? Will we be unable to supply food to Earth’s growing human population?

Bacteria and Fungi: Key Players in Plant Microbiomes

Bacteria and fungi make up more than 90% of a plant’s microbiome. As a result, much research focuses on how these microbes interact with plants.

How can bacteria help plants? Bacteria have been living with plants for hundreds of millions of years, and for centuries bacteria have been known to help plants grow. One of the most well-studied groups of bacteria is rhizobia, which convert nitrogen gas in the atmosphere into ammonia. Plants can use ammonia to make amino acids, the building blocks of proteins (Figure 2A). We call this conversion nitrogen fixation. Nitrogen-fixing bacteria help plants receive the resources they need to remain healthy. However, nitrogen fixation is not the only way that bacteria help their plant hosts. Bacteria also balance plant hormones that are critical for plant growth and development. Many research groups around the world are researching how bacteria and plants help each other.

Figure 2 - Common ways that bacteria and fungi partner with plants.
  • Figure 2 - Common ways that bacteria and fungi partner with plants.
  • (A) Rhizobia or other nitrogen-fixing bacteria can convert atmospheric nitrogen into nitrogen sources that plants can use, like ammonia. Bacteria can then convert ammonia into other usable forms of nitrogen that help themselves and plants grow. (B) Mycorrhizal fungi can trade carbon for nitrogen and phosphorus, which plants need to survive. (C) Microbes and plants also partner when bacteria and mycorrhizal fungi trade resources with plants. Microbes also balance plant hormones, which aids plant growth and development.

How can fungi help plants? Like bacteria, fungi have also been living alongside plants for hundreds of millions of years. Evolution has engineered certain types of fungi, known as mycorrhizal fungi (myco = fungus and rhiza = root), that partner with more than 90% of all plant species on Earth. When mycorrhizal fungi colonize plant roots, they exchange resources each needs for their growth like carbohydrates, amino acids, and water. Research has shown that mycorrhizal fungi take up organic matter from the soil and give plants nutrients like phosphorus, nitrogen, and water (Figure 2B). When and how mycorrhizal fungi identify their plant host are important questions that still need complete answers.

Bacteria and fungi work together to help plants. Bacteria called mycorrhizal helper bacteria have been shown to support the relationships between plants and mycorrhizal fungi [2]. The more nutrients mycorrhizal fungi can provide to their plant host, the higher the chances that the plant will survive and reproduce. It is still unclear how bacteria and mycorrhizal fungi interact, but evidence suggests that mycorrhizal fungi provide nutrients and shelter to some bacteria.

Microbes Support the Health of Forests and Farmlands

Earth has roughly three trillion trees and more than 600 million farms. This means that the microscopic interactions between plants, fungi, and bacteria impact the fate of our forests and food. Research has shown that microbes can be sprayed on plant seeds or soils to boost crop yields [1] and to remove toxic compounds from forest soils [3]. We still do not know how much these microbes will help plants during stressful times, like heatwaves and droughts. Therefore, much research focuses on how climate change will impact plants and their microbiome.

What about the microbes that may not help plants, like pathogens? Researchers predict that global warming will increase the number of plant pathogens [4] and decrease the number of mycorrhizal fungi. We know that the climate controls much of how plants and microbes come together [5]. Changes to Earth’s climate could cause some trees and crops to become less abundant or even extinct. Manufactured goods such as wood and paper, and foods such as rice and vegetables, would be more difficult to produce. It is possible that changes to food production will prevent us from feeding the Earth’s growing population in the next 30 years. Sustainable solutions must be created!

Although these predictions may seem frightening, research continues to focus on ways to preserve our forests and farms by using our knowledge of microbes. How, exactly? Researchers around the world are using DNA sequencing and satellite imaging to find out which microbes pair with which plant types in forests and farmlands (Figure 3). With this information, we can identify the proper microbes and spray them on plant seeds or mix them into the soil, to help plants during heatwaves, droughts, and floods.

Figure 3 - Plants and microbes come together across the globe.
  • Figure 3 - Plants and microbes come together across the globe.
  • (A) Satellites can help us see our world from high above the ground. (B) Satellite images can show us how patterns change over time. This information can help us estimate the amount of food we will be able to produce and how high carbon dioxide levels will become in the future. (C) Researchers are identifying the microbes present in soil samples at various sites all over Earth. (D,E) They are using their findings to understand the connections between plants, microbes and the Earth.

What Have You Learned and How Can You Apply It?

In summary, researchers are focused on understanding the ways microbes can be used to enhance plant growth and development. Mycorrhizal fungi and bacteria can help plants obtain adequate nutrients, which can result in larger, stronger plants. However, global warming may change plant–microbe interactions across the planet. It is important to understand how climate change will impact farmlands and forests.

How can you help? Read, explore, question, and repeat. From articles to stories, pictures, and videos, there are many resources related to plant–microbe interactions online and at local libraries. You will quickly find that there is a ton of free information available (for example, the soil biodiversity atlas). The more you learn about your topic of interest, the better you will be at asking interesting questions and developing interesting experiments to answer those questions.

If you liked this article and want to learn more about plants and microbes, you could also contact a researcher who could teach you more about plant–microbe interactions. You could start by writing an email with your science teacher, parent, guardian, and/or friends to the authors of this article or to other researchers who study plant–microbe interactions. Researchers are often excited to share their findings and to help young people who are interested in science—so do not hesitate to ask questions!


Plant Microbiome: Microbial communities that interact with plants and influence their growth, nutrient uptake, stress tolerance, and resistance to pathogens.

Rhizosphere: The soil within 2 mm of plant roots.

Pathogens: Any organism that can cause disease.

Nitrogen Fixation: The conversion of atmospheric nitrogen to ammonia.

Mycorrhizal Fungi: Fungi that form a symbiotic relationship with plants, in the plant’s root tissue.

Organic Matter: Carbon molecules that are produced from the decomposition of living matter such as leaf litter or fallen tree branches.

Mycorrhizal Helper Bacteria: Bacteria that increase mycorrhizal colonization, growth, and abundance.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


We thank Kyle Alston for his assistance with graphic design. This work was funded, in part, by a National Science Foundation PRFB Grant No. 2109481 awarded to LB and NSF CAREER Award DEB 1845544 to KP. The funders did not contribute to the design of the experiments, data collection, analyses, decision to publish, or the preparation of the manuscript.


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[2] Frey-Klett, P., Garbaye, J., and Tarkka, M. 2007. The mycorrhiza helper bacteria revisited. New Phytol. 176:22–36. doi: 10.1111/j.1469-8137.2007.02191.x

[3] Torres-Cruz, T. J., Hesse, C., Kuske, C. R., and Porras-Alfaro, A. 2018. Presence and distribution of heavy metal tolerant fungi in surface soils of a temperate pine forest. Appl. Soil Ecol. 131:66–74. doi: 10.1016/j.apsoil.2018.08.001

[4] Hutchins, D. A., Jansson, J. K., Remais, J. V., Rich, V. I., Singh, B. K., and Trivedi, P. 2019. Climate change microbiology—problems and perspectives. Nat. Rev. Microbiol. 17:391–396. doi: 10.1038/s41579-019-0178-5

[5] Steidinger, B. S., Crowther, T. W., Liang, J., Van Nuland, M. E., Werner, G. D., Reich, P. B., et al. 2019. Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature. 569:404–408. doi: 10.1038/s41586-019-1128-0