Archaea's Role in Soil Health

Archaea's Role in Soil Health

What are archaea? What do they do to improve my soil health? Here’s a hint: they’re single celled organisms that cycle soil nutrients, among other functions. Let’s look at the amazing microscopic world of the archaea phylum.

For a long time, scientists thought archaea were bacteria that only lived in extreme environments.

Really extreme; hydrothermal vents, hot springs, permafrost, highly saline, acidic, or anaerobic environments.

But in 1977 Carl Woese, an American microbiologist, discovered that archaea have many differences from bacteria and are found in all environments, including your fields or orchard. They are so different they have their them their own branch of the Phylogenetic Tree of Life.(1)

Archaea are the 3rd most abundant microorganism in the world and scientists are still discovering new species. They are microorganisms in your soil, the guts of mammals (including us humans), and in the most extreme environments on earth. This is a rapidly expanding field of study. But what does all that have to do with the productivity of your soil? A good question, but before I can answer that we have to agree on what are the defining characteristics of healthy soil.

How Do You Define Healthy Soil?

Soil, as defined by the Food and Agriculture Organization of the United Nations "…is the capacity of soil to function as a living system, with ecosystem and land use boundaries, to sustain plant and animal productivity, maintain or enhance water and air quality, and promote plant and animal health. Healthy soils maintain a diverse community of soil organisms that help to control plant disease, insect and weed pests, form beneficial symbiotic association with plant roots, recycle essential plant nutrients, improve soil structure with positive repercussions for soil water and nutrient holding capacity, and ultimately improve crop production" (FAO 2008).

This definition can be experienced by you when you walk outside and see many different colors of green from multiple species of trees, shrubs, and plants. When you hear the buzzing of many insects, chirping of birds. When you smell the air after a rain, the fragrance of wild shrubs. When you go into your field with a shovel, dig some soil and smell it, feel it, taste it, and see the earthworms and other arthropods visible to the naked eye. The chances are pretty good you have healthy soil if it smells, feels, tastes, and looks good.

Healthy soil has billions of microorganisms, and is rich in organic matter. It is an amazing ecosystem that responds to weather events, seasons, and even the particular crops we plant. If we treat it well by not tilling or applying synthetics it responds by giving us bountiful harvests, beautiful forests, and a myriad of organisms, microscopic and visible to the eye. Some of those microorganisms are archaea, one-celled microorganisms that are very helpful for soil health.

How Do Archaea Benefit Your Soil?

The archaea family has members who can live in any environment and can use many different organic and inorganic sources for energy. Scientists estimate that up to 10% of the microorganisms in temperate soils are archaea(2). That part of your field that retains water longer into summer becomes inhospitable to aerobic microorganisms so anaerobic archaea move in and cycle nutrients. The rhizosphere around your plant roots can become anaerobic when the soil biota consumes oxygen faster than it can be recirculated. This can be due to locally high moisture or especially in clay soils, compaction. Archaea to the rescue again!

Archaea are also in your fields during the heat of the summer. Archaea species can live in either aerobic or anaerobic conditions. Their versatility is a benefit for your soil health.

"Archaea enhance plant health by promoting growth, including resistance, and elevating abiotic stress tolerance. Nutrient (N, C, P, and S) cycling and siderophore production by archaea could provide nutrients that support and promote plant growth."

"The as-yet unidentified volatile organic compounds (VOC) of archaea trigger plant growth and induced systemic resistance…Functional signatures for resistance to oxidative stress and production of reactive oxygen species (ROS) suggest that archaea could protect plants under abiotic stress conditions." (2)

This means archaea could be very beneficial for maintaining, or even increasing, the productivity of your farm. Archaea work on many fronts at the same time.

Archaea Use Multiple Energy Sources For Soil Health

Archaea have adapted to almost every extreme on the planet and bring that adaptability to your fields. Some archaea, the photoautotrophs, use sunlight as an energy source and carbon dioxide as a carbon source. Their energy process isn’t photosynthetic so they don’t create any oxygen from the process. Other archaea use inorganic chemicals (such as sulfur or ammonia) as their energy source and are called chemotrophs. Some archaea even fix carbon from inorganic sources. Autotrophs use CO2 from the atmosphere as their energy source, effectively fixing carbon in the soil. The adaptability of archaea may prove valuable in the future.

Bacteria like a warm, moist, protein-rich, pH neutral or slightly acidic environment. There are some exceptions but the many different archaea species can handle almost any environment. If you have soil that is saline or sodic archaea can help you bring it back to health. As your soil changes the species of microorganisms changes also. Soil health is dependent on a balance of microorganisms, including bacteria and archaea.

Archaea Are Effective Nutrient Cyclers For Your Plant And Soil Health

Plants and soil get the nutrients in forms most beneficial for optimum health. Archaea often function in tandem with bacteria to break down soil nutrients into plant available forms. Most archaeal nutrient cycling occurs in the plant rhizosphere. Archaea form relationships with other microorganisms and are mutualists, increasing the efficiency of the whole.

Nitrogen is crucial for plant growth. Most N from the soil is in the form of ammonium and nitrate, not plant available forms. Archaea oxidize ammonia into nitrite which is then oxidized by bacteria into nitrate for plant uptake. Because this process happens primarily in the plant rhizosphere the nutrients can be easily taken up by the plant root.

Phosphorus is another important element for plant health. Both archaea and plants can solubilize orthophosphate from organic-P, but archaea have been shown to be more efficient in the process. This means the phosphorus from your soil makes it into your plants without your plants having to use some of their energy for metabolization. That leaves your plants with more energy, and correct P levels, for more growth.

Sulfur exists in all soils primarily in the form of sulfate-esters and sulfonates. These are not plant soluble and need to be metabolized by soil organisms before they are bioavailable. Archaea that use sulfur as an energy source reduce soil sulfates into sulfides through enzymes, gaining energy and making sulfur available to your plants.

Carbon cycling is crucial not only for your plants but for our planet. Healthy soil must have carbon, both for sequestration and strong plant growth. Aerobic archaea and bacteria act as decomposers of organic matter that remains in and on your fields and cycle the carbon into the soil and your crops.

Anaerobic areas such as swamps and wetlands are inhabited by a group of archaea called Methanogens. They cycle carbon and generate methane. Some of the methane is used by anaerobic bacteria and some contributes to atmospheric methane emissions. This is unavoidable in a wetland situation but can be avoided in your fields. You can fend off that wet spot in your field, that will become anaerobic and unproductive, by planting cover crops and avoiding compaction.

Soil Health And Plant Biotic And Abiotic Stresses

Archaea have been found to be beneficial in helping plants avoid biotic and abiotic stress. Their adaptability to extremes has led researchers to examine how archaea can enhance plant responses to stresses.(3)

Are your crops stressed by pathogenic microorganisms, insects, and weeds competing for water and nutrients? This is biotic stress and before you get out the synthetics think about how plants in non-cultivated areas have survived for eons.

Over time plants have developed elaborate defense mechanisms against pathogens and insects. Archaea are being studied as beneficial for triggering an induced systemic resistance (ISR) in plants against pathogens. Gene analysis of archaea species show the production of terpene and bacteriocin, which deter herbivore feeding and microbial colonization. These substances produced by archaea are then in the soil and eventually taken up by the plant. A great partnership of microbe and plant to avoid plant certain death.

Abiotic stresses are becoming more common. Environmental factors such as drought, heat, flood, and other weather extremes are making farming more difficult. Adverse environmental conditions affect and limit crop productivity worldwide, not just on your farm. Decades of conventional farming have brought detrimental soil conditions such as salinity, metal toxicity, and oxidative stress. Studies have shown that archaea can help crops overcome abiotic stresses.(4) Some of the first places archaea were discovered were highly saline, hot, or sulfuric. Perhaps the fact that archaea are found in the most inhospitable places will benefit your fields as they experience abiotic stresses.

Archaea can be a great ally in your cropping system. This microorganism is just beginning to be studied and the complete benefits to you are still unknown. With changing climate conditions farming will become less profitable if you’re not aware of the research about archaea, plant health, and soil health.

"Archaea are known as 'food and survival artists' and for their ability to adapt to chronic energy stress," according to Julian Taffner.(5) Would this trait be valuable for your farm profitability in the future? Or even in the present? For more information on soil health subscribe to our newsletter.


  2. Jihye Jung et al, Archaea, tiny helpers of land plants, Comput and Struct Biotech Journal 18 (2020) 2494-2500
  3. Wang et al, Characterization of the secondary metabolite biosynthetic gene clusters in archaea. Comput Biol Chem, 78 (2019), pp165-169
  4. Taffner, J et al, What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs, mSphere 3 3 10.1128/mSphere.00122-18
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