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Soil microbiome

Also known as
soil microbes, soil biology, soil microorganisms

The soil microbiome is the community of microorganisms living in soil, including bacteria, archaea, fungi, protists and viruses. These organisms decompose organic matter, cycle nutrients, build soil structure and influence plant health.

What is the soil microbiome?

Soil is one of the most biologically diverse environments on Earth. The USDA Natural Resources Conservation Service’s Soil Biology Primer notes that a teaspoon of productive soil generally contains between 100 million and 1 billion bacteria, along with fungi, protozoa and other organisms. The soil microbiome is that whole community and its genetic makeup. Most of its members have never been grown in a laboratory, and modern DNA sequencing has transformed how scientists study it.

What soil microbes do

  • Decomposition. They break down crop residues, roots and manure, forming soil organic matter.
  • Nutrient cycling. They release nitrogen, phosphorus and sulfur from organic matter, carry out nitrification and denitrification, and fix nitrogen; see biological nitrogen fixation.
  • Soil structure. Fungal threads and microbial products bind particles into aggregates that improve water movement and aeration.
  • Plant interactions. Microbes in the rhizosphere, including mycorrhizae and plant growth-promoting rhizobacteria, help plants take up nutrients and resist stress and disease.
  • Disease suppression. Diverse communities can compete with and suppress some soilborne pathogens.

How management affects the soil microbiome

  • Tillage disrupts fungal networks and speeds decomposition.
  • Crop diversity and cover crops feed a wider range of organisms and keep living roots in the soil longer.
  • Organic inputs, such as manure and compost, add food and organisms.
  • Fertilizer and pesticides can shift community composition.
  • Soil conditions, including pH, moisture, compaction and temperature, strongly shape which organisms thrive.

Microbial measures such as soil respiration and active carbon are part of many soil health assessments.

Frequently asked questions

Yes, through microbial inoculants and other biological products. Whether introduced organisms establish depends on the organism, the soil and management. Many practices instead aim to support the microbes already present.

Soil microbes are the individual organisms. The soil microbiome is the whole community, including its diversity and the genes it carries.

  • Rhizosphere

    The rhizosphere is the thin zone of soil immediately surrounding plant roots that is directly influenced by them. Roots release sugars, amino acids and other compounds there, which feed a dense, active community of microorganisms that affects nutrient availability and plant health.

  • Soil health

    Soil health is the continued capacity of a soil to function as a living ecosystem that sustains plants, animals and people. A healthy soil holds and supplies water and nutrients, supports roots and soil life, cycles organic matter and resists erosion.

  • Mycorrhizae

    Mycorrhizae are symbiotic associations between certain soil fungi and plant roots. The fungi extend a network of fine threads into the soil that gathers water and nutrients, especially phosphorus, for the plant, and the plant supplies the fungi with sugars in return.

Sources

  1. Soil Biology Primer, USDA Natural Resources Conservation Service
  2. Soil microbiome and soil health, Peer-reviewed reviews