Below are brief descriptions and interpretations for some of the most common soil health indicators. Also see this NRCS tech note or the Comprehensive Assessment of Soil Health manual for detailed protocols and evaluation of common methods. A thorough field assessment guide is available from the NRCS as well, and these methods may provide good visual evidence of soil health but not allow for rigorous quantitative comparisons. Before you sample, check out our tips for sampling for soil health tests.

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Why use Indicators?

Soil health, like human health, is the interplay among physical, chemical and biological processes. When evaluating human health, we want to know how well a person can function and enjoy what they do, so we measure functions like how far they can run, or indicators such as lung capacity or blood pressure. When evaluating soil health, we want to know how well a soil can support crops or ecosystems, and if it will continue to support those functions. That's hard to measure, so we measure narrower functions, like how well soil takes up and stores water and nutrients, or indicators like “aggregate stability” or “soil respiration”. (Learn more about these measures below.)

To understand how soil health changes over time, researchers need measures that are quantifiable, repeatable, and interpretable (i.e. that them something about soil processes). To monitor the effects of management, farmers also need measures they can repeat and interpret(i.e. that tell them something about how to change their soil management). One of the most valuable indicators is the appearance and structure of the soil when you dig up a shovelful. Soil organic matter is popular because it is easy to measure, but it is hard to interpret its significance.

Challenges of measuring soil microbes

Soil health has brought more attention to biological processes in soil, so many indicators attempt to measure the pool of organic matter that’s available to microbes. (See the microbial indicators below.) Microbial decomposition of organic matter is a critical process that releases nutrients to plants and builds stable soil organic matter, which improves soil structure, so it’s worth trying to measure microbial activity. But there are no ideal indicators of microbial activity.

Measuring microbial activity is tricky because:

  • It changes. Seasonally, daily, weekly--constantly.
    Microbes ingest organic matter as long as they have water and oxygen, and moderate temperatures. Many reproduce rapidly, so the microbial biomass you measure one hour could be different an hour later. Any measurement of the rate of decomposition is just a snapshot of conditions at the time the soil is sampled.
  • Soil micro-environments matter.
    Soil may be rich in organic matter, but if that organic matter is on one side of a pore, and the microbe is on the other, the microbe does not reap the benefits. Microbes are mostly imobile unless the water they live in flows through the soil. Most microbial activity is concentrated around roots, or other “hotspots” where there’s organic matter, air and water in sufficient supply. Since activity can vary so much from hotspots to bulk soil, it makes taking a representative sample very difficult.
  • Diversity.
    According to the Global Soil Biodiversity Index, soil contains archaea, bacteria, fungi, lichens, plant roots, protists, tardigrades, rotifers, nematodes, mites, collembolans (springtails), larvae, worms (enchytraeids and earthworms), ants, termites, centipedes, millipedes, woodlice, burrowing mammals, and more. Some directly feed on plant residue. Some are predators. Even those not directly involved in decomposition and subsequent release of nutrients can have an effect on microbial activity by preying on bacteria or fungi, creating habitat, or shredding residue into more accessible pieces.
    It’s difficult to discern the roles of each species in the soil functions we care about. Most can only be seen with a microscope, and burrowing a microscope into soil is impractical. We can observe them out of the soil, in the lab, but we’re not sure if they behave the same in the lab as they do in soil, and only 10% of soil microbes will grow in the lab.

Organic matter cycling and C sequestration indicators

Organic matter

  • Measured by combustion at high temperatures, presented as % of total soil mass. Generally assumed to be 58% carbon. 
  • Good indicator of overall food source for microbes and fertility of soil

Soil organic carbon

  • Measured by combustion at high temperatures, presented as % of total soil mass. 
  • Good indicator of total soil carbon pool.

Microbial activity indicators

Soil respiration (Solvita, potentially mineralizable carbon (PMC)

  • Measured by sealing soil in jar and measuring CO2 produced by microbes after a period of 1-4 days. Labs vary in how long soil is sealed, moisture and temperature of soil, method of wetting soil, and method of determining CO2 concentration of jars. Presented as mass C/mass soil/day, a rate of C mineralized.
  • Good indicator of both microbial food source and microbial robustness.
  • Shouldn’t be interpreted as absolute rate of decomposition, as these values represent microbial activity under consistent and ideal conditions in the lab.
  • Responsive to management, and suggested to reflect accumulation of rapidly-mineralizing C pools.

Microbial carbon source indicators

Particulate organic matter (POM)

  • Measured by separating large-size organic matter after completely dispersing soil aggregates. Presented as POM/soil mass, or POM-C/soil C.
  • Good indicator of food source for soil organisms, although these particles are likely too large (usually >53 um) for unicellular organisms to decompose. 
  • Tends to decrease with disturbance, like tillage, and build up when it is protected in undisturbed soil.

Permanganate-oxidizable carbon (POXC)

  • Measured by reacting soil with potassium permanganate, which loses color as it reacts with carbon. Presented as POXC/soil mass, or POXC/soil C.
  • Good indicator of readily-available carbon in the soil.
  • Responsive to management, and suggested to reflect the accumulation of stable soil carbon.

Extracellular enzyme activity

  • Measured by providing substrates specific to various enzymes and evaluating how much of substrate reacts, which indicates how many enzymes are available and active. Labs vary in using fresh or frozen soil.
  • Good indicator of microbial enzyme production, especially in relation to specific elements.
  • Responsive to management, but enzymes may increase due to either substrate increase or decrease, making interpretation difficult.

Microbial nitrogen source indicators

Potentially mineralizable nitrogen (PMN)

  • Measured by sealing saturated soil in a jar and measuring ammonium before and after a period of 7-28 days. Presented as mass N/mass soil/day, a rate of N mineralized.
  • Good indicator of how much nitrogen will be mineralized under ideal, anaerobic conditions.
  • Responsive to management, but not predictive of crop N needs.

Autoclaved-citrate extractable protein (ACE protein)

  • Measured by extracting protein at high temperature.
  • Good indicator of soil nitrogen in proteins (a common, microbially-available form).
  • Responsive to management.

Soil organisms indicators

Microbial biomass

  • Measured by extracting carbon and nitrogen after chloroforming soil to kill microbes by disrupting their cell membranes.
  • Good indicator of total microbes in the soil, but includes living, dead, active and dormant microbial cells.
  • Responsive to management.

Phospholipid fatty acids (PLFA)

  • Measured by extracting lipids, which are part of cell walls, and categorizing them by the type of bacteria or fungi which use particular lipids.
  • Good indicator of broad composition of soil microbes. However, most lipids are produced by more than one species or family, and microbes change the lipids they use in cell walls depending on environmental conditions, so these should not be interpreted as microbial diversity.
  • Responsive to management, especially in fungal:bacterial ratios as fungi are more sensitive to physical disturbance.


  • Measured by excavating a known volume (i.e. 1 ft3) of soil, or else spreading mustard solution on the soil to provoke earthworms to surface, and counting worms. Can also look for earthworm casts. 
  • Good indicator of earthworm habitat and food supply (plant residue).
  • Responsive to management, especially physical disturbance which destroys worms and their habitat.

Soil structure and infiltration indicators

Aggregate stability

  • Measured by passing soil through a nest of sieves which separates soil into aggregates of different sizes. Labs vary in soil moisture and sieve sizes used. May be reported as mean weight diameter, with a larger mean weight diameter indicating more large aggregates.
  • Good indicator of structure and porosity, which is important for water-holding capacity and infiltration.
  • Responsive to management, especially physical disturbance which destroys larger aggregates but leaves microaggregates intact.

Bulk density

  • Measured by taking an intact sample of known volume, drying it, and reporting mass per volume.
  • Good indicator of structure, required to interpret long-term changes in soil carbon.
  • Responsive to management, especially compaction, but changes slowly.

Infiltration rate

Slump test