Measures of Soil Biology and Biological Activity

Organic Agriculture June 04, 2012|Print

eOrganic author:

Dr. Michelle M. Wander, University of Illinois


Some content and the structure of the article is based on the consensus about indicators compiled by the North Central Regional Committee (59) on Soil Organic Matter: Formation, Function and Management. Members of the committee will play an ongoing role in the update of information.


Organic management focuses on soil management with the intent to maintain and enhance soil biological activity. There are a variety of ways that biological activity is measured in soils. Few, if any, of these measures are used routinely to test soils in the way that standard chemical assays are used. The various methods of assessing soil biology and biological activity differ in their accuracy, difficulty, and suitability for use. The following table is a summary of measures prepared by the Soil Organic Matter, Formation, Function and Management Committee (NCERA-59) describing the characteristics of widely used measures.

Table 1. Common measures of microbial activity and microbial biomass.
  Soil Respiration Rate (CO2 efflux) Microbial community Microbial community Microbial Biomass
What's measured Proxy for decay rates; can include root respiration when done in field Phospholipids in cell membranes Physiological profiles; BIOLOG plates or other assays that measure increased decay after substrate addition C and N released by fumigation and determined after extraction or through incubation
Standardization Yes Yes Yes Yes
Sensitivity High, maybe too high High Low to medium Medium
Expertise of user Medium Very high Runs low Low to medium
Cost Variable Very high Medium to low High
Difficulty Low Very high Low to medium Low to medium
Special equipment requirements Variable Yes No Some, variable
Accepted interpretation for soil test application No No When used to identify specific organisms grown in pure culture As a proportion of total soil organic matter or indicator of response to management
Scope and/or relevance Low unless done at high spatial and temporal resolution and with appropriate controls

Microbial community composition, mostly for research applications

Use in lab is basis for Solvita® soil test

Metabolic diversity research application

Biomarkers for broad functional groups, e.g., fungi, bacteria, gram+ and gram- bacteria, actinomycetes, protozoa

Used for bacterial id by BBC lab

Biomass size

Used by some alternative testing labs


High variability in-the-field; seasonal, spatial variability

Useful for controlled incubations

Repeatable; seasonal and spatial variability

Used for compost tea and compost assays

Useful for treatment comparisons and assessing influence of management on function Useful for treatment comparisons and possibly to set a benchmark as a proportion of SOC

Table 1, continued.
  Bacterial/Fungal ratios (B/F) Mycorrhizae Microbial abundance Nematodes
What's measured Direct counts of active or total biomass using staining and microscopy Plant associated fungi that assist with nutrient and water uptake Direct counts of bacteria and fungi grown on media abundance, diversity, and/or community structure
Standardization Not standardized Some Yes Yes
Sensitivity Low High Low High, functional level types
Expertise of user High Medium to high Low High for speciation
Cost Medium to high; labor-intensive Medium Labor costs high Labor costs medium
Difficulty Medium Medium High High
Requires special equipment Microscope Microscope Colony counter Microscope
Accepted interpretation for soil test application No; there is considerable interest in developing F/B ratios as an index but weaknesses in the method make many sceptical about its utility Some High High; food web integrator; reflects nutrient enrichment
Scope and/or relevance

Proposed as an index of disturbance and nutrient enrichment; inconsistency in methods has made some conclude that the method has little-to-no practical relevance

Used by Soil Foodweb, Inc.

BBC Labs offers 3 commercial tests: root colonization, spore enumeration, and infectivity potential Limited; used by some testing labs for fungi Now offered by Soil Foodweb, Inc.

Limited agreement between this method and other techniques is problematic

Popular interest reflects the importance of this conceptualization

Varies with season and cropping phase High variability Seasonally variable

Table 1, continued.
  Earthworms Cellulose decomposition, paper disk Cotton strip or buried bag Smell
What's measured Abundance and diversity Mass loss fiber strength subjective
Standardization Yes No No No
Sensitivity High Very high Very high High
Expertise of user High for speciation, low for total numbers None None None
Cost Labor costs medium Low Low Low
Difficulty Low Low Low Low
Requires special equipment No No No No
Accepted interpretation for soil test application Low     Low
Scope and/or relevance Useful for demonstration purposes
Other Sensitive to environment      

Table 2. Enzyme based assays of microbial activity. (Updated by Richard Dick, 2008.)
  ß-Glucosidase Phenol Oxidase FDA Dehydro-genase Phosphatase Arylsulfatase Urease Amidase
Standardization Yes Yes Yes Yes Yes Yes Yes Yes
Sensitivity High Low High Moderate High High High High
Expertise of user Need technical experience
Cost Medium Medium Medium Medium Medium Medium Medium Medium
Difficulty Medium Medium Medium Medium Medium Medium Medium Medium
Requires special equipment Spectrometer
Accepted interpretation for soil test application Not yet; needs correlating with other properties Biological activity index Not yet; needs correlating with other properties
Scope and/or relevance General General General General; must use fresh soil samples General; P cycle General; S cycle General; urea fertilizer use negates results General
Other Best enzyme for index; low coefficient of variability (CV) Moderate CV Moderate to low CV Higher CV Low CV Low CV Moderate CV Moderate CV

References and Citations


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