4.4.4: Laboratory Soil Health Testing

Soil Health Tests: Chemical, Physical and Biological

Chemical Soil Tests

Growers routinely take soil samples and have them analyzed for available nutrients (N-P-K), pH, and total organic matter. In arid regions, it is common to also determine whether the soil is saline (too much salt) or sodic (too much sodium). This provides information on the soil’s chemical/nutrient health and potential imbalances. As mentioned, you get the most benefit from soil tests with regularly scheduled analyses (at least every two years) and good records. If you requested a test on cation exchange capacity (CEC), you should expect it to increase with higher organic matter levels, especially in coarse-textured soils. And, as discussed, soil CEC increases after liming soil, even if there is no increase in organic matter. We devote Chapter 7 to these more familiar tests.

The traditional soil test does not, however, make a comprehensive assessment of soil health, which probably led to the “chemical bias” in soil management. In other words, the widespread availability of good chemical soil tests, although a useful management tool, may also have encouraged the quick-fix use of chemical fertilizers over the longer-term holistic approach promoted in this book. Several soil health tests have been developed to provide a more comprehensive soil assessment through the inclusion of soil physical and biological indicators in addition to chemical ones. Indicators were selected based on the soil processes that they represent, and thereby the tests provide insights into a soil’s ability to provide ecosystem services (like growing healthy crops). They also consider the cost, consistency, and reproducibility of the methodologies, as well as their relevance to soil management.

Pictured below is a different kind of soil test--one for comprehensive SOIL HEALTH that includes physical indicators and biological indicators. This comprehensive soil test shows three categories (left side) of the test--Purple Physical indicators, Green Biological Indicators, and Yellow Chemical indicators. It also flags results (right side). A red box shows a trouble spot--surface hardness. The orange and yellow boxes indicate things can improve, and the green boxes show that all is well for the chemical portions of the soil as well as Available Water Capacity.

Figure \(\PageIndex{1}\): Example of a soil health test report.

The USDA evaluated a set of indicators and methodologies in an attempt to encourage standardization in soil health testing. The proposed methods provide useful insights into aspects of soil health. Currently (in the year 2020) there is no single standard soil health test, but there is universal agreement that a comprehensive soil health test should include indicators that represent all three types of soil processes: physical, biological, and the typical chemical. Also, measured values need to be interpreted based on inherent variation in soils as a result of different climates, soil textures, etc.

Physical Indicators

For physical indicators, aggregate stability relates to infiltration, crusting and shallow rooting, and represents the “tilth” of the soil. It generally shows a fast response after the introduction of new management practices like reduced tillage, cover cropping, or manure or compost additions. Available water capacity relates to plant-available water and is relevant to drought resistance. It is more sensitive to inherent soil texture differences than to changes in management. These soil health indicators have become somewhat widely adopted.

Figure \(\PageIndex{2}\): Results of an aggregate stability test for silt loam vegetable soils: organic (70% stable, left) and conventional (20% stable, right) management. This is a physical soil indicator test.

Biological Indicators

The most common biological indicator is total soil organic matter (SOM) content, which affects almost all important soil processes, including water and nutrient retention, and biological activities. It is often the single most important measurement of soil health, but unfortunately, it is not very sensitive to management. It takes many years to measure a real change in SOM, and farmers would generally want to know earlier about the benefits of a management change.

Active carbon is an inexpensive test that relates to a small fraction of the organic material that is more actively engaged with biological functions, and it has been shown to be very sensitive to changes in soil management. It is therefore a good early indicator of soil health improvements. Active C is assessed as the portion of soil organic matter that is oxidized by potassium permanganate, and the results can be measured with an inexpensive spectrophotometer.

Similarly, soil protein content is an indicator of the soil organic nitrogen potentially available to microorganisms, and it also shows a strong response to management changes, especially when more legumes are introduced.

Respiration (CO₂ released by soil organisms) is widely measured as an indicator that integrates both the abundance and metabolic activity of soil microbes; it is also correlated with nitrogen mineralization potential. Ammonia losses from amino sugars in the soil is a related measurement. There are a number of other biological indicators. The bean root rot bioassay provides an effective and inexpensive assessment of root health and overall disease pressure from various sources (plant-parasitic nematodes; the fungi Fusarium, Pythium, Rhizoctonia). The pictures below show an example of a bioassay.

Figure \(\PageIndex{3}\): Examples of root rot bioassays on bean plants: conventional (left) and organic (right) soil management.Photos by George Abawi.

Microbial Soil Tests

Soils can also be tested for specific biological characteristics—for potentially harmful organisms relative to beneficial organisms (for example, nematodes that feed on plants versus those that feed on dead soil organic matter) or, more broadly, for macro- and microbiology. Two common tests—the phospholipid fatty acid (PLFA) and fatty acid methyl ester (EL-FAME) assays—have shown sensitivity to management changes and are offered by some commercial soil testing labs. They produce an estimate of the soil’s living biomass. Also, the biomarkers, or signature fatty acids, identify the presence or absence of various groups of interest such as different bacteria, actinomycetes, arbuscular mycorrhizal fungi, rhizobia, and protozoa. The relative amounts or activities of each type of microorganism provide insights into the characteristics of the soil ecosystem. Bacterial-dominated soil microbial communities are generally associated with highly disturbed systems with external nutrient additions (organic or inorganic), fast nutrient cycling, and annual plants. Fungal-dominated soils are more common with low amounts of disturbance and are characterized by internal, slower nutrient cycling, and high and stable organic matter levels. Thus, the systems with more weight of bacteria than fungi are associated with intensive agricultural production (especially soils that are frequently plowed), while systems with a greater weight of fungi than bacteria are typical of natural and less disturbed systems. The significance of these differences for the purposes of modifying practices is somewhat unclear, but modifying practices causes biological changes to occur. For example, adding organic matter, reducing tillage and growing perennial crops all lead to a greater ratio of fungi to bacteria. Since networks of mycorrhizal fungal filaments help plants absorb water and nutrients, their presence suggests more efficient nutrient and water use. But we generally want to do these practices for many other reasons—improving soil water infiltration and storage, increasing CEC, using less energy, etc.—that may or may not be related to the ratio of bacteria to fungi.

The study of genetic material recovered directly from soil has advanced in recent years. Routinely characterizing the genetic profile of a soil’s organic matter to obtain a picture of the organisms present is thus becoming commercially feasible. It is challenging to extract specific genetic material from soils due to the high complexity of soil organic matter, and DNA profiling is mostly used for descriptive purposes (for example, how prevalent different types of pseudomonas bacteria are). Some tests are showing promise in identifying specific pathogens that may help farmers better manage their fields.

Chemical soil health indicators, as previously discussed include macro and micronutrients, and soil reaction (pH). Undesirable elements like salts and sodium should be evaluated in arid regions and covered areas, such as inside greenhouses and high tunnels. In urban or industrial environments, toxic elements like heavy metals, salts, radioactive materials, solvents, and petroleum products should be considered when assessing soil health.

Sensing methods are increasingly considered for soil health assessment. Visible near-infrared and mid-infrared reflectance spectroscopy methods are non-destructive approaches that measure the optical reflectance properties of soil, which are influenced by chemical bonds like O-H (abundant in clay minerals), C-H (abundant in organic matter), etc. They therefore can assess certain soil properties rapidly and at a low cost. Such methods appear to be especially efficient when combined with a subset of laboratory-measured properties that can be compared with the spectroscopy results through advanced statistical and machine learning techniques.

Below is a table that summarizes many of the soil health measure. We don't go into detail in this book about the methods, but you should know that these tests are available to help you understand the health of your soil.

Table \(\PageIndex{1}\): USDA-NRCS-Evaluated Laboratory Soil Health Indicators and Methodologies, and Associated Soil Processes They Measure

Soil process	Soil health indicator	Method^1
Organic matter cycling and Carbon sequestration	Soil organic matter content	Dry combustion, Wet oxidation, Loss of ignition
Structural stability	Aggregation	ARS wet aggregate stability, NRCS wet aggregation, Cornell sprinkle
General microbial activity	Short-term C mineralization	CO2 respired—4 day, CO2 respired—24 hours
General microbial activity	Enzyme activity	BG, NAG, Phosphomonoesterases, Arylsulfatase
C food source	Readily available pool	POXC, POM, 28-day mineralization, WEOC, Microbial biomass C, Soluble carbohydrates, Substrate-induced respiration
Biological available N	Available organic N pool	ACE protein, WEON, Correlation with short-term mineralization 7-day anaerobic, PMN, 28-day PMN, Illinois soil N test, NAG, Protease
Microbial diversity	Community structure	PLFA, EL-FAME
^1Acronyms are: BG = β-Glucosidase; NAG = N-acetyl-β-D-glucosaminidase; POXC = Permanganate oxidizable C; POM = Particulate organic matter; WEOC = Cold/hot water-extractable organic C; ACE = Autoclaved citrate extractable (protein); WEON = Cold water-extractable organic C; PMN = Potentially mineralizable N; PLFA = Phospholipid fatty acid; EL-FAME = Ester-linked fatty acid methyl ester profile. Source: USDA (2019)