Renewable Farming

A new measure of soil health can help you evaluate benefits of soil-renewing investments

“The most profitable, fertile soil is the one with the largest population of beneficial microorganisms and a vigorous soil food web.”

June 19, 2018 — That quote from AgriEnergy Resources founder Dave Larson was a typical opening theme for his seminars — in the mid-1980s. He urged farmers to build living soils long before today’s agronomic firms, researchers and Extension began pushing “soil health” into a lead role among farming priorities.

And now, a few scientists are struggling to answer the next challenge: How does a farmer measure soil health? That’s essential to efficiently build toward long-term production of nutritious crops and consistent profit margins.

This report describes a promising lab test that offers useful data on the beneficial bacterial and fungal populations in your soil.  

Soil Microbiologist Lance Gunderson

It’s the “PLFA” test from Ward Labs at Kearney, Nebraska.It was developed at Ward Labs primarily by soil microbiologist Lance Gunderson, who’s the Director of Soil Health and New Test Development — and our source for this report.

PLFA stands for “phospholipid fatty acids.” These fatty acids from soil organisms contain biomarkers which reveal the main communities of bacteria, fungi, actinomycetes, mycorrhizal fungi, rhizobia and protozoa. Ward Labs has been developing this test only for the past six years, so standards for numbers which are “high” and “low” are still taking shape. But already, the test is a useful scorecard for evaluating effects of your soil-building biological management such as cover crops, rotations and enhanced residue recapture. 

Measuring soil minerals such as NPK and micronutrients has become fairly standardized. Strong extraction. Weak extraction. Morgan test. Water soluble test. However, measuring microbes isn’t as familiar. Fortunately, your own close observations are a useful guide to healthy soil. You sense how your soil feels underfoot. You can quickly tell if penetrometer readings show less density. You can watch how quickly rainfall absorbs. Your nose knows that “earthy” odor of good soil. 

Earlier, we’ve reported on another measure of soil health: The Haney soil health calculation, developed by Rick Haney and his colleagues at the USDA/ARS soil laboratory at Temple, Texas. It measures a 24-hour carbon dioxide “burst” from the soil as a guide to microbial life, then factors this into an index number using six other lab measures. You can download a PDF at this link in which Haney describes that test. 

The PLFA analysis offers more specific insights, such as shifts between fungal and bacterial populations. Primary developer of this test at Ward Labs is Lance Gunderson, who provided the background information for this summary. 

Lance points out that laboratories have several other ways to analyze soil organisms. 

Microscopy is useful if you’re looking for specific, known organisms such as fusarium pathogen. Culturing organisms in a petri dish and counting with a microscope is expensive. Anyway, only about 5% of soil microbe species have even been categorized. Most can’t even be isolated and cultured in a petri dish; they’re interdependent in their soil habitat.

Genetic analysis can be helpful if you’re looking for known organisms whose DNA profiles have already been catalogued in an online library. “But the equipment is expensive and training requirements are high,” says Gunderson.

The Solvita 24-hour CO2 burst test indicates a general signal of total biomass, expressed by respiration of soil organisms. This test is one of the ingredients of the Haney test, which Ward Labs also offers.

The PLFA test studies biomarkers in fatty acids extracted from the soil for signals of each type of organism. First, it gives you a Total Living Microbial Biomass indicator, expressed as phospholipid fatty acids in nanograms per gram of soil. A total biomass reading over 3,500 ng/g is considered “Excellent.” That rating is based on an array of thousands of tests on soils nationwide.

It also reveals the balance of fungal organisms versus bacteria. This is especially important in a glyphosate-laced world, because glyphosate tends to shift soil organisms toward fungal dominance.

The Ward Labs website presents a sample lab report at this link. (We also show it at the bottom of this report. You can print out these two pages as a PDF; it will give you an idea of what your own PLFA report might look like.)  

For example, an Indiana grower who has used PLFA tests for several years told us of a PLFA report showing that one of his rented farms indicated a Total Living Biomass reading of only  1,473, which falls in the “Slightly below average” category on Ward Lab’s scale. The grower knew that the soils tend to ‘lay wet,’ which restrains biological activity. He told us, “The landowner is not in favor of installing pattern tile.”  That’s one of the management moves it would take to encourage greater diversity of soil life. Perhaps the hard data of a PLFA report will encourage the landowner to install tile!

This grower’s use of the PLFA analysis on many fields over several years has encouraged him to intensify his use of cover crops, which build and balance soil bacteria and fungal life.

Lance explains that it’s possible to quantify types of organisms in your soil because each functional type carries “signature” fatty acids in their cell structures. Although identifying these biomarkers is time-consuming and costs $59.50 per test, you gain more detailed knowledge than you would with a Haney test ($49.50) or Solvita CO2 burst test ($25). 

Three main groupings are fungi, bacteria and protozoa. There’s a fourth category on the report, “Undifferentiated,” which contains organisms which can’t be clearly sorted out, but still count toward total biomass — and still have biological benefits.

Within the bacterial classification, the report identifies gram positive and gram negative types. Positive or negative refers only to how the bacteria look under a microscope when stained with dye. Gram positive bacteria have an outer cell wall high in peptidoglycan, which retains a violet dye in lab analysis. Their cell walls are single-layer and thick, making them more resilient under stressful conditions such as dry or low-oxygen soil. Gram negative bacteria have double cell walls which make them more resistant to naturally occurring antibodies. However, positive or negative doesn’t indicate pathogens versus beneficial organisms in the soil.

Within the gram positive grouping, the lab analysis can sort out an important filament-structured bacteria: actinomycetes. These bacteria are beneficial in digesting high-carbon residue. They also exude natural antibiotics, which fight off pathogens and thus become part of the crop’s “immune system.” 

Lance notes that actinomycetes are among the organisms which produce the organic compound, geosmin, which gives soil that “sweet, earthy” odor you identify with soil health. Your nose can detect the aroma of geosmin down to a concentration of 5 parts per trillion. Actinomycetes are different from the thread-like mycorrhizae, a fungus which colonizes roots and multiplies the crop’s ability to take up moisture and soil minerals. 

“On the gram-negative side, the bacterial group we look for is rhizobia,” says Lance. These tend to be nitrogen fixers. Some live within nodules and are hard to detect; others are free-living in the soil. All of them generate only one type of fatty acid, so they can’t be classified in detail.

Ward Lab’s PLFA identification of fungi sorts them into two classes.

Saprophytic fungi are the workhorses of residue decomposition. These devour dead, high-carbon stalks and are the main generators of active humus, which becomes the basis for biologically active organic matter. 

Mycorrhizal fungi surround root hairs and reach out for nutrients and moisture

Mycorrhizae are the creatures we often focus on, as the multipliers for moisture and mineral uptake. They colonize living roots, so their numbers fall rapidly when there’s nothing growing in the soil. This is a reason cover crop advocates want to see year-round root life, especially living covers that favor mycorrhizae. The full technical term for these critters is “arbuscular mycorrhizal fungi (AMF).” They colonize the roots of your crop. One end of their microscopic threadlike structure penetrates into a root hair; the outer end reaches far into the surrounding soil to transmit water and nutrients into the roots. The AMF exude enzymes which are up to 10 times more powerful than root hairs to dissolve elements such as nitrogen, zinc and manganese. One major goal of “soil health” is to build and preserve a rich array of mycorrhizae.

Lance emphasizes that the numbers and percentages on your PLFA report show only your soil’s biological life in comparison to averages of thousands of other soils across the nation. He says “We recommend using this test to detect responses to your management moves toward enhancing soil biological activity. It’s a measure you’d want to take to establish a baseline, then make another test two or three seasons later after making a significant management change such as inserting cover crops, or changing a rotation.”

Lance notes that “Most soil tests are designed to point toward a recommendation — advise you how to fix something. The PLFA test is more of a report card allowing you to compare management types and change. There are no benchmarks as to what the score should be.”

A management change could be as simple as using a residue digesting inoculation in the fall. Or no-till versus vigorous tillage. Or more fundamental, like pattern tiling a field.

The scores you’re working toward are a high level of total biomass, and a high level of diversity. Cropping programs like continuous corn under no-till can lead to high total microbial biomass — but poor diversity. 

In case your diversity is low, you can check the levels of functional communities to see what’s missing. Low levels of mycorrhizae during the growing season would definitely indicate a need to diversify your rotation or add cover crops, so your main cash crop has a chance to gain greater ability to take up moisture and nutrients. Mycorrhizae need living roots to survive. At other times they fade into dormancy. 

Dr. Robert Kremer, now-retired ARS/USDA microbiologist at the University of Missouri, says that each species in a cover crop encourages as many as 10 variants of microbial life. That influence varies by crop: Grasses generally favor mycorrhizae. A brassica, like tillage radish or turnip, doesn’t favor mycorrhizae but doesn’t impair them.

Growing crops and moisture levels greatly influence the “bloom” of microbes. So it’s important to sample at about the same time each season — and if possible, when soil moisture conditions are similar to previous sampling times.

If your fungal percentages are consistently high and bacterial percentages low, your soils may be carrying a significant load of residual glyphosate. Some growers have noted this, and they’re looking for ways to remediate that situation. 

All these insights carry us back to our opening view from AgriEnergy’s Dave Larson: If you can achieve a rich and widely varied community of organisms in your soil food web, that’s a strong foundation for highly productive soil.