Humic Acids and Lignins: Prebiotics for Soil


Every grower knows beneficial microbes like rhizobia and mycorrhizal fungi can help plants produce strong, resistant, and resilient crops.  Many growers know that having the right microbes in the soil can reduce or eliminate the need for chemical fertilizers and pesticides.  Far too many growers have fallen for the “bug-in-a-jug,” spending various sums of money on biofertilizers only to see little or no effect after applying these formulas to their fields.  Certainly, there are many biofertilizer formulas on the market.  Some are good.  Some are outstanding.  And still others are not-so-good.  Choosing the right formula for your field can be confounding because infinite environmental variables such as soil type, pre-existing microbial species, the kind of crop you grow, and your management practices can all influence whether a given microbial preparation will thrive in your soil.  Unfortunately, this variability tends to make growers skeptical of efforts to leverage microbial power for crop production.

When you consider your field in the manner that an environmental microbiologist might approach soil remediation for efforts like cleaning up oil spills on contaminated lands, you start to recognize that your biggest job is not to find the best microbes you can add to your soil.  In fact, the best microbes for your environment are probably already be present in your soil or seedstock.  If you have a microscope, a look at the density and diversity of your microbes will help you decide when adding more species may be helpful.  However, the question of what conditions need to be created so that beneficial microbes have a suitable habitat to grow and reproduce in is often more critical.  Afterall, as with any other living creature, microbes become extinct when they lack suitable growing habitat.

Learn to recognize critical soil microbes in our Microbial Analysis for Growers course.
Learn more about soil microbes by joining our Microbial Analysis for Growers course.

Variables that may influence the quality of your soil habitat include crop varieties planted, tillage, aeration, nutrition, and moisture.   Let’s discuss each of these below:

Crop Varieties Planted:

Plants grow best when soils contain complex food webs that represent microbial species from every kingdom.  To feed these diverse food webs, it is helpful to have diverse plant types.  In their meta-analysis of agricultural systems, Lori et. al. found that practices like crop rotations, inclusion of legumes, and use of more complex (ie: organic) inputs were associated with more microbial biomass than was seen in less varied plants systems.  Since it as long been recognized that each plant species has a unique influence on the associated soil microbial populations, it is not surprising that greater plant diversity would result in greater soil microbial diversity.

Tillage Practices:

Deep, horizontal tillage practices that bury crop residues underground can reduce the abundance of eukaryotic soil microbes like microarthopods, and fungi.  These practices also reduce the number of macroscopic soil creatures, like earthworms.  USDA’s Natural Resource Conservation Service now recognizes no-till, ridge till, and strip till practices as the most compatible with soil organisms.   Other groups are reporting positive benefits of vertical tillage options that aerate soils to reduce compaction while minimizing disruption of soil microbial communities.  For small systems, broadforks are preferred over rototillers for preserving critical soil microbes.


Poorly aerated soils tend to accumulate anaerobic bacteria, while failing to support important aerobic microbes like microarthropods and fungi.  Not surprisingly, applying mycorrhizal fungi to a compacted, poorly aerated soil is not going to benefit your crop.  Keyline plows, vertical tillage, or broadforks offer options for improving soil aeration.   Adding organic matter to clay soils also improves aeration.


Anyone who has ever planned a big reunion, meeting, or event knows that if you want people to attend, you better feed them well.  The same is true with soil microbes.  If you want microbes to live long, reproduce, and prosper in your soil, you better feed them.  Soil chemistry labs have spent decades focusing on soil macronutrients like nitrogen, phosphorus, and potassium, while assuming that all carbon necessary for plant growth is provided through photosynthesis.  My own years of working with plants and microbes in arid systems led me to question this assumption, as evidence of bidirectional carbon exchange between plants and fungi became more common.  Johnson et. al. note that low levels of soil carbon are actually detrimental to plant survival.

Conventional wisdom has too often assumed that:

  • soil carbon can be ignored altogether
  • nitrogen, phosphorus, and potassium are key to healthy crops, and
  • micronutrients and trace minerals can be ignored until deficiency symptoms appear.

[box type=”shadow” align=”aligncenter” class=”article-pullquote” width=”100″ ]It seems ironic that we recognize carbon as the primary element from which plants are made, and we know that our atmosphere only contains about 0.01% carbon.  Yet we expect plants to derive all their carbon needs through photosynthesis.  Meanwhile, plants that require only 0.04X as much nitrogen as they require carbon, are thought to require synthetic nitrogen.  Yet nitrogen makes up a whopping 78% of our atmosphere and healthy soil is loaded with nitrogen fixing bacteria![/box]

Two factors are overturning these assumptions.  First, modern analytical techniques make micronutrient and trace element deficiencies much easier to detect.  As growers find multiple trace element deficiencies, they are also finding these easier to correct with complex organic fertilizers, which (like whole foods) add several nutrients simultaneously, than with individual additions of each missing trace element. This is creating a more holistic perspective of soil nutrition, particularly since organic fertilizers often contain bioavailable forms of carbon.

Second, improved recognition of the living component within the soil, now referred to as the soil microbiome, is leading us to view nutrition not only in terms of what mineral elements we are providing, but also in terms of what microbes those elements are supporting. This living soil component was long recognized by indigenous cultures, but frequently swept aside by mainstream science.

Today, we look at restoring beneficial microbes in soil in a manner that is not unlike the way we feed beneficial microbes in our gut.  To keep our gut microbiome happy, we have to balance quickly metabolized foods like starches with insoluble fibers called prebiotics.  These are found in foods like dandelion greens and potato skins.  To keep our soil microbiome happy, we also have to feed it both readily available and slowly decomposing organic materials.  This involves supplying the soil with green, leafy substances and manures that degrade quickly, and also with more slowly decomposing humic acids and woody materials that are rich in lignins.  There are many ways to do this.  Humic acids can be purchased from many commercial vendors. They also occur naturally in composts, and they are formed as organic matter undergoes decomposition.  Lignins, as noted above, come from woody plant material.  Adding straw, sawdust, dry leaves, or even living perennial cover crops with green leaves and large underground root zones will ensure a healthy supply of slow food to help those soil food webs thrive.

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