Soil biology and soil organic matter; What do recent discoveries mean for soil management?

This Changes Everything.

That is how everything is presented in today’s media. New cars, new policies, new science. An example of the latter are the recent advances in the field of soil microbiology, or “soil biology” in pop-ag speak. Soil biology has become the means, the end, and the banner flying over the soil health movement. In particular, the recent focus on the vital role of soil microbes in the production of soil organic matter has become a “This changes everything!” call to arms.

Collage of "This Changes Everything" images generated by Google search
This Changes Everything is a common marketing slogan. Does it apply to the recent advances in soil microbiology? Screen shot of Google search.

I have been hesitant to completely embrace this “soil biology” revolution because of the hype associated with it, and because I am not a soil microbiologist. Back in grad school, I audited a soil microbiology class; I took the class but not for a grade. As an engineer becoming an agronomist, I knew I didn’t have the biology background to succeed in the class, but it was fascinating. Lost in the details, I tried to focus on the larger trends that were applicable to farming. I will again use this strategy here. While the new scientific discoveries are important, revealing the details of microscopic soil life with new clarity, do they change everything? Here is my agronomist take on what has changed, what hasn’t, and what it means for soil management.

Change 1: The microbial pathway to soil organic matter

This change brings soil microbes to the forefront in the formation of soil organic matter (SOM). Rather than only breaking down plant material until what is left is SOM or humus, soil microbes  produce compounds that become SOM (Kallenbach et al., 2016). And when they die, microbe “necromass” can also become SOM. Perhaps 50% or more of the total SOM is formed through this microbial pathway (Kästner and Miltner, 2018).

Change 2: Stable humus concept questioned

The longtime view of humus as a component of SOM resistant to decomposition, and therefore stable and long-lived, is now in question (Lehmann and Kleber, 2015; Woolf and Lehmann, 2019). The alternative view is that humus is created by our extraction methods and that natural SOM is much more dynamic, with constant turnover from protected locations on clay and in aggregates being the norm (A new WSU publication on the nature of SOM).

Change 3: The clay connection to soil organic matter

Recent observations suggest that microbial-derived SOM is most often attached to clay and smaller silt particles (Sokol et al., 2019). The bonding of SOM to clay protects the SOM from microbial decomposition, at least for a while. This SOM is called mineral associated organic matter (MAOM).

SOM is also protected within soil aggregates. But these protections are shorter-lived than we had thought, and even protected pools of SOM are constantly being decomposed and replaced (Woolf and Lehmann, 2019).

Change 4: Roots and root exudates are important

Root biomass and exudates are much more likely, up to 5x by some estimates, (Jackson et al., 2017; Sokol et al., 2018) to become SOM than aboveground plant biomass, mainly because of their location; they are already in the soil in contact with all the microbes waiting there to process them when they die. Furthermore, roots deep in the soil profile are subject to lower decomposition rates than surface roots or surface applied biomass.

Many root exudates are produced by plants for microbes in the soil rhizosphere. Exudates are then rapidly used by microbes in the rhizosphere and so are important for the microbial pathway to SOM. In exchange, microbes supply nutrients, water in some cases, and provide other advantages to plants such as helping them resist plant pathogens. Root exudates and the associated processes are difficult to study (Oburger and Jones, 2018), and complicated. For this reason, exudates are often studied in the lab rather than the field.

What has not changed?

While this new knowledge is important to our understanding of soils, I find the implications of these discoveries on management of soil are overstated, generally not by researchers, but by the popular press and others promoting soil health. They reason that since we have not been able to study soil biology very well until recently, by studying it now with the new tools and guided by new knowledge, all will change.

Here are some things that have not changed.

Plant biomass is still the driver of SOM formation

Just like us, microbes live, either directly or indirectly, on the energy in plant inputs. Plant biomass, produced through photosynthesis, is the raw material and microbes are the processors that transform the material into SOM.

“Plant input fuels the whole system and drives the microbial pump.” Kastner and Miltner 2018

Microbes do not produce all SOM; some SOM is still decomposed plant material, often in sand-sized particles, called particulate organic matter. This type of SOM is more important in low-clay soils because they don’t have clay to protect SOM, but it can be protected in soil aggregates.

No matter the specific mechanisms leading to its formation, the level of SOM in a soil is still a result of SOM gains and losses (Caruso et al. 2018). So, it still holds that using practices to either reduce losses or increase gains of SOM will lead to higher SOM levels.

Increasing SOM levels is still slow and difficult

Regardless of the newly understood microbial and root biomass/exudate pathways to SOM formation, the low conversion rates of plant biomass to SOM, measured for many decades in many types of systems, both managed and unmanaged, still apply. This needs some explanation.

For a long while, we have measured plant biomass flows into the soil, and losses of CO2 from the soil and the resulting levels of soil organic matter without knowing the details of the processes involved. This has been done in managed systems like farms, and in wild ecosystems. Between the measured inputs and the resulting SOM levels was a black box. We did not have the tools to see inside it: most of the components are microscopic; our intrusive methods changed the box’s environment; and most of the life in the box could not be cultured in a lab. We could only guess at what was happening there. Some say we ignored the biology because we were too focused on the chemistry, it being much easier to measure and change. There was some of that, but the lack of tools for identifying and quantifying soil microbes was the biggest factor in keeping the box black closed.

Schematic showing measurable inputs and outputs w/ a black box between them.
Researchers have been measuring inputs to the soil and outputs, the change in soil organic matter levels, for a long time. It is only recently that they have begun to figure out the details of what happens in the black box between.

Nevertheless, researchers made many of these measurements. From them we know that increasing the total amount of organic matter in a soil is not an efficient process; it takes a lot of plant biomass to produce a little soil organic matter. Most of the plant biomass is lost in the black box, used as an energy source by microbes, with the carbon leaving as CO2 and the nutrients being recycled in the microbial biomass.

It varies by input and how it is handled, but only 3-33% of plant material ends up as soil organic matter. (Castellano et al. 2015 review). The conversion rates for pre-digested soil amendments like compost or manure are better. Wuest and Gollany 2013 found that 24-39% of manure or compost became SOM. Other studies give similar results, even those specifically looking at the role of the soil biology. In one of the first papers to show that microbes can directly produce SOM, Kallenbach et al. (2016) still found that only 25% of the added plant materials, in this case glucose, dissolved organic carbon, cellobiose, and lignin, became SOM.

Whatever the input, changing SOM levels requires lots of plant biomass which in practical terms translates to slow change over time unless biomass is imported as with manure and compost.

Roots and root exudates have always been there

What about our imperfect measurements of the inputs, like roots and root exudates? It is true that often only aboveground biomass is measured for calculating the conversion rates. Roots are difficult to measure, and even when we try, the results are questionable (Bolinder et al., 2002). Root exudates are even more difficult because their production varies by plant, time of year, soil conditions, and because they are very short-lived being almost immediately taken up by microbes in the rhizosphere (Oburger and Jones, 2018).

In contrast, our measurements of total SOM have been reasonably reliable over time. Scientists continue to debate the nature of soil organic matter, where it is stored in the soil, the duration of various pools of SOM, but in general, we know how to measure it as a whole. The measurements have not changed much over time and if one picks one of the accepted methods and sticks with it (Roper et al., 2019), the data is reliable.

What happens when we include roots and root exudates in the calculations of the conversion rate? The conversion rate is the change in SOM divided by the inputs. ΔSOM/shoots+roots+exudates. Using some recent estimates of root and exudate biomass quantities in the calculations, we find that our conversion rates decrease not increase:

SOM/shoot biomass = 20/100 = 20%SOM/Shoot + Root biomass = 20/200 = 10%SOM/Shoot + Root + Exudate biomass = 20/260 = 7.7%


This example shows why, in general, our knowledge that microbes are an essential part of the SOM formation does not change everything. Even when we did not know about this process, it was happening. Even when we ignored the inputs from roots and didn’t know about root exudates, they were always there contributing to the process. Even when we incorrectly attributed the entire process to something different than what it was, the process continued just as it does today. Making SOM is no easier just because we know that soil microbes are doing much of the SOM formation and that roots and their exudates are key inputs.

How might this change soil management?

Instead of changing everything and rendering older research obsolete, this new knowledge can explain observations that we have been making for decades.

It explains why perennials, especially grasses, are better at building SOM. Not only because the soil is undisturbed in perennial systems, but because perennial grasses divert more of their available photosynthate to roots and root exudates, and because they are alive all year long (King and Blesh, 2018).

It explains why legumes are particularly good for soils. They are better than non-legumes at building SOM because of their high N content (low C:N ratio) (Kallenbach et al. 2015), making them easy to decompose and so increasing soil microbial populations, which lead to higher conversion rates and higher SOM levels. See also Castellano et al. (2015) and Cotrufo et al. (2013).

It explains why higher clay soils can store more SOM than sandy soils. The microbial-produced SOM is preferentially stored on clay particles. The more clay you have in your soil, the more you can build this type of SOM (mineral associated organic matter).

Improving current and informing new practices

Just because these discoveries don’t change everything doesn’t mean they can’t help us improve farm practices. Here are a few possible ways that this new knowledge could guide us in tweaking the practices already known to build SOM levels.

Focus on producing more microbes

One potential strategy is to focus on producing microbes to increase SOM. This works best on soils with moderate to high clay levels. Higher quality plant materials such as legumes, or other high N, high nutrient status cover crops, might be better at building SOM because they are more easily broken down by microbes, resulting in a better conversion rate to SOM. Green manures may also fit in this strategy. These well-fertilized crops break down quickly, and even with the tillage involved in incorporating them, still end up increasing SOM if they are used regularly (McGuire 2012). One tradeoff here is that hard-to-decompose plant materials, high lignin materials, and high C:N materials, are valuable for protecting the soil surface from erosion.

Maintain continuous living roots

This is not new; it is a common soil health principle. It is what we have had for centuries in unmanaged grasslands and in managed pastures. The strategy can help in annual cropping systems, but there are tradeoffs unless livestock grazing is included as with many regenerative agriculture systems.

Produce more roots and exudates

This is where the science vs. what farmers are trying/claiming gets dicier. One idea is to limit or eliminate fertilizer and other nutrient inputs (manure, compost) to force plants to work to get their nutrients from the soil. And by working, I mean produce more root exudates to feed the rhizosphere microbial community which then grows and produces more SOM. In exchange for the root exudates, plants get nutrients made available to them by the microbes. Mycorrhizal fungi are said to be the key player here, but other microbes are involved as well. Regardless of what the science says about whether this works or not, the clear tradeoffs are important to recognize.

Roots and exudates are produced at the expense of shoot production. There is no win-win as the amount of photosynthate is limited; a gain in one place means a loss in another. We harvest mostly shoots, so this would be a tradeoff in annual crops. We can manage or breed crops to produce more roots and exudates, but then we will have less aboveground crop to harvest. This is why, even in unmanaged natural ecosystems, plants will often respond positively to inputs of nitrogen or phosphorus.

Given the tradeoff, this root-exudate strategy would seem to work best in cover crops, but even with them there are tradeoffs. Less aboveground biomass in cover crops has been shown many times to result in more weeds, less soil protection, less nutrient scavenging, etc.

Focus on stable flow of carbon through soil

Another strategy was presented as a hypothesis by Dr. Markus Kleber, at a Potato Soil Health symposium in December of 2018. Kleber is an Oregon State University soil scientist who knows more about soil organic matter than I ever will. He speculated that we may find carbon flow through a soil may be more important than the level of stable carbon – soil organic matter – in that soil. He bases this on the new view that organic matter can be protected in the soil, but “is never inherently stable.” Microbes are just too good at breaking down organic materials for it to be around long unless otherwise protected.

The question Kleber raises was proposed by Janzen in his 2006 paper, The soil carbon dilemma; Shall we hoard it or use it? When the focus was on stable humus, “hoard it” was the goal. Now, Kleber believes, we may be swinging towards the “use it” tactic. After all, it is the flow of carbon through the soil, from plant to microbe to SOM to CO2 and back again that drives the biological processes. Janzen (2015) concludes in a later paper “…managing carbon flows should take precedence over maximizing carbon stocks.”

Kleber does not discount SOM, “Increasing organic matter content is almost always beneficial to the soil, especially when soils start out low in carbon” but wonders if the goal should be increased flow instead of increased storage. In support of his hypothesis he offered preliminary results from a potato study that found the total SOM levels did not differ between fields with high and low levels of a soilborne pathogen, but soil respiration – a measure of the microbial activity and therefor, of carbon flow – did differ.

He calls for “maintaining a steady supply of carbon” rather than a high or low supply.

This could be connected to the continuous living roots principle; not as concerned with building SOM but rather keeping the C moving through the soil. Cover crops and organic soil amendments would also work for this strategy. The only difficult part is measuring the flow. Perhaps analyses that aim to measure the active carbon portion of SOM, done at the same time of the year, and then compared over the years would help. Active carbon is the part of soil organic matter most available for consumption by soil microbes. An increasing number of commercial soil labs are offering to test for active carbon using the permanganate-oxidizable carbon test or POXC. I am collecting POXC data on a wide range of soils in irrigated Eastern Washington as part of a project funded by the WA Soil Health Committee. Combined with a measurement of carbon mineralization like soil respiration, it is an idea worthy of testing by farmers and researchers.

Detailed description of table linked in image
Soil scientist Markus Kleber thinks that carbon flow may be as or more important than soil organic matter levels. Here is what he proposes we would want in an ideal input to maintain C flow. Used with permission.

Kleber has several ideas of how to keep this steady supply of C to the soil. First, using liquid manure or other organic wastes spoon-fed through center pivot irrigation systems like fertigated nutrients. What may be more feasible for most farmers are roots, root mucilage, and root exudates, as we have covered, through the use of cover crops, which he calls “a technology to supply soil with active carbon.”

Details vs. the Big Picture

That is my take on the big-picture, agronomic view of recent advances in soil science and how they relate to practices in the field. However, when you start looking at the details of an immensely complex environment like the soil, you are bound to find some contradictions. For instance, highly biodegradable materials do not always convert better to SOM (Kallenbach et al. 2019). Science is slow, especially ag field research which can take years or decades to get clear answers to some questions. Compared to farmers for whom every crop is a risky entrepreneurial startup, science is a risk-averse, deliberate method. So, it will take a while to either confirm these ideas or test new ones. In the meantime, there ARE proven benefits of keeping the soil covered (by living plants when possible), cover crops, perennial crops, etc. The real questions are in the details of how far these time-proven practices can take us in improving and managing our soils.


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