Soil carbon sequestration is like a poker machine

Microbes do most of the work to decompose organic matter which is added to the soil. They take carbon from the soil organic matter and respire about two-thirds of it as CO2, which then escapes to the atmosphere. The microbes use the rest of the carbon to grow and divide and so the microbial biomass builds up in the soil and essentially become part of the long-term pool of soil organic carbon.

The carbon going into the soil organic carbon pool is impossible to see and difficult to measure, in the same way that the money flowing from the poker machine to the bank is hidden. In contrast, the carbon which is lost as CO2 escaping to the atmosphere is easy to quantify with simple colour-change tests, just as the pay-out from poker machines can be seen by the punter because it is trumpeted by bells and whistles.

The peculiar aspect of the analogy is that CO2 emissions to the atmosphere affirm that the microbes are active, and that soil carbon sequestration is happening. Great news – which provides encouragement enough to keep adding organic matter to the soil. And as long as organic matter is added, the microbes will keep taking small amounts of carbon into the long-term soil organic carbon pool. It is a perverse winning strategy.

Just Measure Soil Microbial Activity

It has been known for a long time that recycling of organic matter changes the soil environment, and those changes are mostly good for the productivity of plants. And probably for a longer time, villagers and farmers have relied on the decomposition of organic residues and compost, and there has been yonks of scientific studies, my own on cotton and rice included, to understand aspects of the nutrient recycling invoked.

What recently has changed and is most important, is researchers’ collective capability to look at the smallest fractions of organic matter during its decomposition and to better understand not only the structure and function of microbial communities but the molecular changes that occur in that realm.

What also has recently changed is the concentration of CO2 in the earth’s atmosphere, and that situation has understandably given rise to perspectives about the righteousness and longevity of some human activities.

These two shifting standpoints around the essential carbon dynamics of our biological world at least provide scope for musings and opinions, and possibly for considered or ill-considered actions.

As someone committed to science, I have no view on the CO2 conundrum lest I fall victim to the rife scourge of real or perceived biases. But I do attest that it is necessary to understand fully the workings of soil biology, and to that end we are learning more and more about the microbial realm. Thus, we can sensibly commit to use that knowledge to develop efficient and stable technologies, each new one justifiably better.

In my agricultural studies there has always been an obvious (sic) delineation between the growth of plants which we can see and measure, and their interactions with chemistry, physics and biology which create the soil environment in which plant roots grow. In truth it has been frustrating to think about how it all works on a day-to-day or a second-by-second basis. Fortunately, in the case of soil biology, or more precisely soil microbes, technology now lets us know about microbial activity. While we may not easily know which microbes are present or how many of them there are, knowing their activity and knowing much about what they do is an immense help to explaining the effects of microbe on soil organic matter and plant growth.

I recently spent some months reading the current and old literature about organic matter decomposition. There was a lot of it, and it was scary to realise how much I learned and how much I still don’t fully understand. Nevertheless, I gave a presentation about it to a group of compost makers and people interested in the industry and business of organic recycling. The paper was also titled: ‘Just Measure Soil Microbial Activity.’ While the paper was well received, I am sure it contained a bit too much science for most. The corollary of course was to have spoken banally, which would have skimmed over the important detail and been the lesser approach.

I will not rehash all the details of the presentation as you too can read the key papers which are listed below. I am however keen to direct your thinking to the salient ideas, as follows:

The ‘Soil Continuum Model’ is your customer’s environment.

Compost’s Magical Assets are in the smallest fragments.

Mineralisation happens inside the microbe.

Just Measure Soil Microbial Activity

The relatively new Soil Continuum Model is a fascinating representation of organic matter decomposition in soil which simplifies and makes sense of the mineral and molecular interactions in the soil.  It is well-founded in research findings and is engendering new thinking to explain how the soil organic carbon pool is transformed and stabilised. The model may ultimately not be the right one, but it seems to be a rational descriptor of the carbon pathways in the soil. The model’s strengths lie in its size-associated description of the soil environment so, with not too much difficulty, it is possible to imagine the changes to organic matter that take place in both space and time.

Of course, when one looks at compost (or soil for that matter) one sees a physical material with substance and bulk. What one can’t see is that compost is made up of mostly small particles of microbial biomass and products, and organic and inorganic nutrients, plus water and larger undecomposed organic matter. It is my conjecture that the smaller particles hold much of the unexplained benefits of compost that people see in the growth of plants and so happily anecdotally recount.

I think one of the key aspects of the recent discoveries about organic matter focusses on just how small the fragments of organic matter get during the decomposition process. If you close and cover your eyes, you most likely will see little white spots on the back of your eyelids. I am assuming they represent the million or so light receptors on the retina. Compared to each of those spots which are the size of microbes, the organic matter fragments will become 1000 times smaller. In fact, they get so small that it become difficult (at least for me) to imagine the iterations of the processes of organic matter decomposition that are happening all the time.

When the tiny organic matter fragments are assimilated inside of the microbe interesting things happen and carbon transformations are key. About two-thirds of the carbon is combined with oxygen (as happens in all animals) and is respired as CO2 from the microbe to the soil and eventually mostly to the atmosphere. And about one-third of the organic matter carbon is metabolised and used by the microbe to grow and divide and thus increase the soil microbial biomass. And importantly through a process known as mineralization, the nutrients held in the organic matter are transformed to plant-available, inorganic forms and they escape the microbe back into the soil solution.

There is a surprising and important footnote to the mineralisation of the nutrients in soil organic matter. It now seems likely that during the process of fragmentation of organic matter, molecular-sized bits of nutrient-rich materials are released into the soil solution, and these nutrients are quickly absorbed by both microbes and plant roots. A recent paper suggest that this phenomenon could account for 50% or more of organic nitrogen cycling in the soil. Wow!

Large parts of Australia were crops and pastures are widely cultivated are not calibrated by nature to provide sufficient resources to support the plant productivity that can (potentially) be produced from introduced species and the sun and rain or irrigation. Additional resources are nearly always needed to optimise primary productivity and harvestable yields.

One proven management option for the long-term has been to optimise the supply of inorganic fertiliser with respect to the timing of the mineralization of organic nutrients. The difficult aspect of this strategy is that it is hard to see the plant response to organic nutrients unless parts of the crop are grown without fertiliser, and in wholly organic crops it is difficult to correct any constraints to yield due to insufficient or untimely mineralization of nutrients. Establishing reliable patterns of organic nutrient mineralization is a key criterion to efficient plant productivity in both systems. Thus, the final idea was to measure soil microbial activity.

Microbial activity has been known by scientists for a long while to be responsive to the onset of rains after an extended dry period. It is known as the Birch Effect and results in the rapid growth and greening of annual and perennial vegetation. You can see the change in the attached pictures of Mitchell Grass Downs country in north-western Queensland before and four weeks after the onset of the wet-season rains. The enhanced growth was due to both water and (mostly) nitrogen nutrition being mineralised by the soil microbes.

What was fascinating to learn was that those pulses of CO2 escaping to the atmosphere at a landscape scale were also seen by satellite technology. The occurrences were confirmed by flux tower technology located across Australia which also verified the associated wetting of the soil and the rapid growth of soil microbes. The work was published by Metz et al., 2023, but a more accessible TERN News article on the topic written by Mary O’Callaghan is available here.

If you’ve read this far, I’ll need not explain further that the Solvita Soil CO2 Burst test is the most relevant measure of potential soil microbial activity that farmers and land managers can easily use to assess the mineralization of organic nutrients. It is a colour-change, point-of-sample test and is specifically relevant to the local land management practices. It is useful to dissect the landscape CO2 responses so the benefits of microbial activity can be applied to specific plant growth systems. Microbial activity is a must-have dataset for calculating additional nitrogen requirements for optimum plant or crop productivity. Solvita is a technology that I have confidence in, enough to invest time and money in its use and distribution.

And as an associated footnote, soil health (to me) is about making an environment in which microbes and soil fauna can exist and function, and not specifically about making it a good environment for plant roots, although there are obvious connections that can be drawn. It follows that the management of organic matter decomposition in soils may well become a much-valued skill, even a fine art. In relation to pastoral or agricultural pursuits and carbon sequestration per se, a focus on both growing organic materials to add to the soil and supplementing the limiting nutrient supply to plants seems most important. But in the ecological context, making the case to add organic matter to the soil to increase soil organic carbon may not be in the interests of native microbes and fauna and subsequently flora, and may, in either case, be a futile exercise if the soil environment does not favour carbon storage. Well-considered approaches to specific situations and outcomes are called for.

Key Papers

Basile-Doelsch, I., Balesdent, J., and Pellerin, S. (2015). Reviews and syntheses: The mechanisms underlying carbon storage in soil. Biogeosciences, 2020, 17: 5223–5242,

Burgin, A.J., Yang, W.H., Hamilton, S.K., and Silver, W.L. (2011). Beyond carbon and nitrogen: how the microbial energy economy couples elemental cycles in diverse ecosystems. Front. Ecol. Environ., 9(1): 44-52, doi;10.1890/090227.

Daly, A.B., et al. (2021). A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen. Biogeochemistry, 154: 211-229. (Image by Eli Yablonovitch and Harry Deckman).

Jesmin, T., Mulvaney, R.L, and Boutton, T.W. (2023). Residue- and nitrogen-induced mineralization varies with soil fertility status. Soil Sci. Soc. Amer., 87 (3): 541-554. ttps://

Lehmann, J. and Kleber, M. (2015). The contentious nature of soil organic matter. Nature, 528: 60–68, 

Metz et al., (2023). Soil respiration–driven CO2 pulses dominate Australia’s flux variability. Science, 379: 1332–1335.

Matassa et al. (2023). How can we possibly resolve the planet’s nitrogen dilemma?  Microbial Biotechnology, 16: 15-27.

Simunovic, M. (2017). Biology and physics rendezvous at the membrane.

Sun, Q., Meyer, W.S., Koerber, G.R., and Marschner, P. (2015) Response of respiration and nutrient availability to drying and rewetting in soil from a semi-arid woodland depends on vegetation patch and a recent wildfire. Biogeosciences, 12: 5093–5101.

Tao et al., (2023). Microbial carbon use efficiency promotes global soil carbon storage. Nature,