Soil Carbon and the Role of Fungi in the Long-term Sequestering of Carbon in Soil: Associate Professor Peter McGee

3 November 2015 FDI Team

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Key Points

  • Soil organic carbon is the most critically important factor for sustainable use of soil.
  • For a more sustainable agriculture, more long-lived organic carbon is essential.
  • So far efforts to increase long-lived soil organic carbon have failed, in large part because of the need to understand soil physics, soil chemistry and soil microbiology.
  • Much of the organic material contained in soil is quickly degraded and therefore does not contribute to stable and long-term increases in soil organic carbon.
  • Certain types of fungi may have an important role in the long-term sequestering of carbon in soil.



Soil organic carbon (SOC) is recognised and acknowledged as one of the most important components of the complex and interrelated soil environment. SOC is necessary for producing heathy and sustainable agricultural outcomes. Producing and maintaining stores of SOC is, in itself, a complex and multi-faceted process that is still the subject of important research. The current, popular body of knowledge about SOC contains unexplained inconsistencies and possible misconceptions that need further investigation. In the following interview, Associate Professor Peter McGee of the University of Sydney defines and describes the importance of soil organic carbon and in brief outline describes research that may lead to an understanding of the role certain fungi play in facilitating the long-term adding of carbon in soil.


FDI: What do we mean by soil organic carbon (SOC)?  And how does this differ from carbon, soil organic matter and humus?

PM:  In scientific and lay discussion SOC can by referred to by a number of terms and this perceived inconsistency, particularly in non-scientific discussion, can be confusing and misleading. Organic matter constitutes an important component of soil. Plant material is the most common component of soil organic matter though animal and microbial materials also make important contributions.  Organic matter, by definition, must contain carbon, any organic matter in soil can, therefore, be also referred to as soil carbon. Strictly speaking, not all soil carbon is SOC; carbon also occurs in the soil in mineral compounds such as carbonates. The term humus has been used to describe the black mass produced when fresh plant material is structurally broken down by the action of microbes. This substance, once added to soil, rapidly degrades and disappears. The use of the term humus, tends now to be avoided because humus cannot be scientifically defined.

FDI: Why is SOC vital for sustainable, agricultural outcomes?

PM: Organic matter plays an important role in the sustainable management of soil, and the use of soil for agricultural production has an impact on the carbon content of that soil. Organic matter buffers the soil against changes in acidity and salinity. The highly charged surfaces of organic matter hold mineral nutrients (the chemical elements essential or important for plant growth, yield and reproduction), releasing the minerals to soil water as the plant removes the minerals. Indeed, rich plant material slowly releases plant-available minerals as they degrade, spreading the supply of minerals over the growing season of the plant. Slow release is particularly important for plant-available nitrogen, such as its supply by green manure legumes. Organic matter may also enable the flow of water through the soil profile, reducing the erosive vigour of water. This is because, along with roots and the long branching root-like strand structures or hyphae of certain fungi, organic matter is essential for the development of soil structure. The quantity of organic matter is critically important for these characteristics; fluctuations in organic matter in soil also means fluctuations in the various attributes associated with organic matter. Thus, for a more sustainable agriculture, more long-lived organic carbon is essential.

FDI: Are these issues widely known and accepted within the scientific and farming communities and, if not, what needs to be done?

PM: I believe that, while the importance of SOC is understood by science and by much of the agricultural community; the scientific body of knowledge is, however, incomplete and agricultural decisions about SOC are not fully informed. It has been demonstrated that conservation agriculture has unpredictable impact on the quantity of SOC. For instance, the adding of compost, the use of no-till farming and the planting of green manure crops, can improve general soil health but does not necessarily significantly increase SOC over significant periods of time. More research is required.

FDI: How do we increase SOC?

PM: Efforts to increase long-lived carbon have failed so far, in large part because of the need to understand soil physics, soil chemistry and soil microbiology. Indeed, research in soil is extremely difficult because you must break apart the soil just to see the outcomes of any efforts to increase SOC. Issues of scale are also relevant; most attempts to understand the carbon cycle work at the global scale but the processes are microscopic. Our tools tend to be inadequate for the tasks. The development of understanding of SOC is slow and can be highly controversial.

FDI: In a recent FDI Feature Interview with Mr Guy Webb of Soil C Quest 2031, a process was described, where by, SOC could be fixed into the soil and be stable over the long-term. How would you describe this process?

PM: The Carbon content of soil changes rapidly and predictably. Most soil carbon is of recent origin, but a small fraction found protected in micro-aggregates may be hundreds to thousands of years old. Thus understanding the underlying processes of degradation and sequestration is important. Microbes enzymatically degrade linear carbon molecules such as protein, starch and cellulose by the addition of water, a process known as hydrolysis. The microbes gain energy for their growth and development, and, in doing so, release carbon dioxide. Hydrolysis can take place in aerobic (oxygen present) and anaerobic (oxygen absent) conditions, though is slower in the latter. Organic matter may also be oxidized. Carbon can be found in circular compounds called aromatic carbon. Aromatic carbon can form incredibly large and complex combinations, and these are called polyaromatic carbon. Lignin is the most common polyaromatic compound on the planet. Polyaromatic carbon can only be degraded by oxidation. Whether oxidation takes place chemically or by means of fungal enzymes (biological molecules that facilitate complex biochemical reactions), the process requires oxygen. The increase of long-lived organic carbon in soil, then, requires the addition of polyaromatic carbon to the core of micro-aggregates where it is protected from oxidation.

Micro-aggregates are tiny. Theoretically, the size of micro-aggregates is determined by the amount of energy such as water erosion or vibration, required to break them apart. Macro-aggregates break apart easily, and micro-aggregates with much greater difficulty. Practically, if the units of soil are smaller than a quarter of a millimetre, they are called micro-aggregates. Micro-aggregates may last a very long time without much change. If oxygen is allowed to enter the soil, however, oxygen may penetrate the pores of the micro-aggregate, and the structure will start to break apart because the polyaromatic glues are oxidized. The loss of structural integrity of soil following initial cultivation of native lands is explained by the immediate flood of oxygen to the soil profile, and its penetration of micro-aggregates.

Micro-aggregates have a complex structure which can be viewed using specialist microscopes. The outer layer is covered by oxygen dependent microbes; this probably explains why little oxygen enters the structure. The pores and channels of micro-aggregates are tiny and highly variable: commonly between a one thousandth and fiftieth of a millimetre. Plant roots cannot penetrate a pore less than half a millimetre. Thus we can now explain why addition of composts, no-till cropping and green manure cropping has no long term effect on long-lived organic carbon. The polyaromatic lignin molecule, which is abundant in plant structural material, remains in the aerobic zone of soil where it is oxidized. To add long-lived organic carbon to soil, a process to place polyaromatic carbon in to the core of micro-aggregates is necessary. This cannot be achieved with lignin. Melanin is a widely found polyaromatic compound that cannot be easily distinguished from lignin.

Fungi hyphae can penetrate micro-aggregates. Vesicular-arbuscular mycorrhiza (VAM) fungi play a key role in the development and maintenance of aggregate structure and are crucial for the development of structural complexity. Only rare VAM fungi, however, contain aromatic or polyaromatic carbon and these do not survive in cultivated soils. Some soil fungi have melanin in the wall of their hyphae. Thus it was reasoned that if melanised fungi were grown in soil, their growth into micro-aggregates would increase the content of polyaromatic carbon in the micro-aggregates and thus increase the life of the stored SOC. This hypothesis was tested by Tendo Mukasa Mugerwa during his PhD. From his experiments, he observed that organic carbon, and importantly, polyaromatic carbon increased by up to 30% when the melanised fungi were grown in his experimental soils. Clearly, he had no opportunity to determine whether the carbon was long-lived.

Soil is an incredibly competitive environment for microbes. Tendo selected melanised non-harmful fungi that could also grow in the roots of plants. The fungi are called endophytes (within plant), and the melanised endophytes have the acronym MEF. Endophytes have the advantage that the host plant supplies a reliable supply of energy while the fungus grows through adjacent soil. While the plant is alive, the fungus will be fed. Perennial plants are the ideal host, but resupply of endophytes at sowing of annual crops plants should enable the continuity of the MEF.

Experimental data support the concept of carbon sequestration by MEF (outlined above). Commercial development of the exciting discovery by Tendo requires an enormous amount of further research. Determination of the potential under field conditions is essential. Selection of MEF that function in various soils and climates is needed.  Many unpleasant surprises will emerge. For instance, MEF that colonise Canola and clover do not colonise wheat and rye grass, and vice versa. Commercial culture of selected fungi needs to be developed

FDI: What is the place of MEF amongst biologicals of the Future?

PM: The deliberate use of microbes in agriculture has only just commenced. Rhizobium for nitrogen fixation in legumes is well recognized. Microbes that fix nitrogen in leaves of cereals and roots of rice, or release phosphorus from insoluble sources, are now available. Plant growth promotion and structural enhancement may be subject to microbial control. Endophytes that assist the plant to tolerate salinity and heat stress, reduce insect damage and tolerate disease causing microbes are now being researched. In my opinion, the farmer of the near future will be able to select microbes for their specific needs and conditions, and add these with the seed to reduce their use of chemicals and ensure the more sustainable production of their crops.




About the Interviewee: Associate Professor Peter McGee holds an honorary appointment to the School of Biological Sciences, University of Sydney. He retired at the end of 2013 after completing more than 30 years studying soil biology. He and his team researched mechanisms underpinning the sustainable use of soil, and their importance in restoration of soil function. In recent years the team has developed mechanistic models of soil carbon sequestration. He and his group have published more than 70 manuscripts in peer reviewed journals. His research has been supported by rural research bodies, government sources of research funding and commercial entities. He has also encouraged the commercial development of appropriate technologies including inoculums for sustainable agriculture.






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