By Chloe Ward. Chloe is an environmental gardener interested in working towards diversification of agriculture in Wales. Specialising in fruit and perennial systems, she also believes in the importance in developing low impact methods of soil care. She has recently completed an MSc in Food Security at Aberystwyth University, and this article is based on research undertaken for her dissertation.

In the same way that most meat production is an inefficient use of land, use of animal manure can be thought of as an inefficient use of nitrogen fixation. The plentiful nitrogen-rich compounds found in animal manure have originally been produced by biological ‘fixation’ of nitrogen by soil-dwelling bacteria which convert nitrogen gas into a form usable by plants.

These nitrogen compounds are then taken up by plants, which are eaten by animals and concentrated in the animals’ tissues and excrement. However, much of the nitrogen will have been lost along the way through leaching of liquids, and emissions of gases from urine. Therefore, just as the conversion of plant matter into meat loses much of the carbohydrate fixed by photosynthesis, conversion of plant matter into manure loses much of the fixed nitrogen.

An organic system which uses animal manure to fertilise crops is importing nitrogenous compounds which will need to be replaced on the original land to maintain its fertility. In inorganic systems industrially produced nitrogen fertiliser is most commonly used. This has been manufactured by artificial nitrogen fixation by the Haber Bosch process, using fossil fuel as the energy source and so emitting carbon dioxide.

Use of nitrogen fixing green manures, such as clover, avoids the above problems by producing nitrogen compounds by biological fixation which are then used in situ. The relationship between the nitrogen fixing plant and the bacteria is one of the famous symbiotic relationships in which both species benefit, with the bacteria gaining sugars produced by photosynthesis, while the plant gains nitrogen in a usable form.

Not all green manures are nitrogen fixers. Some, for example Hungarian Ryegrass, are ‘nitrogen lifters’ which uptake ready-fixed nitrogen compounds from the soil and hold them in their tissues until they are dug in. All green manures, however, provide organic matter which increases the water holding capacity, and microflora of the soil.

Are we keeping track of our fertility?

By necessity many green manures are incorporated into the soil several weeks before the crops are sown, and the challenge is to prevent loss of the nitrogen compounds before they can be taken up by the crop. A hidden factor of green manure use is the pathway that the nitrogen compounds take after the plant matter has been added to the soil. Organically managed soils generally have high organic matter content, containing much living and once-living material which can ‘soak up’ any spare nitrogen. However, for reasons explained below, it is important to know, as much as possible, about where our fixed nitrogen is going.

Nitrogenous compounds go through a complicated series of reactions in the soil. Our desired destination is for them to be locked up in stable organic compounds until required by crops. However, they can be converted to nitrates which can be leached away in heavy rain, or into the powerful greenhouse gas nitrous oxide. Both of these are bad results – but results that we cannot see.

Biological nitrogen fixation in situ is clearly a low impact method of increasing available nitrogen, but managing that nitrogen so that it stays in the soil in a useful form is not so easy. Incorporation of green manures is, after all, not a natural process. When do we ever see lush green leaves rotting into the soil in a natural system? Plants which die back in autumn re-absorb useful materials into their roots, and those at the end of their lives put proteins into the next generation’s seed, leaving mainly carboniferous material to rot.

Inorganic fertilisers, of course, also emit nitrous oxide, but it can be argued that this is easier to control than for green manures, as liquid or granular fertiliser can be added in small quantities as and when needed (Mueller et al 2012). It is not so easy to do this with green manures.

One criticism sometimes directed at proponents of organics is one of romanticism of assuming that, if a ‒ farm or garden is pretty, then it must be ecologically sound. It is indeed tempting, when we see a visually beautiful farm or garden, to assume that all is well. Gut feelings can tell us something after all. Perhaps, for biodiversity, visual clues are more reliable, but in the world of soil biochemistry, much is hidden from us. In order to maximise the benefits of green manures, it is vital that we progress our understanding of nitrogen pathways so as to conserve fertility and prevent unwittingly emitting large levels of nitrous oxide.

Can mycorrhizal fungi help in preventing nitrous oxide emissions?

Arbuscular mycorrhizal fungi penetrating root cells of sweetcorn (Zea mays). The vesicles of the fungi are stained blue to show up under magnification, this root being about 0.1mm in width

We already know of some factors which affect nitrous oxide emissions from green manures. For example, incorporating green manure into wetter soils results in more emissions (Mueller et al 2012). So there are some good practices that farmers and gardeners can follow in green manure management.

A recent advance in understanding is in the role of arbuscular mycorrhizal fungi (AMF) in nitrogen uptake. AMF, another group of well known symbionts, inhabit plant roots, with the fungal partner gaining sugars from the plant’s photosynthesis, while the plant gains water and nutrients transferred from the soil by the fungus. Fungi are better able than plants to uptake water and nutrients, due to the greater ability of the fine fungal threads to penetrate the soil.

It had, until recently, been thought that AMF did not play a significant role in nitrogen uptake, being better known for their transfer to plants of phosphorous. Of significance to green manure use is research conducted at the University of York which has shown that AMF can take up nitrogen compounds from decomposing grass leaves in soil, and also speed up the decomposition of the grass (Hodge, Campbell and Fitter 2001).

Experiments conducted in 2010 showed that fungi were uptaking and storing nitrogen compounds in their tissues, which led the authors to theorise that the fungal mass of AMF could act as a global reservoir of nitrogen equivalent to that held by fine roots (Hodge and Fitter 2010).

This opens up the possibility that AMF could be a significant factor in retaining nitrogenous compounds in soil, by preventing loss as nitrates through leaching and as the gas nitrous oxide. This past year did indeed bring findings that the presence of AMF can reduce nitrous oxide emissions from soil after fertiliser has been applied (Bender et al 2014). The fertiliser used in these experiments was manufactured nitrogen compounds. However, due to the ability of AMF to take up nitrogen from decomposing plant material, it follows that it could be possible for a healthy AMF population to reduce nitrous oxide emissions from decomposing green manures.

The scientific literature gives results of many experiments which show that various agricultural practices either increase or decrease mycorrhizal populations. It is likely that organic and minimum tillage farming systems are richer in AMF, as fungal populations can be reduced by monocropping, application of excessive fertiliser and ploughing (Oehl et al 2004). However, some of this evidence is contradictory and we need to remember how very little we still know about the organisms and processes involved. It is possible that a diverse and healthy soil, as found in a well maintained organic system, is better able to cope with the unusual event of a sudden gain of a mass of lush green tissue and, perhaps in the near future, the scientific literature will shed more light on the role of AMF in processing decomposing green manures.

One certainty is that we cannot just guess whether our soil management is having a positive impact on the environment. This is all the more reason for stockfree organic growers to educate themselves in soil science, to keep a check on the reality of their actions, actively participate in research, and continue to innovate for best environmental practice.


Bender SF, Plantenga F, Neftel A, Jocher M, Oberholzer HR, Köhl L … & van der Heijden MG (2014). Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil. The ISME journal 8(6), 1336-1345.

Hodge A, Campbell CD, & Fitter AH (2001). An arbuscular mycorrhizal fungus accelerates decomposition and acquires nitrogen directly from organic material. Nature 413(6853), 297-299.

Hodge A & Fitter AH (2010). Substantial nitrogen acquisition by arbuscular mycorrhizal fungi from organic material has implications for N cycling. Proceedings of the National Academy of Sciences 107(31), 13754-13759.

Mueller ND, Gerber JS, Johnston M, Ray DK, Ramankutty N, & Foley JA (2012). Closing yield gaps through nutrient and water management. Nature 490(7419), 254-257.

Oehl F, Sieverding E, Mäder P, Dubois D, Ineichen K, Boller T, & Wiemken A (2004). Impact of long-term conventional and organic farming on the diversity of arbuscular mycorrhizal fungi. Oecologia 138(4), 574-583.

This article appeared in Growing Green International magazine Num 34 (Winter 2014/15), p32.