Soil fertility - Friendly microbes

The role of microbes in maintaining soil fertility needs to be recognised because they can boost industry profit, says Geoff Dixon.

Soil fertility is vital to help feed growing global populations in the face of a changing climate and pressures on land - image: Geoff Dixon
Soil fertility is vital to help feed growing global populations in the face of a changing climate and pressures on land - image: Geoff Dixon

Soil is a non-renewable, finite natural asset. Yet the world's expanding populations are destroying land capital at alarming rates. This reduces opportunities for food production, spaces for recreation and the wilderness needed by nature. We all benefit from conserving soil, while horticulture's profits depend on it. In turn, fertility relies on the populations of microbes of which our understanding is very limited.

How microbes live

Soils are systems of pores and aggregated mineral and organic particles in differing sizes. Within the pores microbes are continuously eating, respiring, reproducing, competing, cooperating, and responding to their environment. They concentrate mainly around roots, which exude sugars providing them with energy. Soil temperature, moisture content, acidity/alkalinity and nutrient availability regulate microbial activity, which changes with the seasons and the way land is used.

For example, adding nitrogen decreases populations of fungi compared with bacteria, while liming tends to favour fungi. Fungi are encouraged by good practices such as reducing the intensity of cultivation, increasing rotations and using cover cropping. Intensive cropping excludes all but one plant from an area of land and reduces its microbial diversity. Subsequent husbandry should aim at restoring fertility because the numbers of beneficial and benign microbes far outweigh and suppress those causing diseases.

Additionally, beneficial microbes enhance crop water-use efficiency and nutrient uptake, particularly phosphorus. Maintaining soil fertility reduces the need for synthetic fertilisers and pesticides and saves growers money.

Degrading dead plants and animals into useful organic matter is a key microbial function. Decomposition underpins sustainable land-use in all managed, agricultural and horticultural, semi-natural and natural soils, part of the natural carbon and nitrogen cycles that are driven by free solar energy captured by plant photosynthesis.

Using the carbon and nitrogen cycles

Carbon from dead plants and animals is recycled naturally back into the atmosphere as carbon dioxide by microbes using chemical energy. Nitrogen is taken by free-living soil bacteria from organic matter and added to the soil.

Associations of bacteria living with legume roots add further nitrogen supplies into soils. Fixation of atmospheric nitrogen by legume-rhizobia deposits 33-46 million tonnes of nitrogen annually into the world's soils. At current fertiliser prices, this is worth US $50-70bn yearly.

Using processes understood only in outline, microbes make soil inorganic phosphorus soluble and available to plant roots. Additionally, the biochemical diversity and adaptability of microbes can be used in repairing polluted land. These processes are further stimulated by adding substances such as active charcoal or biochar.

Suppressing pests and pathogens

Fertile soils rich in microbes suppress plant pathogens. Actively beneficial bacteria include Bacillus spp, Enterobacter spp, Flavobacterium balustinum and Pseudomonas spp and fungi such as Penicillium spp, Gliocladium virens and several Trichoderma spp. Microbes such as Trichoderma spp. offer several beneficial effects. They compete with pathogens for nutrients and soil space, parasitise pathogens and induce plant disease-resistance.

The soil-borne diseases that are reduced and crops that benefit this natural biocontrol include Pythium in turf grass, snow moulds in turf grass and Fusarium, Pythium and Rhizoctonia in tomato and cucumber. Suppression of R. solani attacking cucumber resulted from inoculating seedling compost with Trichoderma asperellum, while a reduction of bacterial leaf spot of radish, lettuce and tomato followed inoculation of compost with T. hamatum. Some free-living soil fungi diminish soil nematode populations very effectively. Their fungal hyphae form nooses that capture the nematodes and then they exude enzymes that dissolve them.

Commercial applications

Commercial use of beneficial bacteria and fungi is gaining ground as part of integrated pest management strategies. Belchim's Contans contains Coniothyrium minitans, which helps control soilborne pathogens such as Sclerotinia sclerotiorum and S. minor. According to specialist Fargro technical and energy director Paul Sopp: "Growers are experimenting with biopesticides such as Serenade (Bacillus subtilis QST713) because this widens their options for pest and disease control. This is especially the case with diseases such as downy mildew on brassicas and onions."

Several formulations of beneficial microbes antagonistic to pathogens are available including Agrobacterium radiobacter active against A. tumefaciens (crown gall, NoGall), Pseudomonas fluorescens active against Sclerotinia, Rhizoctonia and Pythium (Biomonas), Streptomyces griseoviridis active against Fusarium, Phytophthora, Pythium and Rhizoctonia (Mycostop), Trichoderma atroviride active against Sclerotium cepivorum (Plantmate) and T. harzianum active against Pythium, Rhizoctonia and Fusarium (Rootshield, PlantShield).

Developing trends

The current generation of commercially available microbes are actively antagonistic to specific disease-causing pathogens. An alternative and more effective approach is using combinations with differing modes of action. For instance, this might include combining non-pathogenic forms such as strains of F. oxysporum that compete with pathogens for energy sources along with bacterial antagonists that block access to iron.

Alternatively, there is scope for integrating microbial treatments with beneficial husbandry. This approach could be valuable where biofumigant crops are used. A natural suppression of soil-borne pests and pathogens follows the incorporation of green manure or harvest residues from brassicas with high-glucosinolate contents such as Caliente mustard into soil. Adding compost containing growth-promoting rhizobacteria strengthens the control of diseases such as Fusarium wilt and Rhizoctonia damping-off and builds soil fertility further.


Mycorrhizas are mutually beneficial associations of fungi with roots. There are broadly two forms - endomycorrhiza (particularly arbuscular types), where fungal hyphae inhabit plant cells, and ectomycorrhiza, where a hyphae sheath forms round the root surface. Arbuscular mycorrhizas are crucially important for sustainable cropping. Mycorrhizas increase root access to nutrients, particularly phosphorus, improve water uptake and defend them against invading pathogens.

Commercial formulations are available as soil improvers that enhance amenity and fruit tree and shrub establishment. These are useful for controlling specific replant disorders caused by Pythium spp and other pathogens in top and stone fruit and roses. Mycorrhizal preparations are available from Dragonfli or David Austin Roses.

What are soil microbes worth?

Soil microbes provide ecosystem services and only now are these vital benefits being recognised. Economic valuations show nature is worth US $1.5tn a year to agriculture and horticulture worldwide. Nutrient cycling in fertile soils is one of the most vital ecosystem functions that microbes perform.

Working in the Canterbury Plains of New Zealand, Professor Harpinder Sandhu quantified the financial value of ecosystem services from soil microbes that improve fertility as on average US $160.65/ha/year in organic fields and US $142/ha/year in conventionally managed ones.

The future

Microbes and plant roots communicate by exchanging chemical signals. When necessary, they activate their own defences and those of host plants - for example, in mycorrhizal combinations. Exploiting these natural communications offers prospects for developing new generations of environmentally benign fertilisers, crop stimulants and protectants. For example, Isopyrazam (IZM), Syngenta's new cereal fungicide, is a move in this direction.

Good soil care and through that the conservation of beneficial microbes maintaining fertility is of prime importance. We must feed a world population of 10 billion by 2080 from diminishing land assets and in increasingly adverse climates. Microbes and soil fertility are some of our best friends in grappling with these problems.

Professor Geoff Dixon is joint editor with Emma Tilston of Soil Microbiology & Sustainable Crop Production, published by Springer.

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