Soil: nature’s Pandora’s box

Danny Coyne,

Slash-and-burn forest clearance for crop cultivation in West Africa. Photo by Danny Coyne
Slash-and-burn forest clearance for crop cultivation in West Africa. Photo by Danny Coyne

Soil, a natural resource of overwhelming magnitude, is too often taken for granted, even if its importance is recognized at the highest levels. Franklin Delano Roosevelt, for example, lamented that “The nation that destroys its soil, destroys itself” when reflecting on the USA’s dustbowl era.

The “anchor” for the great majority of crops and plants, the soil is a physical support system for crop production and survival. However, it is also a paradoxical Pandora’s box of contrasts and opposing forces. As a refuge for pests and diseases capable of broad-scale crop devastation, it acts to harbor the death knell of the very life it supports. The soil-borne bacterium that causes bacterial wilt, Ralstonia solanacearum, for instance, can inflict 100% mortality to a field of tomatoes; cysts of some nematode species or spores of certain bacteria can lie dormant in the soil for decades, and then wreak havoc on susceptible crops when stimulated.

By contrast, the soil also acts as a treasure trove of beneficial microorganisms. Some are obligate parasites of crop pests and diseases, others facilitate plant access to nutrients, or enable plants to tolerate unfavorable conditions and toxic contaminants. The breadth of microbial biodiversity can also, in effect, be indicative of soil health. The rich tapestry of soil biodiversity involves a highly complex series of interactions, which facilitates biological equilibrium, including the suppression of pests and diseases. Determining how to measure this and relate it to soil health is currently a research topic at IITA. For instance, can a minimum number of non-parasitic nematode genera signify a healthy soil, as suggested by Ferris et al. (2001), and can we rapidly determine this using molecular barcoding? (e.g., Yu et al. 2012).
In Africa, our knowledge of the microbial diversity is particularly sparse and underexplored, and the biological rewards to be reaped vastly underrecognized. At IITA we intend to change this.

Intensifying agriculture in Africa
For Africa to reverse its current trend of declining crop productivity and raise it to a more globally reflective level (Hazel and Wood 2008) intensification of cropping systems is essential (see Vanlauwe this edition). The Asian Green Revolution was successful due to, among other things, the broad-scale use of pesticides to combat pests and diseases. However, their excessive use was a hard lesson learned, and numerous such pesticides are now no longer available.

More ecologically sensitive alternatives are now sought, increasingly so, with soil microbial biodiversity a clear target for exploration. Cropping intensification, however, needs to be carefully managed. The more intensified the system, the greater the selection pressure for pests and disease, and the more severe the problem. The appearance of nematode problems, regularly overlooked and famously misdiagnosed, is an initial indicator of the breakdown of a sustainable system.

Figure 1. AMF species abundance and diversity in relation to agroecological zones and relative water availability in Togo and Benin West Africa, under varying levels of cropping intensification.
Figure 1. AMF species abundance and diversity in relation to agroecological zones and relative water availability in Togo and Benin West Africa, under varying levels of cropping intensification.

At IITA, root-knot nematodes (Meloidogyne spp.) are a key focus of attention. With a short life cycle, rapid multiplication rates, broad host range, and scarcity of suitable management options, they pose a particular nuisance and are probably the most important biotic constraint across Africa (Coyne et al. 2009).

Intensification also results in reduced biodiversity, with many microorganisms unable to survive the heightened soil disturbance or a more uniform cropping pattern. At IITA, in collaboration with Basel University (Switzerland), we investigated the effect of cropping intensification on the diversity and occurrence of arbuscular mycorrhizal fungi (AMF) associated with yam (Dioscorea spp.) (Tchabi et al. 2008).

Yam is viewed as a nutrient-hungry crop, and thus often planted in more fertile soils following the removal (slash and burn) of forest or long-term fallow, an unsustainable and environmentally detrimental practice. It is also particularly afflicted by parasitic nematodes. AMF needs to attach to and grow on plant roots, forming a special relation which is mostly mutually beneficial, creating enhanced nutrient flow to plants. This relatively small and rather unique study showed that yam is associated with a wide array of AMF species and is highly mycorrhizal. The high diversity and incidence of AMF communities, however, decreased dramatically following the removal of forest and cropping intensification (Fig. 1).

Is there a link therefore between yam nutrient access and AMF? And can we exploit this AMF-yam relation to help preserve West African forests? Furthermore, yam tubers were less affected by yam nematodes in the presence of AMF! The limited knowledge of soil microbial diversity in Africa is acutely highlighted with this study, which alone led to four species being newly described and contributed to the revision of the Phylum Glomeromycetes (Oehl et al. 2011).

Balancing ecological equilibrium
At IITA we recognize the potential of healthy soils for crop productivity, in addition to the resource potential of beneficial soil microorganisms for use in pest and disease management. While specialists work on diagnostics, establishing economic importance and developing management solutions for soil-borne pests and disease, similar efforts are focused on the beneficial aspects of soil biodiversity and soil health.

We recently discovered, for example, that fungal antagonists isolated directly from Meloidogyne spp. eggs were far more effective against these pests than those isolated from the soil (see photo), as is the usual practice (Affokpon et al. 2011).

Our plan is to work towards the identification of biological elements, which enhance crop productivity, as well as specific organisms, such as AMF, nitrogen-fixing bacteria and Trichoderma spp., for development as potential products.

As with the pain and suffering that Pandora’s box in the Greek mythology inflicted upon the world, so can the destructive potential to crops that the soil environment harbors be moderated, providing hope by balancing the ecological equilibrium. IITA strives to harness this equilibrium by understanding the mechanisms of the dynamics of healthy soils and determining the key factors that will help curtail pest and disease development.

Affokpon, A., D.L. Coyne, C.C. Htay, L. Lawouin, and J. Coosemans. 2011. Biocontrol potential of native Trichoderma isolates against root-knot nematodes in West African vegetable production systems. Soil Biology and Biochemistry 43: 600‒608.
Coyne, D.L., D. Fourie, and M. Moens. 2009. Current and future management strategies in resource-poor regions. In: Root-knot Nematodes. CAB International, UK. pp. 444‒475
Ferris, H., T. Bongers, and R.G.M. de Goede. 2001. A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Applied Soil Ecology 18: 13‒29.
Hazell, P. and S. Wood. 2008. Drivers of Change in Global Agriculture. Philosophical Transactions of the Royal Society B-Biological Science 363: 495‒515.
Oehl, F., G. Alves da Silva, I. Sánchez-Castro, B.T. Goto, L.C. Maia, H.E.V. Vieira, J-M. Barea, E. Sieverding, and J. Palenzuela. 2011. Revision of Glomeromycetes with entrophosporoid and glomoid spore formation with three new genera. Mycotaxon 117: 297–316.
Tchabi, A., D. Coyne, F. Hountondji, L. Lawouin,  Wiemken, A. and F. Oehl. 2008. Arbuscular mycorrhizal fungal communities in sub-Saharan Savannahs of Benin, West Africa, as affected by agricultural land use intensity and ecological zone. Mycorrhiza 18: 181‒195.
Yu, L., M. Nicolaisen, J. Larsen, and S. Ravnskov. 2012. Molecular characterization of root-associated fungal communities in relation to health status of Pisum sativum using barcoded pyrosequencing. Plant and Soil 357: 395‒405.