Soil borne pathogens on Trojan hosts

By Jan ten Hoopen

The rotation of different crops in one field is one of the oldest agricultural management systems used to suppress pests and weeds, sustain soil fertility or improve soil structure. In its most primitive form it is even as old as agriculture. People would abandon exhausted soil, only to return after long periods of fallow in which forest or other natural vegetation had rehabilitated these soils. Gradually people found out how to use different crops and rotations to sustain fertility or other features of soil health.

Already in the early days of the Roman empire (from 43BC), rotation cropping with fallow or legumes to sustain soil fertility, was common practice and spread throughout the empire. Comparable practices developed independently in all major agricultural areas of the world. The Incas in South-America for example, already in the 15th century had in place a seven years rotation cycle for potatoes to get rid of a persistent nematode. After thousands of years of developing these systems, it was not until recently that pesticides and chemical fertilizers made it possible to produce the same crop more or less continuously in the same field.

Nowadays, crop rotation still is the basis of Organic farming. In conventional production systems it is used as part of Integrated Pest Management (IPM) strategies when soil borne diseases are hard to fight with pesticides or when pesticides are considered too toxic for both people and the environment. In such rotation systems, either organic or conventional, one or more crops might be vulnerable for bacteria, fungi, nematodes or other pests. The strategy is then to select crops that are not hosting the same pests. Without a host or host material like crop residues, the pest will disappear from the soil due to starvation. As these pests are more or less specific for a group of crops, rotations with crops from different groups are the standard. A known example in Europe is the rotation system used in potato production with sugar beets, wheat and barley or feeding maize.

Carolina Leoni Velazco has been working on this subject for a long time now, as part of her job at INIA, the National Agricultural Research Institute of Uruguay. For the past three years she has been combining this work with a PhD at our group and the Biometris group of WageningenUR. In Uruguay, where she is responsible for the area of phytopathology in fruit tree production and soil biology and quality, one of the areas she is working on is the re-designing of cropping systems used by small farmers in the vegetable producing areas in her country. Due to lower prices for vegetables, these farmers were forced to intensify their production to make up for the decreased incomes. This meant increased inputs of seeds, pesticides and fertilizers and a reduced number of crops. Due to this change, the same crops will be grown more often in the same field with all possible consequent effects on soil quality, an increased pressure of soil borne pests being one of them.

While looking at the crop rotation systems, Carolina was puzzled by the heterogeneous results she saw for pest-pressure between farmers. Differences like soil type, soil fertility or management system (i.e. organic or conventional) could not explain these differences. It was then she started thinking of the possibility that some crops used in the rotation systems might actively prolong or shorten the time that the pests survived in the soil. Processes behind this could be that some crops in the rotation system function as an alternative host to the pest, without having symptoms of disease. These kind of alternative hosts are called 'reservoir hosts'. Carolina selected one of the main pathogens of Onions, the fungus Fusarium oxysporum f.sp. cepae (figure 1 and 2), as a model species to look at the possibility of ‘reservoir’ hosts and tested its survival on other crops used in the rotation cycles. As the crops used in the rotation systems studied are of very distinct groups, this would imply that the Fusarium fungus can use a range of hosts with a width not observed before in agricultural systems.

Surprisingly, Carolina found strong indications that several crops she studied indeed do serve as an reservoir host for the Fusarium fungus. In greenhouse and micro-plot experiments the fungus did multiply in several crops that were not part of the onion family. Crops that were formerly considered safe crops then instead might help the fungus remain at high levels in the soil. Model simulations suggest a factor ten difference in pest pressure between using 'dangerous' crops and 'safe' crops as part of the rotation cycle. This could have important implications, not only for the Uruguayan situation, but also for the way we look at crop rotation in general. As Carolina puts it; “this is probably a more common phenomenon in nature, but not known from such distinct crops in agriculture”.

Greenhouses, micro-plots or models are of course simplified systems compared to field conditions on a farm. They are however very good tools to look at specific parts of the system, like the population dynamics of the fungus. To validate the results of the models, Carolina also monitors the rotation cycles of 25 different farms in Uruguay. These farms use different ‘safe’ and ‘dangerous’ crops in their rotation cycles and offer thus good feedback for the model. The crops she suggests to incorporate in the rotation are at the moment not commonly used in Uruguay as green manures, they have however the same functional place in the management system of the farmers. Foxtail millet is a good replacement for Sudan grass, one of the 'dangerous' crops, while Wheat is a good replacement for Black Oat, one of the other ‘dangerous’ crops (figure 3).

Carolina just returned to Uruguay where she will continue monitoring the farms and start analyzing the data gathered in the past three years on these farms. It will be very interesting to see how good her models fit the actual pest-pressure on the farms. With the new insights on the width of the host range of the Fusarium fungus, new tools will be available to improve understanding and design of crop rotation systems in the country. This is not only important for the small-farmers in her study, as these insights are also applicable in other parts of Uruguay where farmers face similar changes and problems (1).

(1) Market prices strongly influence this sector, with low prices for vegetables resulting in intensified production with fewer crops in the area Carolina now studies. In other regions the high prices of soy beans and wheat drive farmers to switch to the production of cash crops solely, whereas it was combined with animal husbandry and permanent grasses before.


Kenneth D White 1970. Fallowing, Crop Rotation, and Crop Yields in Roman Times. Agricultural History 44 (3): 281-290

Brodie, B B and W F Mai 1989. Control of the Golden Nematode in the United States. Annual Review of Phytopathology 27: 443-461