14.1 Fungal diseases and loss of world agricultural production

Standing out among the examples of how damaging a crop disease can be is the Irish famine of 1845/46, which was caused by the failure of the potato crop in Europe because of just one plant disease, the Potato Late Blight (caused by a filamentous fungus-like member of the Oomycota, Phytophthora infestans). This is an astonishing story of how a crop disease affected the structure of our civilisation and our understanding of nature, while causing the deaths of one in eight of the Irish population. It is a story which goes far beyond statistics of number of deaths due to starvation, number of people emigrating, or crop losses and reduction in agricultural yield, and you can read that story in more detail in Chapter 2 of the book Slayers, Saviors, Servants and Sex. An exposé of Kingdom Fungi by David Moore (2000). But it is a piece of our history which we must read about in the knowledge that even today world agriculture suffers significant losses due to plant disease, despite all our scientific advances of the past 150 years. Hopefully, in that time we have learned enough at least to avoid massive calamities like the Irish famine, and today’s losses can be reported in terms of monetary losses. But behind each such statistic there must be personal tragedies in which the lives of individuals and families are changed dramatically.

Although weeds are the major cause of crop loss on a global scale, major losses are suffered by agricultural crops due to insect damage and plant diseases. In rounded (approximate) figures, the world-wide annual production tonnage %age lost to various pests at the start of the 21st century have been estimated as follows:

  • losses due to animal pests, 18%;
  • microbial diseases, 16% (and 70-80% of these losses were caused by fungi);
  • weeds, 34%;
  •  making a grand total of 68% average annual loss of crop production tonnage (data from Oerke, 2006).

Of course, it is not only fungi that cause plant disease (Fig. 1). There are bacteria, viruses, nematode worms (eel worms), aphids and insects as well as fungi. Serious plant diseases are caused by all these other pests, but fungi probably cause the most severe losses due to disease around the world. For one thing there are more plant pathogenic fungi than there are plant pathogenic bacteria or viruses. One survey made several years ago in the American State of Ohio came up with the estimate that the State had one thousand diseases of plants caused by fungi, one hundred caused by viruses and fifty due to bacteria. Crop protection measures include weed control, which can be managed mechanically or chemically, and the control of animal pests or diseases, which relies heavily on synthetic chemicals. Pesticide use has enabled farmers to modify production systems to increase crop productivity while still maintaining some measure of control over the damaging effect of pests. Unfortunately, despite large increases in pesticide use, crop losses have not significantly decreased during the last 40 years.

Crop losses are caused by both biological and physical aspects of the environment that lead to a lower actual yield than the site can be expected to attain (Figs 1 and 2). The attainable yield is the realistic technical maximum under the best achievable growth conditions. It is generally much less than the yield potential, which is the theoretical maximum that cannot be reached under practical growth conditions in the field. Crop losses are best expressed as a proportion of attainable yield but sometimes the proportion of the actual yield is calculated. Pests reduce crop productivity in various ways, for example by:

  • reducing the stand (that is, the population) of plants (pathogens that kill the host [necrotrophs], like damping-off pathogens that kill seedlings, are examples);
  • reducing photosynthetic rate (fungal, bacterial, virus diseases);
  • accelerating plant senescence (most pathogens);
  • shading and ‘stealing’ light (weeds, some pathogens);
  • depleting assimilate (nematodes, pathogens, sucking arthropods);
  • consuming tissue (chewing animals, necrotrophic pathogens);
  • competition for inorganic nutrients (weeds).

Crop losses can be quantitative and/or qualitative, and expressed in absolute terms (kg ha-1, or financial loss ha-1, for example) or in relative terms (% loss in production tonnage, for example):

  • quantitative losses result from reduced productivity giving a lesser yield per unit area;
  • qualitative losses from pests can result from:
    • reduced content of a normal ingredient(s) of the crop,
    • reduced market quality (for example miss-shaped, blemished fruit and vegetables),
    • reduced storage quality,
    • contamination of the harvested product with pests, parts of pests or toxic products of the pests (for example, mycotoxins).
Biological and physical aspects of the environment that lead to a lower crop yield
Fig. 1. Biological and physical aspects of the environment that lead to a lower actual yield than the site can be expected to attain under ideal circumstances. Modified from Oerke (2006).

Agricultural survey statistics make it clear that crop losses directly attributable to fungi are very considerable. Of course, it’s changing all the time because, at least in part, losses depend on the weather, but it appears that world agriculture sustains average losses (in terms of monetary value) of around 16% annually as a result of plant diseases. This overall average conceals instances of good news; with disease loss in the 1 to 2% percent range as well as bad news of a season of unusually heavy pest incidence which might involve losses in the 30 to 40% region. Among crops, the total global potential loss due to all pests varied from about 50% in wheat to more than 80% in cotton production. Other estimated actual losses are 26-29% for soybean, wheat and cotton, and 31, 37 and 40% for maize, rice and potatoes, respectively. Overall, weeds produced the highest potential loss (34%), with animal pests and pathogens each causing about half that loss (Oerke, 2006).

Typical crop losses and yield levels estimated with and without various protection regimes
Fig. 2. Typical crop losses and yield levels estimated with and without various protection regimes. The value of crop protection practices (shown at left as ‘current situation’) can be calculated as the percentage of potential losses prevented by all the crop protection measures that are employed (compare with centre panel). In contrast, the impact of pesticide use on crop productivity (right hand panel) takes into account consequential changes in the agricultural system (for example, use of alternative varieties of the crop, modified crop rotation, reduced fertiliser use), which are provoked by the abandonment of pesticides and which are often accompanied by reduced attainable yield. Redrawn after Oerke, 2006.

Crop losses occur at every stage in the food system; in addition to losses during agricultural production, inefficiencies and consumer behaviour and waste all play a role. Alexander et al. (2017) found that, due to cumulative losses, the proportion of global agricultural dry biomass production finally consumed as food is only 6% of that actually produced. And we do mean SIX percent; that’s not a typographical error. These authors found that the highest rates of loss are associated with livestock production; and although the largest absolute losses of biomass occur before harvest (that is, the field losses due to weeds, pests and diseases as indicated above), losses of harvested crops were also found to be substantial, with 44% of crop dry matter being lost prior to human consumption. Interestingly, in this survey, over-eating was found to be at least as large a contributor to food system losses as consumer food waste; they conclude ‘…the findings suggest that influencing consumer behaviour, e.g. to eat less animal products, or to reduce per capita consumption closer to nutrient requirements, offer substantial potential to improve food security for the rising global population in a sustainable manner...’ (Alexander et al., 2017). So, it’s not just a matter of crop disease.

Efforts to quantify yield losses and identify their causes are still inadequate, and this is especially true for perennial crops, in which this year’s disease will have an adverse effect on next year’s crop. Cerda et al. (2017), researching yield losses caused by pests and diseases in coffee, neatly summarised the situation as follows:

‘…For some authors, crop loss is the reduction of the crop yield, defined both in terms of quantity and quality, that can occur in the field (pre-harvest) or in the storage (post-harvest) due to biotic or abiotic factors. For others, crop loss also includes the decrease in the value and financial returns of the crop. Furthermore, crop losses comprise primary and secondary losses. Primary crop losses are those caused in the specific year when pest and disease injuries occur; secondary crop losses are those resulting from negative impacts of pests and diseases of the previous year. In annual crops, the inoculum accumulation of pathogens in soil or in seeds and tubers remaining from the previous year can cause secondary losses. These losses however can be avoided by implementing crop rotations or chemical treatments. In perennial crops, premature defoliation or the death of stems and branches caused by leaf injuries lead to loss of vigour and decreased production (secondary losses) in subsequent years. In this case, such secondary losses cannot be avoided since they come from already damaged plants...’

The results of their trials over the years 2013-2015 showed that pests and diseases caused high primary yield losses (26%) and even higher secondary yield losses (38%) (Cerda et al., 2017).

Faced with this overabundance of statistics, it’s important to remember that we are talking about ‘twenty-first-century agriculture’, not some primitive agriculture of the distant past. Today, at this very moment, one in every eight crop plants, on average, will fail to yield because of fungal disease and this includes the positive effect of crop protection policies. Without protection of crops in the developed world, loss of crops would range from 50 to 100% (Fig. 2). The assessment of crop yield losses is necessary if improvements are to be made in production systems contributing both to the incomes of rural families and worldwide food security and there is increasing interest in the development of pest and disease models to analyse and predict yield losses. Donatelli et al. (2017) identified five-steps in the simulation of the impacts of plant diseases and pests that need improvement:

  • quality and availability of data for input into models,
  • quality and availability of data for model evaluation,
  • integration with crop models;
  • processes for model evaluation;
  • develop a community of plant pest and disease modellers.

These authors also point out that climate change is a growing challenge as it is likely to impact on agricultural intensification by altering the ranges, both geographical and host ranges, of pests and pathogens by its effects on the environment (Fones et al., 2017). Further aspects of this discussion are developed in the references cited in the following Resources Box.

Resources Box 14.1

Where to find more information about crop diseases, crop losses, plant pathogens and food and agriculture statistics

We have a page giving references to scientific papers and hyperlinks to online resources.

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All groups of fungi and fungus-like organisms can cause serious plant diseases and we will expand on some specific examples, below. Here, just to indicate the range, we will give you the example of rusts and smuts, which are diseases caused by members of the group of fungi which is the most advanced in evolutionary terms, the Basidiomycota; while late blight of potatoes and downy mildew of grapes are diseases caused by the most ancient of fungal-like organisms, belonging to the Oomycota in Kingdom Straminipila. Diseases such as chestnut blight, peach leaf curl, Dutch elm disease, net blotch of barley, beet leaf spot, apple blotch, maple leaf spot and thousands of others are caused by all those fungi in between these extremes. There is an enormous number of plant disease fungi, so many that there’s a rumour about a monastery somewhere in the Himalayas where the monks are listing all the names of plant diseases. When they’ve entered the last one in their list, the Universe ends, and we start all over again. But next time mushrooms rule; OK?

Crop losses due to weeds, pathogens and animal pests can be very substantial (see above) and crop protection measures are needed to safeguard food crops; but not all cultivated crops susceptible to disease are food crops. A disease of the native American chestnut, Chestnut Blight (caused by an introduced parasite), effectively eliminated a valuable timber and nut-crop tree from the United States. A similar loss happened in the UK when large elm trees were killed by Dutch Elm disease (also caused by an introduced parasite but this time the introduction was from the US and into Europe), although this loss is more difficult to quantify because it is a loss of amenity as much as commercial value.

Before the development of fungicides, fungal disease periodically caused massive devastation of crops and consequently mass starvation. The Irish potato famine in the mid-19th century is the prime example (see Resources Box 14.2); but it was caused by Phytophthora infestans (Oomycota). So far in this text we have refused to include these fungus-like organisms of Kingdom Straminipila as true fungi at all (see Section 3.10), but every crop we grow suffers at least one Phytophthora disease (Erwin & Ribeiro, 1996) so we cannot ignore these organisms in a Chapter about plant diseases. Fungi cause most plant diseases, but they figure in only a minority of animal diseases; these will be discussed in Chapter 16.

Resources Box 14.2

The Potato Murrain

The Irish potato famine in the mid-19th century was caused by Potato Late Blight (Phytophthora infestans).

CLICK HERE to visit a page that describes The Potato Murrain

Fungal pathogenesis in the marine environment is poorly researched. One newly identified, but uncultured, marine lineage has been named novel chytrid-like-clade-1 (NCLC1). Ribosomal RNA gene phylogenies demonstrate that NCLC1 is a clade that is either a basal or a sister branch to the Fungi. NCLC1 cells form intracellular infections of diatoms in what appears to be a necrotrophic pathogenic interaction (Chambouvet et al., 2019). This may prove to be an important disease syndrome because diatoms are important planktonic primary producers in so many aquatic environments.

Updated September, 2020