Parasites of plants and other eukaryotes

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Unlike animals in which bacteria and viruses play the most important roles as pathogens, the Basidiomycota and Oomycota are the main parasites in plants, being responsible for 85% of diseases. Note that some protozoa, such as Plasmodiophorida, are also capable of infecting plants. Table 17 gives the ten emerging pathogen species that worry agronomists the most; nine are fungi… On our crops, the damage they cause is at the same levels as that caused by insects or weeds. It is estimated that fungi destroy 15% of crops annually, equivalent to the consumption of 600 million human beings! The use of fungicide is therefore a big expense for agriculture. In France, an average farmer spent in 2011 per hectare around €70 for seeds, €100 for fertilizers, €50 for herbicides, €5 for insecticides and… €75 for fungicides!

The list of important species is too long to quote because each species of cultivated plants can be infected with several species of fungi, most of which are specific. The most important pathogen globally is Magnaporthe grisea/oryzae which infects barley and especially rice, the staple food for more than half of humanity. In France, Mycosphaerella graminicola, also known as Zymoseptoria tritici, causes leaf blotch disease in wheat.

Although very different phylogenetically, the strategies used by Basidiomycota and Oomycota to invade their hosts are very similar. There are two types of plant pathogenic fungi, the virulent pathogens that cause severe disease and the “non-aggressive” that cause mild symptoms. We also distinguish between biotrophic fungi that can live on the plant when it is alive and necrotrophic fungi which kill their host and feed on dead material. Other species have strategies that will successively intervene between the two types of lifestyles; they are said to be semi-biotrophic. Biotrophs are often obligatory and need to keep the plant alive to continue infection. They are generally not able to grow without their host, which complicates studying them. Because of their importance in agronomy, the strategies used by fungi to invade plants are the subject of numerous studies. Their entry points are multiple, mainly the roots and leaves. Sometimes the same species can use both entry points using strategies based on different genes. For example, Magnaporthe grisea uses an appressorium to enter through the leaves and hyphopodia to enter through the root (Figure 376). Other species will pass through the stomata (Figure 376), which they detect by the hormones these structures emit, or by wounds. If the roots are invaded by mycelium, the fungus usually arrives as a spore on the leaves, so they must first germinate. The determinism of this germination is complex and involves recognition by the fungus. These may be specific ligands or physicochemical characteristics, such as hydrophobicity.

Even before entering the plant, the fungus begins a molecular dialogue with it. It emits signal molecules which can be components of its cell wall, secondary metabolites, free radicals or small proteins called “effectors”. The plant has receptors that will detect these signals in order to set up defenses. If the plant does not recognize the fungus because it does not have the right receptors, then it is invaded. Effectors and signals are often encoded by single genes giving a simple genetic determinism for successful invasion between a plant receptor gene and a so-called avirulence gene in fungi (Figure 377). Note that effectors often have the effect of inactivating the plant’s defense systems and therefore, when not recognized, are virulence factors. A race of the Red Queen therefore exists between the plant and its parasite. Polymorphisms for receptor and avirulence genes are often present in populations of plants and fungi which means that among the different varieties of the same plant species, some cultivars are susceptible and others are resistant to particular fungal strains.

The receptors and signaling pathways in plants are similar to those in animals involved in innate immunity with domains rich in leucine (Figure 378). The receptors are either anchored on the external face of the plasma membrane like the “Toll-like” receptors or in the cytosol like the “NOD-like” receptors. These receptors activate MAP kinase signaling pathways, as in the case of innate animal immunity, which in turn cause the activation of defense genes, usually at the level of their transcription. Such genes may encode enzymes that will strengthen the cell wall at the point of contact with the fungus, enzymes that will synthesize toxic secondary metabolites or that will induce the so-called hypersensitive response. This response leads to apoptosis of the cells around the fungus (Figure 379). If the pathogen is a biotroph, its progression is thus stopped. However, it has been shown that this defense mechanism is subverted by certain necrotrophic fungi, such as Botrytis cinerea or Sclerotinia sclerotium. Indeed, these fungi secrete small molecules that activate the hypersensitive response. The fungus can then start invading the plant via these areas of cell death!

Once in the plant, the fungus can feed because it is a rich medium. Depending on the species, it remains extracellular or also invades cells. After a certain time of infection it causes lesions which range from chlorosis, discolorations of the cells, to mildew where the leaves become covered with spores or to the subsequent rotting of the plant (Figure 379).

While humans currently grow mainly plants, we are likely to have to produce more algae and fungi in the future than we do now, especially for producing biofuels (Box 32) or for food. As with plants, the main parasites we will have to deal with are Eumycota, but also other protists of very diverse origins. In the case of freshwater algae, it is more likely to be Chytridiomycota which in nature seem to be their main parasites (Figure 50). In the case of marine algae, it will probably be Oomycota. For fungi, besides nematodes, insects and mites, it will mainly be bacteria and other Eumycota. Indeed, also viruses are capable of causing symptoms in various fungi. They do not seem to have an extracellular phase, instead propagating only through anastomoses or spores. So they will probably be quite easy to control. Table 18, for example, summarizes the main diseases of Agaricus bisporus, the button mushroom.

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