In-soil organisms as drivers of pest and disease control

This section treats the ability of in-soil organisms to act as natural competitors, predators, parasites or antagonists, and thereby as biological control agents for pest species or plant diseases. According to Cook et al. (1996), pests are organisms at population densities that cause death or injury, or constitute a nuisance to crops, livestock, pets, people, or the environment. Pest refers to weeds, plant parasitic nematodes, arthropod pests of plants, animals, plant pathogenic viruses, prokaryotes (including bacteria, mycoplasma-like organisms (MLOs), and spiroplasmas), and fungi. Disease is a process that results from a compatible interaction between virulent pathogen and susceptible plant.

Plant disease refers to infectious diseases caused by plant pathogenic viruses, viroids, bacteria, mycoplasma-like organisms (MLOs), spiroplasma, fungi, and nematodes. Diseases, however, can also be caused by abiotic factors such as unfavourable soil properties, fertility imbalances, moisture extremes, temperature extremes, chemical toxicity, physical injuries (Kennelly et al., 2012).

Pest control has often been highlighted as an important ecosystem service provided by biodiversity and one that is threatened by modern agricultural practices (Wilby and Thomas, 2002). The natural enemies of insect pests are responsible for about 50–90% of the biological pest control occurring in crop fields (Martin et al., 2013). Soils provide habitat to beneficial species that regulate the composition of communities and thus can prevent proliferation of herbivores and pathogens. This service depends not only on the health of the soil, including its abiotic properties, but also on the biological processes driving inter- and intraspecies interactions (symbiosis, competition, host–prey associations) (Aislabie and Deslippe, 2013). A healthy soil community has a diverse food web where beneficial organisms can contribute to suppressing pests and disease-causing organisms through competition, predation, and parasitism. Evidence from natural systems shows that low diversity of an ecosystem can be associated with a higher vulnerability to pests due to altered top-down and bottom-up control mechanisms. In agricultural fields, for example, the soil functioning is modified and, as a consequence, its equilibrium can be altered leading to outbreaks of crop pests (Turbe et al., 2010).

Soil fauna

As a rule, all species of animals are regulated by other living organisms (antagonists) that are not under manipulation by man but occur naturally in crop environments.

Microarthropods and annelids have been shown to contribute significantly to the ecosystem service

‘pest and disease control’. Especially the activity of soil fauna in the control of soil-borne phytopathogenic fungi and their mycotoxins has been investigated (e.g. Schrader et al., 2013). The successful control of fungal biomass and the reduction of deoxynivalenol of Fusarium-infected dead organic matter has been demonstrated for the earthworm species Aporrectodea caliginosa and Lumbricus terrestris (Oldenburg et al., 2008; Wolfarth et al., 2011a,b) and for the collembolan Folsomia candida and the nematode Aphelenchoides saprophilus (Wolfarth et al., 2013, 2015). Sabatini and Innocenti (2001) could show that the selective feeding activity of the collembolan species Onychiurus armatus and Mesaphorura krausbaueri on pathogenic fungi of millet and wheat kernels significantly reduced the severity of the disease complex in winter cereals.

Also, the interaction between the activity of the grazing collembola Proisotoma minuta and Onychiurus encarpatus and those of three biocontrol fungi were studied for suppression of Rhizoctonia solani on cotton (Curl et al., 1988; Lartey et al., 1994). Interestingly, all combinations of collembola and fungi inoculations provided more effective disease suppression than the fungal agents used alone.

It has been argued that such effective control mechanisms result from the combined preference of soil fauna species for some phytopathogenic fungi, their aversion for other fungal species acting as biocontrols and the direct parasitism of the fungus by other agents.

Key drivers Main taxa/

groups Main exposure routes Example species

Bacteria and fungi feeders,

Contact soil/soil pore water Contact litter/litter waterfilm Microorganisms Bacteria Contact soil/contact soil pore water

Mycorrhizal fungi

Contact soil/contact soil pore water Fungi Contact soil/contact soil pore water

Nematodes within agroecosystems provide numerous ecological services and economic benefits for pest and pathogen control. Predatory, entomogenous, and entomopathogenic nematodes (EPNs) and omnivorous nematodes consume insect pests, fungal and bacterial feeders control populations of fungal and bacteria pathogens of plants, as in the case of Aphelenchus spp. (Lagerlof et al., 2011), while plant-feeding nematodes can also affect weeds. Entomogenous nematodes, i.e. nematodes associated (often parasitically) with insects, are a group of insect-killing nematodes. Some species are currently used for biological control or Integrated Pest Management (IPM). EPNs live parasitically inside the infected insect host, and so they are termed as endoparasitic. They carry bacteria that infect many different types of insects living in the soil, like the larvae of moths, butterflies, flies and beetles, as well as adult grasshoppers and crickets. EPNs have been found all over the world and in a range of ecologically diverse habitats. Nine families of nematodes (Allantonematidae, Diplogasteridae, Heterorhabditidae, Mermithidae, Neotylenchidae, Rhabditidae, Sphaerulariidae, Steinernematidae and Tetradonematidae) include species that attack insects and kill or sterilise them, or alter their development. The most commonly studied entomopathogenic nematodes are those that can be used in the biological control of harmful insects: the members of Steinernematidae and Heterorhabditidae families. Entomopathogenic nematodes from the families Steinernematidae and Heterorhabditidae have proven to be the most effective as biological control agents (Kaya and Gaugler, 1993). They are soil-inhabiting organisms and can be used effectively to control soil-borne insect pests, but are generally not effective when applied to control insects in the leaf canopy. When considered as a group of nearly 30 species, each with its own suite of preferred hosts, entomopathogenic nematodes can be used to control a wide range of insect pests, including a variety of caterpillars, cutworms, crown borers, grubs, corn root worm, cranefly, thrips, fungus gnat and beetles. Dozens of different insect pests are susceptible to infection by entomopathogenic nematodes, yet no adverse effects have been shown against beneficial insects or other non-target animals in field studies (Georgis et al., 1991; Akhurst and Smith, 2002). In addition, EPN are often important for the potential control of alien insect species (Landi et al., 2009). Certain nematodes can also parasitise spiders, leeches, annelids, crustaceans and molluscs.

EPNs can be used as biological control agents to suppress a variety of economically important insect pests, especially in IPM and integrated production (IP) systems (Grewal, 2002; De Nardo and Grewal, 2003). The species that have been most studied in this context are those that have been introduced as biopesticides, while few data are available for native EPNs. Duncan et al. (2013) recorded a strong negative correlation between the density of native EPNs and the abundance of the root weevil pest of citrus, Diaprepes abbreviatus, highlighting that EPNs can have an important role in the control of the population of this insect pest. Indeed, when evaluating the potential of the use of chemicals integrated with biological control agents (e.g. EPNs), the International Organization of Biological Control (IOBC) developed a sophisticated approach based on a tiered hierarchy made up of threshold values for lethal and sublethal effects on non-target antagonists (Manachini, 2013).

However, some synergy of EPNs used together with chemical pesticides has been recorded. Control of larvae of Diabrotica virginifera was enhanced by such combination, resulting in a synergistic response and an increase in expected mortality of 24%; the combined effect of the insecticides plus EPNs was greater than either product applied on its own (Nishimatsu and Jackson, 1998). The mechanism for increased nematode efficacy when used together with chemical pesticides is not fully known, although it has been suggested that it could be due to a reduction in the host insect’s immunity and activity even at sublethal dosages (Manachini, 2013). On the other hand, Campos-Herrera et al. (2008) have shown that natural EPN populations isolated from crop fields appeared less active against Galleria mellonella than those isolated from natural areas and field edges, suggesting that agronomic management could affect their natural activity, reducing their virulence and reproductive potential.

In order to support the long-term performance of the functional role of soil fauna in control of pest and pathogens in agricultural soils, it is recommended to define the SPU as the abundance/biomass of population of microarthropods and earthworms as fungal pathogen controller, while it is recommended to define the SPU as the abundance/biomass of nematode species belonging to different functional groups. Nematodes can be allocated to functional groups to condense information efficiently and to determine their contribution to ecosystem processes, e.g. feeding groups as bacterivores, fungivores, plant feeders, vertebrate and invertebrate pathogens, carnivores or omnivores (see e.g. Bongers and Bongers, 1998). These functional groups could be used as indicators to interpret the nematodes’ contribution to the ecosystem services ‘pest and disease control’. Additionally, grouping according to the c-p scale (see Appendix A) could help to interpret changes in the community structure and to indicate a decrease in diversity and ecosystem stability.

Regarding soil microarthropods and earthworms, the species specific preference for fungal pathogens require the definition of SPU at the level of abundance/biomass of populations.

Soil microorganisms

Agricultural systems host numerous microorganisms with the ability to control populations of pests and diseases (Persmark et al., 1995; Kasiamdari et al., 2002; Barrios, 2007; Stewart et al., 2010).

These exert not only control under natural conditions, but also represent a resource that can be tapped for isolates for development of biological pest- and disease-control products. Microbial biocontrol agents include natural enemies and antagonists of pests and pathogens (Cook et al., 1996).

Beneficial species include microbes that support plant growth through increasing nutrient availability and by outcompeting invading pathogens (Aislabie and Deslippe, 2013). Some microbes isolated from soil and other habitats have been developed into biocontrol agents and subsequently marketed as biocontrol products. Examples are antagonistic bacteria and fungi used against fungal plant diseases (Whipps and Gerhardson, 2007), pathogens of pest nematodes (Dong and Zhang, 2006; Wilson and Jackson, 2013), and entomopathogenic fungi and bacteria (Inglis et al., 2001). Species reported to act as biocontrol agents in compost-amended substrates include bacteria, such as Bacillus spp., Enterobacter spp., Flavobacterium balustinum and Pseudomonas spp., and fungi such as Penicillium spp., Gliocladium virens and several Trichoderma spp. (Litterick et al., 2004). These beneficial microorganisms can be released from the compost or the compost may provide nutrients that stimulate the proliferation of antagonistic bacteria and fungi in the rhizosphere (Noble and Coventry, 2005; Green et al., 2006). Four main mechanisms of suppression by the beneficial microbe of the pathogen have been described: competition for nutrients; antibiotic and enzyme production; parasitism and predation; and enhanced resistance to plant diseases (both induced systemic resistance and systemic acquired resistance). Several or all these different mechanisms of disease suppression may occur simultaneously through the activity of one or more beneficial microorganisms present in disease-suppressive soil or composts. For example, several different Trichoderma spp. can compete with pathogens for nutrients and space, exhibit antibiosis, parasitise the pathogen and elicit induced plant resistance. Fungi are the predominant pathogens of insects and play a significant role in the natural regulation of soil-dwelling pests. Insecticidal toxins are produced by most entomopathogenic fungi during pathogenesis. After successfully penetrating the insect cuticle, the fungi enter the haemocoel where they have to overcome insect immune responses in order to colonise and to kill the host.

Generally, these toxins are bioactive secondary metabolites secreted during growth inside the insect.

There is no doubt that soils harbour a high diversity of microorganisms that contribute to biological population regulation and more specifically to natural control of pests and diseases. For practical reasons, however, it is extremely difficult to estimate the total range of this control activity, and the contribution of different microbial groups and species. For example, although there have been estimates of the population densities in soil of the marketed biocontrol entomopathogens Metarhizium spp.

(Bidochka et al., 1998; Schneider et al., 2012) and Bacillus thuringiensis (Eskils and L€ovgren, 2011; Guidi et al., 2011), very little is known regarding their effect on insect populations under natural conditions.

The natural plant disease-control effect is for some diseases manifested as a general soil suppressiveness and it has been known for a long time that certain soils are suppressive to specific soil-borne plant pathogens (Bidochka et al., 1998; Weller et al., 2002; Termorshuizen and Jeger, 2008).

It has been demonstrated that antagonistic microorganisms play a decisive role for this suppressiveness, and for some diseases, the biological basis and contributing microbial groups have been at least tentatively identified (Weller et al., 2002; Mendes et al., 2011).

Mycorrhizal fungi have also been reported among the groups of microorganisms showing antagonism to pathogens, showing the potentials for use as biocontrol agents for soil-borne diseases.

The role of mycorrhizae in disease control has been observed both in arbuscular mycorrhizae and in ectomycorrhizal associations. The most relevant aspects of ectomycorrhizae that make them efficient for plant-disease control are: (i) efficient competition with the ubiquitous soil microflora, (ii) root colonisation and mycorrhiza formation at rates faster than the pathogen invading the roots, (iii) suppressive action against most pathogenic species. For arbuscular mycorrhizae, the possible mechanisms involved in biocontrol are: i) enhanced plant nutrition, ii) biochemical changes in plant tissues, iii) anatomical changes, iv) alleviation from stresses predisposing plants to disease, (v) microbial changes in the rhizosphere (mycorrhizosphere), (vi) induced changes to the root-system morphology, (vii) direct competition between the fungi and the pathogens for physical space or resources, and (viii) induction of systemic resistance (Harrier and Watson, 2004; Mukerji and Ciancio, 2007).

Regarding the entity to protect for these fungal groups, as mentioned above in Section5.3(service of nutrient cycling), the high range in trait expression within arbuscular mycorrhiza species, highly dependent on the plant they establish the symbiosis with, and the high trait variability between

individuals in the case of ectomycorrhizae, as well as the lack of adequacy of the species concept for this fungal group, makes it appropriate to base the risk assessment at the functional group level (arbuscular mycorrhizal and ectomycorrhizal fungi).