Abstract
The majority of arable and annual horticultural field crops within the UK are grown as part of a rotation. This is to manage fertility, particularly in organic production systems, and reduce the incidence of soil-borne pests and disease. Crop rotation and its associated management practices generally disrupt the life cycles of microbial and invertebrate species in the soil, through host alternation and physical disturbance. In recent years there has been considerable interest in, and development of, management practices that increase the diversity of vegetation within fields. These include components of the England Rural Development Programme Environmental Stewardship Scheme, in which Entry Level Stewardship (ELS) aims to tackle countrywide environmental problems (including loss of biodiversity) through, for example, conservation headlands, beetle banks and field corner management. One of the principal aims is to provide additional habitats for animal species in order to increase biodiversity and, where possible, increase levels of natural pest control. As well as increasing plant diversity across the farm, some of these practices also increase the proportion of permanent vegetation within fields, and the temporal and spatial connectivity between patches of non-crop vegetation. In addition, certain cropping practices, such as companion planting and undersowing, also increase plant diversity within fields. These practices may be combined with other operations designed to improve the field environment, such as the use of minimal tillage (widely used in America and gaining increasing attention in the UK) and the application of organic amendments to soil, such as mulches or composted green waste. The benefits of crop rotation for disrupting the life cycles of crop-specific pests and diseases are relatively well understood. However, there are significant gaps in understanding the effects of rotation on other key members of agro-ecosystem communities, particularly soil microorganisms. This is especially true for generalist microbial pathogens in the soil. Pathogen mediated effects are highly significant for the diversity of ecosystems (Hudson et al., 2006), but there is little information on how generalist pathogens in agroecosystems respond to crop rotations and other management practices (although general ecological theory would suggest that they are likely to behave differently, and in more complex ways, than specialists). Similarly, research on the effects of increased within-field plant diversity (e.g. SAPPIO LINK project LK0915 - 3-D farming; HH3123SFV; HL0174LFV) has concentrated on invertebrate species (natural enemies and pests) rather than microorganisms. The focus of this project is on two generalist fungal pathogens; the entomopathogenic fungus Beauveria bassiana and the plant pathogenic oomycete Pythium. Fungi are an important component of the soil microflora (for example up to 5000 species can be commonly found per gram of soil) and – in addition to their role as pathogens - perform important functions related to water dynamics, nutrient cycling, disease suppression and decomposition. Entomopathogenic fungi are naturally widespread in agroecosystems. Defra-funded research at Warwick HRI has shown that populations of entomopathogenic fungi are more abundant in soils from permanent pastureland than arable crops (suggesting that disturbance through tillage could well have a detrimental effect on fungal populations) (Chandler et al., 1997). We have also discovered significant differences in fungal abundance between hedgerows and cropped land. However, we do not know how fungal populations are affected by crop rotations or habitat manipulations such as conservation headlands or organic amendments. In addition, we have little understanding of the mechanisms that determine the interaction between populations of entomopathogenic fungi, their insect hosts, and the environment. This aspect of the project will focus on Beauveria bassiana, which is the dominant species of ascomycete entomopathogenic fungus in natural communities in the UK. New evidence is emerging from research at Warwick HRI and elsewhere that B. bassiana is comprised of a number of genetically distinct groups or clades (sometimes referred to as an ‘aggregate species’). Work at Warwick HRI indicates that four major clades are found in the UK. However, as with many micro-organisms, there is a poor understanding of the factors that determine the diversity of B. bassiana and the occurrence of the clades (Rehner & Buckley, 2005) including the influence of land use and host diversity. The fungus is thought to exhibit a ‘sit and wait’ life cycle comprised of both free-living and host-associated phases (Myers & Rothman, 1995), which suggests that its population biology is influenced by contemporary environmental variation as well as host availability. A combination of host- and habitat- selection could result in local adaptation, which – according to mathematical models – is a key driver of biodiversity in host-pathogen systems (Dybdahl and Storfer, 2003). Because many ascomycete entomopathogenic fungi can infect insects across different trophic levels, they could have complex effects on insect communities. Changes in populations of entomopathogenic fungi could have simultaneous desirable and unwanted effects, depending on the host range of the fungus. For example, habitat manipulations that increase the abundance of Beauveria bassiana, could have positive outcomes, in terms of increased control of insect pests, but they could also have adverse effects on populations of beneficial insects, such as predatory beetles, both directly by causing infections, and indirectly through competition. The oomycetes (formally classified as fungi) are another major component of the soil microflora There are more than 500 species in the Oomycetes. They are filamentous protists that absorb food from the surrounding water or soil, or may be parasitic on other organisms. As such, oomycetes play a critical role in the decomposition and recycling of decaying matter. Pythium is an important genus within the oomycetes, comprising approximately 120 species that occupy diverse habitats ranging from terrestrial ecosystems to salt water estuaries. Many species are plant pathogens, whereas others are strict soil saprophytes, or are parasites of insects, mammals, algae, or fish. Certain non phytopathogenic species show promise as biological control agents capable of protecting plants from attack by pathogenic species. Some phytopathogenic species have broad host ranges, whereas other species infect a narrow spectrum of plants. For example, P. aphanidermatum and P. ultimum infect a number of economic crops, while P. graminicola and P. spinosum have more restricted host ranges. Likewise, different levels of virulence may be observed among species capable of infecting a specific host. Soil-borne diseases caused by phytopathogenic Pythium spp. afflict many crop and non-crop plant species. Pythium spp. are the most important pathogens infecting seeds or seedlings before emergence from the soil, resulting in pre-emergence damping-off. The behaviour of Pythium spp. in the soil is moderated by environmental factors such as moisture, temperature, soil pH, and the presence of specific soil minerals. These environmental parameters can influence fungal growth or development directly or indirectly, through effects on competing or antagonistic soil microorganisms. The environment can also have profound effects on host susceptibility and symptom expression. Although there is considerable literature describing the effects of environmental conditions on Pythium species, there has been no systematic study of changes in, and the movement of, pathogen populations in soil in response to cropping sequences and habitat manipulations. The Countryside Survey is the most comprehensive review of the state of the UK countryside that has been conducted in the UK. It has been designed to provide detailed information about a wide range of habitats and landscape features that are important elements of our countryside. The survey has provided critical information on resources, and an insight into their condition, based on the variety and abundance of the species associated with them. It has provided measures of the current state of the countryside and indicators describing the changes which have taken place. To date, the survey has not made full use of information on soil microbial diversity, in particular fungal diversity. Countryside Survey 2000 has provided the information necessary for reporting on biodiversity in the wider countryside, measuring progress towards sustainable development and detecting the impacts of human activities and global environmental change. In collaboration with the Centre for Ecology and Hydrology, we propose to make use of samples collected for the Countryside Survey 2007. Soil samples from a wide range of habitats will be collected for the survey and DNA will be extracted from the soil by CEH, Oxford (for identification of soil bacteria). DNA from a sub-set of these samples will be available to this project for sampling entomopathogenic fungi and oomycete pathogens.
United Kingdom