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Review of the scientific literature to determine the extent of knowledge on the impact of crop management strategies on soil microbial populations - IF0117

Description
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.
Objective
The aim of this project is to study biodiversity in contemporary cropping systems. The project will provide new insights into the effect of disruptive and non-disruptive crop manipulations on the abundance and diversity of soil microbes in agroecosystems. It will focus on two groups of microbial pathogens; ascomycete entomopathogenic fungi, whose influence within agricultural systems is generally perceived to be benign, and oomycete plant pathogens, whose influence is generally perceived to be detrimental. The project will be designed in a way that will allow the addition of further experimental modules at later stages (e.g. for plant and soil biodiversity) if required.

The component objectives are as follows:
1. Review the scientific literature to determine the extent of knowledge on the impact of crop management strategies on soil microbial populations.
2. Use the information from Objective 1 to finalise the cropping sequences and management options to be studied in experimental systems.
3. Determine the effect of permanent and temporary habitat manipulations and crop rotation on the abundance and diversity of soil populations of an ascomycete entomopathogenic fungus, Beauveria bassiana, and an oomycete plant pathogen, Pythium.
4. Quantify the relationship between the diversity and abundance of populations of insects and entomopathogenic fungi in different agroecosystem habitats.
5. Quantify the relationship between the diversity and abundance of selected Pythium species and plant biodiversity in field margins

Objective 1. Review the scientific literature to determine the extent of knowledge on the impact of crop management strategies on soil microbial populations

The aim of this objective is to identify relevant literature to ensure that this project does not repeat previously undertaken research. As a consequence, it will provide a robust framework for the project.

A literature review will be undertaken to determine the extent of knowledge on:
• Current crop management practices - including trends in rotations.
• Habitat manipulations currently in use through schemes such as the Environmental Stewardship ELS and other potentially innovative habitat manipulations.
• Impact of soil manipulations and perturbations on entomopathogenic fungi and oomycete pathogens.
• Impact of soil biodiversity on plant and insect biodiversity.


Objective 2. Use the information from Objective 1 to finalise the cropping sequences and management options to be studied in experimental systems.

Using the outputs of Objective 1 above, a detailed project plan will be drawn up for discussion with the Defra Project Officer. This will include information on the specific crop rotations and habitat manipulations to be used.

Objectives 3-5 below provide an outline of the experimental plan - although this is likely to be revised in the light of the detailed literature review.


Objective 3. Determine the effect of permanent and temporary habitat manipulations and crop rotation on the abundance and diversity of soil populations of an ascomycete entomopathogenic fungus (Beauveria bassiana) and an oomycete plant pathogen (Pythium).

This Objective will use two field-based experiments to investigate the effects of modern farm practice on microbial populations. The abundance and diversity of B. bassiana and selected Pythium species in soil will be determined using quantitative PCR of DNA extracted from soil, using standard techniques in place at Warwick HRI. Quantitative PCR will be based on specific primers for up to six major Pythium species and the four major clades of B. bassiana found in the UK.

An outline of the experiments is described below. The final design of the experiments, including the cropping sequences and management options used, will be finalised in Objective 2 following completion of Objective 1:

Validation of quantitative PCR. Primers used for Pythium species are already available. Primers for the B. bassiana clades will be designed from sequence information for gene Elongation Factor 1á generated at Warwick HRI in RELU* funded research. Some validation work will be required to optimize the DNA extraction procedure for the different soil types used in the project, optimize PCR conditions, and confirm the specificity of the primers. As a baseline exercise, a bioassay will be done, using quantitative PCR, to relate measures of B. bassiana density in soil to its pathogenicity to two model host insects (Galleria mellonella (Lepidoptera) and Tenebrio molitor (Coleoptera)). (* RELU = Rural Economy and Land Use programme).

Effect of tillage and the application of organic amendments on fungal abundance and diversity. A replicated field experiment will be set up to measure the effect of minimal tillage and the application of organic amendments on the abundance and diversity of B. bassiana and selected Pythium species in soil supporting a cereal crop. Two replicates will be based at Warwick HRI Wellesbourne and the third at our Kirton centre. The experiments will be in place for the life of the project. The intention is to use plots that are sufficiently big to be an accurate reflection of the behaviour of full-scale field crops while still enabling us to use a workable number of treatments and replicates (at present we are planning to use 60 m x 60 m plot sizes, based on our general experience). Each replicate will consist of four treatments: minimal tillage; minimal tillage plus organic amendment; conventionally ploughed crop; conventionally ploughed crop plus organic amendment. Approximately 50 soil samples will be taken from each plot and from surrounding margins/hedgerows on two occasions per year (spring and early autumn) using sampling protocols already in place at Warwick HRI. The abundance and diversity of B. bassiana and selected Pythium species in each plot will be determined using quantitative PCR. The experiment will establish how fungal populations change over time in response to minimal tillage and organic amendments, and the interaction between them.

Effect of crop rotation on fungal abundance and diversity. A second replicated field experiment will be set up to measure the effect of crop rotation on the abundance and diversity of B. bassiana and selected Pythium species in soil. Two replicates will be based at Wellesbourne, the third at Kirton, and the experiments will be in place for the life of the project as described above. Plot sizes are likely to be the same as described above. Each replicate will consist of four treatment plots surrounded by a semi-permanent field margin and a hedgerow. Each plot will contain one crop type in a four crop rotation. Soil samples will be taken twice a year from each plot, plus the field margin and hedgerow, and analysed as described above. The crop rotation will be chosen in Objective 2.

In addition to these replicated experiments, soil samples will be taken from cropped and environmentally-managed areas in commercial crops. This is to provide comparative data on the abundance and diversity of the two species of microorganism. The samples will be obtained via the Countryside Survey or by targeted sampling.


Objective 4. Quantify the relationship between the diversity and abundance of insect and fungal populations

This objective will be done in parallel to Objective 3 and will investigate the relationship between populations of B. bassiana and beetles in agro-ecosystems. The experiment will be done using existing cereal crops at Warwick HRI. Populations of B. bassiana will be sampled from soil collected from cereal crops and their surrounding hedgerows at least twice a year through the life of the project. The abundance and diversity of B. bassiana populations will be determined using quantitative PCR as above. At the same time, populations of ground dwelling beetles will be sampled using ‘live’ pitfall traps and identified using standard taxonomic keys (beetle sampling is already in place at Wellesbourne). The aim is to look for relationships between the abundance and diversity of the fungus, habitat type, and the abundance and diversity of coleopteran species. Quantitative PCR will be used to determine infection levels in beetles. The data will be analysed for: (a) differences in beetle populations between sampling locations; and (b) correlation between fungal abundance and diversity, beetle abundance and diversity, habitat type, and time.


Objective 5 Quantify the relationship between the diversity and abundance of selected Pythium species and plant biodiversity in field margins.

The relationship between the abundance and diversity of Pythium and plant species diversity in field margins will be determined using samples collected via the Countryside Survey - augmented as required by targeted sampling.


References
Chandler, D., Hay, D. B. & Reid, A. P. (1997). Sampling and occurrence of entomopathogenic fungi and nematodes in UK soils. Applied Soil Ecology, 5, 133-141.
Dybdahl, M. F. & Storfer, A. (2003). Parasite local adaptation: Red Queen versus Suicide King
Trends in Ecology and Evolution, 18, 523 – 530.
Hudson, P.J, Dobson, A.P. & Lafferty, K.D. (2006). Is a healthy ecosystem one that is rich in parasites? Trends in Ecology and Evolution, 21, 381 – 385.
Myers, J. H. & Rothman, L. E. (1995). Virulence and transmission of infectious diseases in humans and insects: Evolutionary and demographic patterns. Trends in Ecology and Evolution, 10, 194 – 198.
Rehner, S.A. & Buckley, E. (2005). A Beauveria phylogeny inferred from nuclear ITS and EF1-á sequences: Evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia, 97, 84 – 98.


Project Documents
• Final Report : Review of the scientific literature to determine the extent of knowledge on the impact of crop management strategies on soil microbial populations   (228k)
Time-Scale and Cost
From: 2007

To: 2007

Cost: £49,820
Contractor / Funded Organisations
Warwick - HRI
Keywords
Allocated - WHRI              
Arable              
Biodiversity              
Biological Control              
Crops              
Integrated Farming Systems              
Pest and Weed Control              
Plant Pests and Diseases              
Soils              
Sustainable Farming and Food Science              
Sustainable Farming Systems              
Weed Control