Summary
This project on Pasture Plant Interactions with Soil Organisms in the Rhizosphere was initiated as part of MLA's Pasture Soil Biology Initiative. The objective was to undertake basic science to explore new opportunities for investigating the interaction of soil microorganisms in the rhizosphere of pasture plants. The project aimed to develop and apply new technologies to visualise and quantify the effects of soil microorganisms on plant growth, with a view to identifying and developing management strategies that optimize the contribution of microorganisms to the productivity and sustainable of pasture systems.
Major achievements of the project were:
A survey of the literature showed that biological constraints are an important issue that can potentially reduce the productivity of Australian pastures and that microbial interactions in the rhizosphere may mitigate the severity of root diseases. The importance of disease on the growth of pasture plants was demonstrated in glasshouse experiments using intact cores of field soil. Whilst incidence of disease was highly variable, a number of potentially important root pathogens were identified. Controlled studies in sand culture showed that infection of roots of pasture plants by Pythium sp. significantly reduced root growth, whereas less consistent results were obtained in soil.
New methods for the study of rhizosphere microorganisms were developed. This included a fluorescence-microscopy technique for direct visualisation of Pythium infection on pasture roots and procedures for tagging different species of rhizobacteria with fluorescent proteins. Bacteria that inhibited the growth of Pythium in laboratory media were isolated from the rhizosphere of pasture plants.
A system for the collection of root exudates from pasture plants was established for sand-grown plants and the C composition of the exudate was analysed by GCMS. Defoliation of plants caused a significant change to the allocation of C to root growth and the quantity and composition of C in root exudates, which has important implication for root interactions with soil microorganisms. Attempts to isolate root exudates directly from soil-grown pasture plants were unsuccessful. The presence of various fungal (and oomycete) root pathogens and beneficial fungi in soil and on plant roots was investigated by quantitative DNA analysis (collaboration with SARDI). Although the presence of plant roots increased the DNA content of different fungal groups, no specific effects occurred in response to defoliation. Microbial DNA content of soil was also generally not affected by P status, although higher mycorrhizal content of roots was evident in low P soil, with a possible interaction between the presence of mycorrhizal fungi and reduced presence of Pythium. However, in all cases there was high variability in the fungal DNA content of soil which was exacerbated by the presence of plants. No clear relationship was identified between changes in microbial DNA content in soils with changes in the rhizosphere, and to the extent of fungal infection on plant roots.
Results from the project showed that DNA-based technologies hold considerable promise for investigating the behaviour of specific groups of microorganisms in the rhizosphere of plants. DNA-based techniques provide insight into the response of microorganisms to soil and plant treatments in ways that could not be achieved using more conventional techniques. The study also showed that GCMS has considerable potential for quantifying the C composition of root exudates and to the understanding of how plants respond to treatments that are indicative of management options for pastures. Microbial DNA assays were successfully quantified groups of pathogenic and beneficial microorganisms, directly in bulk soil, rhizosphere soil and within plant roots. However, microbial DNA concentrations in soil were subject to high variability which was largely associated with intrinsic spatial variability in the distribution of the microbial species in field soil which were used as intact cores of soil. High intrinsic variability of different pathogens was further accentuated by the stimulatory presence of plant roots, which meant that it was difficult to interpret results from treatment effects that were imposed under glasshouse conditions.
Whilst a number of measures were undertaken to limit this variability (i.e. increased replication, use of mixed and reconstituted soil cores rather than intact field cores, and controlled inoculation treatments), these also proved to be largely unsuccessful for root pathology studies in the glasshouse. In addition, it was evident from glasshouse studies that the presence of high DNA content of specific pathogens was not necessarily indicative of high incidence of root damage and/or clear evidence of root disease. Further studies to correlate measured DNA content of specific pathogens in soil and incidence of disease on plants roots is required, as this relationship remains poor. Whilst it may be a consequence using glasshouse-grown plants, we are also aware of similar issues under field conditions.
In addition to ensuring that the DNA probes used are representative of causative organisms, further investigation of the importance of environmental factors (e.g. soil type, climatic conditions, management practices, etc) that contribute to the outbreak of root diseases is needed. As well as greater emphasis on use of field sites, this will require input from a plant pathologist. Future studies on the molecular ecology of soil-borne root pathogens, therefore, need to focus on field studies, with glasshouse studies limited to validation (e.g. pathogenicity tests in sand culture) and/or high-throughput germplasm screenings where artificially high inoculum levels can be used without compromising the outcome. Improved understanding of how soil microorganisms interact with plant roots and respond to pasture management will, in the longer term, allow more informed decisions to be made in soil health and the productivity and sustainability of pasture systems. It is expected that such information will be readily available to growers and routinely used within the next 5-10 years.
