The foundation for the group's research in environmental biotechnology is our extensive experience in the area of molecular microbial ecology. Understanding how microbes survive, grow and interact in their ecological niche is fundamental to their exploitation for biotechnological applications to promote sustainable agriculture (Fig. 3).
Microbes do not grow in isolation but interact extensively with other organisms in the environment. A major focus of the group’s research in recent years has been on how signalling between plants and bacteria, and between bacteria and fungi, influences the lifecycle of these organisms. This work has included characterisation of signal molecules (root exudates, amino acid cycling), investigation of the mechanisms by which these signals influence genetic regulatory pathways in target organisms, and analysis of the phenotypic consequences of the signalling systems. We are also actively working on systems for in situ monitoring of microbes, gene expression and microbial interactions using autofluorescent proteins, confocal microscopy, GeneChip technology and Proteomics. This provides an important new dimension to microbial ecology and allows bridging of the gap between molecular studies in laboratory conditions and microbial ecology.
A consequence of our research into ecological interactions has been the development of a research programme in the area of biodiversity. Specifically, we are interested in understanding the factors that influence biodiversity, and in the mechanisms by which changes in biodiversity are effected. One such research program at BIOMERIT is the DAFF research stimulus funded project ‘P-solve’, which specifically addresses how ‘high’ or ‘low’ inputs of phosphate to an agricultural soil system influences the inorganic phosphate solubilizing community. As part of this research theme, we aim to generate a greater understanding of the genetic mechanisms involved in bacterial phosphate mobilisation in the soil and rhizosphere using the soil microbe Pseudomonas fluorescens as a model. Another project which is linked to this area, the EU Sixth Framework project 'Micromaize', will analyse and develop the use of Pseudomonas fluorescens in a consortium with Azospirillum and Glomus arbuscular mycorrhizal fungi for inoculation and growth promotion of Maize crops (Fig. 4). Recently, we have employed genomic techniques to study interactions between plant hosts and bacteria colonising the plant root. This has revealed that plants trigger significant changes in bacterial gene expression and provide one avenue to explore the basis of host selection in these systems. The basic research that we are doing in microbial ecology provides baseline data by which the significance of changes in microbial populations can be assessed. This is of particular relevance to users of GM technology, to regulatory bodies and to public interest groups, who have expressed concerns about the ecological impact of GMOs.
Another area where our research has the potential to be exploited in biotechnology is the development of microbial strains as biocontrol agents. Many microbes have natural biocontrol ability due to the production of secondary metabolites that are inhibitory towards plant pathogens. This aspect of research within the BRC is financed by a second DAFF Research Stimulus Fund, in collaboration with Dr. Max Dow (BRC) and Dr. Fiona Doohan’s research group at UCD. This project examines the biocontrol and biofertilization mechanisms of a variety of bacterial species and the effect of these microbes on the disease resistance and growth promotion of barley and wheat crops.
More recently a Marine Biodiscovery programme has been initiated in the BRC in collaboration with Prof. Alan Dobson (ERI) and Dr. John Morrissey (Microbiology Dept.). This seven year programme has been funded by the Dept. of the Marine Beaufort Marine Research Award scheme, and involves a comprehensive collaborative programme aimed at 1) studying Cell signalling and Biofilm formation in Marine Microorganisms ultimately to help prevent bio-fouling in marine environments and 2) using a Metagenomics approach to exploit Marine Microbial Biodiversity and to identify bioactive compounds with both antimicrobial and anti-fungal activities (Fig. 5). This Beaufort award to the Marine Biodiscovery/Biotechnology cluster at the ERI / Microbiology aims to establish new research competencies in the area of metagenomics and in the screening of unculturable marine microbes and will establish the capability and capacity to isolate and identify novel bioactive compounds and enzymes such as polyketide synthases as well as novel marine microorganisms. Knowledge of novel methods to utilize metagenomic strategies to exploit uncultured microbes from Marine environments is valuable for researchers working in many areas of the life sciences and biotechnology, and exposure to knowledge and training in these technologies will advance the career prospects for researchers involved in this cluster.
A second marine related collaborative project based on the discovery and application of Novel Bioactive Substances from Marine Sponges for the Control of Major Food Pathogens, has also been recently funded by DAFF.