Mark AchtmanTeresa BarbosaDavid ClarkeAvril CoghlanJ. Kevin CollinsAlan DobsonMax DowGerald F. FitzgeraldCormac GahanColin HillJohn MorganJohn P. MorrisseyFergal O' GaraNiall O' LearyPaul O' TooleMichael B. PrenticeMartina ScallanCarmel ShortissDouwe van Sinderen

Biography

Academic Career

1977-1981: BSc in Biochemistry, National University of Ireland, Galway

1981-1985: PhD in Biochemistry, National University of Ireland, Galway

06/1985-03/1986: Post Doctoral Research Fellow in the laboratory of Prof. D. Headon, Department of Biochemistry, National University of Ireland, Galway University College Galway.

03/1986 -09/1988: Post Doctoral Research Associate in the laboratory of Prof. B. O'Malley (Chairman), Dept. of Cell Biology, Baylor College of Medicine, Houston, Texas.

09/1988 - 09/1990: College Lecturer and Post Doctoral Research Scientist in the laboratory of Prof. Fergal O'Gara, Microbiology Department, University College, Cork.

09/1990-1997: College Lecturer in Microbiology, University College, Cork.

1997-2006: Senior Lecturer in Microbiology, University College, Cork, Ireland.

2005: Director Environmental Research Institute, University College, Cork.     

2005: DSc Microbiology & Molecular Biology, National University of Ireland

2006: Associate Professor in Microbiology, University College, Cork.

Additional Positions and Awards

• Member of the European Space Agency, Life Sciences Working Group (July 2000-June 2003).
• Member of Royal Irish Academy [National Commission for Microbiology] (January 2001-December 2003).
• Committee member of the Society for General Microbiology (Irish Area Section), 1998-2000.
• Member of the European Space Agency, Life and Physical Science Advisory Committee (LPSAC) (June 2003-2005).
• Marine Institute- Sea Change Discovery, Marine Biotechnology – Biodiscovery Implementation Team. (May 2007-onwards).
• Appointed as a member of the Panel of Experts to advise the Chief Scientific Adviser to the Irish Government. (March 2009-onwards).
• Member of the Marine Board-European Science Foundation Working Group on Marine Biotechnology- “A European Strategy for Marine Biotechnology” (Oct 2009- onwards).
• Scientific Assessor for Research Proposals: National Agency for Science and Technology (EOLAS, Enterprise Ireland), Stichting Levenswetenschappen (The Netherlands Agency), National Science Foundation (Switzerland), European Space Agency (MAP-Life Support; Mars500/Concordia), European Environmental Research Organisation, Fulbright Scholarship Scheme (Ireland-America), European Union Biotechnology Programmes (5^th, 6^th & 7^th Framework), INTAS, Food Standards Authority (UK),The Nuffield Foundation (UK), The Israel Science Foundation, the Academy of Sciences of the Czech Republic, the Spanish Ministry of Health and Consumer's Affairs, the Environment & Water Industry Development Council (EWI)- Singapore, the Engineering and Physical Sciences Research Council (UK),  the Energy Biosciences Institute at the University of California, the French Polar Institute (IPEV), the Research Fund of Innsbruck Medical University, the U.S. Army Research Office The Netherlands Genomics Initiative (NGI), and the European Science Foundation.

Awards

Fulbright Scholarship 1992.

Royal Irish Academy Senior Visiting Fellowship 1993.

Royal Irish Academy Medal in Microbiology 1999.

CBiol FSB 2005.

Teaching areas

• Food and Industrial Microbiology
• Mycology
• Environmental Microbial Genomics

Research interests and expertise

• Applied Microbiology, Environmental Biotechnology, Marine Biotechnology, Physiology and genetics of bacteria and fungi from marine and terrestrial
• Environments, Functional Metagenomics. Food Mycology/Genetics of Mycotoxigenic fungi, Eukaryotic microbes/Cell Biology.
• Postgraduate students : 21 PhD (of which, 16 have graduated)- 5 currently; 27 MSc ( of which, 26 have graduated)- 1 currently
• Postdoctoral Scientists : 16 (of whom, 8 have completed) – 8 currently

Research

Research Overview

Selected Recent Publications (2004-present)

• Kennedy, J., Baker, P.W., Piper, C., Cotter, P.D., Walsh, M., Mooij, M.J., Bourke, M.B., Rea, M.C., O’Connor, P.M., Ross, P., Hill, C., O’Gara, F., Marchesi, J.R., and Dobson, A.D.W. (2009). Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans isolated from Irish waters. Marine Biotechnology. 11: 384-396.
• Baker, P.W., Kennedy, J., Morrissey, J., O’Gara, F., Dobson, A.D.W. and Marchesi, J.R. (2009). Endoglucanase activities and growth of marine-derived fungi isolated from the sponge Haliclona simulans. Journal of Applied Microbiology. (in press) 10.1111/j.1365-2672.2009.04563.x.
• Abbas, A., Valez, H. and Dobson, A.D.W. (2009). Analysis of the effect of nutritional factors on OTA and OTB biosynthesis and polyketide synthase gene expression in Aspergillus ochraceus . International Journal of Food Microbiology 31; 135, 22-27.
• Bacha, N., Dao, H.P., Atoui, A., Mathieu, F., O’Callaghan, J., Puel, O., Liboz, T., Dobson, A.D.W., and Lebrihi, A. (2009). Cloning and characterization of a novel methylsalicylic acid synthase gene involved in the biosynthesis of isoasperlactone and asperlactone in Aspergillus westerdijkiae. Fungal Genetics & Biology 46 (10): 742-749.
• Baker, P.W., Kennedy, J., Dobson, A.D.W. and Marchesi, J.R. (2009). Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters. Marine Biotechnology. 11, 540-547.
• Forbes, C., O’Leary, N.D., Dobson, A.D.W. and Marchesi, J. (2009). The contribution of “omic” based approaches to the study of enhanced biological phosphorus removal microbiology. FEMS Microbiology Ecology 69, 1-15.
• Gallo, A., Peronne, G., Solfrizzio, M., Epifani, F., Abbas, A., Dobson, A.D.W. and Mulè, G. (2009). Characterization of a pks gene which is expressed during ochratoxin A production by Aspergillus carbonarius. International Journal of Food Microbiology 31;129(1):8-15
• Kabat, B. and Dobson, A.D.W. (2009). Biological strategies to counteract the effects of mycotoxins. Journal of Food Protection 72, (9): 2006-2016.
• Kennedy, J., Codling, C.E, Jones, B., Dobson, A.D.W. and Marchesi, J.R. (2008). Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environmental Microbiology 10 (7): 1888-1902.
• Kennedy, J., Marchesi, J.R. and Dobson, A.D.W. (2008). Marine Metagenomics: Strategies for the discovery of novel enzymes with biotechnological applications from marine ecosystems. Microbial Cell Factories. 7:27.
• Zamocky, M., Schumann, C., Sygmund, C., O’Callaghan, J., Dobson, A.D.W., Ludwig, R., Haltrich, D., Peterbauer, C.K. (2008). Cloning, sequence analysis and heterologous expression in Pichia pastoris of a gene encoding a thermostable cellobiose dehydrogenase from Myriococcum thermophilum . Protein Expression & Purification. 59 (2): 258-265.
• Kennedy, J., Marchesi, J.R. and Dobson, A.D.W. (2007). Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Applied Microbiology & Biotechnology 75, 11-20.
• Tobin, K.M., O’Leary, N.D., Dobson, A.D.W. and O’Connor, K.E. (2007). Effect of heterologous expression of phaG [(R)-3-hydroxyacyl-ACP-CoA transferase] on polyhydroxyalkanoate accumulation from the aromatic hydrocarbon phenylacetic acid in Pseudomonas species. FEMS Microbiology Letters 268, 9-15.
• Hickey, A.M., Gordon, L., Dobson, A.D.W., Kelly, C.T. and Doyle EM (2007). Effect of surfactants on fluoranthene degradation by Pseudomonas alcaligenes PA-10. Applied Microbiology & Biotechology 74, 851-856.
• Mooney, A., O’Leary, N.P. and Dobson, A.D.W. (2006). Cloning and functional characterisation of the styE gene involved in styrene transport in Pseudomonas putida CA-3. Applied & Environmental Microbiology 72, 1302-1309.
• White, S., O’Callaghan, J. and Dobson, A.D.W. (2006). Cloning and molecular characterisation of Penicillium expansum genes upregulated under conditions under conditions permissive for patulin biosynthesis. FEMS Microbiology Letters 255, (1) 17-22.
• Power, T., Ortoneda, M., Morrissey, J.P. and Dobson, A.D.W. (2006). Differential regulation of genes involved in iron metabolism in Aspergillus fumigatus. International Microbiology 9, 281-287.
• Olsen M., Jonsson, N.,Magan, N., Banks, N., Fanelli, C., Rizzo, A., Haikara, A., Dobson, A.D.W., Frisvad, J., Holmes, S., Ollku, J., Persson, S-J and Börjesson, T. (2006). Prevention of ochratoxin A in cereals in Europe. Adv. Exp. Med. Biol. 571, 317-342.
• O'Callaghan, J. and Dobson, A.D.W. (2006). Phylogenetic analysis of polyketide synthase genes from Aspergillus ochraceus. Mycotoxin Research 22, 125-133.
• Olsen M., Jonsson, N.,Magan, N., Banks, N., Fanelli, C., Rizzo, A., Haikara, A., Dobson, A.D.W., Frisvad, J., Holmes, S., Ollku, J., Persson, S-J and Börjesson, T. (2006). Prevention of ochratoxin A in cereals in Europe. In: Advances in Food Mycology. Volume 571, pp 317-342. (Eds. A.D. Hocking, J.I. Pitt, R.A. Sampson and U. Thrane); Springer, New York ).
• O’Callaghan, J., Stapleton, P.M. and Dobson, A.D.W. (2006). Ochratoxin A biosynthetic genes in Aspergillus ochraceus are differentially regulated by pH and nutritional stimuli. Fungal Genetics & Biology 43, 213-221.
• O’Callaghan, J. and Dobson, A.D.W. (2006). Molecular characterization of ochratoxin A biosynthesis and producing fungi. Advances in Applied Microbiology 58, 227-243.
• O’Mahony, M., Dobson, A.D.W., Jeremy Barnes, J. and Singleton, I. (2006). The use of ozone in the remediation of polycyclic aromatic hydrocarbon contaminated soil. Chemosphere 63, 307-314.
• Kabak, B., Dobson, A.D.W. and Var, I. (2006). Strategies to prevent mycotoxin contamination of food and animal feed: a review. Critical Reviews in Food Science and Nutrition. 46, 593-619.
• O’Leary, N.D., Ward, P., Goff, M., O’Connor, K.E. and Dobson, A.D.W. (2005). Genetic characterisation of accumulation of polyhydroxyalkonate from styrene in Pseudomonas putida CA-3. Applied & Environmental Microbiology 71, 4380-4387.
• O’Connor, K.E., O’Leary, N.P., Marchesi, J.R., Dobson, A.D.W., and Deutz, W. (2005). Isolation and characterization of a diverse group of phenylacetic acid degrading microorganisms from pristine soil. Chemosphere. 61, 965-973.
• Dobson, ADW. (2005). Styrene fuels bacterial PHA accumulation. Industrial Bioprocessing 27, 7.
• Terron, M.C., Gonzalez, T., Carbajo, J.M., Yague, A., Arana-Cuenca, A., Tellez, A., Dobson, A.D.W. and Gonzalez, A.E. (2004). Structurally closely-related aromatic compounds have different effects on laccase activity and on lcc gene expression in the ligninolytic fungus Trametes sp. I-62. Fungal Genetics & Biology 41, 954-962.
• Alemayehu, D., Gordon, L.M., O’Mahony, M.M., O’Leary, N.D. and Dobson, A.D.W. (2004). Cloning and functional analysis by gene disruption of a novel gene involved in indigo production and fluoranthene metabolism in Pseudomonas alcaligenes PA-10. FEMS Microbiology Letters 239, 285-293.
• Morrissey, W.F., Davenport, B., Querol, A. and Dobson, A.D.W. (2004). The role of indigenous yeasts in traditional Irish cider fermentations. Journal of Applied Microbiology 97, 647-655.
• Stapleton, P.C., O’ Brien, M.M., O’Callaghan, J. and Dobson, A.D.W. (2004). Molecular cloning of the cellobiose dehydrogenase gene from Trametes versicolor and expression in Pichia pastoris. Enzyme & Microbial Technology 34 (1), 55-63.
• Casey, G.D. and Dobson, A.D.W. (2004). Potential of using real-time –PCR based detection of spoilage yeast in fruit juice-a preliminary study. International Journal of Food Microbiology 91, 327-335.
• Stapleton, P.C., O’Mahony, J. and Dobson, A.D.W. (2004). Real-time PCR analysis of carbon catabolite repression of cellobiose dehydrogenase gene transcription in Trametes versicolor . Canadian Journal of Microbiology. 50, 113-119.
• Mulkerrins, D., Dobson, A.D.W. and Colleran, E. (2004). Parameters affecting biological phosphate removal from wastewaters. Environment International 30, 249-259.
• Mulkerrins, D., O’Connor, E., Lawlee, B. and Dobson, A.D.W. (2004). Assessing the feasibility of achieving biological nutrient removal from wastewater, at an Irish food processing factory. Bioresource Technology 91, 207-214.

Research funding and grants

Various financial sources including the European Commission, The Irish Department of Agriculture and Food, Forbairt/Enterprise Ireland, The Health Research Board, Bioresearch Ireland, The Department of Communication, Marine and Natural Resources as well as industrial sources (national and international).

EU 6^th Framework Programme, Marie Curie Host Development Scheme

Transfer of Knowledge in Microbial Signal Transduction Pathways and Metagenomics.(TRAMWAYS), 2006-2010.

Department of Agriculture & Food, (FIRM Programme)

Novel biotechnological approaches to remove nutrients from wastewaters; 2006 – 2010.

Environmental Protection Agency, (STRIVE Post Doctoral Scholarship Scheme) Recombinant DNA approaches to enhance activity of the pathway for degradation of the toxic pollutant styrene in the bioreactor isolate P. putida CA-3: a biotechnologically significant metabolic route. 2007 – 2010.

Environmental Protection Agency, (STRIVE Doctoral Scholarship Scheme) Investigation of Biodegradable Plastic Production by an Activated Sludge Microbial Consortium Treating Dairy Industry Wastewater. 2007-2010.

Environmental Protection Agency, (STRIVE Doctoral Scholarship Scheme)

Elucidation of global regulatory signals controlling a biotechnologically significant pathway for the degradation of styrene, a toxic pollutant, by the bioreactor isolate Pseudomonas putida CA-3. 2007-2010.

Higher Education Authority (PRTLI 4-Environment and Climate Change

Impacts & Responses - Metagenomic strategies to identify novel bioactive compounds.2007-2011.

Department of Agriculture & Food, (STIMULUS Programme)

Isolation of novel anti-phytopathogen agents from soil bacteria using metagenomic tools, 2007 – 2010.

Department of Communications, Marine & Natural Resources

Beaufort Marine Biodiscovery Programme. 2007-2013.

Department of Agriculture & Food,(FIRM Programme)

Discovery and Application of Novel Bioactive Substances from Marine Sponges for the control of Major Food Pathogens: 2008 – 2011.

Research Groups and collaborators

Marine Biotechnology

Dr Jonathan Kennedy

Dr John O’Halloran

Dr Marlies van der Wal-Mooij

Lekha Margassery

Burkhardt Flemer

Stephen Jackson

Robert Phelan

Environmental Biotechnology

Dr Mark O’Mahony

Dr Christina Forbes

Bill Ryan

Mary Mc Cullagh

Functional Metagenomics

Dr David Lejon

Dr Ruth Henneberger

Catriona Harrington

Key Internal Collaborating Groups

Prof Fergal O’ Gara, Biomerit Research Centre , UCC.

Dr John Morrissey, Microbiology Department, UCC.

Dr Niall O’Leary, Microbiology Department, UCC.

Dr Jerry Murphy, Dept. of Civil & Environmental Engineering, UCC.

Dr Eamon McKeogh, Dept. of Civil & Environmental Engineering, UCC.

Dr Florence McCarthy Analytical & Biological Chemistry Research Facility, UCC

Prof Anita Maguire Analytical & Biological Chemistry Research Facility, UCC

External Academic Collaborators (on funded projects)

Prof Christine Maggs, Queen’s University Belfast (Marine Biodiscovery).

Dr Brendan Gilmore, Queen’s University Belfast (Marine Biodiscovery).

Dr John Hallsworth, Queen’s University Belfast (Marine Biodiscovery).

Prof Mark Johnson, National University of Galway, Ireland (Marine Biodiscovery).

Prof. Mike Guiry, National University of Galway, Ireland (Marine Biodiscovery).

Prof Mike Larkin, Queen’s University Belfast (Metagenomics).

Dr Leonid Kulakov Queen’s University Belfast (Metagenomics).

Prof. Alan Harvey, Strathclyde Institute for Drug Research (SIDR), University of Strathclyde (Marine Biodiscovery).

Dr RuAngelie Edrada-Ebel , Strathclyde Institute of Pharmacy and Biomedical Sciences.

(Marine Biodiscovery).

Prof Lokesh Joshi, National Centre for Biomedical Engineering Science, NUI Galway (Marine Biodiscovery).

Dr Marian Kane, National Centre for Biomedical Engineering Science, NUI Galway

(Marine Biodiscovery).

Dr Julian Marchesi, Cardiff University (Functional Metagenomics)

Dr Fiona Doohan, University College Dublin (Functional Metagenomics)

Research Projects in the group

Environmental Biotechnology

Pseudomonas putida CA-3 is a bioreactor isolate capable of complete degradation of the toxic pollutant styrene, generated by the polymer processing industry. In addition, this organism is capable of generating biodegradable polyesters, (polyhydroxyalkanoate), via styrene degradation. As a result, the potential exists for the application of this organism in whole cell based biotechnological approaches to remediate styrene waste and generate value added products. Extensive characterization of the physiology and molecular biology of this pathway has been performed by our group to date, however one poorly understood aspect is the regulatory mechanisms integrating the pathway into overall carbon metabolism. Current research within the group seeks to address this issue of global regulation of the sty operon and to identify regulatory overlaps between styrene degradation and the production of polyhydroxyalkanoate for exploitation in novel biotechnological applications.

Environmental Biotechnology (Biofuels)

The group is involved in a collaborative project with the Biofuels group from the Sustainable Energy and Environmental Engineering thematic area within the Environmental Research Institute- in the area of Biogas production. The project is focusing on the anaerobic digestion of high solids content biomass including the organic fraction of municipal solid waste, green waste and grass. The effects of enzymatic pre-treatment on biological conversion of high-solid content wastes by employing bacterial and fungal enzyme preparations in pilot-scale conversions, are being studied. The aim is to facilitate maximum biogas conversion efficiencies, with decreased residence times. Molecular microbial ecology approaches are also being employed to monitor and assess the performance of the key microbial populations within the reactors. High throughput robotic-based metagenomic based approaches are being employed to clone and characterise novel hydrolytic enzymes from these microbial populations, with potential value for subsequent use in biogas production and in other biotechnological applications.

Marine Biotechnology

Researchers in the group are currently involved in the establishment of metagenomic based technologies, employing both novel prokaryotic and eukaryotic heterologous expression systems, which can be utilized to perform high throughput screens to identify bioactive compounds with potential antimicrobial, antifungal and anti-biofouling activities; from marine associated microbial ecosystems. The group have chosen to initially focus on bacteria associated with marine sponges, as these are known to produce many novel bioactive compounds, including polyketides. At present, microbial sponge communities and their genomes are poorly understood and a substantial unculturable fraction exists within this micro-environment. Metagenomic libraries are being constructed in high-capacity BAC vectors that can be transferred at high-throughput to a number of different microbial expression hosts including Gram negative Pseudomonas sp and Gram positive Streptomyces sp. These libraries are then been screened by hybridisation for the presence of genes involved in natural product biosynthetic pathways and, in addition; the libraries are being screened for the expression of bioactive compounds. The groupare also employing culture dependent approaches, focusing initially on Actinomycetes associated with the sponge as these are known to be a major source of natural products, including polyketides and nonribosomal peptides. Several actinobacterial strains have been isolated from sponge samples and extracts from these are currently being screened for the production of bioactive compounds. The novel heterologous expression systems being developed by the group will result in the development of a “core capability”, thereby facilitating the high throughput screening of other metagenomic libraries, generated from different types of starting materials from which novel enzymes, such as proteases and many carbohydrate metabolising enzymes (glucanases, lipases, esterases, oxygenases, xylanases, amylases, chitinases and cellulases) which are used by the food pharmaceutical and bioenergy industries.

Functional Metagenomics

A) Isolation of bioactive molecules with activity against foodborne pathogens

Using the aforementioned metagenomic based approaches. researchers in the group are focusing on the discovery of new bioactive substances from marine sponge metagenomic libraries, to combat the emergence of antibiotic resistant foodborne pathogens such as Salmonella sp, Listeria monocytogenis and Campylobacter spp. . This involves the development of screens which can be used to identify novel bioactivities and the subsequent use of these screens in a high throughput fashion with sponge-metagenomic libraries to identify metagenomic clones which are producing natural products with bioactivity against food pathogens. Metagenomic clones which show activity will be subsequently characterized to determine the genes involved and the chemical(s) being produced.

B) Isolation of bioactive molecules with activity against phytopathogenic fungi

Again employing functional metagenomic based approaches researchers in the group are constructing libraries from disease suppressive soils and screening these libraries for activity against Pythium ultimum (damping-off), Gaeumannomyces graminis var. tritici (take-all of cereals), Streptomyces scabies (bacterial potato scab), Phytophthora infestans (late blight of potato), Ralstonia solanacearum (bacterial wilt of tomato), Mycosphaerella graminicola (Septoria tritici blotch of wheat) and Fusarium culmorum (seedling and head blight diseases of cereals). Again metagenomic clones which show anti-fungal activity will be subsequently characterized (using bioinformatic and metabolomic technologies) to determine the genes involved and the chemical(s) being produced.

Fungal Genetics

Researchers are focusing on the cloning and molecular characterisation of the ochratoxin A (OTA) biosynthetic genes in the mycotoxigenic fungi Aspergillus ochraceus and in Penicillium verrucosum . OTA is a common contaminant of grains such as barley, corn, rye, wheat, and oats, with cereal-based products typically accounting for 50–80% of the average consumer intake of the mycotoxin. OTA has also been reported in other plant products including coffee beans, spices, nuts, olives, grapes, beans, and figs. There is a risk to human health not only through the intake of contaminated foods of vegetable origin, but also through foods of animal origin with OTA being reported in animal derived food products, such as poultry and pork meat and in offal and sausages containing pork blood, due to the feeding of mould contaminated fodder to animals. The objective of the work is to determine the influence of a wide variety of nutritional based biotic factors on the production of OTA in these fungi and to evaluate their effects at the transcriptional level by monitoring transcription of the OTA biosynthetic genes. Based on the OTA genes characterized, molecular based detection systems are being developed to monitor fungal contamination of grains and to quantify the level of contamination using real time-RT-PCR and/or QPCR based assay systems. .

Links

http://eri.ucc.ie

http://www.marine.ie/home/research/MIFunded/BeaufortAwards/

http://www.ucc.ie/en/biomerit/

http://www.chiefscientificadviser.ie/aboutus/