Dr David Ryan

Academic and Research Experience

Dr David Ryan has lectured at undergraduate and postgraduate in Microbiology, Biochemistry, Bioinformatics, Communication, Innovation, Research Methods, First Year Experience and has supervised final year research dissertations.  He has been involved in programme development at level 8 and 9 in both the Department of Science and Health and in the Faculty of Life Long Learning and is currently the programme director for Irelands first honours degree in Brewing and Distilling, which he lead the development of.  Dr Ryan’s research interests continue to focus on environmental and societal sustainability and include soil health and bioremediation, the use of endophytic and rhizospheric microbial inoculants for plant growth promotion, microbial metal resistance systems, biofuel and food crops including barley for the brewing and distilling industry.  He has also worked on the development of chemical and microbial based biosensors to detect both contamination and degradation of target compounds, phytotechnologies for biofuel and bioenergy crops, strategies for the acceleration and assessment of the decomposition of biodegradable municipal waste and run off, plant transformation systems, enhancing anaerobic digestion systems.

Dr Ryan has recently become a partner in a consortium including the UCD Centre for Humanitarian Action, Concern Worldwide, Future Analytics, the network on humanitarian action (NOHA) and Wolaita Sodo University (WSU) in Ethiopia as part of a European-funded Horizon 2020 project which aims to ‘Build Resistance Through Education (BRTE)’.  The BRTE programme involves academia working with established relief and development agencies to transform the livelihoods of communities around the world as part of the global effort to meet the commitments to the United Nations 2030 Sustainable Development Goals (https://sustainabledevelopment.un.org).

Dr Ryan has supervised Masters and PhD students, acted as external examiner for levels 8, 9 and 10 and been involved in new programme panels, strategic, programmatic and professional support quality reviews nationally and internationally.  Dr Ryan is based at the enviroCORE research unit (www.envirocore.ie) at SETU Carlow. His research has resulted in the formation of a spin out campus-company, MicroGen Biotech (www.microgenbiotech.com), with a focus on food safety, plant growth promotion, soil health and bioremediation

Engagement and Collaboration

Research projects are all applied in nature, collaborative and focused on maximising impact towards sustainable enviroemntal, societal and economic development.  Current active research collaborations include Technological Universities, Institutes of Technology, Universities, companies and other and organisations including Alltech, TelLabs, Teagasc, MicroGen Biotech, UCD, TUD, DAFM, CONCERN Worldwide, Future Analytics, NOHA, and WIT.  Dr Ryan has also worked with a number of breweries and distilleries on product development innovation and analysis projects.

Applied research projects primarily in microbial plant growth promotion, soil bioremediation, alternative energy and/or heavy metal analysis and the development of commercial and social IP is important in all of my research.  I am planning to expand my focus to include the microbial microbiome and its potential for influencing crops used in the brewing and distilling industries.

Current Research Students

Name of Student

Title of Thesis

PhD/MSc

Completion

Wojciech Nowak

Plant growth promotion potential of novel bacterium Ensifer adhaerens OV14

PhD

2020

Navoditar Bhatnagar

Influence of enzyme supplementation technologies on biogas production and productivity in agriculture

PhD

2019

Evelyn Joyce

In-situ bioremediation and molecular microbiological monitoring of ammonia contamination in shallow groundwater

PhD

2018

Past Research Students

Name of Student

Title of Thesis

PhD/MSc

Completion

Robert Ryan

The generation and molecular analysis of multi-resistant microbial strains and associated operons for the bioremediation of toxic metals

PhD

2005

Jill Hogan

The monitoring of a prokaryotic bioremediation system in PCB contaminated soil and their in-situ quantification

PhD

2006

Kieran Germaine

Construction of endophytic xenobiotic degrader bacteria for improving the phytoremediation of organic pollutants

PhD

2007

Xuemei Liu

Development and application of biosensor technologies for the biodegradation of environmental pollutants

PhD

2008

Elaine Keogh

The isolation and characterisation of bacterial endophytes and their potential applications for improving phytoremediation

PhD

2009

Monica Dempsey

Evaluating microbial biosensors to detect polychlorinated biphenyl (PCB) contamination and degradation in a range of environments and conditions

MSc

2009

Olivia Odhiambo

Developing improved phytoremediation and phytoprotection systems

PhD

2011

Karen Browne

Characterisation of tributyltin resistant microbes isolated from Irish coastal regions

MSc

2011

Nicholas Otieno

Development of endophytic bacterial inoculants possessing plant growth promotion traits for practical application in bioenergy plant species

PhD

2014

Richard Lally

Examination of plant growth promoting bacteria on plant yield and their effect as bio-insecticides.

PhD

2016

Leo Fleming Farrell

A Study of European Medical Device Regulations Effectiveness in the Prevention of Product Recalls 

MSc

2016

Christopher Finnegan

Bioremediation of Tributyltin (TBT) in Irish marine sediments: Microbial screening and process optimisation

PhD

2018

Annija Lace

‘Optochemical detection strategies for heavy metals in water’

PhD

2019

Sinead Morris

Microbial bioremediation and physiochemical treatment of landfill leachate

PhD

2019

Publications and Outputs

Peer Reviewed Journal Articles

Lace, A.., Ryan, D., Bowkett, M., Cleary, J. (2019). Arsenic Monitoring in Water by Colorimetry Using an Optimized Leucomalachite Green Method. Molecules, 24, 339.

Lace, A., Ryan, D., Bowkett, M., Cleary, J. (2019). Chromium Monitoring in Water by Colorimetry Using Optimised 1, 5-Diphenylcarbazide Method. International Journal of Environmental Research and Public Health, 16, 1803.

Lace, A., Ryan, D., Cleary, J. (2019). Arsenic detection in water using microfluidic detection systems based on leucomalachite green method. Analytical method (in review).

Lace, A., Ryan, D., Cleary, J. (2019). A review of microfluidic detection strategies for heavy metals in water. Microchemical journal (in review).

Bhatnagar, N., Ryan, D., Murphy, R. and Enright, A.M. Effect of Co-digestion Ratio and Enzyme Treatment on Biogas Production from Grass Silage and Chicken Litter. (2018) Waste and Biomass Valorization. DOI 10.1007/s12649-018-0377-8

Finnegan, C., Ryan, D., Garcia-Cabellos, G., and Enright, AM Cabellos (2018) A review of strategies for the detection and remediation of organotin pollution, Critical Reviews in Environmental Science and Technology, 48:1, 77-118, DOI: 10.1080/10643389.2018.1443669

Finnegan, C., Ryan, D., Garcia-Cabellos, G., and Enright, AM. Developing Microbial Inocula to Support Biofuel Crop Cultivation on Tributyltin Contaminated Marine Sediments (2017) Journal of Applied & Environmental Microbiology. 2017, 5(2), 47-56. DOI: 10.12691/jaem-5-2-1. 10.12691/jaem-5-2-1.

Finnegan, C., Garcia-Cabellos, G., Enright, AM and Ryan, D. ‘Gas Chromatographic Approach to Evaluate the Efficacy of Organotin Degrading Microbes’ (2017) International Journal of Bioremediation and Biodegradation.

Moreira, AS. Germaine, KJ, Lloyd, A, Lally, RD, Galbally, PT, Ryan, D, Dowling, DN  (2016) Draft Genome Sequence of Three Endophyte Strains of Pseudomonas fluorescens Isolated from Miscanthus giganteus Genome Announcements 4(5):965-981 · DOI: 10.1128/genomeA.00965-16 

Otieno, N., Lally, R., Kiwanuka, S., Lloyd, A., Germaine, K., Ryan, D., Germaine, K., and Dowling D.N. (2015) ‘Plant growth promotion induced by phosphate solubilising endophytic Pseuddomonas isoltes’ Frontiers in Microbiology 6:745:1-8

Xuemei Liu, X., Kiwanuka, S., Ryan, D., Dowling D., and Germaine, K. ‘Use of Ecopiling in a Field Trial to Remediate Heavily Impacted Creosote Contaminated Sediment and Soil. Journal of Environmental pollution in January 2015

Germaine, K., Byrne, J., Liu, X., Keohane, J., Culhane, J., Lally, R., Kiwanuka, S., Ryan, D. and Dowling, D.N. (2015) ‘Ecopiling: a combined phytoremediation and passive biopiling system for remediating hydrocarbon impacted soils at field scale’ Frontiers in plant science 5 (756) 1-6

Lally, R., Moreira, A.S., Galbally, P., Ryan, D., Germaine, K., and Dowling, D.N (2013) Application of Endophytic Bacteria Possessing Plant Growth Promoting Traits for the Use in Bioenergy Crop Brassica napus  Aspects of Applied Biology 120: 9-13

Otieno, N., Culhane, J., Germaine, K., Brazil, D., Ryan, D., and Dowling D.N. (2013) Screening of large collections of plant associated bacteria for effective plant growth promotion and colonisation.  Aspects of Applied Biology 120: 23-28

Power, B, Liu, X., Germaine, K., Ryan, D., Brazil D and D. N. Dowling (2011). Alginate beads as a storage, delivery and containment system for genetically modified PCB degrader and PCB biosensor derivatives of Pseudomonas fluorescens F113. Journal of Applied Microbiology. 110(5):1351-8.

Liu X, Germaine KJ, Ryan D and Dowling D (2010). Genetically modified Pseudomonas biosensing biodegraders to detect PCB and chlorobenzoate bioavailability and biodegradation in contaminated soils. Bioengineered Bugs 1:3, 1-9.

Liu, X., Germaine, K.J., Ryan, D. and Dowling, D.N. (2010).  Whole cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls. Sensors 10: 1377-1398

Germaine K.J., Keogh E., Ryan, D. and Dowling, D.N. (2009). Bacterial endophyte-mediated naphthalene phytoprotection and phytoremediation. FEMS Microbiol. Lett. 2009, 296, 226-234.

Ryan, R.P., Germaine, K., Franks, A., Ryan, D.J. and Dowling, D.N. (2008).  Bacterial endophytes: recent developments and applications. FEMS Microbiol. Lett.  278:1-9

Ryan, R. P., Ryan, D. and Dowling, D. (2007).  Plant protection by the recombinant, root-colonising Pseudomonas fluorescens F113rifPCB strain expressing arsenic resistance: improving rhizoremediation Letters in Applied Microbiology 45: 668-674

Ryan, R. P, Ryan, D., Sun, YC., Li, FM., Wang, Y. and Dowling, D. (2007).  An acquired efflux system is responsible for copper resistance in Xanthomonas strain IG-8 isolated from China FEMS Microbiol Lett. 268: 40-6.

Liu, X., Germaine, KJ., Ryan, D. and Dowling, DN .(2007)  Development of a GFP-based biosensor for detecting the bioavailability and biodegradation of polychlorinated biphenyls (PCBs). (JEELM) Journal of Environmental Engineering and Landscape Management 15:261-268.

Germaine, K.J, Liu, X., Garcia-Cabellos, G., Hogan, J.P., Ryan, D. and Dowling, D.N. (2006).   Bacterial endophyte- enhanced phytoremediation of the organochlorine herbicide 2,4-dichlorophenoxyacetic acid. FEMS Microbiology Ecology 57: 302-310.

Gilmartin, N., Ryan, D. and Dowling, D.N (2005).  Analysis of the C-terminal domain of Burkholderia sp. strain LB400 BphK reveals a conserved motif that affects catalytic activity. FEMS Microbiology Letters 249: 23-30.

Ryan, R.P., Ryan, D. and Dowling, D.N. (2005).   Multiple metal resistant transferable phenotypes in bacteria as indicators of soil contamination with heavy metals. Journal of Soils & Sediments 5:95-100.

Germaine, K, Garcia-Cabellos, G., Borremans B., van der Lelie, N., Barak, T., Oeyen, L., Vangronsveld, J., Porteous-Moore, F., Moore, E., Campbell, C., Ryan, D. and Dowling D. (2004).  Colonisation of Poplar trees by gfp expressing bacterial endophytes FEMS Microbial Ecology 48: 109-118

Hogan, J; Sherlock, O; Ryan, D; Whelan, C; Francesconi, S., Rivilla, R. and Dowling, D.  (2004).  Fluorescence resonance energy transfer (FRET) based molecular detection of a genetically modified PCB degrader in soil.  FEMS Microbiology Letters 236:349-357

Ryan R.. P, Ryan D. and Dowling D. (2004).  “The isolation and characterisation of a multiple heavy metal resistant plasmid pITCRR46 from a heavy metal contaminated site” In: The BioNet Conference ISSN publication.

Gilmartin, N., Ryan, D., Sherlock, O., and Dowling, D., (2003).  A potential role for the bphk gene encoding a Glutathione S-transferase in the PCB breakdown pathway” FEMS Microbial Letters.

Gilmartin, N., Ryan, D., Sherlock, O. and Dowling, D. (2003).  BphK shows dechlorination activity against 4-chlorobenzoate, an end product of bph-promoted degradation of PCBs. FEMS Microbiology Letters 222:251-255.

Ryan, D. and Colleran, E. Arsenical resistance in the IncHI2 plasmids (2002).  Plasmid, 47, 234-240

Books and Book Chapters

Ryan R.P, Ryan, D. and Dowling D. (2008). Heavy metal tolerant rhizobacteria and their phytoremediation potential. In: Phytoremediation and Rhizoremediation: Focus on Biotechnology. Vol 9B. Edited by Mackova M, Dowling DN, Macek T. Springer.

Garcia-Cabellos, G., Byrne, M., Stenberg, M., Germaine, K., Brazil, D., Keohane, J., Ryan, D. and Dowling, D. (2005) A small scale constructed wetland to treat different types of wastewaters. In: Nutrient Management in Agricultural Watersheds: A Wetlands Solution, pp224-229 edited by E. J. Dunne, K.R., Reddy and O.T. Carton. Wageningen Academic Publishers, The Netherlands.

Conference Presentations

Approximately 100 to date

Other Research Outputs

Finnegan, C., Enright, AM., Ryan, D and Garcia-Cabellos, G.  'Bioremediation of Tributyltin (TBT) in Irish marine sediments: Microbial screening and process optimisation'. Presented at Environ 2017 – winner of the ESAI Postgraduate of the Year Award.

Richard D. Lally, David Ryan, Andrew Lloyd, Kieran J. Germaine and David N. Dowling ‘Plant growth promoting Pseudomonads, their colonisation dynamics and agricultural potential’ Winner of the Alltech Young Scientist program 2016.