Dr Kieran J Germaine

BSc (Hons) PhD

Bioenvironmental Lecturer

Room 328, Department of Science & Health, Carlow Campus

e: kieran.germaine@setu.ie      t: 059 9175580

ORCID ID:0000-0003-4026-3414  ResearchGate   Mendeley

  • Research Interests
  • Publications
  • Research Supervision
  • Engagement and Collaboration

Research Interests

My research interests includes isolating and characterising organic pollutant degrading bacteria, isolating heavy metal resistant bacteria, plant growth promoting  bacteria and their growth promoting traits,  bacterial genomics, uses of plant associated bacteria as biocontrol agents, bacterial biosensors, plant microbiomes, waste water bioremediation, human pathogens survival in the plant biosphere, and genetic characterisation of Brassica napus.


Peer Reviewed Journal Articles

Lally R. Moreira AS, Galbally P, Ryan D, Germaine KJ and Dowling, DN.  (2017). Application of endophytic Pseudomonas fluorescens and a bacterial consortium to Brassica napus can increase plant height and biomass under greenhouse and field conditions. Front. Plant Sci. URL

Rathore R, Dowling DN, Forristal PD, Spink J, Cotter PD, Bulgarelli D, Germaine KJ. (2017). Crop establishment practices are a driver of the plant microbiota in winter oilseed rape (Brassica napus). Front Microbiol. 2017 Aug 9;8:1489. doi: 10.3389/fmicb.2017.01489

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 isolatedfrom Miscanthus giganteus. Genome Announc 4(5):e00965-16.doi:10.1128/genomeA.00965-16

 Liu X, Kiwanuka S, Cleary K, Ryan D, Dowling DN, Germaine, KJ. (2016). Use of Ecopiling to   Remediate PAH-Contaminated Storm-water Lagoon Sediment. J Bioremed Biodeg 7: 355.doi:10.4172/2155-6199.1000355

El-sawi, M. Germaine, K. Bourke, P, and Rene Malone (2016). AFLP analysis of genetic diversity     and phylogenetic relationships of Brassica oleracea in Ireland. C R Biol. 339(5-6):163-70. doi:  10.1016/j.crvi.2016.03.002

Germaine KJ, Liu X, Byrne J, Culhane J, Lally R, Kiwanuka S, Keohane J, Ryan D, and Dowling, DN. (2014) Ecopiling: A combined phytoremediation and passive biopiling system for remediating hydrocarbon impacted soil at field scale. Frontiers in Plant Science. 5:756-762

Redondo-Nieto M, Barret M, Morrissey J, Germaine K, Martínez-Granero F, Barahona E, Navazo A, Sánchez-Contreras M, Moynihan JA, Muriel C, Dowling D, O'Gara F, Martín M, Rivilla R. (2013) Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction.  BMC Genomics. 25:14:54. doi: 10.1186/1471-2164-14-54.

El-Sawi, Germaine KJ, Bourke P and Malone R.A (2012) Assessment of Morphological Variation in Irish Brassica oleracea species. Journal of Agricultural Science 4:10. DOI: 10.5539/jas.v4n10p20

Power B, Liu X, Germaine KJ, Ryan D, Brazil D and Dowling DN (2011). Alginate beads as a storage, delivery and containment system for genetically modified PCB degrader and PCB biosensor derivatives of Pseudomonas fluorescens F113. J. Appl. Microbiol. 110 1351-1358.

Germaine KJ, Chhabra S, Song B, Brazil D and Dowling D N (2010). Microbes and sustainable production of biofuel crops: a Nitrogen perspective. Biofuels. 1: 6: 877-888.

Liu X, Germaine K, Ryan D and Dowling D N (2010). Whole-Cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls. Sensors 2010, 10, 1377-1398; doi:10.3390/s100201377.

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.

Germaine KJ, 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., Germaine, K., Franks, A., Ryan, D., Dowling, D. N. (2008). Bacterial endophytes: recent developments and applications. FEMS Microbiology Letters. 278: 1-9

Liu, X., Germaine, K., Ryan, D., Dowling, D. N. (2007). Development of an alginate encapsulated gfp-based biosensor for detecting the bioavailability and biodegradation of polychlorinated biphenyls. Journal of Environmental Engineering and Landscape Management. Vol XV, No 4, 261–268.

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

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

Book Chapters

Germaine, KJ, McGuinness, M, and Dowling, DN. (2013). Improving phytoremediation through plant-associated bacteria. In: Molecular Microbial Ecology of the rhizosphere. Wiley-Blackwell. New Jersey. Chpt. 91. ISBN: 978-1-118-29629-5.

Germaine, KJ, McGuinness, M, and Dowling, DN. (2013). Engineering of microbes for plant and soil systems. In: Applications of microbial engineering (Eds: VK Gupta, M Schmoll, M Maki, M Tunhy and MA Mazutti). Chpt 8: CRC Press.

Germaine KJ and Dowling D N (2010). Improving the phytoremediation potential of plants using endophytic bacteria in Trends in Bioremediation and Phytoremediation, (Editors: Grażyna Płaza). 2010: ISBN: 978-81-308-0424-8.

Garcia–Cabellos, G., Germaine, K., Ryan, D., Dowling, D. N. (2005). Investigating the rhizosphere microbiology of constructed wetlands. Symposium proceedings publication: Nutrient Management in Agricultural Watersheds.

Conference Proceedings and Papers

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

Lally R. Moreira AS, Galbally P, Ryan D, Germaine KJ and Dowling, DN. (2013). Application of Endophytic Bacteria Possessing Plant Growth Promoting Traits for the Use in Bioenergy Crop Brassica napus. Aspects of Applied Biology 120, 9-14.

Other Research Outputs

Gfp microraphs used in: Estibaliz Larrainzar, E., ­ O'Gara, F. and ­ Morrissey, J. (2005). Applications of autofluorescent proteins for in situ studies in microbial ecology. Annual Review of Microbiology. 59: 257-277.

Gfp micrograph featured on front cover of Nature Biotechnology. May, 2004, Volume 22 No 5.

Patents: Ecopiling, A combined phytoremediation and passive biopiling system for remediating hydrocarbon impacted soil. Patent Application No.: S2140311 (patent granted).

Research Supervision

Current Research Students

Ms. R.Rathore (PhD Cadidate); Microbiome of Brassica napus. (Supervisors: Kieran Germaine and David Dowling).

Mr. Edward Lanigan. Novel water treatment system for removing phosphates from  Farmyard dirty water (Supervisors: Kieran Germaine and David Dowling).

Ms. Loriane Mwana Scoe. Characterisation of microplastics in freshwater ecosystems (supervisors: John Cleary, Kieran Germaine and Thomae Kakouli-Duarte).

Mr.Cormac Griffin.  Analysis of heavy metal resistance systems in plant and soil associated bacteria ( supervisors Xuemei Liu, Kieran Germaine, David Dowling and David Ryan).

Past Research Students
  • Richard Lally. PhD. Investigating the application, plant growth promotion and genetic potential of three endophytic Pseudomonas fluorescens isolates for use in sustainable agriculture. 2016.
  • John Culhane. PhD. Investigation of plant growth promotion endophytic isolates as microbial inoculants for application in the bioremediation of oil-contaminated soil. 2016.
  • Nicholas Otieno. PhD. Development of plant growth promotion endophytic isolates as microbial inoculants for practical application in bioenergy plant species.
  • Mohamed El-Sawi. PhD. Assessing the genetic diversity, phylogenetic relationships, and disease resistance genes in Irish Brassica oleracea species. 2012
Areas of interest as a supervisor include
  • Bioremediation
  • Plant growth promoting microbes
  • Microbiome analysis
  • Waste water treatment systems.

Engagement and Collaboration

Over the past 5 years I have been involved in 10 industry based research projects including projects involving  wood spalting fungi, seaweed based fertilisers, improved chemical flocculation in waste water treatment, oil and PAH soil remediation, synthetic chemical markers  for diesel,  and developing  functional food products. I am also involved in secondary school science promotion programs such as the Young Scientist competition and primary school programs such as Cell Explorers. I am a member of professional bodies such as Environmental Sciences Association of Ireland, Association of Applied Biologist and the Society for General Microbiology.