Represented Peer-view Publications

MICROGEN BIOTECH TEAM PUBLICATIONS

Our core team at MicroGen Biotech had over over 70 international peer reviewed publications and over 200 conference and technical publications including presentations, posters and conference proceedings including cover on Nature Biotechnology.

Represented Peer-view Publications
Xuemei Liu, X., Kiwanuka, S., Ryan, D., Dowling D., and Germaine, K. Use of Ecopiling to Remediate PAH-Contaminated Storm-water Lagoon Sediment. Journal of Bioremediation and Biodegradation in June 2016
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
Chhabra, S, Brazil D, Morrissey J, Burke JI., O’Gara F, Dowling DN (2013)  Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome. MicrobiologyOpen Oct; 2(5): 717-24.
Chhabra, S., Brazil, D., Morrissey, J., Burke, J., O’Gara, F., and Dowling DN (2012). Fertilization management affects the alkaline phosphatase bacterial community in barley rhizosphere soil. Biology & Fertility of Soils DOI 10.1007/s00374-0693-2.
Redondo-Nieto,R.,  Barret,M.,  Morrisey,J., Germaine,K., Martínez-Granero,F., Barahona,E., Navazo,A., SánchezContreras,M.,  Moynihan, J., Giddens,S., Coppoolse,E.,  Muriel, C., Stiekema,W., Rainey,P., Dowling,DN., O’Gara,F., Martín,M. and Rafael Rivilla. (2012) Genome sequence of the biocontrol strain Pseudomonas fluorescens F113. J. Bacteriol. 2012, 194(5):1273.
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.
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: 000-000 ISBN: 978-81-308-0424-8.
Liu X, Germaine K, Ryan D and Dowling D N (2010). b-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 10.   McGuinness M and Dowling DN. (2009). Plant-Associated Bacterial Degradation of Toxic Organic Compounds in Soil. International Journal of Environmental Research and Public Health. 6(8):2226-2247
Liu, X., Kieran J. Germaine, David Ryan and David N. Dowling (2010). Genetically modified Pseudomonas biosensing biodegraders to detect PCB and chlorobenzoate bioavailability and biodegradation in contaminated soils. Bioengineered Bugs 1:3, 1-9.
Finlay, W., Orla Cunningham, Matthew Lambert, Xuemei Liu, Brian Fennell. Affinity maturation of a humanized rat antibody for anti-RAGE therapy: comprehensive mutagenesis reveals a high level of mutational plasticity both inside and outside the complementarity-determining regions. J Mol Biol.May 2009
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.
Dowling  D N and Doty SL (2009). Improving phytoremediation through biotechnology. Current Opinion in Biotechnology. 20:204–206.
Brennan E, McGuinness M, Dowling DN. (2009). Bioinformatic analysis and in vitro site-directed mutagenesis of conserved amino acids in BphKLB400, a specific bacterial glutathione transferase.  International Biodeterioration & Biodegradation 63, 928-932 [doi:10.1016/j.ibiod.2009.03.008].
Coffey L, Clarke A, Duggan P, Tambling K, Horgan S, Dowling DN, O’Reilly C. (2009). Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer. Archives in Microbiology 191, 761-767.
Browne P, Rice O, Miller SH, Burke J, Dowling DN, Morrissey JP, O’Gara F. (2009). Superior inorganic phosphate solubilization is linked to phylogeny within the Pseudomonas fluorescens complex. Applied Soil Ecology. 43, 131-138, doi:10.1016/j.apsoil.2009.06.010.
Rice O, Browne P, Chabbra S, Miller SH, Burke J, Dowling DN, Morrissey JP, O’Gara F. (2008).  Meeting the Challenges of sustainable agriculture. T-Research 3, 26-28.
Ryan RP, Germaine KJ, Franks A, Ryan DJ, Dowling DN. (2008). Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett.  278, 1-9.
McGuinness MC, Mazurkiewicz V, Brennan E, Dowling DN. (2007). Dechlorination of Pesticides by a Specific Glutathione S-Transferase), BphK LB400: Potential for Bioremediation. Eng. Life. Sci. 7, 1-6.
Ryan,RP., Ryan, DJ., Sun,Y-C., Li, F-M., Wang,Y., and Dowling,DN. (2007) An acquired efflux system is responsible for copper resistance in Xanthomonas strain IG-8 isolated from China. FEMS Microbiol, Lett. 268; 40-46.
Ryan,RP., Ryan, DJ.,and Dowling,DN. (2007)  Plant protection by recombinant, root-colonizing Pseudomonas fluorescens F113rifPCB strain expressing arsenic resistance: improving rhizoremediation  Letters in Applied Microbiology  45: 668-674.
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.
Yi-Cheng Sun, Yan Li, Hai, Zhang, Hai-Qin Yan, David N. Dowling, and Yi-Ping Wang  (2006) Reconstitution of the enzyme AroA and its glyphosate tolerance by fragment complementation. FEBS Letters 580: 1521-1527.
Germaine, KJ, Liu, X., Garcia-Cabellos, G., Hogan, JP., Ryan, D., and Dowling, DN. (2006)  Bacterial endophyte- enhanced phytoremediation of the organochlorine herbicide 2,4-dichlorophenoxyacetic acid. FEMS Microbiology Ecology 57: 302-310.
McGuinness, M., Ivory, C., Gilmartin, N., and Dowling,DN. (2006) . Investigation of the substrate specificity of wildtype and mutant BphKLB400 (a glutathione S-transferase) from Burkholderia LB400. International Biodeterioration & Biodegradation 58: 203-208.
Villacieros, Marta , Clare Whelan, Martina Mackova, Jesper Molgaard, María Sánchez-Contreras, Javier Lloret, Daniel Aguirre de Cárcer, Roke I. Oruezábal, LuisBolaños, Thomas Macek, Ulrich Karlson, David N. Dowling, Marta Martín and Rafael Rivilla. (2005). PCB Rhizoremediation by Pseudomonas fluorescensF113 derivatives using a Sinorhizobium meliloti nod system to drive bph gene expression. Appl. Environ. Microbiol. 71: 2687-2694
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,DN. (2005)  Multiple metal resistant transferable phenotypes in bacteria as  indicators of soil contamination with heavy metals. J.Soils & Sediments 5:95-100.
Yi-Cheng Sun, Yan-Cheng Chen, Zhe-Xian Tian, Feng-Mei Li, Xin-Yue Wang, Jing Zhang, Zhen-Long Xiao, Min Lin, Niamh Gilmartin, David N. Dowling, and Yi-Ping Wang.   (2005) A novel AroA with high tolerance to Glyphosate encoded by a gene of Pseudomonas putida 4G-1 isolated from an extreme polluted environment in China.  Appl. Environ. Microbiol. 71:4771-4776.
Germaine, K., Keogh, E., Garcia-Cabellos, G., Borremans, B., van der Lelie, D., Barac, T., Oeyen, L., Vangronsveld, J., Porteous Moore, F., Moore, ERB., Campbell CD., Ryan, R., Dowling, D N. (2004) Colonisation of poplar trees by gfp expressing bacterial endophytes. FEMS Microbiology Ecology 48:109-118
Hogan, J ; Sherlock, O; Ryan, D; Whelan, C; Francesconi,, S. , Rivilla, R., and Dowling, D.N.  (2004)  Fluorescence resonance energy transfer (FRET) based molecular detection of a genetically modified PCB degrader in soil.  FEMS Microbiology Letters 236:349-357
Villacieros, M. , B. Power, M. Sánchez-Contreras, J. Lloret, R.I. Oruezabal, M. Martín, F. Fernández-Piñas, I. Bonilla, C. Whelan, David N. Dowling and R. Rivilla. (2003) Colonization behaviour of Pseudomonas fluorescens and Sinorhizobium melilotiin the alfalfa (Medicago sativa) rhizosphere.  Plant and Soil. 251: 47-54
Gilmartin, N., Ryan,D., Sherlock,O. and Dowling,D. BphK shows dechlorination activity against 4-chlorobenzoate, an end product of bph-promoted degradation of PCBs. (2003) . FEMS Microbiology Letters 222:251-255.
Marta Villacieros, Barry Power, María Sánchez-Contreras, Javier Lloret, Roke I. Oruezabal, Marta Martín, Francisca Fernández-Piñas, Ildefonso Bonilla, Clare Whelan, David N. Dowling, Rafael Rivill. Colonization behaviour of Pseudomonas fluorescens and Sinorhizobium meliloti in the alfalfa ( Medicago sativa ) rhizosphere Journal: Plant and Soil – PLANT SOIL , vol. 251, no. 1, pp. 47-54, 2003
J. M. Barea, G. Andrade, V. Bianciotto, D. Dowling, S. Lohrke, P. Bonfante, F. O’Gara, C. Azcon-Aguilar, Consejo Superior de Investigaciones. Impact on Arbuscular Mycorrhiza Formation of Pseudomonas Strains Used as Inoculants for Biocontrol of Soil-Borne Fungal Plant Pathogens .1998
Dunne, C., Y. Moënne-Loccoz, J. McCarthy, P. Higgins, J. Powell, D. N. Dowling, F. O’Gara. Combining proteolytic and phloroglucinol-producing bacteria for improved biocontrol of Pythium-mediated damping-off of sugar beet. Journal: Plant Pathology – PLANT PATHOL , vol. 47, no. 3, pp. 299-307, 1998
Dunne, C., Jer J. Crowley, Y. Moenne-Loccoz, David N. Dowling, s Bruijn, Fergal O’Gara. Biological control of Pythium ultimum by Stenotrophomonas maltophilia W81 is mediated by an extracellular proteolytic activity. Journal: Microbiology-sgm , vol. 143, no. 12, pp. 3921-3931, 1997
Cronin, D., Yvan Moënne-Loccoz, Anne Fenton, Colum Dunne, David N Dowling, Fergal O’Gara Ecological interaction of a biocontrol Pseudomonas fluorescens strain producing 2,4-diacetylphloroglucinol with the soft rot potato pathogen Erwinia carotovora subsp. Atroseptic. Journal: Fems Microbiology Ecology – FEMS MICROBIOL ECOL , vol. 23, no. 2, pp. 95-106, 1997.
Russo, A., Y. Moënne-Loccoz, S. Fedi, P. Higgins, A. Fenton, D. N. Dowling, M. O’Regan, F. O’Gara Improved delivery of biocontrol Pseudomonas and their antifungal metabolites using alginate polymers. Journal: Applied Microbiology and Biotechnology – APPL MICROBIOL BIOTECHNOL , vol. 44, no. 6, pp. 740-745, 1996
Sexton, R., P. R. Gill Jr., D. N. Dowling, F. O’Gara Transcriptional regulation of the iron-responsive sigma factor gene. Journal: Molecular and General Genetics – MOL GEN GENET , vol. 250, no. 1, 1996
McHugh, B., Peter M. Stephens, Fiona I. McConnell, Jeremy D. Glennon, David N. Dowling, Fergal O’Gara Rhizosphere competence of fluorescent Pseudomonas sp. B24 genetically modified to utilise additional ferric siderophores. Journal: Fems Microbiology Ecology – FEMS MICROBIOL ECOL , vol. 19, no. 4, pp. 215-225, 1996
Fedi, S., Dina Brazil, David N Dowling, Fergal O’Gara Construction of a modified mini-Tn5 lacZY non-antibiotic marker cassette: ecological evaluation of a lacZY marked Pseudomonas strain in the sugarbeet rhizosphere. Journal: Fems Microbiology Letters – FEMS MICROBIOL LETT , vol. 135, no. 2, pp. 251-257, 1996
Fedi, S., Dina Brazil, David N Dowling, Fergal O’Gara. Construction of a modified mini-Tn5 lacZY non-antibiotic marker cassette: ecological evaluation of a lacZY marked Pseudomonas strain in the sugarbeet rhizosphere. Journal: Fems Microbiology Letters – FEMS MICROBIOL LETT , vol. 135, no. 2-3, pp. 251-257, 1996
Callanan, M., Raymund Sexton, David N. Dowling, Fergal O’Gara. Regulation of the iron uptake genes in Pseudomonas fluorescens M114 by pseudobactin M114: the pbrA sigma factor gene does not mediate the siderophore regulatory response. Journal: Fems Microbiology Letters – FEMS MICROBIOL LETT , vol. 144, no. 1, pp. 61-66, 1996
Moënne-Loccoz, Y., Brendan McHugh, Peter M. Stephens, Fiona I. McConnell, Jeremy D. Glennon, David N. Dowling, Fergal O’Gara Rhizosphere competence of fluorescent Pseudomonas sp. B24 genetically modified to utilise additional ferric siderophores. Journal: Fems Microbiology Ecology – FEMS MICROBIOL ECOL , vol. 19, no. 4, pp. 215-225, 1996.
Russo, A.,Y. Moënne-Loccoz, S. Fedi, P. Higgins, A. Fenton, D. N. Dowling, M. O’Regan, F. O’Gara. Improved delivery of biocontrol Pseudomonas and their antifungal metabolites using alginate polymers. Applied Microbiology and Biotechnology – APPL MICROBIOL BIOTECHNOL , vol. 44, no. 6, pp. 740-745, 1996
Callanan, M., Raymund Sexton, David N. Dowling, Fergal O’Gara Regulation of the iron uptake genes in Pseudomonas fluorescens M114 by pseudobactin M114: the pbrA sigma factor gene does not mediate the siderophore regulatory response. Fems Microbiology Letters – FEMS MICROBIOL LETT , vol. 144, no. 1, pp. 61-66, 1996
Sexton, R., Paul R. Gill, David N. Dowling, Fergal O’Gara. Transcriptional regulation of the iron-responsive sigma factor gene pbrA. Molecular and General Genetics – MOL GEN GENET , vol. 250, no. 1, pp. 50-58, 1996
Sexton, R., Paul R. Gill, Michael J. Callanan, Daniel J. O’Sullivan, David N. Dowling, Fergal O’Gara Iron-responsive gene expression in Pseudomonas fluorescens M114; cloning and characterization of a transcription-activating factor, PbrA. Molecular Microbiology – MOL MICROBIOL , vol. 15, no. 2, pp. 297-306, 1995
Fedi, S., Y. Moënne-Loccoz, D. N. Dowling, F. O’GaraA versatile most probable number system to quantify lacZY-marked pseudomonads present at low cell numbers in the rhizosphere. Letters in Applied Microbiology – LETT APPL MICROBIOL , vol. 20, no. 4, pp. 220-224, 1995
Ramos, JL., Eduardo Díaz, David Dowling, Victor de Lorenzo, Søren Molin, Fergal O’Gara, Cayo Ramos, Kenneth N. Timmis The Behavior of Bacteria Designed for Biodegradation. Journal: Bio/technology , vol. 12, no. 12, pp. 1349-1356, 1994
Adams, C., David N. Dowling, Dan J. O’Sullivan, Fergal O’Gara Isolation of a gene (pbsC) required for siderophore biosynthesis in fluorescent Pseudomonas sp. strain M114.Molecular and General Genetics – MOL GEN GENET , vol. 243, no. 5, pp. 515-524, 1994
O’Sullivan, DJ., David N. Dowling, Victor DeLorenzo, Fergal O’Gara. Escherichia coli ferric uptake regulator (Fur) can mediate regulation of a pseudomonad iron-regulated promoter. Fems Microbiology Letters – FEMS MICROBIOL LETT , vol. 117, no. 3, pp. 327-332, 1994
Dowling, DN., Daryl F. Dwyer. A DNA module encoding bph genes for the degradation of polychlorinated biphenyls (PCBs). Journal: Fems Microbiology Letters – FEMS MICROBIOL LETT , vol. 113, no. 2, pp. 149-154, 1993
Dowling, DN., and F. O’Gara. Construction of a Rhizosphere Pseudomonad with Potential To Degrade Polychlorinated Biphenyls and Detection of bph Gene Expression in the Rhizosphere
Oteino N., Lally R., Kiwanuka S, Lloyd A, Ryan D, Germaine K and Dowling D.(2015).
Plant growth promotion induced by phosphate solubilising endophytic Pseudomonas isolate. Frontiers in Microbiology. 6: Art: 745
El-sawi, M. Germaine, K. Bourke, P, and Rene Malone (2016). AFLP analysis of genetic diversity and phylogenetic relationships of Brassica oleracea in Ireland. Comptes Rendus Biologies.
El-sawi, M. Germaine, K. Bourke, P, and Rene Malone (2016). Genetic diversity and population structure of Brassica oleracea germplasm in Ireland using SSR markers. Comptes Rendus Biologies.
Books and book chapters
Kieran J. Germaine and David N. Dowling (2010). Improving the phytoremediation potential of plants using endophytic bacteria in Trends in Bioremediation and Phytoremediation, (Editors: Grażyna Płaza). 2010: 000-000 ISBN: 978-81-308-0424-8
Martina Mackova, David N. Dowling, Thomas Macek (2006) Phytoremediation Rhizoremediation. Springer, Science
Patents and Other Publications
A process for the remediation of hydrocarbons and/or heavy metal contaminated soil/sludge/sediment. Patent no. S86631. Issued 02-02-2016
一种修复有害有机物和/或重金属污染基质的方法. China 201510776838.4
Constructed Functional MicroBiome. In application
Hufton Simon, William Finlay, Orla Cunningham, Alfredo Sheehan, Xuemei Germaine, Mathew Lambert. HUMANIZED ANTI-RAGE ANTIBODY. International Patent No. PCT/US2009/05353
Nature Biotechnology Cover. (2004) Kieran J. Germaine,David Ryan and David N. Dowling. Link: Click here