2023

Hajabdollahi Ouderji, Z., Gupta, R. , Mckeown, A., Yu, Z. , Smith, C. , Sloan, W. and You, S. (2023) Integration of anaerobic digestion with heat pump: machine learning-based technical and environmental assessment. Bioresource Technology, 369, 128485. (doi: 10.1016/j.biortech.2022.128485)

2022

Martínez-Rabert, E. , van Amstel, C., Smith, C. , Sloan, W. T. and Gonzalez-Cabaleiro, R. (2022) Environmental and ecological controls of the spatial distribution of microbial populations in aggregates. PLoS Computational Biology, 18(12), e1010807. (doi: 10.1371/journal.pcbi.1010807) (PMID:36534694) (PMCID:PMC9810174)

Birlanga, V. B., McCormack, G., Ijaz, U. Z. , MacCarthy, E., Smith, C. and Collins, G. (2022) Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon. Scientific Reports, 12, 16719. (doi: 10.1038/s41598-022-17008-2) (PMID:36202859) (PMCID:PMC9537138)

Gupta, R. , McRoberts, R., Yu, Z. , Smith, C. , Sloan, W. and You, S. (2022) Life cycle assessment of biodiesel production from rapeseed oil: influence of process parameters and scale. Bioresource Technology, 360, 127532. (doi: 10.1016/j.biortech.2022.127532) (PMID:35772716)

Cholet, F., Lisik, A., Agogué, H., Ijaz, U. Z. , Pineau, P., Lachaussée, N. and Smith, C. J. (2022) Ecological observations based on functional gene sequencing are sensitive to the amplicon processing method. mSphere, 7(4), e0032422. (doi: 10.1128/msphere.00324-22) (PMID:35938727) (PMCID:PMC9429940)

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J. and Ijaz, U.Z. (2022) Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet. npj Biofilms and Microbiomes, 8, 36. (doi: 10.1038/s41522-022-00296-x) (PMID:35508464) (PMCID:PMC9068720)

Martinez-Rabert, E., Smith, C. J. , Sloan, W. T. and González‐Cabaleiro, R. (2022) Biochemistry shapes growth kinetics of nitrifiers and defines their activity under specific environmental conditions. Biotechnology and Bioengineering, 119(5), pp. 1290-1300. (doi: 10.1002/bit.28045) (PMID:35092010)

Thom, C., Smith, C. J. , Moore, G., Weir, P. and Ijaz, U. Z. (2022) Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap. Water Research, 212, 118106. (doi: 10.1016/j.watres.2022.118106) (PMID:35091225)

Khan, A., Akbar, S., Okonkwo, V., Smith, C. , Khan, S., Shah, A. A., Adnan, F., Ijaz, U. Z. , Ahmed, S. and Badshah, M. (2022) Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor. Bioresource Technology, 345, 126219. (doi: 10.1016/j.biortech.2021.126219) (PMID:34813923)

Tatti, E., Duff, A., Kostrysia, A., Cholet, F., Ijaz, U. and Smith, C. (2022) Potential nitrification activity reflects ammonia oxidising bacteria but not archaea activity across a soil-sediment gradient. Estuarine, Coastal and Shelf Science, 264, 107666. (doi: 10.1016/j.ecss.2021.107666)

2021

González-Cabaleiro, R. , Martinez-Rabert, E. , Argiz, L., van Kessel, M. A.H.J. and Smith, C. J. (2021) A framework based on fundamental biochemical principles to engineer microbial community dynamics. Current Opinion in Biotechnology, 67, pp. 111-118. (doi: 10.1016/j.copbio.2021.01.001) (PMID:33540361)

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Ijaz, U.Z. and Smith, C.J. (2021) Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae. Animal Microbiome, 3, 7. (doi: 10.1186/s42523-020-00065-1) (PMID:33500003) (PMCID:PMC7934267)

Champion, T. S., Connelly, S. , Smith, C. J. and Lamberton, P. H.L. (2021) Monitoring schistosomiasis and sanitation interventions—the potential of environmental DNA. Wiley Interdisciplinary Reviews: Water, 8(1), e1491. (doi: 10.1002/wat2.1491)

2020

Cholet, F., Ijaz, U. Z. and Smith, C. J. (2020) Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environmental Microbiology, 22(6), pp. 2383-2402. (doi: 10.1111/1462-2920.15017) (PMID:32285609)

2019

Cholet, F., Ijaz, U. Z. and Smith, C. J. (2019) Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples. Environmental Microbiology, 21(2), pp. 827-844. (doi: 10.1111/1462-2920.14516) (PMID:30585386) (PMCID:PMC6392129)

Keating, C. , Hinchcliff, J., Davies, R. , Wan, A., Davies, S., Fitzgerald, R., Ijaz, U. , Smith, C. and Bolton, M. (2019) Effects of Supplementing a Fishmeal Diet with Algae on the Hindgut Microbiome of Farmed Atlantic Cod (Gadus Morhua) [Poster]. 8th Congress of European Microbiologists, Glasgow, UK, 07-11 Jul 2019.

2018

Zhang, L., Duff, A. and Smith, C. J. (2018) Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems. Environmental Microbiology, 20(8), pp. 2834-2853. (doi: 10.1111/1462-2920.14238) (PMID:29687546)

Reich, I., Ijaz, U. Z. , Gormally, M. and Smith, C. J. (2018) 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Scientific Reports, 8, 10402. (doi: 10.1038/s41598-018-28720-3) (PMID:29991804) (PMCID:PMC6039444)

Keating, C. , Hughes, D., Mahony, T., Cysneiros, D., Ijaz, U.Z. , Smith, C.J. and O‘Flaherty, V. (2018) Cold adaptation and replicable microbial community development during long-term low temperature anaerobic digestion treatment of synthetic sewage. FEMS Microbiology Ecology, 94(7), fiy095. (doi: 10.1093/femsec/fiy095) (PMID:29846574) (PMCID:PMC5995215)

2017

Duff, A. M., Zhang, L.-M. and Smith, C. J. (2017) Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Scientific Reports, 7(1), 13200. (doi: 10.1038/s41598-017-13583-x) (PMID:29038459) (PMCID:PMC5643298)

2016

Tatti, E., McKew, B. A., Whitby, C. and Smith, C. J. (2016) Simultaneous DNA-RNA extraction from coastal sediments and quantification of 16S rRNA genes and transcripts by real-time PCR. Journal of Visualized Experiments(112), e54067. (doi: 10.3791/54067) (PMCID:PMC4927785)

Abberton, C. L., Bereschenko, L., van der Wielen, P. W.J.J. and Smith, C. (2016) Survival, biofilm formation, and growth potential of environmental and enteric escherichia coli strains in drinking water microcosms. Applied and Environmental Microbiology, 82(17), pp. 5320-5331. (doi: 10.1128/AEM.01569-16) (PMID:27342552)

Keating, C. , Chin, J. P., Hughes, D., Manesiotis, P., Cysneiros, D., Mahony, T., Smith, C. J. , McGrath, J. W. and O’Flaherty, V. (2016) Biological phosphorus removal during high-rate, low-temperature, anaerobic digestion of wastewater. Frontiers in Microbiology, 7, 226. (doi: 10.3389/fmicb.2016.00226) (PMID:26973608) (PMCID:PMC4776080)

2015

Reich, I., Gormally, M., Allcock, A. L., McDonnell, R., Castillejo, J., Iglesias, J., Quinteiro, J. and Smith, C. J. (2015) Genetic study reveals close link between Irish and Northern Spanish specimens of the protected Lusitanian slugGeomalacus maculosus. Biological Journal of the Linnean Society, 116(1), pp. 156-168. (doi: 10.1111/bij.12568)

Smith, C. J. , Dong, L. F., Wilson, J., Stott, A., Osborn, A. M. and Nedwell, D. B. (2015) Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient. Frontiers in Microbiology, 6, 542. (doi: 10.3389/fmicb.2015.00542) (PMID:26082763) (PMCID:PMC4451412)

Minogue, E., Tuite, N. L., Smith, C. J. , Reddington, K. and Barry, T. (2015) A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water. BMC Biotechnology, 15(1), p. 6. (doi: 10.1186/s12896-015-0124-1) (PMID:25888294) (PMCID:PMC4342816)

Smith, C. J. , McKew, B. A., Coggan, A. and Whitby, C. (2015) Primers: functional genes for nitrogen-cycling microbes in oil reservoirs. In: McGenity, T. J., Timmis, K. N. and Nogales, B. (eds.) Hydrocarbon and Lipid Microbiology Protocols: Primers. Series: Springer protocols handbooks. Springer: Berlin, pp. 207-241. ISBN 9783662504277 (doi: 10.1007/8623_2015_184)

2014

Papaspyrou, S., Smith, C. J. , Dong, L. F., Whitby, C., Dumbrell, A. J. and Nedwell, D. B. (2014) Nitrate reduction functional genes and nitrate reduction potentials persist in deeper estuarine sediments. Why? PLoS ONE, 9(4), e94111. (doi: 10.1371/journal.pone.0094111) (PMID:24728381) (PMCID:PMC3984109)

2013

Barrett, M., Jahangir, M.M.R., Lee, C., Smith, C.J. , Bhreathnach, N., Collins, G., Richards, K.G. and O’Flaherty, V. (2013) Abundance of denitrification genes under different peizometer depths in four Irish agricultural groundwater sites. Environmental Science and Pollution Research, 20(9), pp. 6646-6657. (doi: 10.1007/s11356-013-1729-3)

2011

Dong, L. F., Sobey, M. N., Smith, C. J. , Rusmana, I., Phillips, W., Stott, A., Osborn, A. M. and Nedwell, D. B. (2011) Dissimilatory reduction of nitrate to ammonium, not denitrification or anammox, dominates benthic nitrate reduction in tropical estuaries. Limnology and Oceanography, 56(1), pp. 279-291. (doi: 10.4319/lo.2011.56.1.0279)

2010

Laverock, B., Smith, C. J. , Tait, K., Osborn, A. M., Widdicombe, S. and Gilbert, J. A. (2010) Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments. ISME Journal, 4(12), pp. 1531-1544. (doi: 10.1038/ismej.2010.86) (PMID:20596074)

McKew, B.A. and Smith, C.J. (2010) Real-time PCR approaches for analysis of hydrocarbon-degrading bacterial communities. In: Timmis, K. N. (ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, pp. 3995-4009. ISBN 9783540775874 (doi: 10.1007/978-3-540-77587-4_311)

2009

Dong, L.F., Smith, C.J. , Papaspyrou, S., Stott, A., Osborn, A.M. and Nedwell, D.B. (2009) Changes in Benthic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne Estuary, United Kingdom). Applied and Environmental Microbiology, 75(10), pp. 3171-3179. (doi: 10.1128/AEM.02511-08) (PMID:19304834) (PMCID:PMC2681644)

Smith, C. J. , Danilowicz, B. S. and Meijer, W. G. (2009) Bacteria associated with the mucus layer of Merlangius merlangus (whiting) as biological tags to determine harvest location. Canadian Journal of Fisheries and Aquatic Sciences, 66(5), pp. 713-716. (doi: 10.1139/F09-035)

Smith, C. J. and Osborn, A. M. (2009) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiology Ecology, 67(1), pp. 6-20. (doi: 10.1111/j.1574-6941.2008.00629.x)

2007

Haynes, K., Hofmann, T. A., Smith, C. J. , Ball, A. S., Underwood, G. J.C. and Osborn, A. M. (2007) Diatom-derived carbohydrates as factors affecting bacterial community composition in estuarine sediments. Applied and Environmental Microbiology, 73(19), pp. 6112-6124. (doi: 10.1128/AEM.00551-07) (PMID:17675437) (PMCID:PMC2075028)

McKew, B. A., Coulon, F., Yakimov, M. M., Denaro, R., Genovese, M., Smith, C. J. , Osborn, A. M., Timmis, K. N. and McGenity, T. J. (2007) Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environmental Microbiology, 9(6), pp. 1562-1571. (doi: 10.1111/j.1462-2920.2007.01277.x) (PMID:17504493)

Smith, C. J. , Danilowicz, B. S. and Meijer, W. G. (2007) Characterization of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus). FEMS Microbiology Ecology, 62(1), pp. 90-97. (doi: 10.1111/j.1574-6941.2007.00369.x) (PMID:17692096)

Smith, C. J. , Nedwell, D. B., Dong, L. F. and Osborn, A. M. (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology, 73(11), pp. 3612-3622. (doi: 10.1128/AEM.02894-06) (PMID:17400770) (PMCID:PMC1932689)

2006

Smith, C. J. , Nedwell, D. B., Dong, L. F. and Osborn, A. M. (2006) Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples. Environmental Microbiology, 8(5), pp. 804-815. (doi: 10.1111/j.1462-2920.2005.00963.x)

2005

Osborn, A. M. and Smith, C. J. (Eds.) (2005) Molecular Microbial Ecology. Series: BIOS advanced methods. Taylor and Francis. ISBN 9781859962831

Smith, C. J. , Danilowicz, B. S., Clear, A. K., Costello, F. J., Wilson, B. and Meijer, W. G. (2005) T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiology Ecology, 54(3), pp. 375-380. (doi: 10.1016/j.femsec.2005.05.002) (PMID:16332335)

Articles

Hajabdollahi Ouderji, Z., Gupta, R. , Mckeown, A., Yu, Z. , Smith, C. , Sloan, W. and You, S. (2023) Integration of anaerobic digestion with heat pump: machine learning-based technical and environmental assessment. Bioresource Technology, 369, 128485. (doi: 10.1016/j.biortech.2022.128485)

Martínez-Rabert, E. , van Amstel, C., Smith, C. , Sloan, W. T. and Gonzalez-Cabaleiro, R. (2022) Environmental and ecological controls of the spatial distribution of microbial populations in aggregates. PLoS Computational Biology, 18(12), e1010807. (doi: 10.1371/journal.pcbi.1010807) (PMID:36534694) (PMCID:PMC9810174)

Birlanga, V. B., McCormack, G., Ijaz, U. Z. , MacCarthy, E., Smith, C. and Collins, G. (2022) Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon. Scientific Reports, 12, 16719. (doi: 10.1038/s41598-022-17008-2) (PMID:36202859) (PMCID:PMC9537138)

Gupta, R. , McRoberts, R., Yu, Z. , Smith, C. , Sloan, W. and You, S. (2022) Life cycle assessment of biodiesel production from rapeseed oil: influence of process parameters and scale. Bioresource Technology, 360, 127532. (doi: 10.1016/j.biortech.2022.127532) (PMID:35772716)

Cholet, F., Lisik, A., Agogué, H., Ijaz, U. Z. , Pineau, P., Lachaussée, N. and Smith, C. J. (2022) Ecological observations based on functional gene sequencing are sensitive to the amplicon processing method. mSphere, 7(4), e0032422. (doi: 10.1128/msphere.00324-22) (PMID:35938727) (PMCID:PMC9429940)

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J. and Ijaz, U.Z. (2022) Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet. npj Biofilms and Microbiomes, 8, 36. (doi: 10.1038/s41522-022-00296-x) (PMID:35508464) (PMCID:PMC9068720)

Martinez-Rabert, E., Smith, C. J. , Sloan, W. T. and González‐Cabaleiro, R. (2022) Biochemistry shapes growth kinetics of nitrifiers and defines their activity under specific environmental conditions. Biotechnology and Bioengineering, 119(5), pp. 1290-1300. (doi: 10.1002/bit.28045) (PMID:35092010)

Thom, C., Smith, C. J. , Moore, G., Weir, P. and Ijaz, U. Z. (2022) Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap. Water Research, 212, 118106. (doi: 10.1016/j.watres.2022.118106) (PMID:35091225)

Khan, A., Akbar, S., Okonkwo, V., Smith, C. , Khan, S., Shah, A. A., Adnan, F., Ijaz, U. Z. , Ahmed, S. and Badshah, M. (2022) Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor. Bioresource Technology, 345, 126219. (doi: 10.1016/j.biortech.2021.126219) (PMID:34813923)

Tatti, E., Duff, A., Kostrysia, A., Cholet, F., Ijaz, U. and Smith, C. (2022) Potential nitrification activity reflects ammonia oxidising bacteria but not archaea activity across a soil-sediment gradient. Estuarine, Coastal and Shelf Science, 264, 107666. (doi: 10.1016/j.ecss.2021.107666)

González-Cabaleiro, R. , Martinez-Rabert, E. , Argiz, L., van Kessel, M. A.H.J. and Smith, C. J. (2021) A framework based on fundamental biochemical principles to engineer microbial community dynamics. Current Opinion in Biotechnology, 67, pp. 111-118. (doi: 10.1016/j.copbio.2021.01.001) (PMID:33540361)

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Ijaz, U.Z. and Smith, C.J. (2021) Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae. Animal Microbiome, 3, 7. (doi: 10.1186/s42523-020-00065-1) (PMID:33500003) (PMCID:PMC7934267)

Champion, T. S., Connelly, S. , Smith, C. J. and Lamberton, P. H.L. (2021) Monitoring schistosomiasis and sanitation interventions—the potential of environmental DNA. Wiley Interdisciplinary Reviews: Water, 8(1), e1491. (doi: 10.1002/wat2.1491)

Cholet, F., Ijaz, U. Z. and Smith, C. J. (2020) Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environmental Microbiology, 22(6), pp. 2383-2402. (doi: 10.1111/1462-2920.15017) (PMID:32285609)

Cholet, F., Ijaz, U. Z. and Smith, C. J. (2019) Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples. Environmental Microbiology, 21(2), pp. 827-844. (doi: 10.1111/1462-2920.14516) (PMID:30585386) (PMCID:PMC6392129)

Zhang, L., Duff, A. and Smith, C. J. (2018) Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems. Environmental Microbiology, 20(8), pp. 2834-2853. (doi: 10.1111/1462-2920.14238) (PMID:29687546)

Reich, I., Ijaz, U. Z. , Gormally, M. and Smith, C. J. (2018) 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Scientific Reports, 8, 10402. (doi: 10.1038/s41598-018-28720-3) (PMID:29991804) (PMCID:PMC6039444)

Keating, C. , Hughes, D., Mahony, T., Cysneiros, D., Ijaz, U.Z. , Smith, C.J. and O‘Flaherty, V. (2018) Cold adaptation and replicable microbial community development during long-term low temperature anaerobic digestion treatment of synthetic sewage. FEMS Microbiology Ecology, 94(7), fiy095. (doi: 10.1093/femsec/fiy095) (PMID:29846574) (PMCID:PMC5995215)

Duff, A. M., Zhang, L.-M. and Smith, C. J. (2017) Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Scientific Reports, 7(1), 13200. (doi: 10.1038/s41598-017-13583-x) (PMID:29038459) (PMCID:PMC5643298)

Tatti, E., McKew, B. A., Whitby, C. and Smith, C. J. (2016) Simultaneous DNA-RNA extraction from coastal sediments and quantification of 16S rRNA genes and transcripts by real-time PCR. Journal of Visualized Experiments(112), e54067. (doi: 10.3791/54067) (PMCID:PMC4927785)

Abberton, C. L., Bereschenko, L., van der Wielen, P. W.J.J. and Smith, C. (2016) Survival, biofilm formation, and growth potential of environmental and enteric escherichia coli strains in drinking water microcosms. Applied and Environmental Microbiology, 82(17), pp. 5320-5331. (doi: 10.1128/AEM.01569-16) (PMID:27342552)

Keating, C. , Chin, J. P., Hughes, D., Manesiotis, P., Cysneiros, D., Mahony, T., Smith, C. J. , McGrath, J. W. and O’Flaherty, V. (2016) Biological phosphorus removal during high-rate, low-temperature, anaerobic digestion of wastewater. Frontiers in Microbiology, 7, 226. (doi: 10.3389/fmicb.2016.00226) (PMID:26973608) (PMCID:PMC4776080)

Reich, I., Gormally, M., Allcock, A. L., McDonnell, R., Castillejo, J., Iglesias, J., Quinteiro, J. and Smith, C. J. (2015) Genetic study reveals close link between Irish and Northern Spanish specimens of the protected Lusitanian slugGeomalacus maculosus. Biological Journal of the Linnean Society, 116(1), pp. 156-168. (doi: 10.1111/bij.12568)

Smith, C. J. , Dong, L. F., Wilson, J., Stott, A., Osborn, A. M. and Nedwell, D. B. (2015) Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient. Frontiers in Microbiology, 6, 542. (doi: 10.3389/fmicb.2015.00542) (PMID:26082763) (PMCID:PMC4451412)

Minogue, E., Tuite, N. L., Smith, C. J. , Reddington, K. and Barry, T. (2015) A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water. BMC Biotechnology, 15(1), p. 6. (doi: 10.1186/s12896-015-0124-1) (PMID:25888294) (PMCID:PMC4342816)

Papaspyrou, S., Smith, C. J. , Dong, L. F., Whitby, C., Dumbrell, A. J. and Nedwell, D. B. (2014) Nitrate reduction functional genes and nitrate reduction potentials persist in deeper estuarine sediments. Why? PLoS ONE, 9(4), e94111. (doi: 10.1371/journal.pone.0094111) (PMID:24728381) (PMCID:PMC3984109)

Barrett, M., Jahangir, M.M.R., Lee, C., Smith, C.J. , Bhreathnach, N., Collins, G., Richards, K.G. and O’Flaherty, V. (2013) Abundance of denitrification genes under different peizometer depths in four Irish agricultural groundwater sites. Environmental Science and Pollution Research, 20(9), pp. 6646-6657. (doi: 10.1007/s11356-013-1729-3)

Dong, L. F., Sobey, M. N., Smith, C. J. , Rusmana, I., Phillips, W., Stott, A., Osborn, A. M. and Nedwell, D. B. (2011) Dissimilatory reduction of nitrate to ammonium, not denitrification or anammox, dominates benthic nitrate reduction in tropical estuaries. Limnology and Oceanography, 56(1), pp. 279-291. (doi: 10.4319/lo.2011.56.1.0279)

Laverock, B., Smith, C. J. , Tait, K., Osborn, A. M., Widdicombe, S. and Gilbert, J. A. (2010) Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments. ISME Journal, 4(12), pp. 1531-1544. (doi: 10.1038/ismej.2010.86) (PMID:20596074)

Dong, L.F., Smith, C.J. , Papaspyrou, S., Stott, A., Osborn, A.M. and Nedwell, D.B. (2009) Changes in Benthic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne Estuary, United Kingdom). Applied and Environmental Microbiology, 75(10), pp. 3171-3179. (doi: 10.1128/AEM.02511-08) (PMID:19304834) (PMCID:PMC2681644)

Smith, C. J. , Danilowicz, B. S. and Meijer, W. G. (2009) Bacteria associated with the mucus layer of Merlangius merlangus (whiting) as biological tags to determine harvest location. Canadian Journal of Fisheries and Aquatic Sciences, 66(5), pp. 713-716. (doi: 10.1139/F09-035)

Smith, C. J. and Osborn, A. M. (2009) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiology Ecology, 67(1), pp. 6-20. (doi: 10.1111/j.1574-6941.2008.00629.x)

Haynes, K., Hofmann, T. A., Smith, C. J. , Ball, A. S., Underwood, G. J.C. and Osborn, A. M. (2007) Diatom-derived carbohydrates as factors affecting bacterial community composition in estuarine sediments. Applied and Environmental Microbiology, 73(19), pp. 6112-6124. (doi: 10.1128/AEM.00551-07) (PMID:17675437) (PMCID:PMC2075028)

McKew, B. A., Coulon, F., Yakimov, M. M., Denaro, R., Genovese, M., Smith, C. J. , Osborn, A. M., Timmis, K. N. and McGenity, T. J. (2007) Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environmental Microbiology, 9(6), pp. 1562-1571. (doi: 10.1111/j.1462-2920.2007.01277.x) (PMID:17504493)

Smith, C. J. , Danilowicz, B. S. and Meijer, W. G. (2007) Characterization of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus). FEMS Microbiology Ecology, 62(1), pp. 90-97. (doi: 10.1111/j.1574-6941.2007.00369.x) (PMID:17692096)

Smith, C. J. , Nedwell, D. B., Dong, L. F. and Osborn, A. M. (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology, 73(11), pp. 3612-3622. (doi: 10.1128/AEM.02894-06) (PMID:17400770) (PMCID:PMC1932689)

Smith, C. J. , Nedwell, D. B., Dong, L. F. and Osborn, A. M. (2006) Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples. Environmental Microbiology, 8(5), pp. 804-815. (doi: 10.1111/j.1462-2920.2005.00963.x)

Smith, C. J. , Danilowicz, B. S., Clear, A. K., Costello, F. J., Wilson, B. and Meijer, W. G. (2005) T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiology Ecology, 54(3), pp. 375-380. (doi: 10.1016/j.femsec.2005.05.002) (PMID:16332335)

Book Sections

Smith, C. J. , McKew, B. A., Coggan, A. and Whitby, C. (2015) Primers: functional genes for nitrogen-cycling microbes in oil reservoirs. In: McGenity, T. J., Timmis, K. N. and Nogales, B. (eds.) Hydrocarbon and Lipid Microbiology Protocols: Primers. Series: Springer protocols handbooks. Springer: Berlin, pp. 207-241. ISBN 9783662504277 (doi: 10.1007/8623_2015_184)

McKew, B.A. and Smith, C.J. (2010) Real-time PCR approaches for analysis of hydrocarbon-degrading bacterial communities. In: Timmis, K. N. (ed.) Handbook of Hydrocarbon and Lipid Microbiology. Springer, pp. 3995-4009. ISBN 9783540775874 (doi: 10.1007/978-3-540-77587-4_311)

Edited Books

Osborn, A. M. and Smith, C. J. (Eds.) (2005) Molecular Microbial Ecology. Series: BIOS advanced methods. Taylor and Francis. ISBN 9781859962831

Conference or Workshop Item

Keating, C. , Hinchcliff, J., Davies, R. , Wan, A., Davies, S., Fitzgerald, R., Ijaz, U. , Smith, C. and Bolton, M. (2019) Effects of Supplementing a Fishmeal Diet with Algae on the Hindgut Microbiome of Farmed Atlantic Cod (Gadus Morhua) [Poster]. 8th Congress of European Microbiologists, Glasgow, UK, 07-11 Jul 2019.