Professor Cindy Smith

  • Professor (Infrastructure & Environment)

Research interests

My overarching research interests are in the field of molecular microbial ecology and water quality, with particular focus on microbial community structure and functioning in natural (coastal sediment), farmed (aquaculture)and engineered (drinking water) ecosystems.  Specifically, research on the nitrogen cycle focuses on unravelling the key drivers, interactions and environmental controls of the microorganisms driving the nitrogen cycle. Drinking water microbiology research focuses on potable water quality with respect to the effects of conditioning shear stress on biofilm development; the fate of pathogens and faecal indicator organisms within water distribution systems and the use of biofiltration to deliver water quality.

Publications

List by: Type | Date

Jump to: 2025 | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2011 | 2010 | 2009 | 2007 | 2006 | 2005
Number of items: 57.

2025

Cholet, Fabien, Vignola, Marta ORCID logoORCID: https://orcid.org/0000-0002-3457-5748, Quinn, Dominic, Ijaz, Umer Z., Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281, 123684. (doi: 10.1016/j.watres.2025.123684) (PMID:40280003)

Thom, Claire, Ijaz, Umer, Moore, Graeme, Weir, Paul and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2025) Evaluation of existing lacZ primers and de novo design of an optimised qPCR assay to quantify coliform bacteria in drinking water. Journal of Applied Microbiology, (doi: 10.1093/jambio/lxaf156) (PMID:40560531) (Early Online Publication)

Li, Xiaobo, Song, Yanqing ORCID logoORCID: https://orcid.org/0000-0002-8338-4016, Glidle, Andrew, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Cusack, Maggie and Yin, Huabing ORCID logoORCID: https://orcid.org/0000-0001-7693-377X (2025) A simple three-dimensional microfluidic platform for studying chemotaxis and cell sorting. Lab on a Chip, 25(3), pp. 343-353. (doi: 10.1039/D4LC00892H) (PMID:39758022)

2024

Fantinelli Franco, Fabiane ORCID logoORCID: https://orcid.org/0000-0002-3891-2334, Malik, Muhammad, Manjakkal, Libu ORCID logoORCID: https://orcid.org/0000-0001-7933-6321, Roshanghias, Ali, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Gauchotte-Lindsay, Caroline ORCID logoORCID: https://orcid.org/0000-0002-4970-5031 (2024) Optimising carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16(47), pp. 65489-65502. (doi: 10.1021/acsami.4c13124) (PMID:39539231) (PMCID:PMC11615855)

Fantinelli Franco, Fabiane ORCID logoORCID: https://orcid.org/0000-0002-3891-2334, Malik, Muhammad Hassan, Manjakkal, Libu, Roshanghias, Ali, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Gauchotte-Lindsay, Caroline ORCID logoORCID: https://orcid.org/0000-0002-4970-5031 (2024) Optimizing carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16(47), pp. 65489-65502. (doi: 10.1021/acsami.4c13124) (PMID:39539231)

Stewart, Kelly, Boerlage, Annette S., Barr, William, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2024) Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea. Animal Microbiome, 6, 65. (doi: 10.1186/s42523-024-00347-y) (PMID:39516952) (PMCID:PMC11549768)

Cholet, Fabien, Agogué, Hélène, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Lachaussée, Nicolas, Pineau, Philippe and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2024) Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. Science of the Total Environment, 946, 174312. (doi: 10.1016/j.scitotenv.2024.174312) (PMID:38936706)

Martin, Signe, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Stewart, Kelly, Barr, William, Cheslett, Deborah, O'Connor, Ian, Swords, Fiona, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and O'Dwyer, Katie (2024) The hepatopancreas microbiome of velvet crab, Necora puber. Environmental Microbiology Reports, 16(5), e70014. (doi: 10.1111/1758-2229.70014) (PMID:39354672)

Quinn, Dominic, Tsagkari, Erifyli ORCID logoORCID: https://orcid.org/0000-0002-7810-3048, Bhandari, Dinesh S. ORCID logoORCID: https://orcid.org/0000-0002-7753-5535, Fish, Katherine, You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Boxall, Joby and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2024) Pseudomonas aeruginosa interactions with drinking water biofilm after an acute spike in annular bioreactors—attachment, persistence, release, and reattachment. In: 3rd International Joint Conference on Water Distribution Systems Analysis & Computing and Control for the Water Industry (WDSA/CCWI 2024), Ferrara, Italy, 01-04 Jul 2024, p. 148. (doi: 10.3390/engproc2024069148)

Shi, X. et al. (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262, 122053. (doi: 10.1016/j.watres.2024.122053)

Singh Bhandari, Dinesh ORCID logoORCID: https://orcid.org/0000-0002-7753-5535, Quinn, Dominic, Tsagkari, Erifyli ORCID logoORCID: https://orcid.org/0000-0002-7810-3048, Fish, Katherine, Pick, Frances, Boxall, Joby, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291 and Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 (2024) Modelling the Dynamics of P. aeruginosa in the Formation of Biofilms. In: 3rd International Joint Conference on Water Distribution Systems Analysis & Computing and Control for the Water Industry (WDSA/CCWI 2024), Ferrara, Italy, 01-04 Jul 2024, p. 141. (doi: 10.3390/engproc2024069141)

Cossu, Laura O., De Aquino, Sérgio Francisco, Filho, César Rossas Mota, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Vignola, Marta ORCID logoORCID: https://orcid.org/0000-0002-3457-5748 (2024) Review on pesticide contamination and drinking water treatment in Brazil: the need for improved treatment methods. ACS ES&T Water, 4(9), pp. 3629-3644. (doi: 10.1021/acsestwater.4c00063)

Hassard, F. et al. (2024) Scaling-up engineering biology for enhanced environmental solutions. ACS Synthetic Biology, 13(6), pp. 1586-1588. (doi: 10.1021/acssynbio.4c00292) (PMID:38903005)

2023

Okonkwo, Valentine, Cholet, Fabien, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Koottatep, Thammarat, Pussayanavin, Tatchai, Polpraset, Chongrak, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Connelly, Stephanie ORCID logoORCID: https://orcid.org/0000-0001-5261-2090 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89(11), e01071-23. (doi: 10.1128/aem.01071-23) (PMID:37874304) (PMCID:PMC10686061)

Vignola, Marta ORCID logoORCID: https://orcid.org/0000-0002-3457-5748, Lenselink, Jeanine, Quinn, Dominic, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Pereira, Ryan, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Connelly, Stephanie ORCID logoORCID: https://orcid.org/0000-0001-5261-2090, Moore, Graeme, Gauchotte-Lindsay, Caroline ORCID logoORCID: https://orcid.org/0000-0002-4970-5031 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2023) Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA: Water Infrastructure, Ecosystems and Society, 72(10), pp. 1837-1851. (doi: 10.2166/aqua.2023.036)

Hajabdollahi Ouderji, Zahra, Gupta, Rohit ORCID logoORCID: https://orcid.org/0000-0001-5246-0883, Mckeown, Andrew, Yu, Zhibin ORCID logoORCID: https://orcid.org/0000-0003-0845-9951, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291 (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, Eloi ORCID logoORCID: https://orcid.org/0000-0002-0583-3103, van Amstel, Chiel, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and Gonzalez-Cabaleiro, Rebeca ORCID logoORCID: https://orcid.org/0000-0002-4000-5928 (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, Victor B., McCormack, Grace, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, MacCarthy, Eugene, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Collins, Gavin (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, Rohit ORCID logoORCID: https://orcid.org/0000-0001-5246-0883, McRoberts, Ruairidh, Yu, Zhibin ORCID logoORCID: https://orcid.org/0000-0003-0845-9951, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291 (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, Fabien, Lisik, Agata, Agogué, Hélène, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Pineau, Philippe, Lachaussée, Nicolas and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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. ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Ijaz, U.Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 (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, Eloi, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and González‐Cabaleiro, Rebeca (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, Claire, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Moore, Graeme, Weir, Paul and Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 (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, Alam, Akbar, Sedrah, Okonkwo, Valentine, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Khan, Samiullah, Shah, Aamer Ali, Adnan, Fazal, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Ahmed, Safia and Badshah, Malik (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, Enrico, Duff, Aoife, Kostrysia, Anastasiia, Cholet, Fabien, Ijaz, Umer ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Rebeca ORCID logoORCID: https://orcid.org/0000-0002-4000-5928, Martinez-Rabert, Eloi ORCID logoORCID: https://orcid.org/0000-0002-0583-3103, Argiz, Lucia, van Kessel, Maartje A.H.J. and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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. ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Ijaz, U.Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, C.J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Teteh S., Connelly, Stephanie ORCID logoORCID: https://orcid.org/0000-0001-5261-2090, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Lamberton, Poppy H.L. ORCID logoORCID: https://orcid.org/0000-0003-1048-6318 (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, Fabien, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Fabien, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Ciara ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Hinchcliff, James, Davies, Robert ORCID logoORCID: https://orcid.org/0000-0002-6342-2222, Wan, Alexander, Davies, Simon, Fitzgerald, Richard, Ijaz, Umer ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Bolton, Majbritt (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, Limei, Duff, Aoife and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Inga, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Gormally, Mike and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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. ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Hughes, D., Mahony, T., Cysneiros, D., Ijaz, U.Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Smith, C.J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 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, Aoife M., Zhang, Li-Mei and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2017) Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Scientific Reports, 7, 13200. (doi: 10.1038/s41598-017-13583-x) (PMID:29038459) (PMCID:PMC5643298)

2016

Tatti, Enrico, McKew, Boyd A., Whitby, Corrine and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Cathy L., Bereschenko, Ludmila, van der Wielen, Paul W.J.J. and Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Ciara ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Chin, Jason P., Hughes, Dermot, Manesiotis, Panagiotis, Cysneiros, Denise, Mahony, Therese, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, McGrath, John W. and O’Flaherty, Vincent (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, Inga, Gormally, Michael, Allcock, A. Louise, McDonnell, Rory, Castillejo, José, Iglesias, Javier, Quinteiro, Javier and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Dong, Liang F., Wilson, John, Stott, Andrew, Osborn, A. Mark and Nedwell, David 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, Elizabeth, Tuite, Nina L, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Reddington, Kate and Barry, Thomas (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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, McKew, Boyd A., Coggan, A. and Whitby, Corrine (2015) Primers: functional genes for nitrogen-cycling microbes in oil reservoirs. In: McGenity, Terry J., Timmis, Kenneth N. and Nogales, Balbina (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, Sokratis, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Dong, Liang F., Whitby, Corinne, Dumbrell, Alex J. and Nedwell, David 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. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, 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, Liang F., Sobey, Milika Naqasima, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Rusmana, Iman, Phillips, Wayne, Stott, Andrew, Osborn, A. Mark and Nedwell, David 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, Bonnie, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Tait, Karen, Osborn, A. Mark, Widdicombe, Steve and Gilbert, Jack 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. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2010) Real-time PCR approaches for analysis of hydrocarbon-degrading bacterial communities. In: Timmis, Kenneth 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. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Danilowicz, Bret S. and Meijer, Wim 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Osborn, A. Mark (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, Kelly, Hofmann, Tanja A., Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Ball, Andrew S., Underwood, Graham J.C. and Osborn, A. Mark (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, Boyd A., Coulon, Frédéric, Yakimov, Michail M., Denaro, Renata, Genovese, Maria, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Osborn, A. Mark, Timmis, Kenneth N. and McGenity, Terry 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Danilowicz, Bret S. and Meijer, Wim 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Nedwell, David B., Dong, Liang F. and Osborn, A. Mark (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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Nedwell, David B., Dong, Liang F. and Osborn, A. Mark (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. Mark and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (Eds.) (2005) Molecular Microbial Ecology. Series: BIOS advanced methods. Taylor and Francis. ISBN 9781859962831

Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Danilowicz, Bret S., Clear, Adrian K., Costello, Fintan J., Wilson, Bryan and Meijer, Wim 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)

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Jump to: Articles | Book Sections | Edited Books | Conference or Workshop Item | Conference Proceedings
Number of items: 57.

Articles

Cholet, Fabien, Vignola, Marta ORCID logoORCID: https://orcid.org/0000-0002-3457-5748, Quinn, Dominic, Ijaz, Umer Z., Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281, 123684. (doi: 10.1016/j.watres.2025.123684) (PMID:40280003)

Thom, Claire, Ijaz, Umer, Moore, Graeme, Weir, Paul and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2025) Evaluation of existing lacZ primers and de novo design of an optimised qPCR assay to quantify coliform bacteria in drinking water. Journal of Applied Microbiology, (doi: 10.1093/jambio/lxaf156) (PMID:40560531) (Early Online Publication)

Li, Xiaobo, Song, Yanqing ORCID logoORCID: https://orcid.org/0000-0002-8338-4016, Glidle, Andrew, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Cusack, Maggie and Yin, Huabing ORCID logoORCID: https://orcid.org/0000-0001-7693-377X (2025) A simple three-dimensional microfluidic platform for studying chemotaxis and cell sorting. Lab on a Chip, 25(3), pp. 343-353. (doi: 10.1039/D4LC00892H) (PMID:39758022)

Fantinelli Franco, Fabiane ORCID logoORCID: https://orcid.org/0000-0002-3891-2334, Malik, Muhammad, Manjakkal, Libu ORCID logoORCID: https://orcid.org/0000-0001-7933-6321, Roshanghias, Ali, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Gauchotte-Lindsay, Caroline ORCID logoORCID: https://orcid.org/0000-0002-4970-5031 (2024) Optimising carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16(47), pp. 65489-65502. (doi: 10.1021/acsami.4c13124) (PMID:39539231) (PMCID:PMC11615855)

Fantinelli Franco, Fabiane ORCID logoORCID: https://orcid.org/0000-0002-3891-2334, Malik, Muhammad Hassan, Manjakkal, Libu, Roshanghias, Ali, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Gauchotte-Lindsay, Caroline ORCID logoORCID: https://orcid.org/0000-0002-4970-5031 (2024) Optimizing carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16(47), pp. 65489-65502. (doi: 10.1021/acsami.4c13124) (PMID:39539231)

Stewart, Kelly, Boerlage, Annette S., Barr, William, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2024) Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea. Animal Microbiome, 6, 65. (doi: 10.1186/s42523-024-00347-y) (PMID:39516952) (PMCID:PMC11549768)

Cholet, Fabien, Agogué, Hélène, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Lachaussée, Nicolas, Pineau, Philippe and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2024) Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. Science of the Total Environment, 946, 174312. (doi: 10.1016/j.scitotenv.2024.174312) (PMID:38936706)

Martin, Signe, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Stewart, Kelly, Barr, William, Cheslett, Deborah, O'Connor, Ian, Swords, Fiona, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and O'Dwyer, Katie (2024) The hepatopancreas microbiome of velvet crab, Necora puber. Environmental Microbiology Reports, 16(5), e70014. (doi: 10.1111/1758-2229.70014) (PMID:39354672)

Shi, X. et al. (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262, 122053. (doi: 10.1016/j.watres.2024.122053)

Cossu, Laura O., De Aquino, Sérgio Francisco, Filho, César Rossas Mota, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Vignola, Marta ORCID logoORCID: https://orcid.org/0000-0002-3457-5748 (2024) Review on pesticide contamination and drinking water treatment in Brazil: the need for improved treatment methods. ACS ES&T Water, 4(9), pp. 3629-3644. (doi: 10.1021/acsestwater.4c00063)

Hassard, F. et al. (2024) Scaling-up engineering biology for enhanced environmental solutions. ACS Synthetic Biology, 13(6), pp. 1586-1588. (doi: 10.1021/acssynbio.4c00292) (PMID:38903005)

Okonkwo, Valentine, Cholet, Fabien, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Koottatep, Thammarat, Pussayanavin, Tatchai, Polpraset, Chongrak, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Connelly, Stephanie ORCID logoORCID: https://orcid.org/0000-0001-5261-2090 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89(11), e01071-23. (doi: 10.1128/aem.01071-23) (PMID:37874304) (PMCID:PMC10686061)

Vignola, Marta ORCID logoORCID: https://orcid.org/0000-0002-3457-5748, Lenselink, Jeanine, Quinn, Dominic, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Pereira, Ryan, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Connelly, Stephanie ORCID logoORCID: https://orcid.org/0000-0001-5261-2090, Moore, Graeme, Gauchotte-Lindsay, Caroline ORCID logoORCID: https://orcid.org/0000-0002-4970-5031 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2023) Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA: Water Infrastructure, Ecosystems and Society, 72(10), pp. 1837-1851. (doi: 10.2166/aqua.2023.036)

Hajabdollahi Ouderji, Zahra, Gupta, Rohit ORCID logoORCID: https://orcid.org/0000-0001-5246-0883, Mckeown, Andrew, Yu, Zhibin ORCID logoORCID: https://orcid.org/0000-0003-0845-9951, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291 (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, Eloi ORCID logoORCID: https://orcid.org/0000-0002-0583-3103, van Amstel, Chiel, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and Gonzalez-Cabaleiro, Rebeca ORCID logoORCID: https://orcid.org/0000-0002-4000-5928 (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, Victor B., McCormack, Grace, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, MacCarthy, Eugene, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Collins, Gavin (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, Rohit ORCID logoORCID: https://orcid.org/0000-0001-5246-0883, McRoberts, Ruairidh, Yu, Zhibin ORCID logoORCID: https://orcid.org/0000-0003-0845-9951, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291 (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, Fabien, Lisik, Agata, Agogué, Hélène, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Pineau, Philippe, Lachaussée, Nicolas and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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. ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Ijaz, U.Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 (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, Eloi, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 and González‐Cabaleiro, Rebeca (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, Claire, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Moore, Graeme, Weir, Paul and Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 (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, Alam, Akbar, Sedrah, Okonkwo, Valentine, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Khan, Samiullah, Shah, Aamer Ali, Adnan, Fazal, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Ahmed, Safia and Badshah, Malik (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, Enrico, Duff, Aoife, Kostrysia, Anastasiia, Cholet, Fabien, Ijaz, Umer ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Rebeca ORCID logoORCID: https://orcid.org/0000-0002-4000-5928, Martinez-Rabert, Eloi ORCID logoORCID: https://orcid.org/0000-0002-0583-3103, Argiz, Lucia, van Kessel, Maartje A.H.J. and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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. ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Ijaz, U.Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, C.J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Teteh S., Connelly, Stephanie ORCID logoORCID: https://orcid.org/0000-0001-5261-2090, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Lamberton, Poppy H.L. ORCID logoORCID: https://orcid.org/0000-0003-1048-6318 (2021) Monitoring schistosomiasis and sanitation interventions—the potential of environmental DNA. Wiley Interdisciplinary Reviews: Water, 8(1), e1491. (doi: 10.1002/wat2.1491)

Cholet, Fabien, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Fabien, Ijaz, Umer Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Limei, Duff, Aoife and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Inga, Ijaz, Umer Zeeshan ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Gormally, Mike and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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. ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Hughes, D., Mahony, T., Cysneiros, D., Ijaz, U.Z. ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Smith, C.J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 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, Aoife M., Zhang, Li-Mei and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2017) Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Scientific Reports, 7, 13200. (doi: 10.1038/s41598-017-13583-x) (PMID:29038459) (PMCID:PMC5643298)

Tatti, Enrico, McKew, Boyd A., Whitby, Corrine and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Cathy L., Bereschenko, Ludmila, van der Wielen, Paul W.J.J. and Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Ciara ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Chin, Jason P., Hughes, Dermot, Manesiotis, Panagiotis, Cysneiros, Denise, Mahony, Therese, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, McGrath, John W. and O’Flaherty, Vincent (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, Inga, Gormally, Michael, Allcock, A. Louise, McDonnell, Rory, Castillejo, José, Iglesias, Javier, Quinteiro, Javier and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Dong, Liang F., Wilson, John, Stott, Andrew, Osborn, A. Mark and Nedwell, David 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, Elizabeth, Tuite, Nina L, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Reddington, Kate and Barry, Thomas (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, Sokratis, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Dong, Liang F., Whitby, Corinne, Dumbrell, Alex J. and Nedwell, David 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. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, 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, Liang F., Sobey, Milika Naqasima, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Rusmana, Iman, Phillips, Wayne, Stott, Andrew, Osborn, A. Mark and Nedwell, David 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, Bonnie, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Tait, Karen, Osborn, A. Mark, Widdicombe, Steve and Gilbert, Jack 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. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Danilowicz, Bret S. and Meijer, Wim 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Osborn, A. Mark (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, Kelly, Hofmann, Tanja A., Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Ball, Andrew S., Underwood, Graham J.C. and Osborn, A. Mark (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, Boyd A., Coulon, Frédéric, Yakimov, Michail M., Denaro, Renata, Genovese, Maria, Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Osborn, A. Mark, Timmis, Kenneth N. and McGenity, Terry 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Danilowicz, Bret S. and Meijer, Wim 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Nedwell, David B., Dong, Liang F. and Osborn, A. Mark (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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Nedwell, David B., Dong, Liang F. and Osborn, A. Mark (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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, Danilowicz, Bret S., Clear, Adrian K., Costello, Fintan J., Wilson, Bryan and Meijer, Wim 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, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, McKew, Boyd A., Coggan, A. and Whitby, Corrine (2015) Primers: functional genes for nitrogen-cycling microbes in oil reservoirs. In: McGenity, Terry J., Timmis, Kenneth N. and Nogales, Balbina (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. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2010) Real-time PCR approaches for analysis of hydrocarbon-degrading bacterial communities. In: Timmis, Kenneth 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. Mark and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (Eds.) (2005) Molecular Microbial Ecology. Series: BIOS advanced methods. Taylor and Francis. ISBN 9781859962831

Conference or Workshop Item

Keating, Ciara ORCID logoORCID: https://orcid.org/0000-0001-9199-3068, Hinchcliff, James, Davies, Robert ORCID logoORCID: https://orcid.org/0000-0002-6342-2222, Wan, Alexander, Davies, Simon, Fitzgerald, Richard, Ijaz, Umer ORCID logoORCID: https://orcid.org/0000-0001-5780-8551, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 and Bolton, Majbritt (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.

Conference Proceedings

Quinn, Dominic, Tsagkari, Erifyli ORCID logoORCID: https://orcid.org/0000-0002-7810-3048, Bhandari, Dinesh S. ORCID logoORCID: https://orcid.org/0000-0002-7753-5535, Fish, Katherine, You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291, Sloan, William T. ORCID logoORCID: https://orcid.org/0000-0002-9450-7384, Boxall, Joby and Smith, Cindy J. ORCID logoORCID: https://orcid.org/0000-0003-4905-0730 (2024) Pseudomonas aeruginosa interactions with drinking water biofilm after an acute spike in annular bioreactors—attachment, persistence, release, and reattachment. In: 3rd International Joint Conference on Water Distribution Systems Analysis & Computing and Control for the Water Industry (WDSA/CCWI 2024), Ferrara, Italy, 01-04 Jul 2024, p. 148. (doi: 10.3390/engproc2024069148)

Singh Bhandari, Dinesh ORCID logoORCID: https://orcid.org/0000-0002-7753-5535, Quinn, Dominic, Tsagkari, Erifyli ORCID logoORCID: https://orcid.org/0000-0002-7810-3048, Fish, Katherine, Pick, Frances, Boxall, Joby, Smith, Cindy ORCID logoORCID: https://orcid.org/0000-0003-4905-0730, You, Siming ORCID logoORCID: https://orcid.org/0000-0003-2175-7291 and Sloan, William ORCID logoORCID: https://orcid.org/0000-0002-9450-7384 (2024) Modelling the Dynamics of P. aeruginosa in the Formation of Biofilms. In: 3rd International Joint Conference on Water Distribution Systems Analysis & Computing and Control for the Water Industry (WDSA/CCWI 2024), Ferrara, Italy, 01-04 Jul 2024, p. 141. (doi: 10.3390/engproc2024069141)

This list was generated on Wed Jul 2 21:04:27 2025 BST.

Grants

Current Grants

  • Gill Health in Scottish Farmed Salmon (2018-2022) £2.3M (£154 694 to UoG) Co-I, The Scottish Aquaculture Innovation Centre
  • How can the water industry move away from the coliform test to a more representative measure of pathogens in drinking water? (2018 - 2023) £63,000 PI, Scottish Water
  • Biofiltration by biological design (2018-2022) £719,000 PI, Royal Academy of Engineering-Scottish Water Senior Reserach Fellowship
  • Biofiltration for sustainable water supply to rural communities (2017-2021) £250,000 PI, Scottish Water
  • ADioS Amoebic Disease of Salmon (2016-2019) €607,924 Co-I, Department of Agriculture, Food and Marine, Ireland.

 Completed Grants

  • Re-engineering Kenyan sand-dams by biological design (2017) £20,000 PI, Royal Academy Engineering Frontiers of Engineering Seed Funding    
  • Manganese mitigation roadmap for Bangladesh (2017) PI £20,000 Co-I, Royal Academy Engineering Frontiers of Engineering Seed Funding.
  • Molecular ecology of ammonia oxidation in coastal sediments (2012-2017) €576,174 PI, Science Foundation Ireland (SFI), Starting Investigator Research Grant (11/SIRG/B2159)
  • Biogeochemical cycling of nitrates in Irish estuaries (2013-2016) €96,000 PI, EPA STRIVE Doctoral Scholarship Scheme (2012-W-PhD-6)     
  • Stable Isotope Probing: linking structure and function (2014) €56,946 PI, Science Foundation Ireland Opportunistic Equipment Fund
  • Microbial Interfaces: SGM Irish Division Meeting (2015) €14,000 PI, SFI Conference and Workshop Call (15/CW/2780)
  • Growth of E. coli in drinking water (2013) €5,994 PI, Irish Research Council New Foundations
  • Pathogen detection, survival and persistence in a model water distribution system (2011-2013) €100,100 PI, Science Foundation Ireland (11:RFP.1:EOB:3243)
  • Development of a functional gene array (FGA) to study bacterial nitrate reducing communities in estuarine sediments (2007)  £4532 Co-I, NERC
  • Biogeochemical cycling of nitrogen in tropical coastal zones: molecular microbial ecology of trace gas production (2006-2009) £261,958 RCo-I, NERC (NE/D013089/1)     

 

Supervision

Current  PhD Students

  • Claire Thom, Part-time PhD Candidate, University of Glasgow, Funded by Scottish Water (2018-2024)
  • Kelly Stewart, PhD Candidate, University of Glasgow, Funded by SAIC (2017 - 2021)
  • Dominic Quinn, PhD Candidate, University of Glasgow, Funded by Scottish Water (2017-2021)
  • Victor Birlanga, PhD Candidate, NUI Galway, Funded by the Department of Agriculture, Food and Marine (2017-2020)
  • Fabien Cholet, PhD Candidate, University of Glasgow PhD studentship (2016-2020)

 

Graduated Students

  • Dr. John Carey, PhD 2017

Thesis: Taxonomy, Parataxonomy and Metabarcoding: an investigation of invertebrate diversity in High Nature Value Wet Grasslands. Irish Research Council and Hardiman Scholarship PhD Studentship

  • Ms Agata Lisik, MSc 2017

       Thesis: Nitrate reduction in Irish estuaries

       EPA: 2012-W-PhD-6

  • Dr. Aoife Duff, PhD 2017

       Thesis: Molecular ecology of ammonia oxidation in coastal sediments.

       SFI:11/SIRG/B2159

  • Dr. Inga Reich, PhD 2016

       Thesis: The EU-protected slug Geomalacus maculosus: An investigation into its phylogenetics, population densities in conifer plantations and its  gut microbial community. Irish Research Council and Hardiman Scholarship PhD Studentship

  • Ms. Cathy Abberton, MSc 2014.

        Thesis: E. coli detection, survival and biofilm potential in drinking water microcosms.

        SFI11:RFP.1:EOB:3243

  

Past Postdoctoral Research Assistants

  • Dr. Aoife Duff, SFI Ammonia Oxidation in Coastal Sediments, 2016-2017.
  • Dr. Enrio Tatti, SFI SIRG  Ammonia oxidation in coastal sediments, 2014-2016.
  • Dr. Limei Zhang, SFI SIRG Ammonia Oxidation in coastal sediments, 2012-2013.
  • Dr. David McCarty, EirCod, Marine Institute, 2011.
  • Chunara, Raheema
    Engineering for Health: Using Qualitative Methods to Inform Water Access Design for Schistosomiasis Control

Teaching

ENG4152: Environmental Biotechnology 4


Professor Cindy Smith on Twitter