UWB Crest

Microbial Pathogen Ecology Group



  • Clements K, Giménez L, Jones DL, Wilson J, Malham SK (2014) Epizoic barnacles act as a reservoir for pathogenic bacteria on commercial shellfish beds: Implications for the shellfish industry. In Proceedings of the 9th International Conference on Molluscan Shellfish Safety (Sydney, March 2013), Food Authority, Newington NSW, Australia. pp 40-43.
  • Duputel, M; Devau, N; Brossard, M; Jaillard, B; Jones, DL; Hinsinger, P; Gerard, F (2014) Reply to the Comment by JP Gustafsson and D. G. Lumsdon on "Citrate adsorption can decrease soluble phosphate concentration in soils: Results of theoretical modeling'' by M. Duputel, N. Devau, M. Brossard, B. Jaillard, DL Jones, P. Hinsinger, and F. Gerard. Applied Geochemistry 46: 90-94.
  • Farrell, M; Macdonald, LM.; Hill, PW.; Wanniarachchi, SD; Farrar, J; Bardgett, RD; Jones, DL (2014) Amino acid dynamics across a grassland altitudinal gradient. Soil Biology & Biochemistry 76: 179-182.
  • Farrell, M; Prendergast-Miller, M; Jones, DL; Hill, PW; Condron, LM (2014) Soil microbial organic nitrogen uptake is regulated by carbon availability. Soil Biology & Biochemistry 77: 261-267.
  • Fathi, R.A., Godbold, D.L., Al-Salih, H.S., Jones, D. (2014) Potential of phytoremediation to clean up uranium-contaminated soil with Acacia species. Journal of Environment and Earth Science 4: 81-91.
  • Flannery, J.; Rajko-Nenow, P.; Winterbourn, J. B.; Malham SK; Jones DL (2014) Effectiveness of cooking to reduce Norovirus and infectious F-specific RNA bacteriophage concentrations in Mytilus edulis. Journal of Applied Microbiology 117: 564-571.
  • Gibbons JM, Williamson JC, Williams AP, Withers PJA, Hockley N, Harris IM, Hughes JW, Taylor RL, Jones DL, Healey JR (2014) Sustainable nutrient management at field, farm and regional level: soil testing, nutrient budgets and the trade-off between lime application and greenhouse gas emissions. Agriculture, Ecosystems & Environment 188, 48-56.
  • Gwyther CL, Jones DL, Gertler C, Edwards-Jones G, Williams AP (2014) Changes in the physicochemical properties and enzymatic activity of waste during bioreduction of pig carcasses. Environmental Technology 35, 1904-1915.
  • Iqbal, Z; Khalid, M; Soleman, N; Jones DL (2014) Differential utilization of dissolved organic and inorganic nitrogen by wheat (Triticum aestivum L.). Journal of Plant Nutrition 37: 2094-2107.
  • Jones, A.K., Jones, D.L., Cross, P. (2014) The carbon footprint of lamb: Sources of variation and opportunities for mitigation. Agricultural Systems 123: 97-107.
  • Jones, AK; Jones, DL; Cross, P (2014) The carbon footprint of UK sheep production: current knowledge and opportunities for reduction in temperate zones. Journal of Agricultural Science 152: 288-308.
  • Jones, DL; Quilliam, RS (2014) Metal contaminated biochar and wood ash negatively affect plant growth and soil quality after land application. Journal Of Hazardous Materials 276: 362-370.
  • Jones, DL; Simfukwe, P; Hill, PW; Mills, RTE; Emmett, BA (2014) Evaluation of Dissolved Organic Carbon as a Soil Quality Indicator in National Monitoring Schemes. PLoS One 9, e90882
  • Lahmer RA, Jones DL, Townsend S, Baker S, Williams AP (2014) Susceptibility of Escherichia coli O157 to chitosan-arginine in beef liquid purge is affected by bacterial cell growth phase. International Journal of Food Science and Technology 49, 515-520.
  • Lucchini, P; Quilliam, RS; DeLuca, TH; Vamerali, T; Jones, DL (2014) Does biochar application alter heavy metal dynamics in agricultural soil? Agriculture Ecosystems & Environment 184, 149-157
  • Lucchini, P; Quilliam, RS; DeLuca, TH; Vamerali, T; Jones, DL (2014) Increased bioavailability of metals in two contrasting agricultural soils treated with waste wood-derived biochar and ash. Environmental Science and Pollution Research 21, 3230-3240
  • Malham, SK; Rajko-Nenow, P; Howlett, E; Tuson, KE; Perkins, TL; Pallett, DW; Wang, H; Jago, CF; Jones, DL; McDonald, JE (2014) The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters. Environmental Science-Processes & Impacts 16: 2145-2155.
  • Millman C, Rigby D, Edwards-Jones G, Lighton L, Jones D (2014) Perceptions, behaviours and kitchen hygiene of people who have and have not suffered campylobacteriosis: A case control study. Food Control 41, 82-90
  • Payvandi, S; Daly, KR; Jones, DL; Talboys, P; Zygalakis, KC; Roose, T (2014) A Mathematical Model of Water and Nutrient Transport in Xylem Vessels of a Wheat Plant. Bulletin of Mathematical Biology 76, 566-596
  • Rousk, Johannes; Hill, Paul W.; Jones, Davey L. (2014) Using the concentration-dependence of respiration arising from glucose addition to estimate in situ concentrations of labile carbon in grassland soil. Soil Biology & Biochemistry 77: 81-88.
  • Rousk, K., Jones, D.L., DeLuca, T.H. (2014) Exposure to nitrogen does not eliminate N2 fixation in the feather moss Pleurozium schreberi (Brid.) Mitt. Plant and Soil 374: 513-521.
  • Rousk, K; Jones, DL; DeLuca, TH (2014) Moss-nitrogen input to boreal forest soils: Tracking 15N in a field experiment. Soil Biology & Biochemistry 72: 100-104
  • Rousk, K; Jones, DL; DeLuca, TH (2014) The resilience of nitrogen fixation in feather moss (Pleurozium schreberi)-cyanobacteria associations after a drying and rewetting cycle. Plant and Soil 377, 159-167
  • Sánchez-Rodríguez, A.R; del Campillo, M. C; Torrent, J; Jones DL (2014) Organic acids alleviate iron chlorosis in chickpea grown on two P-fertilized soils. Journal of Soil Science and Plant Nutrition 14: 292-303.
  • Scullion, J; Smith, AR; Gwynn-Jones, D; Jones DL; Godbold DL (2014) Deciduous woodland exposed to elevated atmospheric CO2 has species-specific impacts on anecic earthworms. Applied Soil Ecology 80: 84-92.
  • Shen, J; Tang, H; Liu, J; Wang, C; Li, Y; Ge, TD; Jones, DL; Wu, JS (2014) Contrasting effects of straw and straw-derived biochar amendments on greenhouse gas emissions within double rice cropping systems. Agriculture Ecosystems & Environment 188: 264-274.
  • Talboys, PJ; Owen, DW; Healey, JR; Withers, PJA; Jones, DL (2014) Auxin secretion by Bacillus amyloliquefaciens FZB42 both stimulates root exudation and limits phosphorus uptake in Triticum aestivum. BMC Plant Biology 14, Article Number 51
  • Wilkinson, A; Hill, PW; Farrar, JF; Jones, DL; Bardgett, RD (2014) Rapid microbial uptake and mineralization of amino acids and peptides along a grassland productivity gradient. Soil Biology & Biochemistry 72, 75-83.
  • Winterbourn JB, Clements K, Lowther J, Malham SK, McDonald JE, Jones DL (2014) Evaluation of spatial contamination patterns for norovirus and faecal indicator bacteria near to a coastal sewage discharge using Mytilus edulis as biosentinels. In Proceedings of the 9th International Conference on Molluscan Shellfish Safety (Sydney, March 2013), Food Authority, Newington NSW, Australia. pp 89-92.
  • Withers, PJA; Sylvester-Bradley, R; Jones, DL; Healey, JR; Talboys, PJ (2014) Feed the crop not the soil: rethinking phosphorus management in the food chain. Environmental Science & Technology 48: 6523-6530.
  • Ransom-Jones, E., Edwards, A., Jones, D.L. and McDonald, J.E. (2014) Environmental Distribution and Diversity of Members of the Cellulolytic Bacterial Phylum Fibrobacteres. Systematic and Applied Microbiology DOI: 10.1016/j.syapm.2014.06.001.


  • Alhelfi, NA; Lahmer, RA; Jones, DL; Williams, AP (2013) Survival and metabolic activity of lux-marked Escherichia coli O157:H7 in different types of milk. Journal of Dairy Research 79: 257-261

  • Coscia I, Robins PE, Porter JS, Malham SK, Ironside JE. (2013) Modelled larval dispersal and measured gene flow: Seascape genetics of the common cockle cerastoderma edule in the southern irish sea. Conserv Genet. 14(2):451-466.

  • Flannery J, Keaveney S, Rajko-Nenow P, O'Flaherty V, Doré W (2013) Norovirus and FRNA bacteriophage determined by RT-qPCR and infectious FRNA bacteriophage in waste water and oysters. Water Research (0).

  • Flannery J, Rajko-Nenow P, Keaveney S, , O'Flaherty V, Doré W (2013) Simulated sunlight inactivatin of norovirus and FRNA bacteriophage in seawater (2013) 115(3):915-922

  • Gwyther, CL; Jones, DL; Golyshin, PN; Williams, AP (2013) Bioreduction of sheep carcasses effectively contains and reduces pathogen levels under operational and simulated breakdown conditions. Environmental Science & Technology 47: 5267-5275.

  • Longshaw M, Malham SK (2013) A review of the infectious agents, parasites, pathogens and commensals of European cockles (Cerastoderma edule and C.glaucum). Journal ofthe Marine Biological Association of the United Kingdom. 93(1), 227-247.

  • Thrupp TJ, Lynch SA, Wootton EC, Malham SK, Vogan CL, Culoty SC, Rowley AF (2013) Infection of juvenile edible crabs, cancer pagurus by a haplosporidian-like parasite. J Invertebr Pathol. 114(1):92-99.

  • Wellington, EMH; Boxall, ABA; Cross, P; Feil, EJ; Gaze, WH; Hawkey, PM; Johnson-Rollings, AS; Jones, DL; Lee, NM; Otten, W; Thomas, CM; Williams, AP (2013) The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria. Lancet Infectious Diseases 13, 155-165

  • Williams, AP; Gordon, HE; Jones, DL.; Killham K; Strachan, NJC; Forbes, KJ (2013) Declining reactivation ability of Escherichia coli O157 following incubation within soil. Soil Biology and Biochemistry 63: 85-88


  • Callaway R,Shinn AP, Grenfell SE, Bron JE, Burnell G, Cook EJ, Crumlish M, Culloty S, Davidson K, Ellis R, Flynn KJ, Fox C, Green DM, Hays GC, Hughes AD, Johnston E, Lowe CD, Lupatsch I, Malham SK, Mendzil AF, Nickell T, Pickerell T, Rowley AF, Stanley MS, Tocher DR, Turnbull JF, Webb G, Wootton E, Shields RJ. (2012) Review of climate change impacts on marine aquaculture in the UK and ireland. Aquat Conserv : Mar Freshwat Ecosyst. 22(3):389-421

  • Flannery F,Keaveney S, Rajko-Nenow P,O'Flaherty V, Doré W (2012) Concentration of norovirus during wastewater treatment and the impact on oyster contamination Applied and Environmental Microbiology 78 (9):3400-3406.

  • Gwyther, CL; Jones, DL; Golyshin, PN; Williams, AP (2012) Fate of pathogens in a simulated bioreduction system for livestock carcasses. Waste Management 32: 933-938.

  • Lahmer, RA; Williams, AP; Townsend, S; Baker, S, Jones, DL (2012) Antibacterial action of chitosan-arginine against Escherichia coli O157 in chicken juice. Food Control 26: 206-211.

  • McDonald, J.E., Rooks, D.J. and McCarthy A.J. (2012) Methods for the isolation of cellulose degrading microorganisms. Methods in Enzymology. 510:375-394.
  • Malham SK, Hutchinson TH, Longshaw M (2012) A review of the biology of European cockles (Cerastoderma spp.) Journal of the Marine Biological Association of the UK. 92 (7) 1563-1577.

  • Quilliam, R.S., Williams, A.P., Jones, D.L. (2012) Lettuce Cultivar Mediates Both Phyllosphere and Rhizosphere Activity of Escherichia coli O157:H7. Plos One 7.

  • Quilliam, RS; Chalmers, RM; Williams, AP; Chart, H; Willshaw, GA; Kench, SM; Edwards-Jones, G; Evans, J; Thomas, DR; Salmon, RL; Jones, DL (2012) Seroprevalence and Risk Factors Associated with Escherichia coli O157 in a Farming Population. Zoonoses and Public Health 59: 83-88.

  • Rajko-Nenow P, Waters A, Keaveney S, Flannery J, Tuite, Coughlan S, O'Flaherty V,  Doré W (2012) .  Norovirus genotypes present in oyster and effluent from a wastewater treatment plant during the seasonal peak of infections in Ireland, 2010 Applied and Environmental Microbiology 79(8):2578-2587

  • Rajko-Nenow P, S Keaveney S, Flannery J, O'Flaherty V, Doré W(2012) Characterisation of norovirus contamination in an Irish shellfishery using real-time RT-qPCR and sequencing analysis. International Journal of Food Microbiology 160(2):105-112.

  • Ransom-Jones, E., Jones, D.L., McCarthy, A.J. and McDonald J.E. (2012) The Fibrobacteres: an important Phylum of cellulose-degrading bacteria. Microbial Ecology 63:271-281.
  • Williams, A.P., Quilliam, R.S., Thorn, C.E., Cooper, D., Reynolds, B., Jones, D.L. (2012) Influence of land use and nutrient flux on metabolic activity of E. coli O157 in river water. Water Air and Soil Pollution 223, 3077-3083.


  • Gwyther, CL; Jones, DL; Golyshin, PN; Williams, AP (2011) The environmental and biosecurity characteristics of livestock carcass disposal methods: A review. Waste Management 31: 767-778.

  • Malpass, MC; Williams, AP; Jones, DL; Omed, HM (2011) Microbiological quality of chicken wings damaged on the farm or in the processing plant. Food Microbiology 27: 521-525.

  • Quilliam, R.S., Williams, A.P., Avery, L.M., Malham, S.K., Jones, D.L.(2011) Unearthing human pathogens at the agricultural-environment interface: A review of current methods for the detection of Escherichia coli O157 in freshwater ecosystems. Agriculture Ecosystems & Environment 140, 354-360.

  • Quilliam, R.S., Clements, K., Duce, C., Cottrill, S.B., Malham, S.K., Jones, D.L. (2011) Spatial variation of waterborne Escherichia coli - implications for routine water quality monitoring. Journal of Water and Health 9, 734-737.

  • Thorn, C.E., Quilliam, R.S., Williams, A.P., Malham, S.K., Cooper, D., Reynolds, B., Jones, D.L ( 2011) Grazing intensity is a poor indicator of waterborne Escherichia coli O157 activity. Anaerobe 17, 330-333.


  • Cotter E, Malham SK, O'Keeffe S, et al. (2010) Summer mortality of the pacific oyster, crassostrea gigas, in the irish sea: The influence of growth, biochemistry and gametogenesis. Aquaculture. 303(1–4):8-21.  

  • Doré W, Keaveney S, Flannery J, Rajko-Nenow P (2010) Management of health risks associated with oysters harvested from a norovirus contaminated area, Ireland, February–March 2010 Eurosurveillance, 2010; 15 (19)

  • McDonald, J.E., Smith, D.L., Fogg, P.C.M., McCarthy, A.J., and Allison, H.E. (2010) Method for Rapid Induction of Prophages from Lysogens and Its Application in the Study of Shiga Toxin-Encoding Escherichia coli Strains. Applied and Environmental Microbiology, 76: 2360-2365.

  • Rooks, D.J., Smith, D.L., McDonald, J.E., Woodward, M.J., McCarthy, A.J., and Allison, H.E. (2010) 454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology. Genes 1(3): 210-226.

  • Rooks, D.J., Yan, Y., McDonald, J.E., Woodward, M.J., McCarthy, A.J. and Allison, H.E. (2010) Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages. Environmental Microbiology 12: 1194-1204. 

Pre 2009

  • Artz RRE, Avery LM, Jones DL, et al. (2006). Potential pitfalls in the quantitative molecular detection of Escherichia coli O157:H7 in environmental matrices. Canadian Journal of Microbiology 52: 482-488.

  • Avery, L.M., Williams, A.P., Killham, K., Jones, D.L. (2009) Heat and lime-treatment as effective control methods for E. coli O157:H7 in organic wastes. Bioresource Technology 100, 2692-2698.

  • Avery, L.M., Williams, A.P., Killham, K., Jones, D.L.(2008) Survival of Escherichia coli, O157:H7 in waters from lakes, rivers, puddles and animal-drinking troughs. Science of the Total Environment 389, 378-385.

  • Avery LM, Killham K and Jones DL (2005). Survival of E. coli O157:H7 in organic wastes destined for land application. Journal of Applied Microbiology 98: 814-822. 2005

  • Avery LM, Hill P, Killham K and Jones DL (2004). Escherichia coli O157 survival following the surface and sub-surface application of human pathogen contaminated organic waste to soil. Soil Biology & Biochemistry 36: 2101-2103.

  • Flannery J, Keaveney S, Doré W (2009)  Use of FRNA bacteriophages to indicate the risk of norovirus contamination in Irish oysters Journal of Food Protection 72 (11) 2358:2362.

  • Jones, DL; Campbell, G; Kaspar, CW (2002) Human enteric pathogens. In Agriculture, hydrology and water quality (Eds Haygarth, PM; Jarvis, SC). Pages: 133-155.

  • Jones DL (1999) Potential health risks associated with the persistence of Escherichia coli O157 in agricultural environments. Soil Use and Management 15, 76-83

  • Lacoste A, Jalabert F, Malham SK, Cueff A, Poulet SA.  (2001) Stress and stress-induced neuroendocrine changes increase the susceptibility of juvenile oysters (crassostrea gigas) to vibrio splendidus. Appl Environ Microbiol. 67(5):2304

  • Lacoste A, Malham SK, Cueff A, Poulet SA. Stress-induced catecholamine changes in the hemolymph of the oyster crassostrea gigas. Gen Comp Endocrinol. 2001;122(2):181-188.

  • Ritchie JM, Campbell GR, Shepherd J, Jones DL et al. (2003). A stable bioluminescent construct of Escherichia coli O157:H7 for hazard assessments of long-term survival in the environment. Applied and Environmental Microbiology 69: 3359-3367.

  • Lacoste A, Malham SK, Gélébart F, Cueff A, Poulet SA (2002) Stress-induced immune changes in the oyster crassostrea gigas. Dev Comp Immunol. 26(1):1-9.

  • Malham SK, Cotter E, O'Keeffe S, et al. (2009) Summer mortality of the pacific oyster, crassostrea gigas, in the irish sea: The influence of temperature and nutrients on health and survival. Aquaculture. 287(1):128.

  • Malham SK, Lacoste A, Gélébart F, Cueff A, Poulet SA.(2003) Evidence for a direct link between stress and immunity in the mollusc haliotis tuberculata. Journal of experimental zoology.Part A, Comparative experimental biology. 295(2):136-144.

  • Williams, AP; Edwards-Jones, G; Jones, DL (2009) In-vessel bioreduction provides an effective storage and pre-treatment method for livestock carcasses prior to final disposal. Bioresource Technology 100: 4032-4040.

  • Williams, A.P., Gordon, H., Jones, D.L., Strachan, N.J.C., Avery, L.M., Killham, K. (2008) Leaching of bioluminescent Escherichia coli O157:H7 from sheep and cattle faeces during simulated rainstorm events. Journal of Applied Microbiology 105, 1452-1460.

  • Williams, A.P., McGregor, K.A., Killham, K., Jones, D.L.(2008) Persistence and metabolic activity of Escherichia coli O157:H7 in farm animal faeces. Fems Microbiology Letters 287, 168-173.

  • Williams AP, Avery LM, Killham K, Jones DL (2007) Persistence, dissipation, and activity of Escherichia coli O157:H7 within sand and seawater environments. FEMS Microbiology Ecology 60: 24-32

  • Williams AP, Avery LM, Killham K, Jones DL (2007). Survival of Escherichia coli O157:H7 in the rhizosphere of maize grown in waste-amended soil. Journal of Applied Microbiology 102: 319-326.

  • Williams, AP; Roberts, P; Avery, LM; Jones DL (2006) Earthworms as vectors of Escherichia coli O157 : H7 in soil and vermicomposts. FEMS Microbiology Ecology 58: 54-64.

  • Williams AP, Avery LM, Killham K and Jones DL (2005). Persistence of Escherichia coli O157 on farm surfaces under different environmental conditions. Journal of Applied Microbiology 98: 1075-1083.

In the Press