Publications of Academic Staff 2016

Academic staff in the School of Biological Sciences published 68 papers in scientific journals during 2016. These are listed below for each staff member (in alphabetical order).

In addition, academic staff also published one edited book, 20 book chapters and 8 referenced conference proceedings. These are listed under “Book chapters” and “Conference proceedings”.

Journal publications

Charles Bishop

Weimerskirch, H., Bishop, C., Jeanniard-du-Dot, T., Prudor, A. and Sachs, G. (2016) Frigate birds track atmospheric conditions over months-long transoceanic flights. Science 353:74-78. Doi 10.1126/science.aaf4374

Henk Braig

Perotti, M. A., Young, D. K. and Braig, H.R. (2016) The ghost sex-life of the paedogenetic beetle Micromalthus debilis. Scientific Reports 6: 27364. Doi 10.1038/srep27364

Gary Carvalho

Carvalho, GR, Hauser, L and Naish, K (2016) Fish, Genes and Genomes: Contributions to Ecology, Evolution and Management. Editorial. Special Issue of Journal of Fish Biology. 89,2471-2478. doi:10.1111/jfb.13228.

Harvey, A. C., Glover, K. A., Taylor, M. I., Creer, S. and Carvalho, G. R. (2016) A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evolutionary Applications. doi: 10.1111/eva.12346

Bylemans, J, Maes, G,  Diopere, E, Cariani, A,  Senn, H, Taylor, MI, Helyar, S,  Bargelloni, L, Bonaldo, A, Carvalho, GR, Guarniero, I, Hans Komen, Martinsohn, J, Nielsen, E, Tinti, F, Volckaert1, F, & Ogden. R (2016) Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics. Aquaculture Environment Interactions, 8: 131–145, doi: 10.3354/aei00164.

Montes, I, Iriondo, M, Manzano, I,   Santos, M, Conklin, D,. Carvalho, GR, Irigoien, X, Estonba, A (2016) No loss of genetic diversity in the exploited and recently collapsed population of Bay of Biscay anchovy (Engraulis encrasicolus, L.). Marine Biology, 163, 98. doi:10.1007/s00227-016-2866-2.

Sinniger, F, Pawlowski, J, Harii1, S, G­ooday, AJ, Yamamoto, H, Chevaldonné, P, Cedhagen, T, Carvalho, GR, & Creer, S (2016) Worldwide analysis of sedimentary DNA reveals major gaps in taxonomic knowledge of deep-sea benthos. Frontiers in Marine Science, http://dx.doi.org/10.3389/fmars.2016.00092.

Llewellyn, M, McGinnity, P, Dionne, M, Letourneau, J, Thonier, F, Carvalho, GR, Creer, S and Derôme, N (2016) The biogeography of the Atlantic Salmon Gut microbiome. The ISME Journal (Nature), 10(5):1280-4. doi: 10.1038/ismej.2015.189.

Harvey, AC, Juleff, G, Carvalho, GR, Taylor, MI, Solberg, MI, Creer, S, Dyrhovden, L,  Matre, IH, and Glover, KA (2016) Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? Royal Society Open Science, DOI: 10.1098/rsos.160152.

Harvey,  AC, Solberg, MF, Glover, KA, Taylor,  MI, Creer, S, and Carvalho, GR (2016) Plasticity in response to feed availability - does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? Journal of Fish Biology, doi: 10.1111/jfb.13076.

Simon Creer

Harvey, A.C., Solberg, M.F., Troianou, E., Carvalho, G.R., Taylor, M.I. Creer, S., Dyrhovden, L., Matre, I.H. and Glover, K.A. (2016). Plasticity in growth of farmed and wild Atlantic salmon: is the increased growth rate of farmed salmon caused by evolutionary adaptations to the commercial diet? BMC Evolutionary Biology. 16:264 doi: 10.1186/s12862-016-0841-7

Harvey, A.C., Solberg, M. F., Glover, K. A., Taylor, M. I., Creer, S., and Carvalho, G.R. (2016).Plasticity in response to feed availability - does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? Journal of Fish Biology. 89:1754-1768. doi: 10.1111/jfb.13076

Harvey, A.C., Juleff, G., Carvalho, G.R., Taylor, M.I., Solberg, M.F., Creer, S.,"Dyrhovden, L., Matre, I.-H., Glover, K.A. (2016). Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? Royal Society Open Science. doi: 10.1098/rsos.160152

Sinniger, F., Pawlowski, J., Harii, S., Gooday, A.J., Yamamoto, H.,Chevaldonne, P., Cedhagen, T., Carvalho, G.R., and Creer, S. (2016).Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos. Frontiers in Marine Science. http://dx.doi.org/10.3389/fmars.2016.00092

Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W.K., Potter, C. and Bik, H.M. (2016). The ecologist’s field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution. 7: 1008-1018. doi: 10.1111/2041-210X.12574

Derycke, S., De Meester, N., Rigaux, A., Creer, S., Bik, H., Thomas, W.K. and Moens, T. (2016). Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability. Molecular Ecology. 25:2093-2110. doi/10.1111/mec.13597/full

Harvey, A. C., Glover, K. A., Taylor, M. I., Creer, S. and Carvalho, G. R. (2016). A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evolutionary Applications. 9:435-449. doi: 10.1111/eva.12346

Christian Dunn

Saraswati, Dunn C., Mitsch W. J. and Freeman C. (2016) Is peat accumulation in mangrove swamps linked to the “enzymic latch” mechanism. Wetlands Ecology and Management. 24:641-650. doi:10.1007/s11273-016-9493-z

Scholz C., Jones T. G., West M., Ehbair A. M., Dunn C. and Freeman C. (2016) Constructed wetlands may lower inorganic nutrient inputs but enhance DOC loadings into a drinking water reservoir in North Wales. Environmental Science and Pollution Research. 23:18192-18199. doi:10.1007/s11356-016-6991-8

Rhymes J., Jones L., Wallace, H. Jones T., Dunn C. and Fenner N.(2016) Small changes in water levels and groundwater nutrients alter nitrogen and carbon processing in dune slack soils. Soil Biology and Biochemistry. 99:28-35. doi:10.1016/j.soilbio.2016.04.018

Nathalie Fenner

Gough, R. Cohen, Y. Fenner, N. Cannon, J. Freeman, C. (2016) Relationships between reservoir water quality and catchment habitat type. International Journal of Environmental Technology and Management (IJETM)19:1.

Rhymes, J. Jones, L. Wallace, H. Jones, T.G. Dunn, C. Fenner. N. (2016) Small changes in water levels and groundwater nutrients alter nitrogen and carbon processing in dune slack soils. Soil Biology & Biochemistry 99:28-35.

Gough, RHolliman P.JFenner, NPeacock, MFreeman, C. (2016) Influence of water table depth on pore water chemistry and trihalomethane formation potential in peatlands. Water Environ Res. 88:107-17. doi:10.2175/106143015X14362865227878.

Menichino, N.M. Fenner, N. Pullin, A. Jones, P. S. Guest, J. Jones, L. (2016) Contrasting response to mowing in two abandoned rich fen plant communities. Ecological Engineering 86:210–222.

Chris Freeman

Hughes, D., Holliman, P., Jones, T., Butler, A.J. & Freeman, C, (2016) Rapid, Semi-Automated fractionation of freshwater dissolved organic carbon using DAX 8 (XAD 8) and XAD 4 resins in tandem. Natural Science 8: 487-498. DOI: 10.4236/ns.2016.811050

Ritson, J.P., Bell, M., Brazier, R.E., Grand-Clement, E., Graham, N., Freeman, C., Smith, D., Templeton, M.R. & Clark, J. (2016) 'Managing peatland vegetation for drinking water treatment' Scientific Reports. Vol 6 Article 36751 DOI: 10.1038/srep36751

Jones, T.G., Evans, C. & Freeman, C. (2016) 'The greenhouse gas (GHG) emissions associated with aquatic carbon removal during drinking water treatment' Aquatic Sciences, 78: 561-572. DOI: 10.1007/s00027-015-0458-8

Jones, T.G., Evans, C.D., Jones, D., Hill, P.W. & Freeman, C. (2016) 'Transformations in DOC along a source to sea continuum; impacts of photo-degradation, biological processes and mixing' Aquatic Sciences, 78:433-446. DOI: 10.1007/s00027-015-0461-0

Scholz, C., Dunn, C., Jones, T., West, M., Ehbair, A. & Freeman, C. (2016) 'Constructed wetlands may lower inorganic nutrient inputs but enhance DOC loadings into a drinking water reservoir in North Wales' Environmental Science and Pollution Research, 23:18192-18199. DOI: 10.1007/s11356-016-6991-8

Williamson, J., Mills, G., Hayes, F., Jones, T. & Freeman, C. (2016) 'How do increasing background concentrations of tropospheric ozone affect peatland plant growth and carbon gas exchange?' Atmospheric Environment, 127:133-138.

Gough, R.S., Holliman, P.J., Fenner, N., Peacock, M. & Freeman, C. (2016) 'Influence of water table depth on pore water chemistry and trihalomethane formation potential in peatlands' Water Environment Research, 88: 107-117. DOI: 10.2175/106143015X14362865227878

Dunn, C., Jones, T., Roberts, S. & Freeman, C. (2016) 'Plant Species Effects on the Carbon Storage Capabilities of a Blanket bog Complex' Wetlands, 36:47-58 DOI: 10.1007/s13157-015-0714-7

Gough, R., Cohen, Y., Fenner, N., Cannon, J. & Freeman, C. (2016) 'Relationships between reservoir water quality and catchment habitat type' International Journal of Environmental Technology and Management,  19:16-39. DOI: 10.1504/IJETM.2016.074799

Saraswati, S., Dunn, C., Mitsch W.J., & Freeman C. (2016) Is peat accumulation in mangrove swamps influenced by the “enzymic latch” mechanism?. Wetlands Ecology and Management 24:641-650, DOI:10.1007/s11273-016-9493-z

Olga Golyshina

Golyshina, O.V, Kublanov, I.V., Tran, H., Korzhenkov, A.A., Lünsdorf, H., Nechitaylo, T.Y., Gavrilov, S.N., Toshchakov, S.V. and Golyshin, P.N. (2016) Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments. Scientific Reports. 2016;6:39034. doi: 10.1038/srep39034.

Golyshina O.V., Lünsdorf H., Kublanov I.V., Goldenstein N.I., Hinrichs K.U. and Golyshin P.N. (2016) The novel, extremely acidophilic, cell wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new Family of Cuniculiplasmataceae fam. nov., order Thermoplasmatales. International Journal of Systematic and  Evolutionary Microbiology  66:332-340. doi: 0.1099/ijsem.0.000725.

Ferrer, M., Martínez-Martínez, M., Bargiela, R, Streit, W.R., Golyshina, O.V. and Golyshin, P.N. (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microbial Biotechnology 9:22-34. doi:10.1111/1751-7915.12309.

Peter Golyshin

Golyshina, O.V, Kublanov, I.V., Tran, H., Korzhenkov, A.A., Lünsdorf, H., Nechitaylo, T.Y., Gavrilov, S.N., Toshchakov, S.V. and Golyshin, P.N. (2016) Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments. Scientific Reports. 2016;6:39034. doi: 10.1038/srep39034.

Bourguignon, N., Bargiela, R., Rojo, D., Chernikova, T.N., de Rodas, S.A.,García-Cantalejo, J., Näther, D.J., Golyshin, P.N., Barbas, C., Ferrero, M. and Ferrer, M. (2016) Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data. World Journal of Microbiology and Biotechnology. 32:201. doi 10.1007/s11274-016-2163-8

Zapata-Pérez, R., García-Saura, A.G., Jebbar, M., Golyshin, P.N. and Sánchez-Ferrer, A. (2016) Combined whole-cell high-throughput functional screening for identification of new nicotinamidases/pyrazinamidases in metagenomic/polygenomic libraries. Frontiers in Microbiology 7:1915. doi: 10.3389/fmicb.2016.01915.

Ramírez-Escudero, M., Del Pozo, M.V., Marín-Navarro, J., González, B., Golyshin, P.N., Polaina J., Ferrer M. and Sanz-Aparicio J. (2016). Structural and functional characterization of a ruminal β-glycosidase defines a novel subfamily of glycoside hydrolase family 3 with permuted domain topology. Journal of Biological Chemistry 291:24200-24214. doi: 10.1074/jbc.M116.747527

Yakimov, M.M., Crisafi, F., Messina E., Smedile, F., Lopatina, A., Denaro, R., Pieper, D.H., Golyshin, P.N. and Giuliano, L. (2016) Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME. Environmental Microbiology Reports 8:508-519. doi:10.1111/1758-2229.12424.

Hajighasemi, M., Nocek, B.P., Tchigvintsev, A., Brown, G., Flick, R., Xu, X., Cui, H., Hai, T., Joachimiak, A., Golyshin, P.N., Savchenko, A., Edwards, E.A. and Yakunin, A.F. (2016) Biochemical and structural insights into enzymatic depolymerization of polylactic acid and other polyesters by microbial carboxylesterases. Biomacromolecules. 17:2027-39. doi: 10.1021/acs.biomac.6b00223.

Messina, E., Denaro, R., Crisafi, F., Smedile, F., Cappello, S., Genovese, M., Genovese, L., Giuliano, L., Russo, D., Ferrer, M., Golyshin, P. and Yakimov M.M. (2016) Genome sequence of obligate marine polycyclic aromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME, isolated from petroleum deposits of the sunken tanker Amoco Milford Haven, Mediterranean Sea. Marine Genomics. 25:11-13. doi: 10.1016/j.margen.2015.10.006

Golyshina O.V., Lünsdorf H., Kublanov I.V., Goldenstein N.I., Hinrichs K.U. and Golyshin P.N. (2016) The novel, extremely acidophilic, cell wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new Family of Cuniculiplasmataceae fam. nov., order Thermoplasmatales. International Journal of Systematic and Evolutionary Microbiology 66:332-340. doi: 0.1099/ijsem.0.000725.

Sorokin, D.Y., Kublanov, I.V., Gavrilov, S.N., Rojo, D., Roman, P., Golyshin, P.N., Slepak, V.Z., Smedile, F., Ferrer, M., Messina, E., La Cono, V., Yakimov, M.M. (2016) Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon. The ISME Journal 10:240-252. doi: 10.1038/ismej.2015.79.

Ferrer, M., Martínez-Martínez, M., Bargiela, R, Streit, W.R., Golyshina, O.V. and Golyshin, P.N. (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microbial Biotechnology 9:22-34. doi:10.1111/1751-7915.12309.

Matt Hayward

Creel, S., Becker, M., Christianson, D., Dröge, E., Hammerschlag, N., Hayward, M.W., Karanth, U., Loveridge, A., Macdonald, D.W., Matandiko, W., M'soka, J., Murray, D., Rosenblatt, E. and Schuette, P. (2016) Policy for hunting large carnivores can and should be improved. Science, 350, eLetter: https://d2ufo47lrtsv45s.cloudfront.net/sites/default/files/response_attachments/2016/2006/Creel_et_al.pdf

Hayward, M.W., Kamler, J.F., Montgomery, R.A., Newlove, A., Rostro-García, S., Sales, L.P. and Van Valkenburgh, B. (2016) Prey preferences of the jaguar Panthera onca reflect the post-Pleistocene demise of large prey. Frontiers in Ecology and Evolution, 3, e148 http://dx.doi.org/110.3389/fevo.2015.00148.

Hayward, M.W., Ripple, W.J., Plotz, R.D. and Garnett, S.T. (2016) Don't bank African rhinos in Australia. Nature, 534, 475.

Hayward, M.W., Ward-Fear, G., L'Hotellier, F., Herman, K., Kabat, X. and Gibbons, J.M. (2016) Could biodiversity loss have increased Australia's bushfire threat? Animal Conservation, 19, 490-497.

Linnell, J.D.C., Trouwborst, A., Boitani, L., Kaczensky, P., Huber, D., Reljic, S., Kusak, J., Majic, A., Skrbinsek, T., Potocnik, H., Hayward, M.W.,

Milner-Gulland, E.J., Buuveibaatar, B., Olson, K.A., Badamjav, L., Bischof, R., Zuther, S. and Breitenmoser, U. (2016) Border security fencing and wildlife: The end of the transboundary paradigm in Eurasia? PLoS Biol, 14, e1002483.

Luther, D.A., Brooks, T.M., Butchart, S.H.M., Hayward, M.W., Kester, M.E., Lamoreux, J. and Upgren, A. (2016) Determinants of bird conservation action implementation and associated population trends of threatened species. Conservation Biology, 30, 1338-1346.

Ripple, W.J., Chapron, G., Lopez-Bao, J., Durant, S., Macdonald, D.W., Lindsey, P.A., Bennett, E.L., Beschta, R.L., Bruskotter, J., Campos-Arceiz, A., Corlett, R.T., Darimont, C., Dickman, A., Dirzo, R., Dublin, H.T., Estes, J.A., Everatt, K.T., Galetti, M., Goswami, V., Hayward, M.W., Hedges, S., Hoffmann, M., Hunter, L., Kerley, G.I.H. and Levi, T. (2016) Saving the world's terrestrial megafauna. BioScience, biw092.

Ward-Fear, G., Hayward, M.W., L'Hotellier, F., Herman, K., Kabat, A.P. and Gibbons, J.P. (2016) The implications of biodiversity loss for the dynamics of wildlife in Australia. Animal Conservation, 19, 504-505.

Eldred, T., Meloro, C., Scholtz, C. and Hayward, M.W. (2016) Does size matter for horny beetles? A geometric morphometric analysis of interspecific and intersexual size and shape variation in Colophon haughtoni Barnard, 1929, and C. kawaii Mizukami, 1997 (Coleoptera: Lucanidae). Organisms Diversity and Evolution, 16, 821-833. DOI: 10.1007/s13127-016-0289

Hofman, M.P.G., Signer, J., Hayward, M.W. and Balkenhol, N. (2016) Spatial ecology of a herd of white-lipped peccaries (Tayassu pecari) in Belize using GPS telemetry: challenges and preliminary results. Therya, 7, 21-37. DOI: 10.12933/therya-16-335

Van Valkenburgh, B., Hayward, M.W., Ripple, W.J., Meloro, C. and Roth, V.L. (2016) The impact of large terrestrial carnivores on Pleistocene ecosystems. Proceedings of the National Academy of Sciences of America, 113, 862-867 DOI: 10.1073/pnas.1502554122.

Richard Holland

Kareclas, K., Elwood, R.W. and Holland, R.A. (2016). Plasticity varies with ‘boldness’ in a weakly-electric fish. Frontiers in Zoology, 13:22. doi 10.1186/s12983-016-0154-0.

McAroe, C., Craig, C. and Holland, R.A. (2016). Place versus response learning in fish: a comparison between species. Animal Cognition, 19:153-161. doi 10.1007/s10071-015-0922-9.

Barrie Johnson

Holanda, R., Hedrich, S., Ňancucheo, I., Oliveira, G., Grail, B.M. and Johnson, D.B. (2016) Isolation and characterisation of mineral-oxidising “Acidibacillus” spp. from mine sites and geothermal environments in different global locations. Research in Microbiology 167:613-623. doi org/10.1016/j.resmic.2016.04.008

Nuňez, H., Covarrubias, P.C., Moya-Beltrán, A., Issotta, F., Atavales, J., Acuňa, L.G., Johnson, D.B. and Quatrini, R. (2016) Detection, identification and typing of Acidithiobacillus species and strains: a review. Research in Microbiology 167:555-567. doi org/ 10.1016/j.resmic.2016.05.006

Santos, A.L. and Johnson, D.B. (2016) The effects of temperature and pH on the kinetics of an acidophilic sulfidogenic bioreactor and indigenous microbial communities.  Hydrometallurgy. doi.org/10.1016/j.hydromet.2016.07.018

Ňancucheo, I., Rowe, O.F., Hedrich, S., and Johnson, D.B. (2016) Solid and liquid media for isolating and cultivating acidophilic and acid-tolerant sulfate-reducing bacteria. FEMS Microbiology Letters 363, fnw083. doi: 10.1093/femsle/fnw083
Sánchez-Andrea, I, Stams, A.J.M., Weijma, J., Gonzalez Contreras, P., Dijkman, H., Rozendal, R.A. and Johnson, D.B. (2016) A case in support of implementing innovative bio-processes in the metal mining industry. FEMS Microbiology Letters 363, 2016, fnw106. doi: 10.1093/femsle/fnw106

Falagán, C. and Johnson, D.B. (2016) Acidithiobacillus ferriphilus sp. nov.: a facultatively anaerobic iron- and sulfur-metabolising extreme acidophile. International Journal of Systematic and Evolutionary Microbiology.66:206-211.

Ñancucheo, I., Oliveira, R., Dall'Agnol, H., Johnson, D.B., Grail, B.M., Holanda, R., Nunes, G., Orellana, S. and Oliveira, G. (2016) Draft Genome Sequence of a Novel Species of Acidophilic Iron-oxidizing Firmicute, "Acidibacillus ferrooxidans" (SLC66T). Genome Announcements 4: e00383-16. doi:10.1128/genomeA.00383-16.

Dall'Agnol, H., Ñancucheo, I., Johnson, D.B., Oliveira, R., Leite, L., Pylro, V.,  Carvalho, N., Nunes, G., Tzotzos, G., Fernandes, G., Dutra, J., Orellana, S. and Oliveira, G. (2016). Draft genome sequence of "Acidibacillus ferrooxidans" ITV01, a novel acidophilic Firmicute isolated from a chalcopyrite mine drainage site in Brazil. Genome Announcements 4: e01748-15. doi 10.1128/genomeA.01748-15

Florence, K., Sapsford, D.J., Kay, C.M., Johnson, D.B. and Wolkersdorfer, C. (2016) Iron mineral accretion from acid mine drainage and its application in passive treatment. Environmental Technology 37:1428-1440, DOI: 10.1080/09593330.2015.1118558

Matthies, R., Henjy, H., Hirsch, K., Kahnt, R., Marten, H. and Johnson, D.B. (2016) Biobasierte in-situ-gewinnung und industriemetallen aus unzuganglichen lagerstatten zur EU-rohstoffsicherung. Georesources Zeitschrift 3:34-38 (in German; title translates as “Bio-based in situ-recovery of industrial metals from inaccessible deposits to secure the supply of raw materials for the EU”)

James McDonald

Doonan, J., Denman, S., McDonald, J.E., and Golyshin, P.N. (2016) Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities. Metagenomics 1539; 85-97 [Link]

Hassard, F., Gwyther, C.L., Farkas, K., Andrews, A., Jones, V., Cox, B., Brett, H., Jones, D.L, McDonald, J.E. and Malham, S.K. (2016) Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review. Frontiers in Microbiology 7:1692. doi: 10.3389/fmicb.2016.01692 [Link]

Denman, S., Barrett, G., Kirk, S.A, McDonald, J.E. and Coetzee, M.P.A (2016) Identification of Armillaria species on declined oak in Britain: implications for oak health. Forestry doi:10.1093/forestry/cpw054[Link]

Ransom-Jones, E. and McDonald, J.E (2016) Draft Genome Sequence of Clostridium sp. strain W14A isolated from a cellulose-degrading biofilm in a landfill leachate microcosm. Genome Announcements 4(5):e00985-16.   doi:10.1128/genomeA.00985-16. [Link]

Winterbourn, J.B., Clements, K., Lowther, J.A., Malham, S.K., McDonald, J.E. and Jones, D.L. (2016) Use of Mytilus edulis biosentinels to investigate spatial patterns of norovirus and faecal indicator organism contamination around coastal sewage discharges. Water Research 105: 241–250. [Link]

Denman, S., Plummer, S., Kirk, S., Peace, A. and McDonald, J.E. (2016) Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline. Systematic and Applied Microbiology 39(7): 484–490. [Link]

McDonald, J.E., Larsen, N., Pennington, A., Connolly, J., Wallis, C., Rooks, D.J., Hall, N., McCarthy, A.J. and Allison, H.E. (2016) Characterising the canine oral microbiome by direct sequencing of reverse-transcribed rRNA molecules. PLoS ONE 11(6): e0157046. [Link]

Emmett, B.A., Cooper, D., Smart, S., Jackson, B., Thomas, A., Cosby, B., Evans, C., Glanville, H., McDonald, J.E., Malham, S.K., Marshall, M., Jarvis, S., Rajko-Nenow, P., Webb, G.P., Ward, S., Rowe, E., Jones, L., Vanbergen, A.J., Keith, A., Carter, H., Pereira, G.P. et al. (2016) Spatial patterns and environmental constraints on ecosystem services at a catchment scale. Science of The Total Environment 572: 1586-1600. [Link]

Perkins, T.L., Perrow, K., Rajko-Nenow, P., Jago, C.F., Jones, D.L., Malham, S.K. and McDonald, J.E. (2016) Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations. Science of The Total Environment 572: 1645-1652. [Link]

Robins, P.E., Skov, M.W., Lewis, M.J., Giménez, L., Davies, A.G., Malham, S.K., Neill, S.P., McDonald, J.E., Whitton, T.A., Jackson, S., Jago, C.F., (2016) Impact of climate change on UK estuaries: A review of past trends and potential projections. Estuarine, Coastal and Shelf Science 169: 119-135. [Link]

John Mulley

Braasch, I, Gehrke, AR, Smith, JJ, Kawasaki, K, Manousaki, T, Pasquier, J, Amores, A, Desvignes, T, Batzel, P, Catchen, J, Berlin, AM, Campbell, MS, Barrell, D, Martin, KJ, Mulley, JF, Ravi, V, Lee, AP, Nakamura, T, Chalopin, D, Fan, S, Wcisel, D, Cañestro, C, Sydes, J, Beaudry, FEG, Sun, Y, Hertel, J, Beam, MJ, Fasold, M, Ishiyama, M, Johnson, J, Kehr, S, Lara, M, Letaw, JH, Litman, W, Litman, RT, Mikami, M, Ota, T, Saha, NR, Williams, L, Stadler, PF, Wang, H, Taylor, JS, Fontenot, Q, Ferrara, A, Searle, SMJ, Aken, B, Yandell, M, Schneider, I, Yoder, JA, Volff, J-N, Meyer, A, Amemiya, CT, Venkatesh, B, Holland, PWH, Guiguen, Y, Bobe, J, Shubin, NH, Di Palma, F, Alföldi, J, Lindblad-Toh, K, Postlethwait, JH (2016) ‘The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons’ Nature Genetics 48: 427-437. doi:10.1038/ng.3526

Graeme Shannon

Shannon, G., Crooks, K.R., Wittemyer, G., Fristrup, K.M. and Angeloni, L.M. (2016) Road noise causes earlier predator detection and flight response in a free-ranging mammal. Behavioral Ecology 27:1370-1375.

Shannon, G., McKenna, M.F., Angeloni, L.M., Crooks, K.R., Fristrup, K.M., Brown, E., Warner, K.A., Nelson, M.D., White, C., Briggs, J., McFarland, S. and Wittemyer, G. (2016) A synthesis of two decades of research documenting the effects of noise on wildlife. Biological Reviews 91:982-105. doi.org/10.1111/brv.12207

McKenna, M.F., Shannon, G. and Fristrup K. (2016) Characterizing anthropogenic noise to improve understanding and management of impacts to wildlife. Endangered Species Research 31:279-291. doi.org/10.3354/esr00760

Simon Webster

Hoelters, L., O’Grady, J.F., Webster, S.G. and Wilcockson, D.C. (2016) Characterization, localization and temporal expression of crustacean hyperglycemic hormone (CHH) in the behaviourally rhythmic peracarid crustaceans, Eurydice pulchra (Leach) and Talitrus saltator (Montagu). General and Comparative Endocrinology 237:43-52. doi org/10.1016/j.ygcen.2016.07.024

Nia Whiteley

Penney, C. M., Patton, R. L., Whiteley, N. M., Driedzig, W. R., and McGaw, I. J. (2016). Physiological responses to digestion in low salinity in the crabs Carcinus maenas and Cancer irroratus. Comparative Biochemistry and Physiology A. 191: 127-139. DOI: 10.1016/j.cbpa.2015.10.007

McCarthy, I. D., Nicholls, R., Malham, S. K., and Whiteley, N. M. (2016). Validation of the flooding dose technique to determine fractional rates of protein synthesis in a model bivalve species, the blue mussel Mytilus edulis (L.). Comparative Biochemistry and Physiology A. 191: 166-173. DOI: 10.1016/j.cbpa.2015.10.019

Wolfgang Wüster

Maddock, S.T., Childerstone, A., Fry, B.G., Williams, D.J., Barlow, A. and Wüster W. (2017) Multi-locus phylogeny and species delimitation of Australo-Papuan blacksnakes (Pseudechis Wagler, 1830: Elapidae: Serpentes). Molecular Phylogenetics and Evolution 107:48–55. doi.org/10.1016/j.ympev.2016.09.005  (dated 2017, but published 2016 with page numbers)
Zancolli, G., T.G. Baker, A. Barlow, R.K. Bradley, J.J. Calvete, K.C. Carter, K. de Jager, J.B. Owens, J.F. Price, L. Sanz, A. Scholes-Higham, L.

Shier, L. Wood, C.E. Wüster & W. Wüster (2016) Is hybridization a source of adaptive venom variation in rattlesnakes? A test, using a Crotalus scutulatus x viridis hybrid zone in southwestern New Mexico. Toxins 2016:8:188. doi:10.3390/toxins8060188

Stümpel, N., M. Rajabizadeh, A. Avcı, W. Wüster & U. Joger (2016) Phylogeny and diversification of mountain vipers (Montivipera, Nilson et al., 2001) triggered by multiple Plio–Pleistocene refugia and high-mountain topography in the Near and Middle East. Molecular Phylogenetics and Evolution 101:336–351. http://dx.doi.org/10.1016/j.ympev.2016.04.025

Books & book chapters

Christian Dunn/Nathalie Fenner/Anil Shirsat/Chris Freeman

Dunn C., Fenner N., Shirsat A. and Freeman, C. (2016) Options for geoengineering the climate via microorganisms: a peatland case study. In: Climate Change and Microbial Ecology: Current Research and Future Trends (Marxsen, J. ed) Caister Academic Press, Norfolk, UK, pp. 185-200

Kang H. and Freeman, C. (2016) Microbes, Environmental Change and the Global Carbon Cycle. In: Climate Change and Microbial Ecology: Current Research and Future Trends (Marxsen, J. ed) Caister Academic Press, Norfolk, UK, pp. 153-166

Matt Hayward

Hayward, M.W. and Slotow, R. (2016) Wildlife management of reintroduced populations. In: Reintroduction of Fish and Wildlife Populations: 319-340. Jachowski, DS and Slotow, R (Eds.). University of California Press, California, USA.

Olga Golyshina

Golyshina OV, Ferrer M and Golyshin PN. (2016) Diversity and Physiologies of acidophilic Archaea. In: Acidophiles. Life in extremely acidic environments. Ed. Quatrini R. and Johnson DB. Caister Academic Press. pp.93-107. doi.org/10.21775/9781910190333.06.

Golyshina OV, Lünsdorf H and Golyshin PN. (2016) The family Ferroplasmaceae. In: Bergey's Manual of Systematics of Archaea and Bacteria. Ed. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 1–3. doi: 10.1002/9781118960608.fbm00273.

Golyshina OV, Lünsdorf H and Golyshin PN. (2016) The genus Ferroplasma. In: Bergey's Manual of Systematics of Archaea and Bacteria. Ed. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 1–6. 
doi: 10.1002/9781118960608.gbm01373.

Golyshina OV, Lünsdorf H and Golyshin PN. (2016) The genus Acidiplasma. In: Bergey's Manual of Systematics of Archaea and Bacteria. Ed. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 1–7. doi: 10.1002/9781118960608.gbm01372.

Peter Golyshin

Golyshina OV, Ferrer M and Golyshin PN. (2016) Diversity and Physiologies of acidophilic Archaea.  In:  Acidophiles. Life in extremely acidic environments. Ed. Quatrini R. and Johnson DB. Caister Academic Press. pp.93-107. doi.org/10.21775/9781910190333.06.

Golyshina OV, Lünsdorf H and Golyshin PN. (2016) The family Ferroplasmaceae. In:  Bergey's Manual of Systematics of Archaea and Bacteria. Ed. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 1–3. doi: 10.1002/9781118960608.fbm00273.

Golyshina OV, Lünsdorf H and Golyshin PN. (2016) The genus Ferroplasma. In: Bergey's Manual of Systematics of Archaea and Bacteria. Ed. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 1–6.  doi: 10.1002/9781118960608.gbm01373.

Golyshina OV, Lünsdorf H and Golyshin PN. (2016) The genus Acidiplasma. In: Bergey's Manual of Systematics of Archaea and Bacteria. Ed. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 1–7. doi: 10.1002/9781118960608.gbm01372.

Barrie Johnson

Quatrini, R. and Johnson, D.B. (eds.) (2016): Acidophiles: Life in Extremely Acidic Caistor Academic Press, Haverhill, UK, 310pp

Johnson, D.B. and Quatrini, R (2016) Acidophile microbiology in space and time. In: Acidophiles: Life in Extremely Acidic Environments (Quatrini, R. and Johnson, D.B., eds) Caistor Academic Press, Haverhill, UK, pp.3-16

Johnson, D.B. (2016) Microbial communities and interactions in low pH environments. In: Acidophiles: Life in Extremely Acidic Environments (Quatrini, R. and Johnson, D.B., eds) Caistor Academic Press, Haverhill, UK, pp.121-138

Nia Whiteley

Whiteley, N. M. and Mackenzie, C. L. (2016). Physiological responses to thermal stress in marine invertebrates. In: Stressors in the Marine Environment. Physiological and Ecological Responses; Societal Implications. Editors M. Solan and N. M. Whiteley. Chp 4 pp. 56-72. Oxford University Press, UK.

Solan, M. and Whiteley, N. M. (2016). Stressors in the Marine Environment. Physiological and Ecological Responses; Societal Implications. Oxford University Press, UK, 356 pp.

Isabelle Winder

Winder, N. and Winder, I. (2016) Integrative Research and the Stakeholder Problem. In: The Quest for a Model-Stakeholder Fusion, the COMPLEX Final Report Vol. 1 (Winder, N., Liljenström, H. and Seaton, R., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 157-175. Volume DOI: 10.13140/RG.2.2.12592.35847

Winder, N. and Winder, I. (2016) Anticipatory Modelling and Innovation Management. In: The Quest for a Model-Stakeholder Fusion, the COMPLEX Final Scientific Report Vol. 1 (Winder, N., Liljenström, H. and Seaton, R., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 176-179. Volume DOI: 10.13140/RG.2.2.12592.35847

Winder, N. and Winder, I. (2016) Modelling the Modelling Process. In: The Quest for a Model-Stakeholder Fusion, the COMPLEX Final Scientific Report Vol. 1 (Winder, N., Liljenström, H. and Seaton, R., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 180-188. Volume DOI: 10.13140/RG.2.2.12592.35847

Winder, N. and Winder, I. (2016) The Description of Work (DOW) as a Model. In: The Quest for a Model-Stakeholder Fusion, the COMPLEX Final Scientific Report Vol. 1 (Winder, N., Liljenström, H. and Seaton, R., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 189-199. Volume DOI: 10.13140/RG.2.2.12592.35847

Winder, N. and Winder, I. (2016) Using the DOW for Decision-Support. In: The Quest for a Model-Stakeholder Fusion, the COMPLEX Final Scientific Report Vol. 1 (Winder, N., Liljenström, H. and Seaton, R., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 200-210. Volume DOI: 10.13140/RG.2.2.12592.35847

Winder, N. and Winder, I. (2016) The COMPLEX Approach to Innovation Management. In: The Quest for a Model-Stakeholder Fusion, the COMPLEX Final Scientific Report Vol. 1 (Winder, N., Liljenström, H. and Seaton, R., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 211-219. Volume DOI: 10.13140/RG.2.2.12592.35847

Winder, N. and Winder, I. (2016) Darwin’s Goldilocks Problem. In: Non-Linearities and System-Flips, the COMPLEX Final Scientific Report Vol. 2 (Winder, N. and Liljenström, H., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 11-15. Volume DOI: 10.13140/RG.2.2.19303.24482

Winder, N. and Winder, I. (2016) Saltation. Emergence and Non-Linear Dynamics. In: Non-Linearities and System-Flips, the COMPLEX Final Scientific Report Vol. 2 (Winder, N. and Liljenström, H., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 16-29. Volume DOI: 10.13140/RG.2.2.19303.24482

Winder, N. and Winder, I. (2016) Fit Genes Hide. In: Non-Linearities and System-Flips, the COMPLEX Final Scientific Report Vol. 2 (Winder, N. and Liljenström, H., eds) Sigtunastiftelsen, Sigtuna, Sweden, pp. 30-35. Volume DOI: 10.13140/RG.2.2.19303.24482

Conference proceedings

Barrie Johnson

Johnson, D.B., Santos, A.L., Falagan, C., Jones, R.M., Grail, B.M., Holanda, R. and Hedrich, S. (2016) Developing sustainable biotechnologies for mine water treatment in the 21ST century. In: Mining Meets Water – Conflicts and Solutions, Proceedings of the International Mine Water Association Symposium, Leipzig, Germany. July 2016, Drebenstedt, C and Paul, M (eds.) pp.782 789.

Falagán, C., Smail, I., Grail, B.M. and Johnson, D.B. (2016) Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom. In: Mining Meets Water – Conflicts and Solutions, Proceedings of the International Mine Water Association Symposium, Leipzig, Germany. July 2016, Drebenstedt, C and Paul, M (eds.) pp.796-803.

Falagán, C., Sánchez-España, J., Yusta, I. and Johnson, D.B. (2016) New insights into the microbiology of meromictic acidic pit lakes in the Iberian Pyrite Belt (Spain). In: Mining Meets Water – Conflicts and Solutions, Proceedings of the International Mine Water Association Symposium, Leipzig, Germany. July 2016, Drebenstedt, C and Paul, M (eds.) pp. 192 - 198.

Santos, A-L. and Johnson, D.B. (2016) Potential use of micro-algal biomass in sulfidogenic bioreactor systems used to remediate acidic metal-rich wastewaters. In: Proceedings of Biohydrometallurgy ’16, Falmouth, Cornwall, June 2016, Wills, B. (ed.). Minerals Engineering International.

Falagán, C., Grail, B.M. and Johnson, D.B. (2016) New approaches for extracting and recovering metals from mine tailings. In: Proceedings of Biohydrometallurgy ’16, Falmouth, Cornwall, June 2016, Wills, B. (ed.). Minerals Engineering International.

Falagán, C., Yusta, I., Sánchez-España, J. and Johnson, D.B. (2016) Biologically-induced precipitation of aluminium in synthetic acid mine water. In: Proceedings of Biohydrometallurgy ’16, Falmouth, Cornwall, June 2016, Wills, B. (ed.). Minerals Engineering International.

Pakostova, E., Grail, B.M. and Johnson, D.B. (2016) Indirect oxidative leaching of a polymetallic black schist sulfide ore: development of a protocol for in situ bioleaching of deep-buried ore bodies. In: Proceedings of Biohydrometallurgy ’16, Falmouth, Cornwall, June 2016, Wills, B. (ed.). Minerals Engineering International.

Smith, S.L., Grail, B.M. and Johnson, D.B. (2016) Reductive bioprocessing of cobalt-bearing limonitic laterites. In: Proceedings of Biohydrometallurgy ’16, Falmouth, Cornwall, June 2016, Wills, B. (ed.). Minerals Engineering International.