Publications

2021

Lee S, Sieradzki ET, Nicolas AM, Walker RL, Firestone MK, Hazard C*, Nicol GW*. 2021. Methane-derived carbon flows into host-virus networks at different trophic levels in soil. bioRxiv doi.org/10.1101/2020.12.16.423115

Finn DR, Lee S, Lanzén A, Bertrand M, Nicol GW, Hazard C. 2021. Agricultural management that improves richness conveys increased resistance and resilience to fungal, but not prokaryote, communities. bioRxiv doi.org/10.1101/2020.03.15.992560

Finn DR, Bergk-Pinto B, Hazard C, Nicol GW, Tebbe C, Vogel TM. 2021. Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. FEMS Microbiology Ecology, 97:fiab068. doi.org/10.1093/femsec/fiab068

Ramos, D.T., Corseuil, H.X., Vogel T.M. 2021. Back to the wild: polluted sites remediation and biosphere resilience. bioRxiv doi.org/10.1101/2021.04.22.441002

Norton, G.J., Travis, T., Ruang-Areerate, P., Nicol, G.W., Adeosun, A.A., Hossain, M., Islam, M.R., Douglas, A., and Price, A.H. 2021. Genetic loci regulating cadmium content in rice grains. Euphytica, 217:1-16. doi.org/10.1007/s10681-020-02752-1

Hazard C, Prosser JI, Nicol GW. 2021. Use and abuse of potential rates in soil microbiology. Soil Biology & Biochemistry, 157:108242. doi.org/10.1016/j.soilbio.2021.108242

Hung Y, Jing J, Yan M, Hazard C, Chen Y, Guo C, Xiao X, Lin J. 2021. Contribution of pathogenic fungi to N2O emissions increases temporally in intensively managed strawberry cropping soil. Applied Microbiology and Biotechnology, 105:2043-2056. doi.org/10.1007/s00253-021-11163-8

Sanchez-Cid, C.; Guironnet, A.;Wiest, L.; Vulliet, E.; Vogel, T.M. 2021. Gentamicin adsorption onto soil particles prevents overall short-term effects on the soil microbiome and resistome. Antibiotics, 10:191. doi.org/10.3390/ antibiotics10020191

 
Larose, C., Maccario, L., Vogel,T.M. 2021. Microbiology of the Cryosphere: Diversity, Habitat Constraints and Ecology. Chapter in Advances in Atmospheric Chemistry – Volume 3, World Scientific Publishing Company. https://www.worldscientific.com/series/acca

 

2020

 

Prosser, J.I., Hink, L., Gubry-Rangin, C., and Nicol, G.W. 2020. Nitrous oxide production by ammonia oxidisers: community composition matters. Global Change Biology, 26:103-118. doi.org/10.1111/gcb.14877

Stein, L.Y. Klotz, M.G., Lancaster, K.M., Nicol, G.W., Qin, W., Schleper, C., Stahl, D., Ward, B.B., Yoon, S. 2020. Comment on “a critical review on nitrous oxide production by ammonia-oxidizing Archaea”. Environmental Science & Technology, 55:797-798. doi.org/10.1111/1462-2920.15192

Aigle, A., Gubry‐Rangin, C., Thion, C., Estera‐Molina, K.Y., Richmond, H., Pett‐Ridge, J., Firestone, M.K., Nicol, G.W., and Prosser, J.I. 2020. Experimental testing of hypotheses for temperature‐and pH‐based niche specialization of ammonia oxidizing archaea and bacteria. Environmental Microbiology, 22:4032-4045. doi.org/10.1111/1462-2920.15192


Papadopoulou, E.S., Bachtsevani, E., Lampronikou, E., Adamou, E., Katsaouni, A., Vasileiadis, S., Thion, C., Menkissoglu-Spiroudi, U., Nicol, G.W., Karpouzas, D.G. 2020. Comparison of novel and established nitrification inhibitors relevant to agriculture on soil ammonia-and nitrite-oxidizing isolates. Frontiers in Microbiology, 10:1571. doi.org/10.3389/fmicb.2020.581283

 

Tignat-Perrier, R., Dommergue, A., Thollot, A., Magand, O., Amato, P., Joly, M., Sellegri, K., Vogel, T.M., Larose, C. 2020. Seasonal shift in airborne microbial communities. Science of the Total Environment, 716:137129. doi.org/10.1016/j.scitotenv.2020.137129

Zhu, C., Miller, M., Lusskin, N., Bergk Pinto, B., Lorrie Maccario, L., Haggblom, M., Vogel, T.M., Larose, C., Bromberg, Y. 2020.  Snow microbiome functional analyses reveal novel microbial metabolism of complex organic compounds. MicrobiologyOpen, 9:e1100. doi.org/10.1002/mbo3.1100

Tignat-Perrier, R., Dommergue, A., Vogel, T.M., Larose, C. 2020. Microbial ecology of the planetary boundary layer. Atmosphere, 11: 1296. doi:10.3390/atmos11121296


Finn, D.R., Yu, J., Ilhan, Z.E., Fernandes, V.M.C., Penton, C.R., Krajmalnik-Brown, R., Garcia-Pichel, F., Vogel, T.M. 2020. MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data. FEMS Microbiology Ecology, 96:fiaa131. doi: 10.1093/femsec/fiaa131


Holland AT, Bergk Pinto B, Layton R, Williamson CJ, Anesio AM, Vogel TM, Larose C and Tranter M. 2020. Over winter microbial processes in a Svalbard snow pack: an experimental approach. Frontiers in Microbiology, 11:1029. doi:10.3389/fmicb.2020.01029


McCarty, P.L., Criddle, C.S., and Vogel, T.M. 2020. Retroperspectives on microbial transformations of chlorinated organics. Environmental Sciences: Processes & Impacts, 22:512-517. doi.org/10.1039/C9EM00575G


Beaulne J.-S., Mishra S.R., Suar M., Panda A.N., Rastogi G., Pattnaik A.K., Raina V. & Vogel T.M. 2020. Spatial analysis of bacteria in brackish lake sediment. International Journal of Sediment Research, 35:227-236. doi.org/10.1016/j.ijsrc.2020.01.003

 

2019

 

Bergk Pinto B, Maccario L, Dommergue A, Vogel TM and Larose C. 2019. Do organic substrates drive microbial community interactions in arctic snow? Fronteries in Microbiology, 10:2492. doi:10.3389/fmicb.2019.02492

Nicol, G.W., Hink, L, Gubry-Rangin, C., Prosser, J.I., and Lehtovirta-Morley, L.E. 2019. The genome sequence of “Candidatus Nitrosocosmicus franklandus” C13, a terrestrial ammonia oxidising archaeon with a high tolerance to ammonium. Microbiology Resource Announcements, 40:e00435-19. doi:10.1128/MRA.00435-19

Wu X, Wang Y, Zhu Y, Tian H, Qin X,Cui C, Zhao L, Simonet P, Zhang X. 2019.Variability in the response of bacterial community assembly to environmental selection and biotic factors depends on the immigrated bacteria, as revealed by a soil microcosm experiment. mSystems, 4:e00496-19. doi.org/10.1128/mSystems.00496-19

Els, N., Baumann-Stanzer, K. Tignat-Perrier, R., Keuschnig, C., Vogel, T.M., Larose, C. 2019. Microbial composition in seasonal time series of free tropospheric air and precipitation reveals community separation. Aerobiologia, 35:671–701. doi:10.1007/s10453-019-09606-x

Tignat-Perrier, R., Dommergue, A., Thollot, A., Christoph Keuschnig, Olivier Magand, Timothy M. Vogel & Catherine Larose. 2019. Global airborne microbial communities controlled by surrounding landscapes and wind conditions. Scientific Reports, 9:14441 doi:10.1038/s41598-019-51073-4

Hoyos-Hernandez, Caroline, Christelle Courbert, Caroline Simonucci, Sebastien David, Timothy M Vogel, Catherine Larose. 2019. Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima, FEMS Microbiology Letters, 366:180. doi.org/10.1093/femsle/fnz180

Wang, Z., Cao, Y., Zhu-Barker, X., Nicol, G.W., Wright, A.L., Jia, Z., and Jiang, X. 2019. Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biology and Biochemistry, 135:392-395. doi.org/10.1016/j.soilbio.2019.06.004

Baloh P, Els N, David RO, Larose C, Whitmore K, Sattler B and Grothe H. 2019. Assessment of artificial and natural transport mechanisms of ice nucleating particles in an alpine ski resort in Obergurgl, Austria. Frontiers in Microbiology, 10:2278. doi:10.3389/fmicb.2019.02278

Sekkour, Sonia; Bekki, Abdelkader; Bouchiba, Zoulikha; Vogel, Timothy M; Navarro, Elisabeth. 2019. The diversity of cultivable hydrocarbon-degrading bacteria isolated from crude oil contaminated soil and sludge from Arzew refinery in Algeria. The Journal of Microbiology, Biotechnology and Food Sciences, 9:70. doi:10.15414/jmbfs.2019.9.1.70-77

Maccario, L., Carpenter, S.D., Deming, J.W. Vogel, T.M., Larose, C. 2019. Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover. Scientific Reports, 9:2290.  doi:10.1038/s41598-019-38744-y

Els N, Baumann-Stanzer K, Larose C, Vogel TM, Sattler B. Beyond the planetary boundary layer: Bacterial and fungal vertical biogeography at Mount Sonnblick, Austria. Geo: Geography and Environment. 2019:e00069. doi.org/10.1002/geo2.69

Dommergue A, Amato P, Tignat-Perrier R, Magand O, Thollot A, Joly M, Bouvier L, Sellegri K, Vogel T, Sonke JE, Jaffrezo J-L, Andrade M, Moreno I, Labuschagne C, Martin L, Zhang Q and Larose C. 2019. Methods to investigate the global atmospheric microbiome. Frontiers in Microbiology, 10:243. doi:10.3389/fmicb.2019.00243

2018

 

Zhu, Yong-Guan; Gillings, Michael; Simonet, Pascal; Stekel, Dov; Banwart, Steven; Penuelas, Josep. 2018. Human dissemination of genes and microorganisms in earth’s critical zone. Global Change Biology, 24:1488-1499. doi:10.1111/gcb.14003

Vasileiadis, S., Puglisi, E., Papadopoulou, E. S., Pertile, G., Suciu N., Pappolla, R. A., Tourna, M., Karas, P. A., Papadimitriou, F., Kasiotakis, A., Ipsilanti, N., Ferrarini, A., Sułowicz, S., Fornasier, F., Menkissoglu-Spiroudi, U., Nicol, G. W., Trevisan, M., and Karpouzas, D. G. 2018. Blame it on the metabolite: 3,5-dichloraniline rather than the parent compound is responsible for decreasing diversity and function of soil microorganisms. Applied and Environmental Microbiology, 84:e01536-18. doi:10.1128/AEM.01536-18

Lu, X., Nicol, G.W., and Neufeld, J.D. 2018. Differential responses of soil ammonia-oxidizing archaea and bacteria to temperature and depth under two different land uses. Soil Biology and Biochemistry, 120:272-282. doi.org/10.1016/j.soilbio.2018.02.017

Stein, L.Y., and Nicol, G.W. 2018. Nitrification. eLS. doi.org/10.1002/9780470015902.a0021154.pub2

Hink, L., Gubry-Rangin, C., Nicol, G.W., and Prosser, J.I. 2018. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. The ISME Journal,  12:1084-1093. doi.org/10.1038/s41396-017-0025-5

Li, Y., Chapman, S.J., Nicol, G.W., and Yao, H. 2018. Nitrification and nitrifiers in acidic soils. Soil Biology and Biochemistry, 116: 290–301. doi.org/10.1016/j.soilbio.2017.10.023

Hily, J. M., S. Demaneche, N. Poulicard, M. Tannieres, S. Djennane, M. Beuve, E. Vigne, G. Demangeat, V. Komar, C. Gertz, A. Marmonier, C. Hemmer, S. Vigneron, A. Marais, T. Candresse, P. Simonet and O. Lemaire. 2018. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. Plant Biotechnology Journal, 16:208-220. doi.org/10.1111/pbi.12761

Hazard C, Johnson D. 2018. Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? New Phytologist, 220:1122-1128. doi.org/10.1111/nph.15010

Djeran-Maigrea, I., Dubujet, P., Vogel, T.M. 2018. Variation over time of excavated soil properties treated with surfactants. Environmental Earth Sciences, 77:67. doi.org/10.1007/s12665-018-7230-z

2017

 

Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S and Penuelas J. 2017. Microbial mass movements. Science, 357:1099-1100. doi:10.1126/science.aao3007

Ramirez K, Knight C […] Thion C, van der Heijden M & de Vries F. 2017. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology, 3:189-196. doi:10.1038/s41564-017-0062-x

Nicol, G.W. 2017. Archaea and the Nitrogen Cycle. Microbiology Today, 44:106-109. https://microbiologysociety.org/publication/past-issues/archaea/article/archaea-and-the-nitrogen-cycle.html

Nielsen, T.K., Rasmussen, M., Demaneche, S., Cecillon, S., Vogel, T.M. and Hansen, L.H. 2017. Evolution of Sphingomonad gene clusters related to pesticide catabolism revealed by genome sequence and mobilomics of Sphingobium herbicidovorans MH. Genome Biology and Evolution, 9:2477–2490. doi.org/10.1093/gbe/evx185

Hink, L., Lycus, P., Gubry‐Rangin, C., Frostegård, A., Nicol, G.W., Prosser, J.I., Bakken, L.R. 2017. Kinetics of NH3‐oxidation, NO‐turnover, N2O‐production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environmental Microbiology, 19:4882-4896. doi:10.1111/1462-2920.13914

Hazard C, Kruitbos L, Davidson H, Mbow FT, Taylor AFS, Johnson D. 2017. Strain identity of the ectomycorrhizal fungus Laccaria bicolor is more important than richness in regulating plant and fungal performance under nutrient rich conditions. Frontiers in Microbiology, 8:1874. doi.org/10.3389/fmicb.2017.01874

Catão E, Thion C, Krüger R & Prosser JI. 2017. Ammonia oxidizers in a non-nitrifying Brazilian savanna soil. FEMS Microbiology Ecology, 93. doi:10.1093/femsec/fix122

Demanèche S, Schauser L, Dawson L, Franqueville L, Simonet P. 2017. Microbial soil community analyses for forensic science: Application to a blind test. Forensic Science International, 270:153–158. doi.org/10.1016/j.forsciint.2016.12.004

Blanchard LS, Monin A, Ouertani H, Touaibia L, Michel E, Buret F, Simonet P, Morris CE and Demanèche S. 2017. Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions. FEMS Microbiolgy Ecology, 93. doi:10.1093/femsec/fix057

Simonet P. 2017. Fiche thématique n°7, Apport de la metagénomique pour évaluer la capacité d’adaptation du microbiote du sol aux changements environnementaux, notamment climatiques. Fiches thématiques Partie 1 « Les mécanismes biologiques d’adaptation aux changements climatiques », 3 – Ecosystèmes, Dans Institut de France. Rapport de l’Académie des Sciences : « Les mécanismes d’adaptation de la biodiversité aux changements climatiques et leurs limites » (87-91).

Royet D, Hériveaux Y, Marchalot J, Scorretti R, Dias A, Dempsey NM, Bonfim M, Simonet P and Frénéa-Robin M. Using injection molding and reversible bonding for easy fabrication of magnetic cell trapping and sorting devices. Journal of Magnetism and Magnetic Material, 427:306-313.  doi.org/10.1016/j.jmmm.2016.10.102

Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S and Penuelas J. 2017. Increased abundance of antibiotic resistance in earth’s critical zone: A paradigm for human dissemination of genes and microorganisms. Global Change Biology, 24:1488-1499. doi.org/10.1111/gcb.14003

Hazard C, Kruitbos L, Davidson H, Mbow FT, Taylor AFS, Johnson D. 2017. Strain identity of the ectomycorrhizal fungus Laccaria bicolor is more important than richness in regulating plant and fungal performance under nutrient rich conditions. Frontiers in Microbiology, 8:1874. doi:10.3389/fmicb.2017.01874

Hazard C, Kruitbos L, Davidson H, Taylor AFS, Johnson D. 2017. Contrasting effects of intra- and interspecific identity and richness of ectomycorrhizal fungi on host plants, nutrient retention and multifunctionality. New Phytologist, 213:852-86. doi.org/10.1111/nph.14184

Herbold, C.W., Lehtovirta‐Morley, L.E., Jung, M.-Y., Jehmlich, N., Hausmann, B., Han, P., Loy, A., Pester, M., Sayavedra‐Soto, L.A., Rhee, S.-K., Prosser, J.I., Nicol, G.W., Wagner, M., Gubry‐Rangin, C. 2017. Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics. Environmental Microbiology, 19:4939-4952. doi.org/10.1111/1462-2920.13971

Gubry-Rangin, C., Novotnik, B., Mandič-Mulec, I., Graeme W. Nicol, J. I. Prosser. 2017. Temperature responses of soil ammonia-oxidising archaea depend on pH.  Soil Biology and Biochemistry, 106:61-68. doi.org/10.1016/j.soilbio.2016.12.007

 

Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, Gafny R, Simonet P, Jurkevitch E and Z Pasternak. 2017. Soil characterisation by bacterial community analysis for forensic application: a quantitative comparison of environmental technologies. Forensic Science International: Genetics, 26:21-29. doi.org/10.1016/j.fsigen.2016.10.005

Nacke, H., Schöning, I., Schindler, M., Schrumpf, M., Daniel, R., Nicol, G.W., and Prosser, J.I. 2017. Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity. FEMS Microbiology Ecology, 93:fix14. doi.org/10.1093/femsec/fix144

Müller, J. B., Ramos, D. T., Larose, C., Fernandes, M., Lazzarin, H. S.C., Vogel, T. M., Corseuil, H. X. 2017. Combined iron and sulfate reduction biostimulation as a novel approach to enhance BTEX and PAH source-zone biodegradation in biodiesel blend-contaminated groundwater. Journal of Hazardous Materials, 326:229-236. doi.org/10.1016/j.jhazmat.2016.12.005

Paitier, A., Godain, A., Lyon, D., Haddour, N., Vogel, T.M., Monier, JM. 2017. Microbial fuel cell anodic microbial population dynamics during MFC start-up. Biosensors and Bioelectronics, 92:357-363. doi.org/10.1016/j.bios.2016.10.096

Elling, F.J., Könneke, M., Nicol, G.W., Stieglmeier, M., Bayer, B., Spieck, E., de la Torre, J.R., Becker, K.W., Thomm, M., Prosser, J.I., Herndl, G.J., Schleper, C. and Hinrichs, K.-U. 2017. Chemotaxonomic characterization of the thaumarchaeal lipidome. Environmental Microbiology, 19:2681–2700. doi.org/10.1111/1462-2920.13759

Fedrizzi, F., Ramos, D.T., Lazzarin, H.S.C.,  Fernandes., Larose, C., Vogel, T.M., Corseuil, H.X. 2017. A modified approach for in situ chemical oxidation coupled to biodegradation enhances light nonaqueous phase liquid source-zone remediation. Environmental Science & Technology, 51:463–472. doi.org/10.1021/acs.est.6b03604

Simonet P and A Maître. 2017. De la santé de l’environnement à la santé humaine. Les Big Data à découvert In Bouzeghour, M. and R. Mosseri (ed.), Les Big Data à découvert. CNRS Editions, Paris, France (202-203).

Alizon S, F Angelier, G Bécard, L Bézin, F Courchamp, S. Dutreuil, L Guidi, U Hibner, M Jebbar, O Klatz, F Heullier, O Loudet, P Simonet, J Tost, N Vergnolle. 2017. L’être vivant dans son environnement.  pour les sciences de la vie du XXIème siècle . In Jessus, C. (ed.), Etonnant vivant. Découvertes et promesses du XXIème siècle (Livre blanc). CNRS Editions, Paris, France (183-241).

2016

Hink, L., Nicol, G.W., and Prosser, J.I. 2016. Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environmental Microbiology, 19:4829-4837. doi.org/10.1111/1462-2920.13282

Ramos, D. T., H. S. Lazzarin, P. J. Alvarez, T. M. Vogel, M. Fernandes, M. Do Rosario and H. X. Corseuil. 2016. Biodiesel presence in the source zone hinders aromatic hydrocarbons attenuation in a B20-contaminated groundwater. Journal of Contaminated Hydrology, 193:48-53. doi.org/10.1016/j.jconhyd.2016.09.002

Ufarte, L, S Bozonnet, E Laville, D A Cecchini, S Pizzut-Serin, S Jacquiod, S Demaneche, P Simonet, L Franqueville and G Potocki-Veronese. 2016. Functional Metagenomics: Construction and High- Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes. In Martin, F and S Uroz (ed.), Microbial Environmental Genomics (MEG). Springer Science + Business Media, New York.

Subirats J, A Sànchez-Melsió, CM Borrego, JL Balcázar and P Simonet. 2016. Metagenomic analysis reveals bacteriophages are reservoirs for antibiotic resistance genes. International Journal of Antimicrobial Agents, 48:163-167. doi.org/10.1016/j.ijantimicag.2016.04.028

Pylro VS, Mui TS, Rodrigues JLM, Andreote FD, Roesch LFW and the Working Group supporting the INCT Microbiome (P Simonet, T.M. Vogel members of the working group). 2016. A step forward to empower global microbiome research through local leaderships. Trends in Microbiology, 24:767-771. doi.org/10.1016/j.tim.2016.07.007

Smalla K, P Simonet, J Tiedje and E Topp. 2016. Opinion Paper/Editorial. Co-editors, Special section of FEMS Microbiology Ecology on the environmental dimension of amoxicillin antibiotic resistance. FEMS Microbiology Ecology, 92: fiw17. doi:10.1093/femsec/fiw172

Masy, T., Demanèche, S., Tromme O, Thonart P, JacquesP, Hiligsmann S, Vogel, T.M. 2016. Hydrocarbon biostimulation and bioaugmentation in organic carbon and clay-rich soils. Soil Biology & Biochemistry, 99: 66-74. doi.org/10.1016/j.soilbio.2016.04.016

Nesme, Joseph, WafaAchouak, SpirosN.Agathos, MarkBailey, PetrBaldrian, Dominique Brunel, ÅsaFrostegård, ThierryHeulin, JanetK.Jansson, Edouard Jurkevitch , KristiinaL.Kruus, GeorgeA.Kowalchuk, AntonioLagares, HilaryM.Lappin-Scott, PhilippeLemanceau, DenisLePaslier, InesMandic-Mulec, J. ColinMurrell , DavidD.Myrold, RenaudNalin, PaoloNannipieri, Josh D.Neufeld, FergalO’Gara, JohnJ.Parnell, AlfredPühler, VictorPylro, Juan L.Ramos, LuizF.W.Roesch, MichaelSchloter, ChristaSchleper , Alexander Sczyrba, AngelaSessitsch , SaraSjöling, JanSørensen, Søren J.Sørensen, ChristophC.Tebbe, EdwardTopp, GeorgeTsiamis , Jan DirkvanElsas , GeertjevanKeulen, FrancoWidmer, MichaelWagner, TongZhang, XiaojunZhang, LipingZhao, Yong-GuanZhu, Timothy M.Vogel and Pascal Simonet. 2016. Back to the future of metagenomics. Frontiers in Microbiology, 7 doi:10.3389/fmicb.2016.00073

Lehtovirta-Morley, L.E., Sayavedra-Soto, L.A., Gallois, N., Schouten, S., Stein, L.Y., Prosser, J.I., and Nicol, G.W. 2016. Identifying potential mechanisms enabling acidophily in the ammonia-oxidising archaeon ‘Candidatus Nitrosotalea devanaterra’. Applied and Environmental Microbiology. 82:2608-2619. doi:10.1128/AEM.04031-15

Lehtovirta-Morley, L.E., Ross, J., Hink, L, Weber, E.B., Gubry-Rangin, C., Thion, C., Prosser, J.I., and Nicol, G.W. 2016. Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiology Ecology, 92:fiw057. doi:10.1093/femsec/fiw057

Bao, Q., Huang, Y., Wang, F., Nie, S., Nicol, G.W., Yao, H., and Ding, L. 2016. Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Applied Microbiology and Biotechnology, 100:5989–5998. doi.org/10.1007/s00253-016-7377-z

Ighilhariz S., de Lajudie P., Bekki A., Ighilhariz Z., Duponnois R., Reboulet J., Navarro E. 2016. Effect of anthropisation and revegetation efforts on soil bacterial community structure in Terga sandpit, Algeria. Journal of Biodiversity and Environmental Sciences, 9:283-296.

Nicol, G.W., and Prosser, J.I. 2016. Ecology of Archaea. Oxford Bibliographies. Oxford University Press. doi:10.1093/obo/9780199363445-0041.

Prosser, J.I. and Nicol, G.W. 2016. Candidatus Nitrosotaleales. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.

Prosser, J.I. and Nicol, G.W. 2016. Candidatus Nitrosotaleaceae. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.

Prosser, J.I. and Nicol, G.W. 2016. Candidatus Nitrosotalea. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.

2015

David MM, Cecillon S, Warne BM, Prestat E, Jansson JK, Vogel TM. 2015. Microbial ecology of chlorinated solvent biodegradation. Environmental Microbiology, 17:4835–4850. doi.org/10.1111/1462-2920.12413

Maccario L, Sanguino L, Vogel TM, Larose C., 2015. Snow and ice ecosystems: not so extreme. Res Microbiol, 166:782-95. doi:10.1016/j.resmic.2015.09.002

Zhu, C. Delmont, TO. Vogel, T M. Bromberg, Y. 2015. Functional basis of microorganism classification. PLoS Computational Biology, 11:e1004472. doi:10.1371/journal.pcbi.100447

O. Fabrègue, E. Navarro, R. Scorretti, J. Reboulet, P. Simonet, L. Dawson and S. Demanèche. 2015. RisaAligner software for aligning fluorescent data between Agilent 2100 Bioanalyzer chips: application to soil microbial community analysis. BioTechniques, 59:6. doi/10.2144/000114363

Sanguino, L. Franqueville, L., Vogel, TM., Larose, C. 2015. Linking environmental prokaryotic viruses and their host through CRISPRs. FEMS Microbial Ecology, 91:fiv046. doi.org/10.1093/femsec/fiv046

Delmont, TO. Eren, AM. Maccario, L. Prestat, E. Esen, OC. Pelletier, E. Le Paslier, D. Simonet, P. Vogel, TM. 2015. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Frontiers in Microbiology, 6:00358. doi.org/10.3389/fmicb.2015.00358

Oton, E.V., Quince, C., Nicol, G.W., Prosser, J.I. and Gubry-Rangin, C. 2015. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal, 10:85-96. doi.org/10.1038/ismej.2015.101

2014

Maccario L, Vogel T.M. and Larose C. 2014. Potential drivers of microbial community structure and function in Arctic spring snow. Frontiers in Microbiology, 5:413. doi:10.3389/fmicb.2014.00413

Nesme J and Simonet P. 2014. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environmental Microbiology, 17:913-930. doi:10.1111/1462-2920.12631

Mathieu A, Vogel TM and Simonet P. 2014. The Future of Skin Metagenomics. Research in Microbiolgy, 165:69-76. doi:10.1016/j.resmic.2013.12.002

Pivetal J, Ciuta G, Frenéa-Robin M, Haddour N, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Magnetic nanoparticle DNA labeling for individual bacterial cell detection and recovery.  Journal of Microbiology Methods,  107:84-91. doi.org/10.1016/j.mimet.2014.09.006

Pivetal J, Toru S, Frénéa-Robin M, Haddour N, Cecillon S, Dempsey NM, Dumas-Bouchiat F and Simonet P. 2014. Selective isolation of bacterial cells within a microfluidic device using magnetic probe-based cell fishing. Sensors and Actuators B: Chemical, 195: 581–589. doi.org/10.1016/j.snb.2014.01.004

Le Digabel, Y., Demanèche, S., Benoit, Y., Fayolle-Guichard, F., and Vogel, T.M. 2014. Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments. Journal of Hazardous Materials, 279:502-510. doi.org/10.1016/j.jhazmat.2014.07.013

Nesme, J., Cécillon, S., Delmont, T.O., Monier, J-M., Vogel, T.M., Simonet, P. 2014. Large-scale metagenomic-based study of antibiotic resistance in the environment. Current Biology, 24:1–5. doi.org/10.1016/j.cub.2014.03.036

Delmont, T.O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M.T., Nannipieri, P., Simonet, P., Vogel, T.M. 2014. Microbial community and unseen diversity development in inoculated sterile soil. Biology and Fertility of Soil, 50:1069-1076. doi:10.1007/s00374-014-0925-8

Jacquiod S, Demanèche S, Delmont TO, Ausec L, Dunon V, Franqueville L, Mandic-Mulec I, Springael D, Vogel TM and Simonet P. 2014. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. Journal of Biotechnology, 190:18-29.  doi:10.1016/j.jbiotec.2014.03.036

2013

Delmont, T.O., Simonet, P., Vogel, T.M. Mastering methodological pitfalls for surviving the metagenomic jungle.. BioEssays, 2013, 35 (8), pp. 744-54. doi.org/10.1002/bies.201200155

Mathieu, A. Tom Delmont, T.O., Vogel, T.M., Patrick Robe, P., Nalin, R., Simonet, P. Life on human surfaces: skin metagenomics. PLoS ONE, 2013, 8 (6), pp. e65288. doi.org/10.1371/journal.pone.0065288

Simonet, P. 2013. Évolution de l’antibiorésistance dans le sol. ANSES: Les cahiers de la Recherche: Santé, Environnement, Travail. Octobre 2013 :42-44.

Le Digabel, Y., Demanèche, S., Benoit, Y., Vogel, T.M., and Fayolle-Guichard, F. 2013. Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer. Applied Microbiology and Biotechnology, 97:10531-10539. doi:10.1007/s00253-013-4803-3

Bowman, J. S., C. Larose, T. M. Vogel and J. W. Deming. 2013. Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere. Environmental Microbiology Reports, 5:575-582. doi:10.1111/1758-2229.12047

Jacquiod, S., Franqueville, L., Cecillon, S., Vogel, T.M., Simonet, P. 2013. Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach. PLoS ONE, 8:0079699. doi:10.1371/journal.pone.0079699

Larose, C., Dommergue, A., Vogel, T.M. 2013. The dynamic Arctic snow pack: an unexplored environment for microbial diversity and activity. Biology, 2:317-330. doi.org/10.3390/biology2010317

Gaze WH, Krone SM, Larsson DGJ, Li X-Z, Robinson J, Simonet P, Smalla K, Timinouni M, Topp E, Wellington EM, Wright GD, Zhu Y-G. 2013. The impact of humans on the evolution and mobilization of the environmental antibiotic resistome. Environmental Health Perspectives, 19:eid1907. doi:10.3201/eid1907.120871

2012

Delmont, T.O., Simonet, P., Vogel, T.M. 2012. Describing microbial communities and performing global comparisons in the ‘omic era. ISME Journal, 6:1625-1628. doi.org/10.1038/ismej.2012.55

Zhang X, Nesme J, Simonet P, Frostegård Å. 2012. Fate of invading bacteria in soil and survival of transformants after simulated uptake of transgenes, as evaluated by a model system based on lindane degradation.  Research in Microbiology, 163:200-210. doi.org/10.1016/j.resmic.2012.01.007

Delmont, T.O., Prestat,E., Keegan,K.P., Faubladier,M., Robe,P., Clark,I.M., Pelletier, E., Hirsch,P.R., Meyer,F., Gilbert,J.A., Le Paslier, D., Simonet, P., Vogel, T.M. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME Journal, 6: 1677-1687. doi.org/10.1038/ismej.2011.197

Douglas, T.A., Lisa Loseto, Robie Macdonald, Peter Outridge, Aurélien Dommergue, Alexandre Poulain, Marc Amyot, Tamar Barkay, Torunn Berg, John Chételat, Philippe Constant, Marlene Evans, Christophe Ferrari, Nikolaus Gantner, Matthew Johnson, Jane Kirk, Niels Kroer, Catherine Larose, David Lean, Torkel Nielsen, Laurier Poissant, Sigurd Rognerud, Henrik Skov, Søren Sørensen, Feiuye Wang, Simon Wilson, Christian Zdanowicz. The fate of mercury in Arctic terrestrial and aquatic ecosystems, a review. 2012. Environmental Chemistry, 9:321-355. doi.org/10.1071/EN11140

Castro, L., A. Dommerguet, C. Larose, C. Ferrari, L. Maron. A theoretical study of abiotic methylation reactions of gaseous Elemental mercury by halogen-containing molecules. 2012. Journal of Physical Chemistry A, 115:5602-5608. doi.org/10.1021/jp200643n

Eric Dugat-Bony, Corinne Biderre-Petit, Faouzi JAZIRI, Maude David, Jérémie Denonfoux, Delina Lyon, Jean-Yves Richard, Cyrille Curvers, Delphine Boucher, Timothy Vogel, Eric Peyretaillade, Pierre Peyret. In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. 2012. Microbial biotechnology, 5:642-653. doi.org/10.1111/j.1751-7915.2012.00339.x

2011

Delmont, T.O. Cedric Malandain, C., Prestat, E. Catherine Larose, C. Monier, J-M., Simonet, P. Vogel, T.M. 2011. Metagenomic mining for microbiologists. ISME Journal, 5:1837-1843. doi.org/10.1038/ismej.2011.61

Monier J-M, Demanèche S, Delmont TO, Mathieu A, Vogel, T.M. and Simonet P. 2011. Metagenomic exploration of antibiotic resistance in soil. Current Opinion in Microbiology, 14:236-243. doi:10.1016/j.mib.2011.04.010

Lombard N, Prestat E, Van Elsas JD and Simonet P. 2011. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiolgy Ecology, 78:31-49. doi:10.1111/j.1574-6941.2011.01140.x

Simonet P., Plomion C and Martin F. Quand la génomique rencontre l’écologie. 2011. Biofutur, 319:26-29.

Demanèche S, Monier J-M, Dugat-Bony E and Simonet P. 2011. Exploration of horizontal gene transfer between transplastomic tobacco and plant‐associated bacteria. FEMS Microbiology Ecology, 78:129-136. doi:10.1111/j.1574-6941.2011.01126.x

Larose, C., Dommergue, A., De Angelis, M., Cossa, D., Averty, B., Marusczak, N., Soumis, N., Schneider, D., and Ferrari, C. 2011. Springtime changes in snow chemistry lead to new insights into mercury methylation in the arctic, Geochimica et Cosmochim Acta, 74:6263-6275. doi.org/10.1016/j.gca.2010.08.043

Demanèche S, Brard C, Lima O, Binet F and Simonet P. 2011. Development of a new tool to improve gene transfer frequency calculations. Journal of Microbiology Methods, 86:255-257. doi:10.1016/j.mimet.2011.05.014

Delmont TO, Robe P, Clark I, Simonet P and Vogel TM. 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches. Journal of Microbiology Methods, 86: 397-400. doi.org/10.1016/j.mimet.2011.06.013

Delmont, T. O., L. Franqueville, S. Jacquiod, P. Simonet and T. M. Vogel. 2011. Soil Metagenomic Exploration of the Rare Biosphere. In De Bruijn, F. J. (ed.), Handbook of Molecular Microbial Ecology, Volume I: Metagenomics and Complementary Approaches, First Edition. Wiley-Blackwell.

Simonet P. 2011. Approches métagénomiques pour l’étude de la microflore du sol et implications dans le domaine de la santé. Revue du Rhumatisme 78S

Petric I, Philippot L, Abbate C, Bispo A, Chesnot T, Hallin S, Laval K,  Lebeau T, Lemanceau P, Leyval C, Lindstrom K, Pandard P, Romero E, Sarr A, Schloter M, Simonet P, Smalla K, Wilke BM and Martin-Laurent F. 2011. Inter-laboratory evaluation of the ISO standard 11063 “Soil quality – Method to directly extract DNA from soil samples”.Journal of Microbiology Methods, 84:454-460. doi.org/10.1016/j.mimet.2011.01.016

Gilbert, J., O’Dor, R., Vogel, T. 2011. Survey data are still vital to science. Nature, 469:162. doi:10.1038/469162a

Delmont T.O., Robe P, Cecillon S, Clark I.M., Constancias F, Simonet P, Hirsch P.R., Vogel TM. 2011. Accessing microbial diversity for soil metagenomic studies. Applied Environmental Microbiology, 77:1315–1324. doi:10.1128/AEM.01526-10

2010

Nemir, A., David, M.M., Perrussel, R., Sapkota, A., Pascal Simonet, P., Jean-Michel Monier, J.M., Vogel, T.M. 2010. Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils. Chemosphere, 80:600-607. doi:10.1016/j.chemosphere.2010.03.036

Sapkota AR, Berger S, Vogel T.M. 2010. Human pathogens abundant in the bacterial metagenome of cigarettes. Environmental Health Perspective, 118:351-6. doi:10.1289/ehp.0901201

Héry M, Sanguin H, Perez Fabiel S, Lefebvre X, Vogel T.M., Paul E, Alfenore S. 2010. Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques. Water Research, 44:6133-43. doi:10.1016/j.watres.2010.07.003

Pontiroli A, Ceccherini MT, Poté J, Wildi W, Kay E, Nannipieri P, Vogel T.M., Simonet P, Monier JM. 2010. Long-term persistence and bacterial transformation potential of transplastomic plant DNA in soil. Research in Microbiology, 161:326-34. doi:10.1016/j.resmic.2010.04.009

Lyon, D., Buret, F., Vogel, T.M., Monier J-M. 2010. Is resistance futile? Changing external resistance does not improve microbial fuel cell performance. Bioelectrochemistry, 78:2-7. doi.org/10.1016/j.bioelechem.2009.09.001

Lyon, D. Y., Monier, J-M.,  Dupraz, S., Freissinet, C., Simonet, P., and Vogel, T.M. 2010. Integrity and biological activity of DNA after UV exposure. Astrobiology, 10:285-92. doi:10.1089/ast.2009.0359

Larose, C., Sibel Berger, Christophe Ferrari, Elisabeth Navarro, Aurélien Dommergue, Dominique Schneider, Vogel, T.M. 2010.  Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway.  Extremophiles, 14:205-12. doi.org/10.1007/s00792-009-0299-2

Malandain, C., Fayolle-Guichard, F., Vogel, T.M. 2010. Cytochromes P450-mediated degradation of  fuel oxygenates by environmental isolates. FEMS Microbial Ecology, 72:289-96. doi:10.1111/j.1574-6941.2010.00847.x

Dommergue A, Larose C, Faïn X, Clarisse O, Foucher D, Hintelmann H, Schneider D, Ferrari CP. 2010. Deposition of mercury species in the Ny-Alesund area (79 degrees N) and their transfer during snowmelt. Environmental Science and Technology, 44:901-7. doi.org/10.1021/es902579m

Lyon, D. Y., Pivetal, J., Blanchard, L. and Vogel, T.M. 2010. Bioremediation via in situ electrotransformation. Bioremediation Journal, 14:109-119. doi.org/10.1080/10889861003767092

Poté J, Ceccherini MT, Rosselli W, Wildi W, Simonet P and Vogel T.M. 2010. Leaching and transformability of transgenic DNA in unsaturated soil columns. Ecotoxicology and Environmental Safety, 73:67-72. doi.org/10.1016/j.ecoenv.2009.09.009

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