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Publications

For citation information, please refer to my Google-Scholar profile page or my ResearcherID profile.

2017

Eyice, Ö., Myronova, N., Pol, A., Carrión, O., Todd, J., Smith, T.J., Gurman, S.J., Cuthbertson, A., Mazard, S., Mennink-Kersten, M.A.S.H., Bugg, T.D.H., Andersson, K.K., Johnston, A.W.B., Op den Camp, H.J.M., Schäfer, H. 2017. Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. The ISME Journal.

Jameson, E., Taubert, M., Coyotzi, S., Chen, Y., Eyice, O., Schäfer, H., Murrell, J.C., Neufeld, J.D., Dumont, M.G. 2016. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Metagenomics – Methods and Protocols Vol: 1539 Page: 57-74.
DOI: 10.1007/978-1-4939-6691-2_5.

2016

Zhu, Y., Ksibe, A.Z., Schäfer, H., Blindauer, C.A., Bugg, T.D.H., Y. Chen. 2016. O2-independent demethylation of trimethylamine N-oxide by Tdm of Methylocella silvestris. FEBS Journal 283, 3979-3993. doi: 10.1111/febs.13902

Kowalczyk, A., Price, O.R., van der Gast, C.J., Finnegan, C.J., van Egmond, R.A. Schäfer, H., G.D. Bending. 2016. Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol. Chemosphere 164, 355-362.

Lidbury, I., Kröber, E., Zhang, Z., Zhu, Y., Murrell, J.C., Chen, Y., and H. Schäfer. 2016. A mechanism for bacterial transformation of DMS to DMSO: a missing link in the marine organic sulfur cycle. Environ. Microbiol. 18, 2754-2766. doi: 10.1111/1462-2920.13354

Eyice, Ö., and H. Schäfer. 2016. Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments. Arch. Microbiol. 198:17-26; doi: 10.1007/s00203-015-1160-x

2015

Kowalczyk, A., Eyice, Ö., Schäfer, H., Price, O., Finnegan, C., van Egmond, R., Shaw, L., Barrett, G., and G.D. Bending. Characterization of para-nitrophenol degrading bacterial communities in river water using functional markers and stable isotope probing. Appl. and Environ. Microbiol. 81:6890-6900. doi: 10.1128/AEM.01794-15

Eyice, Ö., Namura, M., Chen, Y., Mead, A., Samavedam, S., and H. Schäfer. 2015. SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment. ISME J. 9, 2336-2348; doi:10.1038/ismej.2015.37 OPEN ACCESS

Kowalczyk, A., Martin, T.J., Price, O.R., Snape, J.R., van Egmond, R.A., Finnegan, C.J., Schäfer, H., Davenport, R.J., and G.D. Bending. 2015. Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques. Ecotoxicology and Environmental Safety 111, 9-22

2014

Kappler, U. and H. Schäfer. 2014. Transformations of dimethylsulfide. In "The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment", Eds P.M.H. Kroneck, M.E. Sosa Torres; Vol. 14 of Metal Ions in Life Sciences, Eds A. Sigel, H. Sigel, R.K.O. Sigel, Springer Science + Business Media B.V., Dordrecht, 2014, Chapter 11.

Chan, J.Z-M., Millard, A.D., Mann, N.H. and H. Schäfer. 2014. 'Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes.' Frontiers Microbiol. 5, article 506, 1-14. doi: 10.3389/fmicb.2014.00506

Zhu, Y. Jameson, E., Parslow, R.A., Lidbury, I., Fu, T., Dafforn, T.R., Schäfer, H. and Yin Chen. 2014. Identification and characterization of trimethylamine N-oxide (TMAO) demethylase and TMAO permease in Methylocella silvestris BL2. Environ. Microbiol. 16, 3318-3330. doi: 10.1111/1462-2920.12585

Zhu, Y., Jameson, E., Cosatti, M., Schäfer, H., Rajakumar, K., Bugg T. D. H. and Y. Chen. 2014. 'Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota' Proceedings Of The National Academy Of Sciences (USA) 111 (11), 4268-73. doi: 10.1073/pnas.1316569111.

Mazard, S, and H. Schäfer. 2014. 'Stable isotope probing to study functional components of complex microbial ecosystems' in Methods in Microbiology. Environmental Microbiology - Methods and Protocols, 2nd Ed, Editors: I.T. Paulsen and A.J. Holmes, Humana Press.

2013

Davies, L.O., Bramke, I., France, E., Marshall, S., Oliver, R., Nichols, C., Schäfer, H., and G. Bending. 2013. Non-UV light influences the rate of crop protection product degradation. Environ. Sci. & Technol. 47, 8229-8237.

Davies, L.O., Schäfer, H., Marshall, S., Bramke, I., Oliver, R.G., and G.D. Bending. 2013. Light structures phototroph, bacterial and fungal communities at the soil surface. PLoS One, 8, 69048.

2012

Cox, M.J., Schäfer, H., Nightingale, P.D., McDonald, I.R., and J.C. Murrell. 2012. Diversity of methyl halide-degrading microorganisms in oceanic and coastal waters. FEMS Microbiol. Lett., 334, 111-118.

2011

Boden, R., Murrell, J.C., and H.Schäfer. 2011. Dimethylsulfide is an energy source for the heterotrophic marine bacterium Sagittula stellata. FEMS Microbiol. Lett. 322, 188-193. DOI:10.1111/j.1574-6968.2011.02349.x.

Boden, R., Ferriera, S., Johnson, J., Kelly, D.P., Murrell, J.C., and H.Schäfer. 2011. Draft genome sequence of the chemolithoheterotrophic, halophilic methylotroph Methylophaga thiooxydans DMS010. J. Bact. 193, 3154-3155. DOI:10.1128/JB.00388-11.

Boden, R., Borodina, E., Wood, A.P., Kelly, D.P., Murrell, J.C., and H. Schäfer. 2011. Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans. J. Bact. 193, 1250-1258. DOI: 10.1128/JB.00977-10.

2010

Chen, Y., Scanlan, J., Song, L., Crombie, A., Rahman, T., Schäfer, H., and J.C. Murrell. 2010. γ-glutamylmethylamide is an essential intermediate for the metabolism of methylamine by Methylocella silvestris. Appl. Environ. Microbiol. 76, 4530-4537.

Boden, R., Kelly, D.P., Murrell, J.C., and H. Schäfer. 2010. Oxidation of dimethylsulfide to tetrathionate by Methylophaga thiooxidans sp. nov.: a new link in the sulfur cycle. Environ. Microbiol. 12, 2688-2699. DOI: 10.1111/j.1462-2920.2010.02238.x

Schäfer, H., Myronova, N., and R. Boden. 2010. Microbial degradation of dimethylsulfide and related C1-sulfur compounds: organisms and pathways controlling fluxes of sulfur in the biosphere. J. Exp. Bot. 61, 315-334; DOI:10.1093/jxb/erp355

Latypova, E., Yang, S., Wang, Y.-S., Wang, T. Chavkin, T.A., Hackett, M., Schäfer, H., and M.G. Kalyuzhnaya. 2010. Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5. Mol. Microbiol. 75, 426-439; DOI: 10.1111/j.1365-2958.2009.06989.x

2009

Cunliffe, M., Whiteley, A.S., Newbold, L. Oliver, A., Schäfer, H., and J.C. Murrell. 2009. Comparison of bacterioneuston and bacterioplankton dynamics during a phytoplankton bloom in a fjord mesocosm. Appl. Environ. Microbiol. 75, 7173-7181.

Cunliffe, M., Harrison, E., Salter, M., Schäfer, H., Upstill-Goddard, R.C., and J.C. Murrell. 2009. Comparison and validation of sampling strategies for the molecular microbial analysis of surface microlayers. Aquat. Microb. Ecol. 57, 69-77; DOI: 10.3354/ame01330

2008

Neufeld, J.D., Boden, R., Moussard, H. Schäfer, H. and J.C. Murrell. 2008. Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment. Appl. Environ. Microbiol. 74, 7321-7328.

Cunliffe, M., Schäfer, H., Harrison, E., Cleave, S., Upstill-Goddard, R. and J.C. Murrell. 2008. Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary. ISME J. 2, 776-789.

2007

Schäfer, H., Ferdelman, T.G., Fossing, H., and G. Muyzer. 2007. Microbial diversity in deep sediments of the Benguela Upwelling System. Aquat. Microb. Ecol., 50, 1-9.

Neufeld, J.D., Schäfer, H., Cox, M.J., Boden, R., McDonald, I.R., and J. C. Murrell. 2007. Stable isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 1, 480-491.

Schäfer, H. 2007. Isolation of Methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide. Appl. Environ. Microbiol. 73, 2580-2591.

Schäfer, H., Miller, L., Oremland, R., and J. C. Murrell. 2007. Bacterial cycling of methyl halides. In: Ed. Laskin, A.I., Sariaslani, S., and G. Gadd (eds.), Adv. Appl. Microbiol. 61, 307-346. DOI: 10.1016/S0065-2164(06)61009-5

2005

Lin, J.L., Joye, S.B., Scholten, J.C.M., Schäfer, H, McDonald, I.R. and J. C. Murrell. 2005. Methanotroph diversity in Mono Lake, a meromictic soda lake, as determined by pmoA clone library and DGGE analysis suggests a change in community structure which correlates with increased aerobic methane oxidation activity. Appl. Environ. Microbiol. 71, 6458-6462.

Schäfer, H., McDonald, I. R., Nightingale, P. D. and J. C. Murrell. 2005. Evidence for presence of a CmuA methyltransferase pathway in novel marine methyl halide-oxidising bacteria. Environ. Microbiol. 7, 839-852.

2003

Muyzer G., Yildirim E., Roosken P., Abbas B., and H. Schäfer. 2003. PCR-DGGE analysis of mixed bacterial populations. In: van Belkum A, Duin B., and J.P. Hays (eds.), Experimental approaches for assessing genetic diversity among microbial pathogens, pp. 71-80, Dutch working party on epidemiological typing and Dutch Society for Microbiology, The Netherlands.

2002

Schäfer H., Abbas B., Witte H., and G. Muyzer. 2002. Genetic diversity of 'satellite' bacteria present in cultures of marine diatoms. FEMS Microbiol. Ecol. 42, 25-35.

Troussellier, M., Schäfer, H., Batailler, N., Bernard, L., Guindulain, T., Petit, M., Pukall, R., Courties, C., Lebaron, P., Muyzer, G., Servais, P., Stackebrandt, E. and J. Vives-Rego. 2002. Bacterial activity and genetic richness along an estuarine gradient (Rhône river plume, France). Aquat. Microb. Ecol. 28, 13-24.

2001

Schäfer, H., Bernard, L., Courties, C., Lebaron, P., Servais, P., Pukall, P., Stackebrandt, E., Troussellier, M., Guindulain, T., Vives-Rego, J., Muyzer G. 2001. Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol. Ecol. 34, 243-253.

Lebaron, P., Servais, P., Troussellier, M., Courties, C., Muyzer, G., Bernard, L., Schäfer, H., Pukall, P., Stackebrandt, E., Guindulain, T., and J. Vives-Rego. 2001. Microbial community dynamics in Mediterranean nutrient-enriched mesocosms: changes in abundances, activity, and composition. FEMS Microbiol. Ecol. 34, 255-266.

Schäfer, H. and G. Muyzer. 2001. Denaturing gradient gel electrophoresis in marine microbial ecology. In: Paul J.H. (ed.), Methods in Microbiology, 30: 425-468, Academic Press, London.

Bernard, L., Courties, C., Duperray, C., Schäfer, H., Muyzer, G., and P. Lebaron. 2001. A new approach to determine the genetic diversity of viable and active bacteria in aquatic ecosystems. Cytometry 43, 314-321.

2000

Schäfer, H., Servais, P., and G. Muyzer. 2000. Successional changes in the genetic diversity of a marine bacterial assemblage during confinement. Arch. Microbiol. 173, 138-145.

Bernard, L., Schäfer, H., Joux, F., Courties, C., Muyzer, G., and P. Lebaron. 2000. Genetic diversity of total, active and culturable marine bacteria in coastal seawater. Aquat. Microb. Ecol. 23, 1-11.

Casamayor, E. O., Schäfer, H., Bañeras, L., Pedrós-Alió, C., and G. Muyzer. 2000. Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 66, 499-508.

1999

Lebaron, P., Servais, P., Troussellier, M., Courties, C., Vives-Rego, J., Muyzer, G., Bernard, L., Guindulain, T., Schäfer, H., and E. Stackebrandt. 1999. Changes in bacterial community structure in seawater mesocosms differing in their nutrient status. Aquat. Microb. Ecol. 19, 255-267.

Rosselló-Mora, R., Thamdrup, B., Schäfer, H., Weller, R., and R. Amann. 1999. The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions. Syst. Appl. Microbiol. 22, 237-248.

1998

Muyzer, G., Brinkhoff, T., Nübel, N., Santegoeds, C., Schäfer, H., and C. Wawer. 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 1-27. In: A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (eds.), Molecular Microbial Ecology Manual, vol. 3.4.4. Kluwer Academic Publishers, Dordrecht.