Publications
For more information refer to Publons/ResearcherIDLink opens in a new window profile.
2024
Allison A. Fong, Clara J. M. Hoppe*, Nicole Aberle, Carin J. Ashjian, Philipp Assmy, Youcheng Bai, Dorothee C. E. Bakker, et al. .2024. Overview of the MOSAiC expedition: Ecosystem, Elementa, accepted.
Luo, W., Zhao, M., Dwidar, M., Gao, Y., Xiang, L., Wu, X., Medema, M. H., Xu, S., Li, X., Schäfer, H., Chen, M., Feng, R. & Zhu, Y. 2024. Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn’s disease development. Microbiome, 12, 152.
2023
Tebbe, D.A., Gruender, C., Dlugosch, L., Lõhmus, K., Rolfes, S., Könneke, M., Chen, Y., Engelen, B. and H. Schäfer. 2023. Microbial drivers of DMS-reduction and DMS-dependent methanogenesis in saltmarsh sediments. ISME Journal, 17, 2340-2351. doi:https://doi.org/10.1038/s41396-023-01539-1Link opens in a new window
2022
Mock, T., Boulton, W., Balmonte, J.-P., Barry, K., Bertilsson, S., Bowman, J. et al. 2022. Multiomics in the central Arctic Ocean for benchmarking biodiversity change. PLOS Biology 2022 Vol. 20 Issue 10 Pages e3001835, DOI: 10.1371/journal.pbio.3001835
Ghosh, D., Whitworth, D.E., Schäfer, H., Krishnamurthi, S., and P. Saha. 2022. Editorial: Microbial mitigation of hazardous compounds in agro-ecosystems. Frontiers in Microbiology 13:1015111. doi: 10.3389/fmicb.2022.1015111
Kröber, E., Mankowski, A., and H. Schäfer. 2022. Microorganisms associated with Sporobolus anglicus, an invasive dimethylsulfoniopropionate producing salt marsh plant, are an unrecognized sink for dimethylsulfide. Frontiers in Microbiology, 13, 950460. doi: 10.3389/fmicb.2022.950460
Tebbe, D.A., Geihser, S., Wemheuer, B., Daniel, R., Schäfer, H., and Engelen, B. 2022. Seasonal and zonal succession of bacterial communities in North Sea salt marsh sediments. Microorganisms, 10, 859. DOI: 10.3390/MICROORGANISMS10050859
Wang, J., Chu, Y.-X., Schäfer, H., Tian, G., and R. He. 2022. CS2 increasing CH4-derived carbon emissions and active microbial diversity in lake sediments. Environmental Research. Accepted.
2021
Palmer, J.L., Hilton, S., Picot, E., Bending, G.D. and H. Schäfer. 2021. Tree phyllospheres are a habitat for diverse populations of CO-oxidising bacteria. Environmental Microbiology, 23, 6309-6327. DOI: https://doi.org/10.1111/1462-2920.15770Link opens in a new window
Picot, E., Hale, C.C., Hilton, S., Teakle, G., Schäfer, H., Huang, Y., Perryman, S., West, J.S., and G.D. Bending. 2021. Contrasting responses of rhizosphere bacterial, fungal, protist and nematode communities to nitrogen fertilisation and crop genotype in field grown oilseed rape (Brassica napus). Frontiers Sustainable Food Systems., 5, 613269, doi: https://doi.org/10.3389/fsufs.2021.613269Link opens in a new window
2020
Cook, S., Price, O., King, A., Finnegan, C., van Egmond, R., Schäfer, H., Pearson, J.M., and G.D. Bending. 2020. Bedform characteristics and biofilm community development modify hyporheic exchange in a recirculating flume environment. Science of the Total Environment., 749, 141397, DOI: https://doi.org/10.1016/j.scitotenv.2020.141397Link opens in a new window
Dixon, J.L., Hopkins, F.E., Stephens, J.A. and H. Schäfer. 2020. Seasonal changes in microbial dissolved organic sulfur transformations in coastal waters. Microorganisms, 8, 337. DOI: https://doi.org/10.3390/microorganisms8030337
Cook, S., Chan, H.-L., Abolfathi, S., Bending, G.D., Schäfer, H. and J.M. Pearson. 2020. Longitudinal dispersion of microplastics in aquatic flows using fluorometric techniques. Water Research, 170, 115337, DOI: https://doi.org/10.1016/j.watres.2019.115337Link opens in a new window
2019
Kröber, E. and H. Schäfer. 2019. Identification of proteins and genes expressed by Methylophaga thiooxydans during growth on dimethylsulfide and their presence in other members of the genus. Frontiers in Microbiology, 10, 1132, DOI: 10.3389/fmicb.2019.01132Link opens in a new window
Chen, Y. and H. Schäfer. 2019. Towards a systematic understanding of structure–function relationship of dimethylsulfoniopropionate‐catabolizing enzymes. Molecular Microbiology 111 (6), 1399-1403. DOI: 10.1111/mmi.14230Link opens in a new window
Schäfer, H. and Ö. Eyice. 2019. Microbial cycling of methanethiol. pp. 173-182. In: Methylotrophs and Methylotroph Communities (Editor: Chistoserdova, L.), Caister Academic Press, Norfolk UK. DOI: 10.21775/9781912530045.09Link opens in a new window
2018
Veras, D., Armstrong, D.J., Blake, J.A., Gutiérrez-Marcos, J.F., Jackson, A.P., and H. Schäfer. 2018. Dynamical and biological panspermia constraints within multi-planet exosystems. Astrobiology, 19 (9), published online 12 Sep 2018. DOI: 10.1089/ast.2017.1786Link opens in a new window
Pol, A., Renkema, G.H., Tangerman, A., Winkel, E.G., Engelke, U.F., de Brouwer, A.P.M., Lloyd, K.C., Araiza, R.S., van den Heuvel, L., Omran, H., Olbrich, H., Oude Elberink, M., Gilissen, C., Rodenburg, R.J., Sass, J.O., Schwab, K.O., Schäfer, H., Venselaar, H., Sequeira, J.S., Op den Camp, H.J.M., and R.A. Wevers. 2018. Mutations in SELENBP1, encoding a novel human methanethiol oxidase, cause extraoral halitosis. Nature Genetics 50, 120-129; published online 18 Dec 2017. DOI: 10.1038/s41588-017-0006-7Link opens in a new window.
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., and H. Schäfer. 2018. Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. The ISME Journal 12 (1), 145-160. DOI: 10.1038/ismej.2017.148Link opens in a new window.
2017
Jameson, E., Taubert, M., Coyotzi, S., Chen, Y., Eyice, O., Schäfer, H., Murrell, J.C., Neufeld, J.D., and M.G. Dumont. 2017. 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.Link opens in a new window
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: 10.1111/1462-2920.13354Link opens in a new window
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.D. 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.