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Focused metagenomics

Functional Metagenomics and Stable Isotope Probing of Marine Methylotrophs. Funded by the Moore Foundation

One carbon (C1) compounds such as methane, methanol and methylamine are used as carbon and energy source by microbes known as methylotrophs. In the marine environment, where these compounds can sometimes be found in surprisingly high concentrations, methylotrophs responsible for metabolising them seem to be ubiquitous. By turning over these compounds in the water column and sediments, methylotrophic organisms therefore play key roles in major biogeochemical cycles. Investigation of the role of methylotrophic bacteria in the marine environment will thus be of significance to answer key questions about the cycling of carbon and nitrogen in marine microbial food webs.

The central questions this project aims to answer by functional investigation of the microbial communities are those regarding the activity and identity of the microbes present, or, to put it simply, “who is doing what, where and when?” Also of importance are measurements of methylotrophic activity to develop a better understanding of the impact of these processes in marine ecosystems. Also, the interactions of methylotrophs with other organisms and the influence of environmental parameters on their activity are being investigated.

Principal investigators: Prof JC Murrell, UEA (PI); Dr.Y Chen, Warwick (Co-PI)

Associated staff: Dr. Carolina Grob; Dr. Martin Taubert; Alexandra Howat; Oliver Burns

Selected key publications on focused metagenommics

  • Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow H.H., Jehmlich N., von Bergen M., Chen, Y. and Murrell, J.C. (2015) 'Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph.', Environmental Microbiology, in press
  • Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Dixon, J.L., Chen, Y. and Murrell, J.C. (2015) 'XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments', Environmental Microbiology, in press
  • Zhang, D., Berry, J., Zhu, D., Wang, Y., Chen, Y., Jiang, B., Huang, S., Langford, H., Li, G., Davision, P.A., Xu, J., Aries, E., Huang, W.E. (2015) 'Magnetic nanoparticle mediated isolation of functional bacteria in a complex microbial community.', ISME Journal, i9 603 - 614.
  • Y Wang, Y Chen, Q Zhou, S Huang, K Ning, J Xu, RM Kalin, S Rolfe, WE Huang (2012) 'A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community', PLoS One, 7 (10), e47530
  • Chen, Y., Dumont, M. G., Neufeld, J. D. and Murrell, J. C. (2011) 'Towards 'focused metagenomics': a case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics', in Handbook of molecular microbial ecology I: metagenomics and complementary approaches, 491- 496, Editors: De Bruijn, F. J. (9780470644799) John Wiley & Sons
  • Chen, Y. and Murrell, J. C. (2010) 'When metagenomics meets stable-isotope probing: progress and perspectives', Trends In Microbiology, 18 (4), 157 - 163.
  • Neufeld, J. D., Chen, Y., Dumont, M. G. and Murrell, J. C. (2008) 'Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics', Environmental Microbiology, 10 (6), 1526 - 1535.
  • Chen, Y., Dumont, M. G., Neufeld, J. D., Bodrossy, L., Stralis-Pavese, N., McNamara, N. P., Ostle, N., Briones, M. J. I and Murrell, J. C. (2008) 'Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands', Environmental Microbiology, 10 (10), 2609 - 2622