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Functional Metagenomics and Stable Isotope Probing of Marine Methylotrophs

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.

Fig. 1. Location of L4 sampling site in the English Channel, UK


Fig. 2. Location of the shallow methane seep sampling site off the Island of Elba, Italy

Two main sites are being studied during this project. The first is a coastal sampling station, named Station L4, located 10 km off the coast of Plymouth in the English Channel (50º15.00 N; 004º13.02 W; Fig 1). Sampled regularly since 1988, L4 is an established and important site for which there is a large historical database available. At this site, methanol and methylamine uptake by methylotrophs will be studied within the water column. The second site is a shallow (12m) seep located 100 m off Pomonte in the Island of Elba (42º48.00 N; 10º18.00 E; Fig. 2), Italy, where methane of thermogenic origin is being constantly released into the water column.

The project makes extensive use of both metagenomics combined with DNA Stable Isotope Probing (DNA-SIP) and single cell ecophysiological techniques (Raman-FISH) for functional investigations of marine microbial populations. The incorporation of the heavy isotopes into microbial DNA is being analysed to follow carbon and nitrogen fluxes through microbial communities, from methylotrophs to heterotrophs. 13C labeled DNA of methylotrophs is then used for high-throughput sequencing to reconstruct genomes of these marine organisms. Key functional genes are being analysed by PCR and qPCR. We are therefore able to identify active methylotrophs in complex marine microbial communities, and quantify their contribution to marine nutrient fluxes. Raman microspectroscopy in combination with optical tweezers based on specific FISH probes is also being used for isolation of potential novel methylotrophs and single cell genomics.

This project is revealing novel insights into marine microbial communities driven by methylotrophic metabolism. The identification of novel methylotrophs and new variants of enzymes involved in methylotrophic processes allows a better understanding of these metabolic processes. Knowledge of key organisms and their pathways is yielding valuable insights into the impact of methylotrophs on carbon and nitrogen cycling in marine ecosystems.


Gordon and Betty Moore Foundation (GBMF)

Principal investigators
Prof JC Murrell, UEA (PI)
Prof Y Chen, Warwick (Co-PI)

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

Project Partners
Dr Jo Dixon (Plymouth Marine Laboratory)
Prof Wei Huang (University of Oxford)