Functional Metagenomics and Stable Isotope Probing of Marine Methylotrophs
One carbon (C1) compounds such as methane, methanol and methylated amines are used as carbon and energy source by microbes known as methylotrophs. In the marine environment, where these compounds can be found in relatively 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 and their study will help us to answer key questions about the cycling of carbon and nitrogen in marine microbial food webs.
Functional investigations of these microbial communities are aimed at understanding the activity and identity of the microbes present, or, to put it simply, “who is doing what, where and when?” Measurements of methylotrophic activity help us to develop a better understanding of the impact of these processes in marine ecosystems. We also study the interactions of methylotrophs with other organisms and the influence of environmental parameters on their activity.
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 have been studied.The first is a coastal sampling station, named Station L4, located 10 km off the coast of Plymouth in the English Channel (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 has been studied within the water column. The second site is a shallow (12m) seep located 100 m off Pomonte in the Island of Elba (Fig. 2), Italy, where methane of thermogenic origin is being constantly released into the water column.
Our research 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 can then be used for high-throughput sequencing to reconstruct genomes of these marine organisms. Key functional genes are analysed by PCR and qPCR 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 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. This work has been funded by the Gordon & Betty Moore Foundation and carried out in collaboration with Yin Chen, University of Warwick, Jo Dixon and colleagues at Plymouth Marine Laboratory, Miriam Weber and colleagues at The Hydra Institute, Elba and Anne-Kristin Kaster and colleagues at Karlsruhe Institute of Technology.
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Taubert, M., Grob, C., Crombie, A.T., Howat, A.M., Burns. O.J., Weber, M., Lott, C.,Kaster, A.K., Vollmers, J., Jehmlich, N., von Bergen, M., Chen., Y and Murrell, J.C. (2019) Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environmental Microbiology, 21, 3780-3795.
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Howat, A.M., Vollmers, V., Taubert, M., Grob, C., Dixon, J.L., Todd, J.D.,Chen, Y.,Kaster, A-K., Murrell, J.C. (2018) Comparative genomics and mutational analysis reveals a novel XoxF-utilising methylotroph in the Roseobacter group. Frontiers of Microbiology, 9:766.
Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Pratscher, J., Jehmlich, N., von Bergen, M., Richnow, H.H., Chen, Y., J Colin Murrell, J.C. (2017) Methylamine as a nitrogen source for microorganisms from a coastal marine environment. Environmental Microbiology, 19, 2246-2257.
Sargeant, S., Murrell, J.C., Nightingale, P.D and Dixon, J.L. (2016) Seasonal variability in microbial methanol utilisation in coastal waters of the western English Channel. Marine Ecology Progress 550, 53-64.