Lipids, containing carbon, nitrogen, phosphorus and sulfur, are a major component of all living cells and are constantly released into the oceans due to programmed cell death, viral infections and zooplankton grazing. Current estimates suggest that lipids can account for ~10% of total dissolved organic matter (DOC) in the oceans. However, our knowledge on microbial lipid transformation in the oceans is very limited. Neither the identities of the microbes involved, nor the mechanisms by which lipids are degraded, have been well understood.
A major hurdle in understanding the microbial lipid cycle lies in the difficulty in characterizing and quantifying numerous lipid classes in marine samples. Commonly observed lipids in marine ecosystems include phospholipids, glycolipids and amino acid-containing lipids. Recent advances in technologies such as liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS) has enabled high throughput identification and quantification of thousands of cellular lipid molecular species (Shevchenko, 2010), which now enables lipid characterization both qualitatively and quantitatively. Indeed, lipidomics is starting to complement the rapid progress made in genomics, metagenomics, transcriptomics and proteomics.
Here in this project, we will combine laboratory and filed based methodologies to fully uncover the lipid cycle in marine waters. The aim of this project is thus twofold,
Firstly, we aim to establish a high throughput workflow for simultaneous determination of common lipids species in marine surface waters using our in house HPLC MS platform. This will involve examining samples from the Western English Channel, collected via the Marine Biological Association research vessel, Sepia.
Secondly, we aim to determine the identity and activity of key microbial populations in the recycling of representative lipids in marine surface waters and coastal marine sediment using integrated omics approach, e.g. high throughput sequencing of 16S/18S rRNA, metagenomics, metagenomics and lipidomics.
This project is not suitable for CASE funding
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Microbial lipids identification will be carried out by liquid chromatography-mass spectrometry (LC-ESI-MS).
Nutrients and key intermediates in lipid degradation pathways will be analysed by established chromatography techniques, such as ion-exchange chromatography and gas chromatography, and analysis guided by our previous extensive characterisation of laboratory strains.
Microbial community analyses will be carried out using amplicon sequencing of 16S rRNA genes, metatranscriptomics and metagenomics.
DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.
The Supervisory team has an excellent record in PhD supervision. 12 PhD students have graduated from Chen’s group to date, all of whom have published at least two papers in high profile journals (PNAS) or leading journals of the discipline (ISME J). This exciting project provides cutting-edge training on contemporary omics approaches, including lipidomics, transcriptomics and metagenomics. It will also provide excellent training in wider aspects of marine microbiology, biogeochemistry and molecular biology using cutting edge molecular ecology techniques as well as in a variety of analytical techniques currently available at Birmingham, Warwick and the Marine Biological Association, Plymouth, including gas chromatography, ion-exchange chromatography, liquid chromatography-mass spectrometry.
The supervisors are world-leading experts in marine microbiology and publish regularly on high profile interdisciplinary journals (e.g. Proc. Natl. Acad. Sci. USA, Current Biology) and field specific high impact journals (e.g. The ISME Journal). They have complementary expertise in marine microbiology and biogeochemical cycles. Current research in the groups is well-funded by NERC, the Leverhulme trust and The European Union. Further details on their research activities and their group members can be found via the links below.
Prof Yin Chen www.yinchenlab.org
Dr. Katherine Helliwell https://scholar.google.co.uk/citations?user=0K3xhvoAAAAJ&hl=en
Dr. Michaela Mausz https://warwick.ac.uk/fac/sci/lifesci/people/mmausz/
The student will also have access to research resources available at the MBA including the Plymouth Culture Collection of Marine Algae, the MBA research vessel, and seawater samples.
Year 1: Mass spectrometry-based identification of bacterial lipids in marine systems (lipidomics).
Year 2: Microbial lipid cycling in anaerobic sediment, microcosm setup and measurement of lipid degradation, amplicon sequencing, metagenomics and metatranscriptomics sequencing and bioinformatics.
Year 3: microbial lipid cycling in marine waters, microcosm setup, amplicon sequencing, metagenomics sequencing and bioinformatics.
Shevchenko A, Simons K. 2010 Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol. 11:593-598.
Westermann et al., 2023 Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles. Science Advances 9 (17), eadf5122
Merchant SS, Helmann JD 2012 Elemental Economy: Microbial Strategies for Optimizing Growth in the Face of Nutrient Limitation. Adv Microb Physiol 60:92-210.
Guillonneau, et al 2022 Trade-offs of lipid remodeling in a marine predator–prey interaction in response to phosphorus limitation. Proceedings of the National Academy of Sciences 119 (36), e2203057119
Applicants should hold a BSc and/or MSc degree in relevant subjects. Informal enquires can be made to Prof Yin Chen ([email protected] )
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 7th January 2026.