Project highlights

  • Marine microbes meet omics
  • World-leading supervisory team on marine microbiology and ecology
  • Uniquely opportunity at Warwick to apply cutting-edge techniques on integrated omics

Overview

The growth of marine bacteria in the vast open ocean ecosystem is limited by the availability of nutrients (Scanlan et al, 2009; Merchant & Helmann, 2012). Marine cyanobacteria are responsible for the generation of around half of oxygen in the atmosphere. Heterotrophic marine bacteria play a crucial role in marine elemental cycling which regenerates essential nutrients for oceanic primary production. Global warming and the rise of sea surface temperature are predicted to enhance nutrient limitation on our oceans. Understanding how marine bacteria meet their nutrient demand and how organic macromolecules are recycled in the oceans holds the key to predicting the future Oceans’ functioning under natural and anthropogenic changes.

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.

The aim of this project is therefore 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 (see above figure 1). Secondly, we aim to determine the identity and activity of key microbial populations in the recycling of representative lipids in marine surface waters and costal marine sediment using integrated omics approach, e.g. high throughput sequencing of 16S rRNA, metagenomics, metagenomics and lipidomics.

 

Host

University of Warwick

Theme

  • Organisms and Ecosystems

Supervisors

Project investigator

  • Prof Yin Chen, University of Warwick

 

Co-investigators

  • Prof David Scanlan, University of Warwick

How to apply

Methodology

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. Microbial community analyses will be carried out using amplicon sequencing of 16S rRNA genes, metatranscriptomics and metagenomics.

Training and skills

The Supervisory team has an excellent record in PhD supervision. The last two PhD students completed from the Chen group has published 4 and 3 first-authored papers respectively, including 2 in PNAS, 1 in the ISME Journal, 3 in Environmental Microbiology and 1 in the FEBS Journal. 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 Warwick, including gas chromatography, ion-exchange chromatography, liquid chromatography-mass spectrometry.

Partners and collaboration

The supervisors are world-leading experts in marine microbiology and publish regularly on high profile interdisciplinary journals (e.g. Proc. Natl. Acad. Sci. USA) 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 Chen’s group: http://www2.warwick.ac.uk/fac/sci/lifesci/people/ychen

Prof Scanlan’s group http://www2.warwick.ac.uk/fac/sci/lifesci/people/dscanlan

 

Further details

Applicants should hold a BSc and/or MSc degree in relevant subjects. Informal enquires can be made to Prof Yin Chen (y.chen.25@warwick.ac.uk)

Please visit the University of Warwick website for application guidance: https://warwick.ac.uk/fac/sci/lifesci/study/pgr/studentships/nerccenta/

Possible timeline

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.

Further reading

Shevchenko A, Simons K. 2010 Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol. 11:593-598. [link]

Scanlan et al., 2009 Ecological Genomics of Marine Picocyanobacteria. Microbiol Mol Biol Rev 73:249-299. [link]

Merchant SS, Helmann JD 2012 Elemental Economy: Microbial Strategies for Optimizing Growth in the Face of Nutrient Limitation. Adv Microb Physiol 60:92-210. [link]

Sibastian M, Smith AF, Gonzalez JM, Fredricks HF, Van Mooy B, Koblizek M, Brandsma J, Koster G, Mestre M, Mostajir B, Pitta P, Postle AD, Sanchez P, Gasol JM, Scanlan DJ, Chen Y. (2016) Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency. The ISME Journal,  10 (4) 968-978.

AF Smith, B Rihtman, R Stirrup, E Silvano, MA Mausz, DJ Scanlan, Chen Y (2019) Elucidation of glutamine lipid biosynthesis in marine bacteria reveals its importance under phosphorus deplete growth in Rhodobacteraceae. The ISME journal 13 (1), 39-49

COVID-19

In unforeseen circumstances where wet lab work is not feasible due to COVID outbreak, the project will shift towards bioinformatic analyses of proteomics and lipidomics datasets which are already collected in Scanlan/Chen labs. These include structural determination of novel lipids from high resolution MS datasets and comparative proteomics datasets of bacterial culture grown on various lipids.