Project Overview
The aim is to resolve gene expression of individual cells in marine samples by a new sequencing approach. This information can help us understand how microbes turn over nutrients, mutually interact, and adapt their physiology to environmental change such as coastal water pollution and climate change.
Project Description
Microbial eukaryotes are important drivers of marine nutrient cycles but most of them remain uncultured and little known. Sequencing of bulk environmental RNA has revealed patterns in the metabolism of whole microeukaryotic ‘phyla’, but it lacks resolution at the level of species and populations, where much metabolic variation underlying nutrient flows occurs [1]. One way of linking metabolism to species and populations (‘who does what’) is by microfluidics-based separation and sequencing of individual cells. This novel approach has been increasingly popular in Biomedicine [2] but scarcely applied to environmental microbiology.
You will use the flexible DropSeq platform [3] to bring high-throughput single-cell sequencing to environmental microbiology. You will first optimise microfluidic cell separation on laboratory cell cultures, then use your pipeline to process samples of coastal phytoplankton across natural and human-induced gradients (water pollution, harmful algal blooms). By assembling and analysing transcriptomes from thousands of cells per sample, you will model dominant metabolic pathways and nutrient flows, and identify the involved genes. You will then proceed functionally characterize selected, understudied metabolic genes involved in carbon, phosphorus and nitrogen conversion by phytoplankton and other processes (DMS release, bioluminescence). This work will involve mutant complementation, heterologous gene expression, and/or gene knockout in laboratory models, such as E. coli, Synechocystis and Phaeodactylum.
Your work will introduce a powerful and reconfigurable analytic method to environmental microbiology. Your results will improve our understanding of physiology, interactions and metabolic variation in phytoplankton and other microbes, and have implications for coastal ecology, climate change and human health.
All doctoral candidates will enrol in the Graduate School of NOCS (GSNOCS), where they will receive specialist training in oral and written presentation skills, have the opportunity to participate in teaching activities, and have access to a full range of research and generic training opportunities. GSNOCS attracts students from all over the world and from all science and engineering backgrounds. There are currently around 200 full and part-time PhD students enrolled (~60% UK and 40% EU & overseas). Specific training will include:
- DropSeq microfluidics, device and method optimisation.
- Cultivation of algae.
- Collection of phytoplankton samples.
- High-throughput sequencing sample preparation.
- Transcriptome assembly and analysis (Cellxgene, Seurat, Cellenics).
- Modeling nutrient conversion by phytoplankton.
- Gene cloning, complementation & over-expression in bacteria and/or eukaryotes
- Networking, presentation of results, public outreach.
The student will be hosted at the School of Biological Sciences.
[1] Kolody BC, Harke MJ, Hook SE, Allen AE. 2022. Transcriptomic and Metatranscriptomic Approaches in Phytoplankton: Insights and Advances In: Clementson LA, Eriksen RS, Willis A, editors. Advances in Phytoplankton Ecology. Elsevier. pp. 435–485. doi:10.1016/B978-0-12-822861-6.00022-4
[2] Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. 2015. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161:1202–1214. doi:10.1016/j.cell.2015.05.002
[3] Vallejo AF, Davies J, Grover A, Tsai C-H, Jepras R, Polak ME, West J. 2021. Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering. iScience 24:102147. doi:10.1016/j.isci.2021.102147
