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B411: Shining a light on microbial dark matter: a role for the forgotten B vitamins in marine algal communities? (Lead Supervisor: Alison Smith, Plant Sciences)

Supervisors: Alison Smith (Plant Sciences) and Katherine Helliwell (Marine Biological Association of the UK

Importance of the area of research:

A significant proportion of microbial diversity is inaccessible to biological experimentation due to our inability to culture such taxa. This research project has potential to bring ‘unculturable’ microeukaryotes into the laboratory by examining the importance of largely ignored organic micronutrients for their growth. In doing so the research will not only provide essential insight into the basic biology of some of these elusive microbes, but also advance our understanding of algal cofactor requirements, and thus fundamental aspects of eukaryote metabolism more broadly.

Project summary:

This project will investigate the exchange of B vitamins between marine microbes, providing insights into what holds communities together, and offering the possibility to culture the unculturable – the so-called ‘microbial dark matter’, revealed by environmental molecular surveys. Metagenomics datasets from various marine and fresh-water environments will be analysed to establish which species are capable of B-vitamin biosynthesis, and which are likely auxotrophs (requirers). The bioinformatics approach will be complemented with experimental mesocosm work to compare the effect of B vitamin fertilisation on microeukaryote growth (community composition and productivity) in natural samples. Finally, auxotrophic algal will be generated by CRISPR/Cas9, and then tested for their ability to interact with marine bacteria that can provide the micronutrients.

What the student will do:

There are three strands to the project

1) Metagenomic and metatranscriptomic analysis of data sets such as the time series from the Western English Channel Observatory (http://www.westernchannelobservatory.org.uk/), and those from the Tara Oceans Project will be mined for genes involved in B vitamin biosynthesis, uptake and use, and correlated with the species composition to establish patterns of requirers and producers.

2) Bioassay bottle incubation experiments of uncultured taxa will be carried out in which natural environmental samples, from both freshwater and marine locations, are amended with different B vitamins. Microbial abundance and community composition will be compared before and after nutrient amendment in the different treatments.

3) CRISPR/Cas9 will be used to generate auxotrophic mutants in a model marine alga, targeting known B vitamin biosynthesis genes. RNAseq would be carried out to determine changes in gene expression when the mutants are grown with B-vitamin producers and compared with genes identified in part 1.

Please contact the lead supervisor directly for further information relating to what the successful applicant will be expected to do, training to be provided, and any specific educational background requirements.

References:

Croft MT, Lawrence AD, Raux-Deery E,  Warren MJ, Smith AG. (2005) Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438: 90-93

Helliwell KE, Collins S, Kazamia E, Purton S, Wheeler GL, Smith AG. 2015. Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution. The ISME journal 9: 1446-1455., doi: 10.1038/ismej.2014.230

Kazamia E, Helliwell KE, Purton S, Smith AG (2016) How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes. Ecol Lett, 19: 810-822; doi: 10.1111/ele.12615

Follow this link to find out about applying for this project.

Other projects available from the Lead Supervisor can be viewed here.

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