Harvesting the Photonic Properties of Self-Organising Bacteria Colonies

Lead Research Organisation: University of Cambridge
Department Name: Chemistry


The overarching aim of the project is to investigate and utilise the photonic properties of colonies of a novel type of Flavobacterium (strain IR1), which self-assembles into photonic crystals. The strain is a rod-shaped marine bacterium with a diameter of roughly 400nm, that packs in colonies with a tight hexagonal lattice. The colonies appear bright, sparkling green since a part of the visible spectrum is strongly reflected by this organisation. The effect can be described by photonic crystal theory and does not involve pigmentation. In particular we wish to understand:
(i) how light scattering relates to the structural organisation (periodicity, regularity) such that we can screen them optically;
(ii) how genetic modifications change the optical properties and reveal the important genetic pathways for colouration;
(iii) how to fixate the bacterial colonies while retaining their optical properties.

We have identified a wide range of methods to reversibly and irreversibly change organisation (and hence colour) of the living colonies through growth conditions and many types of external stimuli. The studentship will use our well-established characterisation methods and knowledge to explore how this bacterial system can be modified towards controlled photonic applications. This will involve a wide range of traditional microbiology tools ranging from screening of growth conditions to DNA genetics via CRISPR.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011194/1 01/10/2015 31/03/2024
2110570 Studentship BB/M011194/1 01/10/2018 30/09/2021 Laura Caton Alcubierre
Description Edwin Leong Travel Grant, Hughes Hall
Amount £500 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 10/2021 
End 10/2021
Description Research Visit Grant
Amount £3,000 (GBP)
Organisation Microbiology Society 
Sector Learned Society
Country United Kingdom
Start 03/2022 
End 06/2022
Description Collaboration with Dr. Raymond Staals - CRISPR Cas tools 
Organisation Wageningen University & Research
Department WU Agrotechnology & Food Sciences
Country Netherlands 
Sector Academic/University 
PI Contribution Create new structural colour Flavobacterium IR1 mutants based on tailor-made gene knockouts using SIBR-Cas technology and their further optical characterization
Collaborator Contribution Development of a novel CRISPR Cas gene editing system, SIBR-Cas, compatible with our model bacteria organism
Impact Research Visit Grant Award to have a hands-on approach to understanding the design and technology available in the collaborator's laboratory. The introduction of CRISPR Cas technology has a major impact on the understanding of the molecular genetics of structurally colour in Flavobacteria. Publication in progress
Start Year 2021