Genetic insights shed light on how and where bacteria form brightly coloured colonies without pigments

Genetic insights shed light on how and where bacteria form brightly coloured colonies without pigments

Iridescent bacteria even found in deep ocean

Some bacteria form colonies that display striking, reflective colours. New genetic insights into the formation of such colours allowed an interdisciplinary, international team of researchers to identify the environments and bacterial groups in which these colours are found. Doing so, the team has made a start in understanding the function of these colours in bacteria. The findings, which are published today in the scientific journal Proceedings of the National Academy of Sciences (PNAS), might have implications for the development of new innovative materials that use bacteria to replace non-sustainable dyes.

The striking, vibrant colours that we know from butterfly wings and peacock feathers are not the result of dyes or pigments. Instead, they are created by tiny, ordered structures that interact with light, creating a vibrant display of hues that is often perceived as iridescence (changes in colours depending on the angle of view or illumination). Such 'structural colour' is widespread in nature, and also exist in bacteria.

The same Petri dish containing the marine bacterium Muricauda ruestringensis, viewed from three different angles. Image: Colin Ingham, Hoekmine BV

Structural colour is not displayed by individual single-cell bacteria, but by colonies of certain bacteria. Previous studies showed that specific genes involved in motility allow these bacteria to precisely align and form highly structured colonies that are able to produce iridescence.

The exact function of structural colour in bacteria, as well as the genetics behind them, up to now remained largely unknown. In other life forms, structural colour plays a role in display, camouflage or protection from light, amongst others.

Specific genes

To gain more insight into the genetics behind structural colour in bacteria, the first step the researchers took was to collect 87 structurally coloured bacterial isolates, alongside 30 closely related non-iridescent strains. They then determined the sequence of the DNA of these bacteria. By comparing the DNA-sequences of the different strains, the researchers found that the bacteria that exhibited structural colours shared specific genes that were absent in non-iridescent bacteria, even though the iridescent bacteria belonged to very diverse and different bacterial groups.

Colonies of the marine bacterium Marinobacter algicola HM-28' showing bright structural colours. Image: Colin Ingham, Hoekmine BV

"This suggested that genes leading to structural colour may be shared between bacteria that are not directly related,", says Bas Dutilh, visiting professor at Utrecht University and professor of Viral Ecology and Omics at the University of Jena. "Being able to trace the evolution of this colony characteristic, which is so striking to us, may help us to understand its function in bacteria." Interestingly, some of the genes that were associated with structural colour in bacteria also contribute to the phenomenon in butterfly wings.

This really shows the power of machine learning to predict biological functions from very complex genetic data.

Machine learning

Combining the genetic insights with the data of the 117 DNA-sequences, the researchers also trained a computer model to be able to predict whether bacteria would display iridescence based only on their DNA-sequence. They used a technique called machine learning, a form of artificial intelligence that uses mathematical models to allow computers to learn without giving them direct instructions. "The machine learning model unexpectedly also predicted structural colour in new groups of bacteria, which we confirmed in the lab. This really shows the power of machine learning to predict biological functions from very complex genetic data", says UU-researcher Aldert Zomer.

Distribution of structural colour

With the machine learning model in hand, then-PhD student Bastiaan von Meijenfeldt screened and analysed 250,000 publicly available bacterial DNA-sequences and 14,000 metagenomes, complete sets of DNA-sequences found in environmental or clinical samples. Using this data, Von Meijenfeldt set out to map the distribution of structural colour in the bacterial tree of life, and across habitats.

The researcher found that bacteria that live in or on hosts, such as our gut bacteria, almost never showcase structural colour. In contrast, structural colour was predicted to be abundant in bacteria that live in marine waters and lakes, and in interfaces between surface and air such as on glaciers and in intertidal areas. The latter finding could suggest that the function of the structuring in these bacterial colonies is indeed to interact with light. However, this does not always seem to be the case.

Image: Colin Ingham, Hoekmine BV

Von Meijenfeldt: "We were very surprised to see that the abundance of genes involved in structural colour increased in deeper waters, where light does not penetrate. This is not what you would expect if breaking of light plays a role in bacterial structural colour. We did find support for a hypothesis that bacterial structural colour is associated with floating particles at these dark depths, which potentially could mean that the structuring has other advantages and structural colour in this case is a byproduct."

Interdisciplinary collaboration

The study was a highly interdisciplinary collaboration. The researchers from Utrecht combined their expertise on genomics, the field that focuses on the study of the complete set of DNA of organisms, and machine learning with Henk Bolhuis's (NIOZ) knowledge of marine microbes. Richard Hahnke (Leibniz Institute DSMZ) contributed rare bacterial isolates and Silvia Vignolini (University of Cambridge and Max Planck Institute of Colloids and Interfaces) performed experiments that proved the colony structuring.

The new fundamental insights in structural colour in bacteria might serve as the foundation for the future development of innovative materials.

Colin Ingham, founder of biotech company Hoekmine BV and initiator of the study, contributed their research and strain collection related to structural colour. Ingham explains the potential value of structurally coloured bacteria for biotechnology: "The idea is to create colour from non-harmful bacteria to replace dyes that are often polluting and do not suit a sustainable economy". The new fundamental insights in structural colour in bacteria might therefore serve as the foundation for the future development of innovative materials.

Publication

Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype
Aldert Zomer, Colin J. Ingham, F. A. Bastiaan von Meijenfeldt, Álvaro Escobar Doncel, Gea T. van de Kerkhof, Raditijo Hamidjaja, Sanne Schouten, Lukas Schertel, Karin H. Müller, Laura Catón, Richard L. Hahnke, Henk Bolhuis, Silvia Vignolini, and Bas E. Dutilh
PNAS, 11 July 2024. DOI: https://doi.org/10.1073/pnas.2309757121

This research was supported by a ZonMW Enabling Technologies Hotels grant (40-43500-98-4102/435004516).