Colour in the Microbial World

Bacterial Pigments, Survivability, Implications, and Applications


Colour in the microscopic world differs greatly from colour in the macroscopic world in its purpose. In the macroscopic world it is used for camouflage by many animals, to show off to potential mates by birds, and to express ourselves as humans. But most microbes cannot see, and those that can are pretty bad at it, so their colour is not used for any purpose at all, it’s just a side effect of the functionality of various pigments they use¹. For example, autotrophic microbes are green because of the chlorophyll they use in photosynthesis to create their food; other microbes are yellow, orange, or red, due to the carotenoids they use to protect against environmental stresses¹. Think of the fact that most plants are green because of the chlorophyll they use to perform photosynthesis: that’s analogous to the way all colour is produced in the microbial world.

Carotenoids protect against environmental stresses

To begin, carotenoids are the major class of pigments that protect against environmental stresses such as UV radiation, aid in the reparation of cellular damage, and are involved in energy-harvesting². They are accessory pigments coloured yellow, orange, or red that are present in microbes and some plants¹.

Some bacteria like Haematococcus and Euglena sanguinea are normally green due to their chlorophyll but turn red by producing astaxanthin, a carotenoid, in excess UV light¹. While the former actually turns into a near-indestructible cyst, both produce this pigment because it helps protect them from the damage that UV radiation can do, almost like microbial sunscreen¹. Extremely halophilic microorganisms (microorganisms that thrive in very salty environments), use the carotenoids bacterioruberin and salinzanthin to help them survive in this hostile environment². For example, bacterioruberin is largely responsible for the red colour of the Halobacteriacaea family of archaea².

Likewise, carotenoids such as myxoxanthophyll and echinenone are present in cyanobacteria such as Aphanothece halophytica, Cyanothece, and Halothece which live in the upper layers of saltern sediments, colouring them yellow or orange². In the Antarctic, all microorganisms are specially adapted to the harsh freeze-thaw cycles and excessive UV radiation that the environment brings, including the use of carotenoids³. Most bacteria in the environment are Gram-positive, indicating thick cell walls, and are spore-forming, but the ones that produce carotenoids largely do not fulfil either of these qualifications, indicating that the carotenoids are their main adaptation³.

It has been shown that carotenoids play a role in the stabilization of cell plasma membranes which has been suggested as a possible explanation of why they enhance survivability of these bacteria in freeze-thaw cycles³. The results of this study also showed that carotenoids may confer resistance against UV damage in this environment by mitigating damage caused by toxic oxygen species³. Overall, it is clear that carotenoids are great survivability enhancers in a range of extreme environments. Bacteria and archaea that produce these pigments are present in environments of high salinity, high UV radiation, and extreme temperatures.

Other pigments also enhance survivability

Other microorganisms use pigments to enhance their survivability by inhibiting or killing their competition. For example, Pseudomonas aeruginosa produces a killer pigment that eliminates certain Gram-negative bacteria in its immediate environment, giving it a growth advantage⁴. This pigment is called pyocyanin and kills by generating reactive oxygen intermediates which lethally alter membrane permeability and produce chromosome breaks⁴. Since the pigment targets Gram-negative bacteria other than itself, and P. aeruginosa is also Gram-negative, this means that over time it can become the dominant bacteria of its kind in its immediate environment⁴.

Another bacteria that enhances its survivability by killing its competition are the violacein-producing Duganella bacteria, notably the relatively newly discovered strains inhabiting the rhizospheres (the regions immediately surrounding a plant’s roots) of wild and cultivated olive trees in Southern Spain⁵. Violacein, in contrast to pyocyanin, inhibits Gram-positive bacteria but has little to no effect on fungi and Gram-negative bacteria⁵.

These bacteria are certainly not the only ones that produce violacein though; many other Gram-negative bacteria do too, likely because of its evolutionary advantage as a survivability enhancer⁵. However, these bacteria are notable for producing violacein even without favourable conditions, unlike many other violacein-producing species⁵. This is important because violacein is of interest in biotechnology due to possible uses in dermatological and oncological clinical applications⁵.

Another bacteria producing a lethal pigment is Vibrio sp. DSM 14379⁶. This bacteria was proven through a study of it in co-culture with Bacillus sp. to use its red pigment as an antibacterial weapon⁶. Notably though, the bacteria, an isolate of the pigment, and a non-pigmented mutant of the bacteria all had antibacterial activity, meaning that while the pigment is antibacterial, it is not the only such feature of the bacteria⁶. These three bacterial examples are not the only ones of colour as a side effect of a killer pigment in the microbial world. The lethal properties of many microorganisms is part of the reason microbial communities are constantly changing⁴.


The most well known use of pigment in the microbial world is in photosynthesis. This is because since we were in the third grade our teachers have explained, in third-grader-friendly terms at that point of course, that plants are green because of a chemical that helps them make their own food, in a process called photosynthesis. Well before plants though, microbes were doing the same thing; in fact, today’s plants gained their ability to photosynthesise because their microbial ancestors absorbed cyanobacteria⁷. Early microbes, especially cyanobacteria, evolved this pigment, which absorbs red and blue wavelengths for energy to produce carbohydrates as food, and reflects green wavelengths, hence its green appearance¹.

Cyanobacteria is also known as blue-green algae though, and what is less well known is the origins of the ‘blue’ part of that name. This comes from a cyan pigment in these bacteria called phycocyanin, not to be confused with the killer pyocyanin discussed earlier, which is an accessory pigment that helps boost photosynthesis by absorbing more wavelengths¹. This means that the cyanobacteria can survive and even thrive in environments where the water above them has already absorbed or diverted most of the red and blue wavelengths that chlorophyll uses, thereby maximizing the survivability of cyanobacteria¹, and everything above them in the micro- and macroscopic food chain⁷. Billions of years ago, these organisms caused the Great Oxidation Event, a mass extinction that led to the world as we know it now⁷. The importance of the green and blue photosynthetic pigments is incredible. It is the reason we exist.


To conclude, microbial colour is clearly not for aesthetics, but for survival. It is a fortunate side-effect of the pigments they use to defend themselves against the environment, kill their competitors, and create food for themselves. However, microbial colour is also useful to humans, in our search for life beyond Earth. Carotenoids in particular could be excellent biomarkers for use in detecting life on other planets². Alongside some other selected pigments, they could be tested for using a technology like Raman spectroscopy that can be easily miniaturized for use on a Mars rover, for example⁷. This means that the implications of colour in the microbial world are vast, even though the producers of the colour themselves are not very good at seeing it.


  1. Green, Hank., Andrew Huang, Matthew Gaydos, Mark Olsen, James Weiss, Deboki Chakravarti. The Colours of the Microcosmos. Journey to the Microcosmos. October 28, 2019. YouTube video. 9:37.
  2. Jehlička, Jan., Howell G. M. Edwards, Kateřina Osterrothová, Julie Novotná, Linda Nedbalová, Jiří Kopecký, Ivan Němec, & Aharon Oren. “Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology.” Philosophical Transactions: Mathematical, Physical, and Engineering Sciences 372, no. 2030 (December 13, 2014): 1-17
  3. Dieser, Markus., Mark Greenwood, & Christine M Foreman. “Carotenoid Pigmentation in Antarctic Heterotrophic Bacteria as a Strategy to Withstand Environmental Stresses.” Arctic, Antarctic, and Alpine Research 42, no. 4 (November 2010): 396-405.
  4. Benathan, Isaiah A., & Marion Saccardi. “Killer Pigments in Bacteria: An Ecological Nightmare.” The American Biology Teacher 62, no. 9 (Nov-Dec, 2000): 649-651.
  5. Aranda, Sergio., Miguel Montes-Borrego, & Blanca B Landa. “Purple-Pigmented Violacein-Producing Duganella spp. Inhabit the Rhizosphere of Wild and Cultivated Olives in Southern Spain.” Microbial Ecology 62, no. 2 (August 2011): 446-459.
  6. Starič, Nejc., Tjaša Danevčič, & David Stopar. “Vibrio sp. DSM 14379 Pigment Production–A Competitive Advantage in the Environment?” Microbial Ecology 60, no. 3 (October 2010): 592-598.
  7. Green, Hank., Andrew Huang, Matthew Gaydos, Mark Olsen, James Weiss, Deboki Chakravarti. How Cyanobacteria Took Over the World. Journey to the Microcosmos. February 24, 2020. YouTube video. 12:56.

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