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We see the colors of the microcosmos every single week, but let's stop and ask why our some microbes are bright green, while others are a golden brown.

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This amoeba is making its home out of a drop of water, taken from a larger sample and then sandwiched between a glass slide and a coverslip before being placed onto a microscope, oh so carefully.

And perched above, is us, peering down through the lens to see a magnified version of its daily life. And coming from underneath the slide is white light, often passing through microbial bodies so that they appear transparent, like moving outlines.

But white light is a fracturable thing, made up of different wavelengths that can interact in their own particular ways with the world they encounter, absorbed by some materials and reflected by others. For wavelengths that lie in the visible spectrum, that reflected light gives us color. Like the inside of this ciliate, its clear body rendered kaleidoscopic following a colorful meal.

We often link color to perception: how we see it, how it makes us feel, how we pick and choose our favorites. Colors signal, not just like traffic lights, but in nature. Feathers that attract, bright markings that warn, and patterns that camouflage.

But setting aside our own voyeurism, there are no complex eyes on you when you’re microscopic. The colors that emerge are entirely incidental, in a sense stripped down to their fundamental natures: the product of light absorbing and reflecting at different wavelengths, these colors do not exist to communicate or signal, they’re just the color they are, and when we find beauty here, it’s not because there’s any advantage to that beauty, it’s just luck. Maybe the easiest color to translate from what we see on a daily basis to what we observe under the microscope is green, the color of photosynthesis, and thus of many plants and photosynthetic microbes.

This is, of course, not a coincidence, but a monochromatic pattern of evolution and endosymbiosis, the product of an ancient cyanobacterium that made its home in a plant and brought the green pigment chlorophyll along for the ride. When light hits chlorophyll, the molecule absorbs energy from the red and blue wavelength, exciting electrons and powering the reactions that produce storages of chemical energy. What remains to the observer, to us, are the green wavelengths that reflect.

Other photosynthetic microbes rely on chlorophyll as well, sometimes containing different forms of the pigment that allow them to access other wavelengths of light. While chlorophyll is essential to cyanobacteria, the “cyano-” in their name implies another important color: blue. This is the product of phycocyanin, which—combined with chlorophyll—gives the organisms that color that makes them often known as “blue green algae.” Phycocyanin is an accessory pigment, it’s nature’s way of hedging its photosynthetic bets.

Relying strictly on chlorophyll, after all, would restrict what kind of light an organism can take advantage of. For cyanobacteria, this can be particularly problematic if that light gets absorbed by water or by other organisms above them. So it relies on assemblies of phycocyanin to absorb additional wavelengths, creating alternate sources of excitation energy for photosynthesis.

But there are, as always, exceptions. Other microbes use a class of molecules called carotenoids as accessory pigments, which bring pops of yellow, orange, and red. Like chlorophylls, these are a type of chemistry that we’re familiar with from plants and vegetables we see everyday, like the orange carotene of carrots.

Translate them into the microbial world, and you get diatoms like this one, its beautiful golden brown color derived from the carotenoid fucoxanthin. But carotenoids can serve other purposes, like the red pigment astaxanthin, which we see on a more regular basis in the pinkish color of shrimp. The most plentiful source of astaxanthin is this microscopic Haematococcus, which we found in a cemetery birdbath.

When conditions are good, the Haematococcus is green. But if the sun becomes too intense or nutrients become scarce, they form protective cysts and produce large amounts of astaxanthin, which shields the cells from harmful ultraviolet light. These cysts are almost indestructible, valiant against chemical and mechanical attempts to break them until conditions return to normal, allowing the Haematococcus to do the same.

Euglena sanguinea use astaxanthin to protect themselves as well, rapidly reddening in response to large amounts of light to protect themselves from the dangerous rays of the sun. These pigments have implications beyond their microbial uses or even their visceral beauty. Scientists have converted pigments like phycocyanin into a fluorescent tool that allows us to map out the interiors of other cells, and Haematococcus and diatoms are objects of study for the potential health benefits their carotenoids may confer.

Their colors are observed and utilitarian in our hands, guiding and identifying and indicating. Earlier, we stated a simple premise of the microcosmos: that its inhabitants live in a world largely unobserved. We made that statement while casually setting aside the obvious: that you and I, we are here, watching these microbes, both colorful and not.

They did not evolve to be seen, in fact we went almost our entire history without ever seeing one, but now they have certainly captured our attention. These colors developed long before we were around to notice them, independent of our preferences and our needs. But we have bodies and minds that have evolved to take note.

Even the examples we’ve highlighted today emphasize our own observational bias, focusing on wavelengths that are visible to us as a species even while light extends far beyond that spectrum. Color is, to us, often subjective, but it’s a product of light of physics and of chemistry that has impacts at all scales. Even if the way we process it varies, the underlying physics does not.

What the microcosmos helps us understand is that there is more to color than what we see, that our perception of it is only one facet of what it means to live in an illuminated world. Thank you for coming on this journey with us as we explore the unseen world that surrounds us. Journey to the Microcosmos is a production of Complexly which is a company that makes stuff for YouTube and right now at Complexly we’re trying something really new.

We’re trying three new things. It’s a pilot season. We’re launching three brand new shows, each on their own channel and each will run for three episodes.

And then we’ll decide if any of those will continue on. Now, we love all of these ideas but we can’t make all of them happen so we’d love your feedback and what you think should continue. Please check them out and share your thoughts.

And thank you to all of these people who support this channel on Patreon so that we can continue making these very cool videos. If you’d like to join them, and we would love it if you did, you can check us at And if you want to see more from our Master of Microscopes, James, check our Jam and Germs on Instagram.