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When you first start looking through a microscope at microorganisms, it’s very obvious that each little cell is its own thing.

But then, as time goes on, and you start to understand their relationships and their dependence on each other, and also everything’s dependence on them, each microbe starts to feel like a piece of some much broader, even global organism. And of course, species of all kinds and sizes have their ecological impacts.

And this actually becomes much more obvious when you make that ecosystem less global by, say, putting it in a little box. And you might have seen one of these boxes recently...maybe in your home, or at a restaurant, or the doctor's office. We are talking, of course, about aquariums.

This tank is just one of those tanks at a mall aquarium store. It's got some reefs and some fishes swimming around, living in full display for people passing by. But just give it a moment...just a few seconds.

And there. That is the disembodied hand of an aquarium shop worker who probably went to work expecting the usual aquarium shop business, until James, our master of microscopes, came in and asked if he could please have some water from the tank. Science is always a team effort, and fortunately, this shop worker was a willing collaborator, searching around for biofilm and other bits from the tank in response to various requests thrown his way.

Of course, there are plenty of macroscopic animals in the aquarium to admire. Have you ever wanted to see what a starfish looks like when you're really up close? Yeah.

I mean, of course you have. But the real focus of this expedition wasn’t the fishes or the large invertebrates that we can clearly see with our own eyes. What we want to see is what else is in that tank.

This question is actually pretty important for any aquarium you might want to set up at home. Sure, you might be most excited about the fish. But fish waste is full of ammonia, which can accumulate to toxic levels if left unchecked.

In nature, microbes play an essential role in the nitrogen cycle, including taking extremely stable atmospheric nitrogen and turning it into nutrients like these Trichodesmium do, or by consuming nitrogenous waste. To make sure that aquatic ecosystems have the same cleaning abilities built in, people install bio filters that contain nitrogen-consuming bacteria in their aquariums. It’s sort of like building wastewater treatment into the artificial ecological neighborhood.

And beyond the basic care of keeping tanks, scientists have been studying the microbial composition of aquariums to explore all sorts of questions. One group collected tank water from seven Rhode Island pet shops to examine the diversity of microbial communities between them, finding potential sources of pathogens that might require further study. Another group observed that freshwater aquarium bio filters are dominated more by ammonia-oxidizing archaea than they are by bacteria.

There are, of course, also large aquariums. Like very large. So large you have to drive out to visit them so you can stand in awe.

And yes, scientists have been studying the microbiomes of these large tanks too. This includes a study of the Ocean Voyager exhibit in Georgia, one of the largest aquariums in the United States, where 14 months of tracking the microbial community of the exhibit revealed a surprising dynamic and changing community despite the relative stability of the water itself. Just for reference, the Ocean Voyager exhibit contains about 6.3 million gallons of artificial seawater, and it houses very cool, odd animals including the blacktip reef shark, the longcomb sawfish, and the porcupine ray.

In contrast, the mall aquarium has a lot less water in it, and the fish are not quite as varied. But fortunately, we don’t need millions of gallons of water to find fascinating ecological diversity. We just need a microscope.

So we were pretty impatient to see what was in that carefully obtained, mall tank water. One of the first organisms that caught our attention was foraminifera, this kind of conch shell-looking thing. Foraminifera, or forams for short, are protists, and they can be found living all over the ocean, both in terms of depth and geographical location.

There are around 4,000 species of forams around the world, of which we found only a handful in this sample. Their shells come in different shapes and are made up of different material depending on what species they are. Now forams may look innocuous, but they've been around for over 500 million years.

And with all those forams living and dying over that long period, their shells have built up on the deep ocean floor, accumulating to the point where in death, they’re practically a geological entity. In turn, the chemical composition of their shells has helped us better understand how our oceans and climate have changed over millions of years. But while we were watching our new foram friends, something else came along.

You can see it here, that long, thin line snaking between the magnified sand grains. It looks like a worm, but we think it’s actually a Tracheloraphis, and I do not know if we’re pronouncing that correctly, a mysterious single-celled organism. It's difficult to find a lot of information on Tracheloraphis, probably because it’s been difficult to culture in a lab for further study.

Even filming it turned out to be a challenge. The slide we were watching it on had too much sand and debris in it for us to get a good recording. So we tried moving it over to a new slide, taking off the coverslip and using a micropipette to grab it.

Except that once we removed the coverslip, that little guy just disappeared! It took 3 hours to find it and prepare it in this sample, but it was worth it for this close up view of just how weird this unicellular organism is. What else did we find?

An amoeba spreading against microbial fauna as its own internal crystals sparkle, like an opening in tree branches that give way to a galaxy. There also long cyanobacteria stalks, the idling dinoflagellates, the stunning trichodesmium filaments, and this ciliate who seemed to not quite know what it wanted to be doing. I know that feel, buddy.

And all of this from some scoops taken from a mall aquarium...all of these organisms make those clear boxes of glass not just a storage tank for some pretty fish, but a living ecosystem with millions of organisms all depending on each other to turn the basics of chemistry into the majesty of life. Thank you for coming on this journey with us as we explore the unseen world that surrounds us. And if you like this show, who you really want to thank are these people whose names are on the screen right now, our patrons on Patreon who make it possible for us to search through grains of sand for hours so that we can get a good picture of a weird microbe.

Thank you for indulging with us and allowing us to indulge in this curiosity. If you want to see more from our Master of Microscopes James, check out Jam & Germs on. Instagram.

And if you want to see more from us, you can find us at