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Know your microbes: Round things with motion inside

Identifying amoebae in a soil sample can be quite easy. It can also be tricky. For those new to soil microscopy, it’s easy to imagine all sorts of objects – spores, cysts, mineral particles, random bits of decomposing material – are amoebae, because they may resemble in some way the protective shell, or “test,” that lots of soil amoebae build and live in.


The same thing often happens with “naked” amoebae. In the video below, you’ll see two examples of a particular type of naked amoeba, those that form into spherical shapes. And as you might expect, spherical amoebae are not the only round objects commonly found in soils and composts – not even the only round object with motion visible inside.



It may all seem confusing and overwhelming, but only at first. There are distinct differences between these objects, and they’re easy to notice once you’ve trained your eye. Notice the ciliate cyst’s larger size, its not-perfectly-round shape, and its wall structure. But there’s also the movement – subtle, but distinct. You can see there’s a single, solid object just slightly rolling back and forth. By comparison, the movement inside the amoebae looks distinctly like a liquid flow. That’s the movement of vacuoles, organelles and smaller objects floating around in the cytoplasm of this single-celled organism.


Why is it so important to know the difference? Because these microbes can indicate different soil conditions. Naked amoebae are usually found in conditions of high biological activity, like fresh compost or high-quality soil in springtime. A ciliate in the process of encysting or emerging – we can’t say which, without observing it until it emerges or goes completely dormant – can suggest a couple of things: either soil conditions are becoming more aerobic and therefore improving (because it’s going dormant), or oxygen levels are dropping (because it’s emerging), which is bad for plants and their aerobic microbe friends.


And of course there’s also the question of nutrient-cycling activity, a necessity for plant health. Amoebae and ciliates both consume bacteria, and therefore cycle nutrients; only amoebae do so in an oxygen-rich environment.


But also keep in mind that, in order to decide what is happening, you don’t necessarily need to continue watching that one cyst. Instead, look around at the other clues: What’s the moisture level of this soil? The color? What other organisms currently appear active? It takes a bit of training to confidently assess the condition of a soil from the microbes that appear, or don’t appear. But in most cases, it’s a lot like these round objects – confusing at first, but with a little practice, not too difficult to discern.

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