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  • Alex Cloherty

A lively soil

Way back in 2011, little baby teenage Alex was learning introductory microbiology at UBC Okanagan. To this day, I still remember my first-year, intro to biology professor explaining protists. And, I distinctly remember just not getting it. Amoebas were protists - I knew those ones from kids' science shows on the BBC - but they could also have shells? What? I just couldn't wrap my head around these guys.


And to be honest, I've largely avoided writing about protists because these guys have simply boggled my mind for the last decade. However, my interest in these puzzling protists was newly piqued in the last week.


It all started with a question about the differences between different types of microbes, which I wrote briefly about last week. Then I got to talking about soil microbiology with a few different people. Most recently, after hearing Danny Daniels' winning Climate Change Communicators pitch on composting, and Malaysia's top science communicator Daniel Nesan on soil health, I asked my green-thumbed horticulturist extraordinaire friend Robin about how she cares for her finicky poinsettias. She said that ideally, she would be feeding them a brew with a mix of fungi, bacteria, nematodes… and protists. And, fascinatingly, Robin cited a fact from her textbook Soil Science and Management: "I just learned that a lot of soil nitrogen is held in the bodies of bacteria, and only becomes available to the plants once they are eaten by protozoa! So soil with more life in it is also more nutritious and needs fewer inputs."


Those protists again! So, finally, a decade after my first attempt to learn about them, I've tried again - with more success this time. And I'd like to share with you what I learned.


After getting caught up on the scientific literature, I have some compassion for my seventeen-year-old self and her confusion. It's understandable - protists are indisputably a weird mix of little guys. As the authors of my main scientific source for today write, "Protists constitute the invisible majority of eukaryotes" - in other words, they include all "eukaryotes" - i.e. cells with a nucleus, that are not plants, fungi, or animals. Already, this is a strange way to define a group of organisms: by what they are not, rather than by what they are.


To make things even more complicated, there is seemingly no rhyme nor rule to the lifestyles of these highly varied microbes. Protists can be found everywhere on earth - from the soils to the seas, from the heat extremes of deserts and hot springs to the cold extremes of the poles, in acidic and basic environments, and in any other place that you can think of. They range in size from the smaller-than-bacteria "Picoeukaryotes" ('pico' being a measurement prefix that is smaller than 'nano' or 'micro'), to the larger-than-life Caulerpa, which are the biggest single-celled organisms known to us, to forming multicellular constructions of multi-meter-long brown algae. Protists can be 'naked' - i.e. have sort of flexible cells, kind of like our own human cells - or armoured, coated with a tough silicon shell. And depending on the protist, it might get its nutrients by photosynthesizing like a plant (i.e. 'phototrophic' protists, 'photo' meaning light and 'trophic' referring to eating), eating other organisms like us (i.e. 'heterotrophic' protists), or a mix of the two.


To put it simply, protists are a weird and wild bunch.


In fact, the word 'Protist' encompasses such a diverse bunch of microbes that they are actually now divided into many different sub-categories that span the whole tree of life. In the past, protists were grouped together kind of on the basis of being weird - again, being eukaryotes, but not being fungi, plants, or animals. Over the years, as we have learned more and more about these inarguable weirdos, the classification of protists has grown and changed with our increasing knowledge. There is actually a group known as the International Society of Protistologists that is dedicated to not only the study, but also the classification of these little guys, and you can follow the evolution of their thoughts about their study subject through the years by tracking successive publications from 1964, 1980, and 2012.





The tree of life, or more completely, the 'Phylogenetic tree of life', is a representation of how scientists think that all life on earth evolved. At the base of the tree is the one cell to rule them all. We call him/her/they Luca. No, really. The base of the tree represents the first cell that ever existed, from which everything else - all bacteria, plants, animals, fungi, protists, archaea, EVERYTHING - descended. Luca actually stands for "Last Universal Common Ancestor". Anyways, protists are all mixed up all over the place in the tree of life. You can see them represented in this particular tree as slime moulds, ciliates, and flagellates, for example. Fun fact plus nerd alert: I have this tattooed down my spine.



Like many things in science, the 'facts' have steadily grown closer and closer to the truth as our understanding deepens.


Now, we know that protists aren't actually one inter-related group on the tree of life. They actually form a lot of different branches on the tree, with names like Amoebozoa, Obazoa, Archaeplastida, SAR (thus named because it includes Stramenopila, Alveolata, and Rhizaria), and Excavata. Yes, scientists like complicated names. In other words, unlike bacteria, animals, and plants, protists don't actually share one common ancestor. As a result, some protists are more closely related to, for example, animals, than they are to other protists. https://www.micropia.nl/en/discover/microbiology/protists/ Technically, it's now more correct to refer to them more individually with the names of their branches on the tree of life - as Amoebozoa, Obazoa, or Excavata, for instance - but for ease of communication, many scientists still use the catch-all name Protist.


So far, the take-away messages from this article would be, 1) there is still a lot for us to learn about the highly varied microorganisms that comprise protists, and that 2) because of all that we are still learning about protists, this is a fast-moving field. But I would like to leave you with a third take-away message before we go, namely: although there is a lot that we still don't know about protists, we can be sure that they have massive impacts on the world around us.


For instance, if we start with a self-centered view, protists can very directly impact our human lives. Diseases like malaria, beaver fever, African sleeping sickness, and the nasty intestinal disease amoebiasis are all caused by protists - and more specifically by Plasmodium falciparum, Giardia duodenalis, and Entamoeba histolytica respectively. Other protists like the difficult-to pronounce Phytophtora infestans have had massive impacts on human food security. It was Phytophtora infestans that caused the 19th century Irish potato famine, and thereby indirectly caused millions of deaths and a great exodus towards, for example, Canada.


But there are also good guys! And, circling back to where we started, some of those helpful protists can be found beneath our feet. In the soil.


Depending on the lifestyle of soil protists, they can have different effects on the soil - but whether they are phototrophs (using the power of the sun to make their own food) or heterotrophs (eating up stuff that they can predate or scavenge), all can have a major positive role on soil ecosystems.


Let's start with the phototrophs. Although phototrophic protists are less commonly found on land than sea, soil phototrophic protists likely have some impact on their earthy environment. As these authors conservatively put it, phototrophic protists' "contribution to the soil organic carbon input is non-negligible". In other words, we know that phototrophic protists help fix some carbon, but in most soil ecosystems, we don't know exactly how much. This is one of those areas of protist research where we simply don't know much yet.


What we do know, though, is that heterotrophic protists have a great impact on soil fertility, as Robin's quote at the beginning of this article alluded to. Heterotrophic protists can be predatory, hunting anything from bacteria to fungi, or even small animals or other protists in the soil. By eating up these other microbes, and then pooping out the waste, they basically act as fertilizers of the soil. The nutrients contained within the bodies of the other microbes are pre-digested by heterotrophic protists, and then let loose into the soil for plants to use for their own growth.


By preying on other soil microorganisms, protists also help keep the levels of those other soil microbes in balance. They act as a cougar does in the mountains of British Columbia: ensuring that the deer, rodents, and Chihuahuas don't multiply beyond what the environment can sustain. Predators like protists, cougars, and lions are essential in natural environments for keeping a healthy balance of their prey in the ecosystem.


Finally, even upon their death, protists contribute to the fertility of soils. Some protists, as I mentioned earlier, can grow tough shells made of silica or calcium carbonate. Upon the death of these protists, the silicon or calcium in their shells will stay in the soil - where plants can suck it up (sometimes through the help of fungi!). Plants need micronutrients like silicon and calcium to grow, and without the build-up of decomposing protists in the soil, they would be hard-pressed to get enough of those two particular elements.


As with my recent article on forest fungi and the dance of carbon sequestration, I have to acknowledge here that this story is unquestionably incomplete. We simply don't know enough yet about protists to have the full picture about how they contribute to the lives of our soils. But in the end, that is the beauty of science. Science is but a process, a way of thinking that we scientists use to dive into the data, argue it out, and, slowly and carefully, come to a consensus that approximates the Truth to the highest possible degree. As new data will come up, our idea of the Truth will shift accordingly. It can be confusing - and the case of protists is a perfect example for this. As we slowly find out more about these microbes, our understanding of them must naturally change with the newest, best data, to our newest approximation of Truth. With protists, as with, ahem, viruses.


Until next time,

~ Alex

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