The many roles of protists in soils

By Dr. Enrique Lara, University of Neuchâtel, Switzerland

This is part two in four part soil protist series!  Part 1 can be read here.


Protists are extremely diverse in soils, often reaching thousands of species of protists and fungi per gram. If we bring these numbers to our scale of perception, this means that a little piece of soil the size of a fingernail hosts a number of species comparable to the diversity of insects in a hectare of tropical rainforest! Like in the jungle, the different organisms play various roles in the soil ecosystem. Globally, these roles can be divided in three great categories: osmotrophs, phototrophs and phagotrophs.


Figure 1: This unidentified amoeba is one of the members of the extremely diverse protist community inhabiting the soil of a common indoor flower pot; new species can be found even in the least exotic environments! This species feeds on yeasts and bacteria.

Osmotrophs absorb their food from the environment; they are unable to engulf preys. They play a fundamental role in the decomposition of dead organic matter produced by plants. Mostly fungi take this role, but they are not alone! Another very common group of soil osmotrophs is the oomycetes, which closely resemble fungi but are now classified within the stramenopiles- a group very distant to fungi together with many algae such as the marine kelps! Some organisms evolved from photosynthetic ancestors to live in the absence of light and became secondarily osmotrophs, like the green alga Polytomella. Osmotrophic organisms often tend to become parasites during evolution; they start the evolutionary process as mostly free-living organisms that infect occasionally any potentially weakened host. Then, they become gradually more and more specialized and virulent. Many species of fungi and oomycetes are well known plant parasites, and are responsible for huge economic losses every year. Others infect animals (including humans) and even other fungi! Other groups are entirely parasitic such as the Phytomyxea (plant parasites) and the Apicomplexans (animal parasites, including amongst others the agent of malaria Plasmodium falciparum), which can be extremely abundant and diverse in soils. However, osmotrophs can also become Mr. Niceguy and collaborate with plants: mycorrhiza are the most widespread and famous example.


Being a phototroph, obtaining energy from the sun like a plant, in soils may seem contradictory; however, phototrophic organisms are numerous and diverse as well. Logically, they are limited to the upper part of the soil that is reached by light; they are responsible (together with mosses and cyanobacteria) for the formation of so-called cryptogamic crusts, which are common in deserts and high altitude soils. Some of these groups are well known in lakes and rivers (like diatoms, green algae, xanthophytes), but most often species are specific to soils as they went through specific adaptations to be able to colonize these environments.


Many protists in soils are phagotrophic, which means that they prey on other organisms through phagocytosis (just like the macrophages of our immune system). Bacteria are a common food source for them, and it has been shown that predation by protists is the main source of mortality for soil bacteria. By eating these preys, nutrients are released and taken up by plants; it has been shown that this phenomenon, coined the soil microbial loop, is key in driving plant productivity. However, all bacteria are not equally preyed upon by protists, and food preferences vary drastically even between closely related protist species. On the other hand, bacteria are by no means defenceless and produce secondary metabolites that can kill protist predators. This make trophic interactions between protists and bacteria extremely complex. But bacteria are by no means the only prey of protists. Fungi are also consumed, and some species of ciliates possess a cytostome (=cell mouth) that prevents them from eating anything else; they are simply unable to consume bacteria! Others are top predators and will feed only on other protists. Some, like the tiny shelled amoeba Cryptodifflugia, are able to kill even nematodes, and practice a kind of pack hunting to slay their victims which weigh about hundred times more than them! 


Figure 2: A testate amoeba, Centropyxis aerophila, hunting for small protists and fungi in its favourite environments, forest litter. It uses its pseudopod to move forward and capture preys by immobilizing them before engulfing.

The situation is complicated even more as some organisms may belong to two functional categories at the same time. Many soil flagellates and amoebae are capable of both actively hunting for preys and absorbing nutrients from the environment, thus combining phagotrophy and osmotrophy. Phototrophy and phagotrophy are also often combined, especially in wet soils like in peatlands (where it is largely practised by golden alga like Ochromonas, Synura and Mallomonas). Altogether, functional diversity of eukaryotes in soils is immense. Our knowledge on their diversity is now at a turning point where it starts to be evaluated, but still remains an open field for new, exciting discoveries.