Protists, the overseen guardians of soil microbiome function

By Assistant Professor Dr. Alexandre Jousset, Utrecht University, The Netherlands


This is part 3 in a 4 part blog series on soil protist

Left:  Cercomonas sp., a bacterivorous amoebae.


Soil microbes provide essential functions supporting soil fertility and plant health. Recent advances in sequencing technologies have favored a boom in studies investigating soil microbiome diversity and function. However, to date most studies have focused on bacteria and fungi, neglecting other trophic levels. This focus may be very convenient, as many functional genes are now described. It however oversees the function of predators as regulators of microbial communities.

Soil bacterial and fungal communities are typically top-down controlled. In other words, the main selective pressure is predation, not resource availability. The main predators of bacteria are protists and nematodes. These organisms, albeit unrelated, have been historically grouped as “microfauna”, reflecting that protist have been mostly investigated by zoologists and botanists, not by microbiologists. This discipline separation has contributed to neglecting protists in environmental microbiology. With these lines I aim at bridging these two research fields.

Protists can affect bacterial communities and soil fertility in several ways: By massively consuming bacteria, they release the nutrients contained in their preys, accelerating nutrient cycling. This increased nutrient availability can stimulate plant growth as well as nitrification process. Further, by reducing bacterial biomass, they alleviate competition and allow for more synergies between competing species. Protists are further very selective and will ingest only specific preys. They select preys based on their morphology, surface properties and toxicity. This selection has a strong impact on microbial functions linked to soil fertility. For instance, bacteria producing large amounts of exopolysaccharides may be better protected. These compounds play an important role in gluing soil particles together. We can thus expect that protozoa predation may improve soil structure. A range of studies have also revealed the functional overlap between antibiotics linked to disease suppression and protozoa inhibition. Several bacteria can naturally protect plants against disease by producing antibiotics and are seen as a promising alternative to pesticides. However, most attempts to use these bacteria in natural soil have failed. They either die out or evolve to lose their plant protective ability. Protists are here the guardians that “force” bacteria to produce antibiotics. They eat up bacteria lacking antibiotics, creating more space for the well-defended – and coincidentally plant protecting ones. Previous experiments in my group have shown that adding bacterivorous amoebae to soil can increase the success of plant-beneficial microbes by a factor three. In addition, bacterivorous protists are sensed by bacteria, that upregulate antibiotics production as a defense mechanism. These different protists-bacteria interactions can have a profound effects on soil fertility. We could for instance show that addition of bacterivorous protists could induce soil suppressiveness against the fungal pathogen Fusarium oxysporum. First commercial application of protozoa are already on the market and help for instance mineralize organic fertilizers and promote plant growth in sustainable agriculture.

I conclude that protozoa should be included in further microbiome studies and green biotechnology strategies aiming at reducing fertilizer and pesticide use in the agriculture.


Lettuce grown on compost, left without addition of protists, right with addition of Cercomonas sp