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The more we know about the protists,
the better we can understand the microbial jungle.


What are Protists?

Protists are all of the eukaryotic organisms except plants, animals and fungi, which makes them the vast majority of the eukaryotes.

Protists are among the most diverse and dominant microbial groups and play important roles in various ecosystems as

  • Phototrophs (carbon fixation),

  • Phagotrophs (predators),

  • Decomposers,

  • Animal parasites,

  • Plant pathogens.

Protist Research in LAP

Applied protistology is still at its infancy stage as still less is known about protist ecology & function. Indeed, protists are referred as the "dark matter of biodiversity". Although protists are promising, in order to use protists in applied sciences, first we need to fill the basic knowledge gap in protistology.

Thus, in LAP, our first aim is to increase the basic knowledge on protist ecology & function through natural and environemental sciences, and then, apply the scientific knowledge we have gained to develop practical & sustainable applications of protists in agriculture and life. 


Predatory Protists

Predatory protists are the most dominant eukaryotic organisms, especially in the soil ecosystem. 

They include amoeba, flagellates and ciliates. Although they mainly feed on bacteria, they also feed on fungi, nematodes, and other protists. 


Fig 1.. Effects of predatory protists on rhizosphere bacteria. 

Protists selectively feed on bacteria; hence, bacterial species targeted by protists markedly decreases (Fig. 1A). Simultaneously, several bacterial species benefit the protist predation through reduced bacterial competition. Therefore, the protist predation alters bacterial community composition in the rhizosphere (Fig. 1A).

When protists feed on bacteria, protists excrete excess nutrients (that would otherwise be locked up in bacterial biomass) into the rhizosphere (Fig. 1B), making it available for plant uptake.


Moreover, protists increase bacterial activities (Fig. 1C), such as the production of secondary metabolites and plant growth hormones. Some protists can directly prey upon plant pathogens and contribute to disease suppression.


Altogether, protists enhance soil fertility and plant productivity (Fig. 1D).


Protists are considered as ‘puppet masters’ of the rhizosphere microbiome due to their role in controlling bacterial communities and functions. Manipulating the rhizosphere microbiome by protists for sustainable and high-yield agricultural productivity is a current hot topic

At LAP, we study with a few model predatory protist species to understand their impact on bacterial communities & functioning. Effect of predators on bacteria depends on various factors such as water availability, soil type, temperature etc. We also study how environmental factors shape prey-predator interactions.  

* Please note that predatory protists are also known as phagotrophic protists, heterotrophic protists, and protozoa (not preferred anymore). Terminology should be carefully selected depending on the context. 

Top-down & Bottom-up Concepts

The bottom-up & top-down concepts refer to the two main factors determining the composition and population of communities in the ecosystem. 


The bottom-up concept refers to organisms being resource-limited, and resources shape communities at each trophic level [1]. The most outstanding example is that plants determine the community and population of herbivores. Later, this theory was questioned with the famous “green world” hypothesis (i.e., HSS hypothesis)[2]: “why do not herbivores eat all the available food and change the world into brown?” Hairston et al. [2] suggested that predators keep the herbivore population in control so that herbivores do not consume all of their food supplies. This takes us to the top-down concept; organisms are predator-regulated, and upper-level predators determine communities of lower-level organisms. Although the two contradictory points of view have been studied independently for decades, recent studies provided unequivocal evidence that both top-down and bottom-up controls interact to shape natural communities [3].  






Although the bottom-up & top-down concepts are extensively used in animal ecology studies, the concepts have been adopted to microbiology research only in the last decades.

In the soil ecosystem, bacterial communities are top-down regulated by microbial predators, mainly protists, and bottom-up regulated resources, mainly fertilizers, soil nutrients, and plant root exudates. In our previous study [4], we created a controlled laboratory environment in which the position of the bacteria at the trophic level is centred between soil nutrients (i.e., bottom-up) and bacterial predators (i.e., top-down).  The results showed that the top-down effects of protists were greater than the bottom-up effects of the applied fertilisers on the formation of bacterial communities, which provided unique information on the importance of protists in regulating bacterial communities in paddy field soil, which is likely to affect bacterial activities and agricultural productivity. 

In LAP, part of our research is focused on understanding the relative contribution of top-down and bottom-up effects on bacterial communities, and how top-down and bottom-up factors interact with each other. 


1. Elton, C. Animal Ecology. (The Macmillan Company, 1927).

2. Hairston, N. G., Smith, F. E. & Slobodkin, L. B. Community Structure, Population Control, and Competition. The American Naturalist 94, 421–425 (1960).

3. Leroux, S. J. & Loreau, M. Theoretical perspectives on bottom-up and top-down interactions across ecosystems. in Trophic Ecology (eds. Hanley, T. C. & La Pierre, K. J.) 3–28 (Cambridge University Press, 2015). doi:10.1017/CBO9781139924856.002.

4. Asiloglu, R. et al. Top-down effects of protists are greater than bottom-up effects of fertilisers on the formation of bacterial communities in a paddy field soil. Soil Biology and Biochemistry 156, 108186 (2021).


Protists & Plant Growth

Protists have profound impact om plant growth. Predatory protists enhance plant growth through nutrient turnover and regulation of microbial communities, while pathogenic protists have negative impacts on plant health. 

The Positive Impact


To overcome the global problem of food shortage through supporting sustainable life on Earth, we must appreciate critical importance of soil microorganisms—the key drivers of essential ecosystem services such as nutrient cycling and plant productivity. A better understanding of plant-microbe interaction could revolutionize agriculture through manipulating the plant-microbe interactions to sustainably increase crop production. 


The plant-microbe interactions mainly occur in rhizosphere: a narrow zone of soil surrounding roots of living plants. Plant roots deposit chemicals, making the rhizosphere a nutrient-rich habitat for bacteria, which increases bacterial populations in the rhizosphere. Since bacteria are the primary food source of protists, the bacteria-enriched rhizosphere attracts protists, creating everlasting prey-predator dynamics, which has enormous benefits for plant health. 

As summarized in the Predatory Protists section, predatory protists enhance plant growth through 

1)  Increased Nutrient Turnover,

2) Altering bacterial communities and enhancing their activities,

3) Enhancing beneficial bacterial populations,

4) Directly and indirectly suppressing plant pathogens.

The Negative Impact

Protists include important plant pathogen species, many of them belongs to Oomycetes. The below figure shows the negative impact of Pythium species on rice plant growth (Buyten and Hofte, 2013). 

Screen Shot 2022-03-09 at 14.04.45.png

Fig. Effect of Pythium on rice growth.

Image credit:Buyten and Hofte, 2013

At LAP, we recently started to study plant pathogen species of protists, as well as their impact on plant growth and their interaction with other microbes. 


Protist Ecology


Protists, the vast majority of the eukaryotes, are among the most diverse and dominant microbial groups in the soil ecosystem (Geisen et al., 2018). Their taxonomic diversity results in versatile functionalities. Phagotrophic protists (microbial predators) regulate microbial populations and shape microbial communities (Gao et al., 2019). The predatory activities of phagotrophic protists alter bacterial functionalities, accelerate nutrient turnover, and increase plant nutrient uptake (Clarholm, 1985; Kuikman and Van Veen, 1989; Bonkowski, 2004). Several protists play essential roles in nutrient cycling by organic matter degradation and carbon fixation (Jassey et al., 2015; Kramer et al., 2016). Some protists are plant pathogens having enormous negative impacts on plant production. Animal and microbial parasites negatively affect their hosts’ health (Latijnhouwers et al., 2003; Mah ́e et al., 2017). The taxonomic and functional diversity of protists provides valuable information to understand the soil ecosystem dynamics. 

Soil protists are highly sensitive to environmental factors and respond differently to the biotic and abiotic factors from bacteria and fungi (Geisen et al., 2018). Among the environmental factors, fertilizer-induced changes on protist communities, especially on phagotrophs, were stronger than that on bacterial and fungal communities (Zhao et al., 2019, 2020). Along with the fertilisers, changes in the soil pH, soil moisture, and organic matter content due to agricultural land usage affect protist diversity (Santos et al., 2020). Changes in soil nutrients and porosity by biochar amendments differently affected phagotrophic and autotrophic protists (Asiloglu et al., 2021b). Scherber et al. (2010) showed that bottom-up effects of plant diversity affect higher trophic levels (phagotrophs) more strongly than the lower trophic levels (bacteria). Taken together, protists are more susceptible to changes induced by environmental factors, especially soil water availability, climate (temperature and precipitation), soil nutrients, and the rhizosphere effects of plants, than their counterparts (bacteria and fungi). 

*(Above paragraphs are copied from Asiloglu et al. 2021. For full references, please see the article: ). 


At LAP, we research on protist ecology to answer two basic questions: 

1)    Who are there?

2)    How they are affected by environmental factors?

Pro eco

Graduate School of Science and Technology / Faculty of Agriculture
Niigata University

8050 Ikarashi 2-no-cho, Nishi-ku Niigata City, Niigata 950-2181 Japan

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