原生生物について知れば知るほど
微生物ジャングルをより深く理解することができます。
原生生物とは？
原生生物は、植物、動物、菌類を除くすべての真核生物であり、真核生物の大部分を占める。
原生生物は最も多様で支配的な微生物群の一つであり、生態系において重要な役割を担っている。
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光栄養生物（炭素固定）
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貪食性（捕食者）
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分解者
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動物寄生虫
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植物病原菌
LAPにおける原生生物の研究
原生生物学は、原生生物の生態や機能に関する知見がまだ少ないため、応用原生生物学はまだ発展途上の段階にある。実際、原生生物は「生物多様性のダークマター」とも呼ばれている。原生生物は有望であるが、原生生物を応用科学に利用するためには、まず原生生物学の基本的な知識のギャップを埋める必要がある。
そこで、LAPでは、まず、自然科学や環境科学を通じて原生生物の生態や機能に関する基礎知識を深め、得られた科学知識を応用して、原生生物の農業や生活への実用的かつ持続可能な応用を開発することを目的としています。
研究テーマ(英語版のみ）
捕食性原生生物
捕食性原生生物は、特に土壌の生態系において最も支配的な真核生物である。
アメーバ、鞭毛虫、繊毛虫などが含まれる。主にバクテリアを捕食するが、菌類、線虫、他の原生生物も捕食する。
図1. 細菌の捕食者（原生生物）が根圏細菌に及ぼす影響。
原生生物はバクテリアを選択的に捕食するため、原生生物に狙われるバクテリア種は著しく減少する（図1A）。同時に、原生生物に捕食されない細菌種や原生生物に捕食されても生き残ることができる細菌種は、原生生物の存在によって細菌の競争が減り、利益を得ることができる。したがって、原生生物による捕食は、根圏の細菌群集組成を変化させる（図1A）。
原生生物がバクテリアを捕食すると、原生生物は（バクテリアのバイオマスに閉じ込められていた）過剰な栄養素を根圏に排泄し（図1B）、植物が摂取できるようになる。
さらに、原生生物は、二次代謝産物や植物成長ホルモンの生産など、細菌の活動を活発化させる（図1C）。原生生物の中には、植物の病原菌を直接捕食し、病気の抑制に貢献するものもいる。
これらを総合すると、原生生物は土壌の肥沃度を高め、植物の生産性を向上させます（図1D）。原生生物は、細菌群集や機能を制御する役割を持つことから、根圏微生物群の「操り人形」と考えられている。持続的かつ高収量の農業生産性を実現するために、原生生物による根圏微生物群を操作することは、現在のホットな話題である。
LAPでは、いくつかのモデル捕食性原生生物種を用いて、細菌群や機能に対する影響を理解するための研究を行っています。捕食性原生生物がバクテリアに与える影響は、土壌水分、土壌の種類、温度など様々な要因に依存します。環境要因が餌生物と捕食者の相互作用をどのように形成しているかを研究しています。
トップダウン・ボトムアップ概念 (英語のみ）
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].
Herbivores
Plants
Carnivores
Image credit: Dorling Kindersley
https://www.dkfindout.com/us/animals-and-nature/food-chains/energy-pyramid/
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.
References
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).
原生生物と植物成長 (英語のみ）
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).
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.
原生生物生態学 (英語のみ）
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: https://doi.org/10.1016/j.soilbio.2021.108397 ).
At LAP, we research on protist ecology to answer two basic questions:
1) Who are there?
2) How they are affected by environmental factors?
