Rhizosphere protists are key determinants of plant health

Xiong et al. Microbiome (2020) 8:27 https://doi.org/10.1186/s40168-020-00799-9 RESEARCH Open Access Rhizosphere protists are key determinants of plant health Wu Xiong1,2†, Yuqi Song1†, Keming Yang1, Yian Gu1, Zhong Wei1*, George A. Kowalchuk2, Yangchun Xu1, Alexandre Jousset1,2, Qirong Shen1 and Stefan Geisen1,3,4 Abstract Background: Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators—protists—are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. Results: We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. Conclusions: We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. Keywords: Rhizosphere, Pathogen of Ralstonia solanacearum, Protists, Predator-prey interactions, Secondary metabolite genes, Plant health Background Plant pathogens can colonize the rhizosphere and have a severe influence on plant health [1, 2]. However, pathogen success and plant health are ultimately controlled by other biota, particularly the rhizosphere microbiome [3, 4]. The plant rhizosphere microbiome is a complex * Correspondence: † Wu Xiong and Yuqi Song contributed equally to this work. 1 Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People’s Republic of China Full list of author information is available at the end of the article assembly of diverse microorganisms, including bacteria, fungi, and protists that together influence plant health [5–8]. Despite the fact that the microbiome consists of diverse groups, most research aiming to understand the role of the microbiome in plant health or disease suppression has focused on bacteria [9–11] and fungi [12, 13]. A whole-microbiome view to decipher the main microbial determinants and their potential interactions that determine plant performance is currently missing [14]. As such, a more complete microbiome analysis is needed to identify the microbial groups and potential interactions that help predicting plant health. © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Xiong et al. Microbiome (2020) 8:27 In particular, protists that steer the taxonomic and functional composition of the rhizosphere microbiome through trophic predator-prey interactions have so far rarely been included in microbiome analyses linked to plant performance [8]. Protists, especially microbialfeeding phagotrophs [15, 16], have various functions within the rhizosphere [6, 17, 18]. For instance, some of these phagotrophs can directly prey on plant pathogens [19]. Studies using model protists have shown that protists control microbiome diversity and structure leading to plant growth promotion [17, 18, 20]. These changes are at least partly explained by the fact that protists feed selectively on microbial prey taxa, which differs between protistan species [21, 22]. Through this selective predation, protists can, for instance, increase those bacteria that produce pathogen-suppressive secondary metabolites [23, 24]. Yet, all these studies investigating potential links of protists with plant performance were carried out under artificial laboratory or greenhouse conditions focusing on one or few protistan species. As such, we have yet to identify the links between a complex diversity of protists, the microbiome and plant performance, especially in agricultural systems under field conditions. Protists and their interactions with other microorganisms are also subject to change throughout plant growth [14, 25]. Yet, the composition of the microbiome is often investigated only once during plant growth, usually at the time of plant maturity or after disease has already developed. Such approaches make it difficult to disentangle causality between plant health and potentially underlying characteristics in microbial communities, especially for diseased plants that host high amounts of pathogens. Recently, it was shown that bacterial communities at plant establishment can predict plant health at maturity [26]. Yet, other microbial groups might be even better indicators to predict Page 2 of 9 plant health, as for instance, protist communities were shown to respond more strongly to environmental inputs and vary more in their composition between seasons than bacteria and fungi [27]. To investigate potential key microbiome groups that might predict plant health, we here used a rhizobox system in an agricultural system under field conditions, in which we grew tomato plants. Soils we (...truncated)