Harnessing the potential of predatory protists to support a beneficial soil microbiome

Abstract

The application of micro-organisms has been increasingly suggested as sustainable agricultural approach. Soil micro-organisms include bacteria, archaea, fungi and protists. The majority of soil protists are free-living predators that feed, among others, on bacteria. Through their predatory activity, they typically unlock nutrients that can benefit plants. In addition, because soil protists do not equally feed on all bacteria, they influence their prey community structure which can further lead to an enrichment in plant-beneficial taxa. One challenge but also an opportunity of soil protist ecology lies in the high phylogenetic diversity of protists that likely mirrors an equally high functionality: each protist species could have a distinct impact on plant development. Most of the current understanding is, however, based on few model species and successful protist application typically follows a trial and error methodology with little a priori knowledges. In the present work, we investigated the potential of phylogenetically diverse soil protists to support plant development, especially via their impact on the bacterial community composition. We first pursued to identify relevant protist and bacterial traits to better understand and predict predator-prey interactions. We were able to relate the ability of bacteria to inhibit their predators to their ability to suppress pathogens (Chapter 2). We identified for each of the protist tested distinct prey consumption patterns which were related to their predatory impacts on soil bacterial communities: protist species that could feed on the same set of bacteria in a plate assay had a similar impact on the bacterial community structure in the soil (Chapter 3). After investigating the predator-prey interactions, we examined different aspects of protist application to best support plant development by using lettuce, Lactuca sativa, as model plant. We found that the effect on the plant varied depending on the protist species inoculated (Chapter 4) and that application of protists before transferring the plant into the soil led to the best yield (Chapter 5). In chapter 6, I synthesized the obtained results, further examined the context-dependency of the predatory impact of protists and suggested plate assays to be promising in soil protist ecology. The results of this work highlight that protist predatory impact is taxon specific, both on its prey community and on plant development. Further, effects on plant development are not necessarily beneficial or related to an overall change of the bacterial community composition. We conclude that predatory protists are an essential component of the soil microbiome functioning and have the potential to support plant development.