Cristina Rotoni

Cristina Rotoni MSc

PhD Candidate


Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands


My PhD project aims to understand soil microbial farming to increase plant productivity: reducing nutrient inputs to enhance plant-microbe interactions and managing soil microbial diversity.


I’m a PhD candidate currently working at the Netherlands Institute of Ecology (NIOO-KNAW) in collaboration with Utrecht University (UU). I’m part of PE&RC graduate school and my promotor is Prof. Dr. Ir. Eiko Kuramae (NIOO-KNAW, Utrecht University) and co-promotor is Prof. dr. G.A. Kowalchuk (Utrecht University).





Peer-reviewed publicaties

  • Applied Soil Ecology

    Cultivar governs plant response to inoculation with single isolates and the microbiome associated with arbuscular mycorrhizal fungi

    Cristina Rotoni, Marcio Fernandes Alves Leite, Lina Wong, Cátia S. D. Pinto, Sidney L. Stürmer, Agata Pijl, Eiko Kuramae

    Plant Growth-Promoting Microbes (PGPM) have the potential to enhance sustainable agriculture, but there is still a limited understanding of how the complex interplay between plant genetic variability, the native soil community, and soil nutrients affects PGPM recruitment. To address this challenge, we investigated the impact of bacteria isolates and arbuscular mycorrhizal fungi (AMF) along with their accompany microbiome (AMFc) derived from a wild chrysanthemum on the growth of five different commercial chrysanthemum cultivars (Chic, Chic 45, Chic Cream, Haydar and Barolo), as well as their rhizosphere microbiomes, within a nutrient-rich complex substrate environment. We found 23 bacterial strains capable of producing siderophore, 14 strains capable of producing Indole-3-acetic acid, and 18 strains capable of solubilizing phosphate. The AMFc had six AMF species, and the bacterial and fungal communities associated with AMF belonged to different phyla. Using generalized joint models, we investigated the impact of the three most effective bacterial strains and the AMFc on plant growth (shoot and root dry mass) while integrating information on plant genotype, environment, and microbes. The impact of PGPM inoculation varied from positive to negative effects depending on the cultivar, with Chic Cream showing the highest increase in root biomass after inoculation with both bacterial strain SMF006 (57 %) and AMFc inoculation (79 %). Our study demonstrates that PGPM from wild relative can impact the growth and assembly of the chrysanthemum root microbiome, but this impact is cultivar-dependent. Furthermore, inoculation with a complex AMF containing community (AMFc) induced greater changes in the rhizosphere microbiome than with a single bacterial isolate. Our study shows that inoculation of a complex community of beneficial microbes results in more effective plant growth promotion.
  • FEMS Microbiology Ecology

    Rhizosphere microbiome response to host genetic variability

    Cristina Rotoni, Marcio Fernandes Alves Leite, Agata Pijl, Eiko Kuramae
    Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.
  • Science of the Total Environment

    Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome

    Viviane Cordovez da Cunha, Cristina Rotoni, Francisco Dini-Andreote, Ben Oyserman, Victor Carrion Bravo, Jos M. Raaijmakers
    Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.

Projecten & samenwerkingen


  • Microbial Farming to increase plant productivity

    Project 2018–Present
    Plant-growth promoting microbes (PGPM) are a viable alternative to traditional fertilizers for enhancing plant productivity and improving soil quality without environmental pollution. The use of PGPM in agriculture has been hampered by a lack of reproducible results and the difficulty of transferring this technology to the field. This inconsistent success primarily reflects competition or resistance of the original soil microbiome to inoculants, as well as the negative effects of management practices such as fertilization on plant interactions with the soil microbiome and the efficiency of ecosystem services delivered by PGPM. We were the first to circumvent this problem under field conditions by manipulating the soil microbiome to successfully obtain consistent, positive effects of inoculated microbes on plant productivity (Cipriano et al., 2016; However, the influence of the indigenous soil microbiome on plants remains largely unknown. We propose to investigate this tripartite, PGPM-plant-soil microbiome interaction in plant quality and productivity using state-of-the-art ‘omics’ and bioinformatics approaches to investigate facilitation (positive interactions) and competition (negative interactions) by both microbes and PGPM within the plant realized niche following gradients of both soil diversity and nutrient availability. This research will facilitate the development of innovative methods for agricultural and horticultural starting material production using PGPM for sustainable crop production by combining techniques to reduce nutrient input and enhance the efficiency and long-lasting effects of PGPM. This research proposal will integrate approaches to obtain a fundamental understanding of these tripartite interactions in a smart microbiome engineered plant production system for sustainable high-quality crop production.
    Soil microbial farming to increase plant productivity: reducing nutrient inputs to increase plant-microbe interactions and managing soil microbial diversity