Interactions of soil microbiome, plant defenses and domestication in tomato
- Autores: Lisanne Smulders
- Directores de la Tesis: M. Jose Pozo Jiménez (codir. tes.), Emilio Benítez León (codir. tes.)
- Lectura: En la Universidad de Granada ( España ) en 2022
- Idioma: inglés
- ISBN: 9788411175166
- Número de páginas: 157
- Tribunal Calificador de la Tesis: Ainhoa Martinez Medina (presid.), Inmaculada Sampedro Quesada (secret.), Arjen Biere (voc.)
- Programa de doctorado: Programa de Doctorado en Biología Fundamental y de Sistemas por la Universidad de Granada
- Materias:
- Enlaces
- Tesis en acceso abierto en: DIGIBUG
- Resumen
Domestication and breeding were often focused on plant morphology, while resistance and defence traits were usually left aside. Furthermore, crop domestication could alter interactions of plants with herbivores and their natural enemies at all trophic levels. In the introduction we integrate plant-microbe-arthropod (PMA) interactions from an ecological point of view focusing on interactions with beneficial organisms both below and aboveground. Interactions with beneficial organisms are thought to be reduced during domestication and breeding but experimental evidence for this is lacking. Here we discuss how domestication and breeding can affect plant constitutive and induced defenses and if results are consistent in this direction. Thus, we show the complexity of studying domestication effects on plant and soil microbiome, resistance and defence mechanisms and propose ideas for future research to advance our understanding in this exciting field. The objective of this thesis was to study how tomato domestication influenced belowground microbial communities, focusing on bacteria and arbuscular mycorrhizal fungi (AMF), and dive deeper into how these belowground communities affect aboveground indirect defences in tomato. This general objective was divided into two specific ones 1) To address top down effects of tomato domestication on plant microbial communities and 2) To investigate bottom up effects of microbial communities and Spodoptera exigua attack on volatile production and attraction of the predator Chrysoperla carnea. First, we explored how tomato domestication affected belowground root-associated bacterial communities, focusing on community composition (chapter 1) and functionality (chapter 2). In chapter 1, two main bacterial classes were found to dominate the tomato rhizosphere of all varieties, Alphaproteobacteria and Actinobacteria. Some minority phyla, such as Acidobacteria and Gemmatimonades, were increased in modern tomato varieties compared to wild tomato varieties. Tomato fruit traits varied following the domestication degree, where wild tomatoes produced more but smaller tomatoes while modern tomatoes produced a higher plant biomass and yield. However, no effect of tomato fruit traits on the root associated bacterial community was found. On the other hand, resistance traits explained an important fraction of variation between tomatoes, especially between domesticated varieties. Lastly, evidence was found for a positive correlation between bacterial diversity and reduced resistance, suggesting that susceptible varieties harbour more diverse bacterial communities. It could be that there are other unmeasured morphological traits, such as root-associated traits, that could be linked with belowground bacterial communities. In chapter 2, we show that all bacterial predicted functions were present in all tomato domestication types. The bacterial communities of wild tomato showed a higher level of aromatic degradation pathways and the Krebs cycle, indicating that modern tomato species lost degradation of recalcitrant organic compounds capacity. In line with this, reduced expression of biochemical cycles such as nitrates, sulphates and urea formation were detected in modern cultivars. Thus, it seems that the increased use of agrochemicals in modern agriculture might be connected with a reduction in metabolic pathways levels due to certain biochemical cycles. Other pathways were more highly expressed in modern tomato species, such as the synthesis of gamma-aminobutyric acid (GABA), fatty acids and jasmonic acid (JA), with plant produced JA being involved in defence against biotic stress and plant-microbe interactions, but an unclear role in the soil. Tomato landraces and wild tomato species were more connected to each other compared to modern:wild or modern:landraces pairs in terms of predicted bacterial functions in their rhizosphere. Then, we had a look at how 1) tomato domestication and spatial location affected symbiosis with root glomeromycotan fungal communities and 2) how variation in fungal communities drives the expression of aboveground plant traits (chapter 3). We found similar AMF communities between varieties and no evidence for selection of particular AMF families or genera by the different tomato genotypes. AMF communities were mainly influenced by location, especially AMF phylogenetic turnover. It therefore seems that AMF communities were driven by an unidentified environmental (soil) gradient. Despite the similarity of AMF communities, colonization levels significantly differed among tomato genotypes independently from their domestication degree, thus not supporting the hypothesis that modern tomatoes lost mycorrhizal capacity.. Aboveground plant traits also differed between varieties, with wild tomatoes generally showing increased symptom development despite lower viral incidence, higher tomato numbers and lower fruit weight. Location had a major influence on aboveground plant fruit and resistance traits. After location, AMF community composition and phylogenetic turnover explained variation in most traits, tomato variety mainly explained resistance traits and colonization while domestication explained differences in both resistance and fruit traits. Lastly, we found taxa of four different AMF genera with varying effects on aboveground plant traits, suggesting that symbiosis outcomes depend on the presence of certain AMF and can vary between taxa. Some taxa were found to positively affect plant morphology (biomass and tomato production), albeit negatively affecting resistance. We therefore believe that diverse AMF communities in the soil can be helpful in increasing plant growth and promoting tolerance to biotic stress. Finally, in chapter 4 we studied the effect of the natural soil microbial community and Spodoptera exigua attack on volatile production and attraction of the predator Chrysoperla carnea. As expected, the soil microbial community differed between sterile soil and natural soil treatments. However, Rhizophagus irregularis inoculation of natural soil did not affect soil bacterial beta diversity in the wild LA1589, while changes were observed in the modern Monita. .Feeding by S. exigua affected volatile production in both tomato species, but only in LA1589 an effect of soil microbiome was observed. This could be due to differences in the defense strategies between the two species, as LA1589 contains type VI trichomes, while Monita contains the Mi resistance gene. For both tomato species, the predator C. carnea preferred the sterile soil (SS) treatment, followed by inoculated natural soil (NS+Ri) and finally the non-inoculated natural soil (NS) treatment. Some volatiles were detected that could explain differences in attractiveness, with δ-elemene (LA1589) and 3-hexen- 1-ol (Monita) explaining most differences in behavior. Indeed, both δ-elemene and 3-hexen-1-ol have been described as involved in insect resistance. Some S. exigua induced volatiles in both tomato species were described as toxic to pests, such as octanal and 2-decanone. Some volatiles were even only present after pest attack, or only induced in one of the tomato species. Other detected volatiles have been described affecting natural enemy behavior. The effect of volatiles on natural enemies may depend on the natural enemy species, as some volatiles could be attractive to one natural enemy and repellent to another. In natural soil, Rhizophagus irregularis inoculation enhanced the atractiveness of C. carnea. These differences in C. carnea behavior could be caused by differences in AMF colonization as we detected a moderate but significant increase in fungal root colonization in the inoculated natural soil compared to the non-inoculated natural soil. This indicated that R. irregularis has a high competitive ability. The reduced attraction of C. carnea to natural soil could indicate that the microbial community may promote direct defenses at the cost of indirect defenses, which requires future experiments for confirmation. In conclusion, this thesis showed how agronomic practices and domestication affected soil bacterial communities, and the ecosystem services they provide, especially those functions related to the accumulation of organic matter in the soil. It also evidenced that soil bacterial and fungal communities of different tomato species and varieties were affected by different parameters. Bacterial communities were influenced mainly by resistance traits, which were generally non-targeted by domestication. In contrast, spatial location had profound effects on root fungal communities as well as aboveground plant traits. However, when location is taken into account, fungal communities were found to affect aboveground plant traits as well. Diving deeper into how soil communities affect above-ground plant defence, we evidenced that pest attack affected volatile profiles in both wild and modern tomato, with soil treatment only affecting volatiles significantly in wild tomato. We identified different volatiles induced by S. exigua attack, some of them potentially functioning as pest or natural enemy repellents. Also, R. irregularis inoculation in natural soil increases C. carnea attraction, and could therefore be a sustainable method to enhance tomato indirect defenses.
