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While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.

Plant defence systems consist of many components and are activated by a wide range of microbe associated molecular patterns (MAMPs). In this thesis we focus on the specific immune responses classified as induced systemic resistance (ISR) and how this is activated by the strain WCS417 of Pseudomonas fluorescens from the rhizosphere. We examine the mechanisms behind ISR in relation to systemic acquired resistance and investigate how WCS417 can trigger ISR in the model plant A. thaliana, without triggering a MAMP triggered immunity response from the plant. We also examine the MAMPs of WCS417, with a main focus on flagellin and a secondary focus on lipopolysaccharides, as these are relevant for WCS417’s interactions with A. thaliana as a plant growth promoting rhizobacterium in relation to ISR, we also investigate the mechanisms behind priming, as this is believed to be the main way ISR enhances defence in the plant. We can conclude that WCS417 is a promising candidate to enhance defence in A. thaliana through ISR, even though more research is needed to understand when the priming effect happens.

Glucosinolates are a group of thioglycosides that act as a defence molecule in some plant species. These defence molecules are a central part of the plant defence system. Glucosinolates were commonly regarded as a secondary metabolite and not as important as primary metabolites. So far research has been made to understand glucosinolates importance in plants defence systems and their function. Glucosinolates are used in the plant to store sulphate, and utilise nitrogen. Different glucosinolates profiles have been shown to be produced and upregulated under nutrient availability. For plant species like Arabidopsis thaliana, applying a hormone like jasmonic acid you can imitate the plant, experiencing a real herbivore or insect attack that normally would activate glucosinolate accumulation and regulation. These plants utilise their resources like nutrients to a great extent to optimise their growth and defence. This thesis seeks to uncover if there are further connections between a plants prioritising of defence molecules under nutrient deficiency of elements like nitrogen and sulphate. This thesis aims to draw a new understanding of the effect of nutrient deficiency on glucosinolates, and the relative change under these stressful situations, compared to sufficient levels of sulphate and nitrogen. This will further be supported by measuring the hormones present as salicylic acid, after applying the plant to the deficiencies or sufficient nutrient variations and hormones as jasmonic acid. Understanding these complex conditions better, will lead us to achieve an overall better understanding of the plants utilising the strategy of nutrients for defence and growth.

Behovet for afgrøder med særlige egenskaber og/eller tilpasninger er steget markant grundet de seneste klimaforandringer. Skabelsen af disse nye afgrøder vil ofte kræve mange specifikke genetiske manipulationer, hvilket sjældent er let at opnå med moderne genredigeringsteknologier. Ligeledes er der også mange gener, man ikke kender funktionen af i mange planter, og disse er heller ikke altid nemme at redigere i med moderne genredigeringsteknologi. Dette projekt er en undersøgelse af mulighederne for at skabe genomsyntese-delen i en maskine, der skal kunne syntetisere afgrøder ud fra DNA-fri celler, der får indsat syntetiserede genomer baseret på et digitalt genom uploadet fra en computer. Denne maskine omtales som planteprinteren. Planteprinteren skal da kunne nøjagtigt syntetisere disse genomer baseret på det digitale genom, der på computeren nemt skal kunne redigeres til præcis det genom, man ønsker at indsætte. I dette projekt er der blevet undersøgt og diskuteret mulighederne for den optimale opdeling af genomet til mindre enkeltstrengede oligonukleotider vha. software, syntesemulighederne for disse ved brug af SPS og EDS til at skabe et DNA-bibliotek, amplifikation af oligonukleotiderne vha. bridge amplification, omdannelsen til dobbeltstrengede chunks ved korresponderende antisense-strenge og overhang extension synthesis, opbevaringen og sorteringen vha. Si-capsules med påsatte bar-koder, og sammensætningen af chunks til kromosomer vha. Gibson Assembly. Yderligere er der også blevet undersøgt mulighederne for at løse problemer ifm. de epigenetiske modifikationer og kromosomernes struktur vha. dCas9-fusionsproteiner og syntetiske histoner, samt hvordan fejlraten undervejs kan minimeres vha. brug af proofreading-polymeraser og MMRS-enzymer, og hvordan og hvornår der bør verificeres undervejs via sekventering og fluorescens-detektion af fluorescerende nukleotider. Undersøgelsen har vist, at syntesedelen i planteprinteren med moderne teknologi og tekni, The need for crops with certain abilities and/or adaptations has increased significantly because of the latest climate changes. The creation of these new crops will often require many specific genetic manipulations which rarely are easy to achieve with modern gene editing technologies. Likewise, there are also many genes whose functions are unknown in many plants, and these are also not always easy to edit with modern gene editing technology. This project is an investigation into the possibilities of creating the genome synthesis part of a machine that shall be able to synthesize crops from DNA-free cells that have synthesized genomes inserted based on a digital genome uploaded from a computer. The machine is called the plant printer. The plant printer will then be able to accurately synthesize these genomes based on the digital genome, which can be easily edited on the computer to the exact genome one wants to insert. There has in this project been investigated and discussed the possibilities for the optimal division of the genome into smaller single-stranded oligonucleotides using software, the synthesis possibilities for these using SPS and EDS to create a DNA library, amplification of the oligonucleotides using bridge amplification, the conversion to double-stranded chunks by using corresponding antisense strands and overhang extension synthesis, the storage and sorting using Si-capsules with barcodes attached, and the assembly of chunks into chromosomes using Gibson Assembly. In addition, there has been an investigation of the possibilities for solving problems related to the epigenetic modifications and the structures of the chromosomes using dCas9 fusion proteins and synthetic histones as well as how the error rate along the way can be minimized by using proofreading polymerases and MMRS enzymes and how and when there should be verified along the way via sequencing and fluorescence detection of fluorescent nucleotides. The study has shown that the

Arbuscular mycorrhizal fungi (AMF) establish symbiosis with many plant species. During the symbiosis, AMF may modify the plant immune system and elicit an induced resistance response. In this experiment I investigated AMF inoculated plants under different light levels (aiming to change C-allocation to roots and AMF), focusing on the changes in plants immunity and induced resistance.  I compared the physiological and nutritional parameters under high light and low light conditions and conditions as well as short, medium and long treatment periods to understand the physiological and immunity responses of plants and the impact of AMF.  Plants were accidentally infected with powdery mildew and showed different severity of symptoms under different treatments, indicating AMF induced resistance might change under different light conditions. Relevant genes that regulate plant defense and AMF symbiosis were selected for transcript analysis.  The experiment showed that high AMF infection will weaken the plant defense system especially against biotrophic pathogens under low light conditions. At the same time, plants also suppress AMF infection. However, the suppression can hardly compensate for the damage caused by AMF under low light conditions.

Phytoalexins are antimicrobial plant metabolites elicited by microbial attack or abiotic stress. We investigated phytoalexin profiles after foliar abiotic elicitation in the crucifer Barbarea vulgaris and interactions with the glucosinolate-myrosinase system. The treatment for abiotic elicitation was a foliar spray with CuCl2 solution, a usual eliciting agent, and three independent experiments were carried out. Two genotypes of B. vulgaris (G-type and P-type) accumulated the same three major phytoalexins in rosette leaves after treatment: phenyl-containing nasturlexin D and indole-containing cyclonasturlexin and cyclobrassinin. Phytoalexin levels were investigated daily by UHPLC-QToF MS and tended to differ among plant types and individual phytoalexins. In roots, phytoalexins were low or not detected. In treated leaves, typical total phytoalexin levels were in the range 1–10 nmol/g fresh wt. during three days after treatment while typical total glucosinolate (GSL) levels were three orders of magnitude higher. Levels of some minor GSLs responded to the treatment: phenethylGSL (PE) and 4-substituted indole GSLs. Levels of PE, a suggested nasturlexin D precursor, were lower in treated plants than controls. Another suggested precursor GSL, 3-hydroxyPE, was not detected, suggesting PE hydrolysis to be a key biosynthetic step. Levels of 4-substituted indole GSLs differed markedly between treated and control plants in most experiments, but not in a consistent way. The dominant GSLs, glucobarbarins, are not believed to be phytoalexin precursors. We observed statistically significant linear correlations between total major phytoalexins and the glucobarbarin products barbarin and resedine, suggesting that GSL turnover for phytoalexin biosynthesis was unspecific. In contrast, we did not find correlations between total major phytoalexins and raphanusamic acid or total glucobarbarins and barbarin. In conclusion, two groups of phytoalexins were detected in B. vulgar

Although ammonium (NH4+ ) is a key intermediate of plant nitrogen metabolism, high concentrations of NH4+ in the soil provoke physiological disorders that lead to the development of stress symptoms. Ammonium nutrition was shown to induce the accumulation of glucosinolates (GSLs) in leaves of different Brassicaceae species. To further understand the link between ammonium nutrition and GSLs, we analysed the ammonium stress response of Arabidopsis mutants impaired in GSL metabolic pathway. We showed that the MYB28 and MYB29 double mutant (myb28myb29), which is almost deprived of aliphatic GSLs, is highly hypersensitive to ammonium nutrition. Moreover, we evidenced that the stress symptoms developed were not a consequence of the lack of aliphatic GSLs. Transcriptomic analysis highlighted the induction of an iron (Fe) deficiency response in myb28myb29 under ammonium nutrition. Consistently, ammonium-grown myb28myb29 plants showed altered Fe accumulation and homeostasis. Interestingly, we showed overall that growing Arabidopsis with increased Fe availability relieved ammonium stress symptoms and that this was associated with MYB28 and MYB29 expression. Taken together, our data indicated that the control of Fe homeostasis was crucial for the Arabidopsis response to ammonium nutrition and evidenced that MYB28 and MYB29 play a role in this control.

A growing world population as well as the need to enhance sustainability and health create challenges for crop breeding. To address these challenges, not only quantitative but also qualitative improvements are needed, especially regarding the macro- and micronutrient composition and content. In this review, we describe different examples on how the nutritional quality of crops and the bioavailability of individual nutrients can be optimised. We focus on increasing protein content, the use of alternative protein crops, and improving protein functionality. Furthermore, approaches to enhance the content of vitamins and minerals as well as healthy specialised metabolites and long-chain polyunsaturated fatty acids are considered. In addition, methods to reduce antinutrients and toxins are presented. On the one hand, these approaches could help to decrease the ‘hidden hunger’ caused by micronutrient deficiencies. On the other hand, a more diverse crop range with improved nutritional profile could help to shift to healthier and more sustainable plant-based diets.