| 1. |
- Aballay, Erwin
(författare)
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Rhizobacteria associated to Vitis vinifera and their effect on the control of Xiphinema index, Meloidogyne ethiopica and Vitis growth
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plant-parasitic nematodes are one of the most important pests affecting the growth of vineyards due to the destruction of new roots. Several species are associated with this problem, the most important being the ectoparasite Xiphinema index and the endoparasite Meloidogyne ethiopica. The search for new pest and disease control methods based on bioantagonist microorganisms is an important aspect of modern agriculture and the development of tools based on the use of rhizobacteria is becoming a widely evaluated alternative. The present study on suppressive soils started with a survey undertaken in productive Chilean vineyards to explore the younger roots of grapevines and identify the presence of rhizobacteria. More than 1800 soils were surveyed and a set of 11 vineyards were selected and considered suitable for bacteria isolation, as they showed low densities of plant-parasitic nematodes. A total of 400 bacterial isolates in 25 genera were obtained using tryptic soy broth agar and identified with fatty acid profiling. Two of the most frequently isolated species were Pseudomonas putida (35.1%) and P. fluorescens (6.1%). The effect of these isolates on the parasitism and reproduction of X. index was assessed through assays using potted vine plants (cv. Thompson Seedless) and a bacterial suspension containing 1×106 CFU/mL. Some isolates from Bacillus megaterium, B. brevis, B. mycoides, B. sphaericus, B. thuringiensis, Pseudomonas corrugata, P. putida, P. alcaligenes, P. savastanoi, P. fluorescens, P. pseudoalcaligenes, P. viridiflava, Stenotrophomonas maltophilia, Serratia plymuthica, Cytophaga johnsonae, Rahnella aquatilis, Stenotrophomonas sp., Variovorax paradoxus and Curtobacterium flaccumfaciens reduced root damage and suppressed populations. Isolates of B. brevis, Comamonas acidovorans, B. megaterium, Pantoea agglomerans and P. savastanoi increased plant growth or root weight, but did not control nematodes. Most of the culture filtrates obtained from isolates from four vineyards were effective in killing X. index and decreasing egg hatching, which was not related to damage or population control. It was estimated that 89, 32 and 16% of the isolates were effective against X. index under supernatant conditions, in potted plants growing in sterile substrate and in potted plants growing in field soil, respectively. Sixteen bacterial isolates previously assessed were also evaluated on M. ethiopica in vine cv. Chardonnay. Seven isolates (Serratia marcescens, C. acidovorans, P. agglomerans, Sphingobacterium spiritivorum, B. mycoides, Alcaligenes piechaudii and S. plymuthica) decreased damage or reproduction, showing that different species of nematodes can respond differently to a particular isolate.
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| 2. |
- Abd El-Daim, Islam Ahmed Moustafa
(författare)
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Use of rhizobacteria for the alleviation of plant stress
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plant growth promoting rhizobacteria are beneficial microbes able to induce plant stress tolerance and antagonise plant pathogens. The present study showed that wheat seedlings pre-treated with Bacillus thuringiensis AZP2 had better tolerance to severe drought stress and showed 78% greater plant biomass and five-fold higher survivorship compared to wheat seedlings not treated with the bacterium. The effect of B. thuringiensis AZP2 also resulted in improved net assimilation and reduced emission of stress volatiles. The study investigated the effect of the inactivation of sfp-type phosphopantetheinyl transferase in plant growth promoting bacterium Paenibacillus polymyxa A26. The inactivation of the sfp gene resulted in loss of NRP/PK production such fusaricidins and polymyxins. In contrast to the former Bacillus spp. model the mutant strain compared to wild type showed greatly enhanced biofilm formation ability. Its biofilm promotion is directly mediated by NRP/PK, as exogenous addition of the wild type metabolite extracts restores its biofilm formation level. Further, increased biofilm formation was connected with enhanced ability of the sfp inactivated strain to remarkably protect wheat seedlings by improving its survival and biomass under severe drought stress conditions compared to wild type. Fusarium graminearum and F. culmorum are the causing agents of a destructive disease known as Fusarium head blight (FHB). The disease is the leading cause of contamination of grain with Fusarium mycotoxins that are severe threat to humans and animals. Biological control has been suggested as one of the integrated management strategies to control FHB causing agents. The present study showed that P. polymyxa A26 is a potent antagonistic agent against F. graminearum and F. culmorum. In order to optimize strain A26 production, formulation and application strategies traits important for its compatibility need to be revealed. Hence, a toolbox comprising of dual culture plate assays and wheat kernel assays including simultaneous monitoring of the FHB causing pathogens, A26 and mycotoxins produced was developed in the present study. Using this system results showed that, besides the involvement of lipopeptide antibiotic production by P. polymyxa in the antagonism process, biofilm formation ability may play a crucial role in the case of A26 F. culmorum antagonism.
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| 3. |
- Aboshady, Hadeer Moursy
(författare)
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Genomic variation and molecular mechanisms of the host response to gastrointestinal nematodes in small ruminants
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papers and General discussion. In paper Ⅰ, a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper Ⅱ, transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In paper Ⅲ, the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper Ⅳ, the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway.
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| 4. |
- Abrahamsson, Malin
(författare)
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Patterning during embryo development in Pinus : with special emphasis on somatic embryogenesis in Scots pine (Pinus sylvestris L.)
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Somatic embryogenesis is an attractive method to propagate conifers vegetatively. However, many species belonging to Pinus are recalcitrant to somatic embryo development. The overall aim of this thesis has been to gain a better understanding of the developmental pathway leading to cotyledonary somatic embryos of Scots pine (Pinus sylvestris). By comparing the developmental pathway of somatic embryos in a normal and in an abnormal cell line, differences between the cell lines were identified. An important difference was the high ratio of early and late embryos carrying supernumerary suspensor cells in the abnormal cell line compared to embryos in the normal cell line. This unbalanced ratio between the embryonal mass and the suspensor is at least partly caused by a disturbed polar auxin transport. Furthermore, a high proportion of early and late embryos degenerated in both cell lines. The degenerating embryos in the normal cell line were eliminated in a similar way as subordinate embryos in the seed. Contrastingly, the degenerating embryos in the abnormal cell line were not eliminated; instead the degenerated embryos started to differentiate new embryos creating a loop of embryo degeneration and embryo differentiation. During initiation of embryogenic tissue, the protruding early zygotic embryo(s) started to degenerate before a proliferating embryogenic culture was established, indicating that the initiation of embryogenic cultures is not a direct continuation of cleavage polyembryony. The results further suggest that there is a high risk that cell lines initiated from early zygotic embryos at the stage of cleavage develop abnormally. To be able to use more differentiated tissues as explants for initiation of embryogenic cultures, more knowledge is needed about totipotence and embryogenic potential. Treatment with the histone deacetylase inhibitor trichostatin A (TSA) during maturation of somatic embryos of Norway spruce inhibited the maturation progression of the embryos. Furthermore, although TSA-treatment maintained the embryogenic potential in germinating somatic embryos, it did not enable the embryos to regain embryogenic potential after it was lost. By analysing global changes in gene expression during early zygotic embryo development in Scots pine, we identified genes and processes that might be important for regulating the cleavage process and for the development of a dominant embryo. Together these results contribute to the knowledge that in turn can lead to improved protocols for large scale propagation of Pinus species via somatic embryos.
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| 5. |
- Abrahamsson, Sara
(författare)
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Genetic dissection of quantitative traits in Scots pine
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The phenotypic expressions of Scots pine, have been extensively studied over the years, but the gene regulation behind the traits has only just begun to be elucidated. The overall aim of this thesis was to start dissecting the genetics behind a number of adaptive traits in Scots pine and examine how they are influenced by relatedness using different molecular tools. In a full-sib family of Scots pine the genetic variation in autumn frost hardiness and height growth was revelead by measuring open-pollinated offspring. A significant genetic variation for both traits was found, a prerequisite to identify quantitative trait loci (QTL). A conceptual statistical model in the Bayesian framework for identifying QTLs in dynamic traits i.e. traits that vary over time, was developed and applied in a QTL study based on a full-sib family of 250 trees. A set of 160 AFLPs were utilized. QTLs for three latent traits were identified: one for the slope (growth) and two for the quadratic term (growth cessation). As a tool to identify candidate genes for the study of quantitative adaptive traits, gene regulation under continuous red (cR) and far-red (cFR) light was studied in hypocotyls from open-pollinated seeds from a natural population in northern Sweden using microarray technology. The gene expression patterns for the light response pathway in Scots pine under cFR show clear differences from those of angiosperms, wherein we observed up-regulation of cryptochrome1. This gene has, therefore, become a strong candidate gene that deserves further studies to elucidate the genetics behind Scots pine adaptation. Not knowing the genetic relationship and inbreeding of trees, and how it influences the phenotypic expression, can lead to over- or underestimation of additive genetic values resulting in biased heritability estimates. A natural population of Scots pine, earlier identified as being highly inbreed, was used to investigate the influence of inbreeding by the correlation between heterozygosity and propotion of sound seed (PSS), average seed weight and proportion of rare alleles (PRA). Heterozygosity fitness correlation (HFC) was found positive for PSS and negative for PRA most likely due to recessive deleterious alleles purged in homozygotes. The study provided evidence that, as predicted by theory, inbreeding enhances HFC in a species with high outbreeding rate and high number of lethal equivalents as Scots pine.
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| 6. |
- Abro, Rani
(författare)
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Digestion and metabolism of carbohydrates in fish
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with the digestion and metabolism of carbohydrates in Arctic charr, Eurasian perch and tilapia. Two sources of carbohydrates, native starch (wheat) and chitin (zygomycete biomass), were evaluated. Gut tissue of Arctic charr displayed significant chitinase activity, of both endo- and exo-chitinase forms. Moreover, the distribution pattern along the gastrointestinal tract of Arctic charr differed between endo-chitinase and exo-chitinase. The endo-chitinase activity in stomach tissue and in the distal intestine was several hundred-fold higher than the exo-chitinase activity in stomach tissue. The greatest exo-chitinase activity was found in the distal intestine fed a zygomycete-based diet. Disturbed intestinal integrity and increased uptake rate of the amino acid lysine were observed in the distal, but not proximal, intestine of fish fed the zygomycete-based feed. A ¹HNMR metabolomics approach revealed no differences in metabolic profile in liver tissues of Arctic charr fingerlings fed a zygomycete-based diet and a fish-meal based diet. The inclusion of wheat starch did not affect α-amylase activity in gut tissue of Arctic charr and Eurasian perch. Overall, α-amylase activity was correlated with the trends obtained for starch digestibility. The apparent digestibility (AD) of crude protein, starch, crude fat and energy differed between the fish species, with on average higher values for all parameters in Eurasian perch than in Arctic charr. Within fish species, dietary starch level had no effect on AD of dry matter, crude protein, crude fat and energy. Studies of the metabolic response to wheat starch inclusion in Arctic charr and tilapia using ¹HNMR base metabolomics indicated metabolic effects in tilapia, while inclusion of starch in the diet of Arctic charr resulted in partial or negligible metabolism effects. Thus there are species-related differences in the metabolic response to dietary starch inclusion.
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| 7. |
- Abro, Shahid, hussain
(författare)
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Molecular characterization and detection of infectious bronchitis virus
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with the molecular characterization and detection of infectious bronchitis virus (IBV), an important pathogen that causes heavy losses in the poultry populations worldwide. The aim of the research was to better understand the molecular characteristics of the virus and to investigate the factors behind the continuous emergence of new genetic variants and the occurrence of outbreaks. The studies showed that the viral genome is under a continuous evolution, due to mutations, strong selective pressure and recombination events. These forces lead to a wide genetic diversity and the generation of new variants of this virus. The viral genes encoding the spike, envelope and membrane proteins can be considered the main genomic regions, which are indicating the evolution processes of IBV. The various strains contain specific structural and functional motifs in their genes and the alterations in these motifs may affect the infection biology of the virus. The constant emergence of new variants in Sweden is likely due to the introduction of novel IBV strains from other European countries through the import of poultry products, or by the continuous migration of wild birds. The in silico investigations of the spike glycoprotein coding regions of the Massachusetts and QX-like genotypes demonstrated molecular differences between these genotypic variants. It is hypothesized that the genetic diversity in the spike gene of IBV and of other avian coronaviruses, as well as of human, bat, and other animal coronaviruses could be associated with the adaptation and host specificity of these infectious agents. The data obtained by molecular characterization approach was also used for the development of a new molecular method for the improved detection and genotyping of this virus. A microarray platform was developed for the simultaneous detection and rapid typing of IBV variants. This assay provides a practical tool for better diagnosis, for studying the effectiveness of vaccination and for performing large-scale epidemiological studies.
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| 8. |
- Abubaker, Jamal
(författare)
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Effects of fertilisation with biogas residues on crop yield, soil microbiology and greenhouse gas emissions : recycling of plant nutrients from bioenergy production
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The amount of residues generated by biogas production has increased dramatically due to worldwide interest in using renewable energy. Biogas residues (BRs) originate from anaerobic degradation of different types of rural and urban organic wastes and have been proposed as organic fertilisers because of their high content of ammonium and other valuable macro- and micro-nutrients. However, application of BRs to agricultural soils may be accompanied by environmental risks, since they may contain heavy metals and organic pollutants. Therefore the effects of BRs on crop production and on the soil ecosystem and environment urgently need to be investigated before their wider use. This thesis evaluated and compared different types of BRs against cattle slurry, pig slurry, compost and mineral fertiliser with respect to their (1) ability to provide plants with necessary nutrients, (2) impact on the soil microbial ecosystem and (3) effects on emissions of the greenhouse gas nitrous oxide (N₂O). The results from short-term laboratory experiments and a long-term field trial showed that BRs increased crop yield to the same extent or more than conventional mineral fertiliser and compost, but less than pig slurry. BRs generated from source-separated organic household waste had a tendency to give higher crop yield and soil microbial activities than other BRs. BRs had no general negative effect on soil respiration, but substrate-induced respiration decreased significantly in organic soil on addition of BRs. Although all BRs initially inhibited potential ammonium oxidation and potential denitrification activity, no long-term negative effects were detected. BRs stimulated ammonium assimilation, which can temporarily decrease nitrogen availability to the plant. Furthermore, the bacterial community structure in the sandy soil was altered by BRs and cattle slurry, but no significant change was seen in the community structure of clay and organic soil. Application of BRs and animal slurry increased N₂O emissions, but the total losses and flux patterns were affected by fertiliser type and soil type. In conclusion, the fertiliser value of BRs should be regarded as high and they apparently have no long-term adverse effects on soil microbial functions and structures. Thus the problematic amounts of residues associated with expansion of biogas production could be turned to advantage, as these residues seem to be safe and competitive fertilisers.
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| 9. |
- Adevi, Anna
(författare)
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Supportive nature - and stress : wellbeing in connection to our inner and outer landscape
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many benefits are claimed for the interplay between humans and nature, such as nature’s potentially positive effect on wellbeing and health. The main aim with the present work was to increase the understanding of how nature nvironments can support and contribute to health improvement from stress related experiences. Different landscape types’ effect on stress was studied in Sweden. Single case-studies focused on factors considered being essential in the recovery process for people diagnosed with exhaustion disorder within a stress rehabilitation-program through garden therapy in Alnarp, Sweden. A simplified conclusion of the thesis would be that the childhood landscape seems to play a significant role affecting the choice of the adult’s recreational setting - and recreational activity when stress is included. People feel more at home in the type of landscape they grew up in and more often chose to settle down in this type of landscape; even if they have moved from their childhood region. People also prefer qualities connected to their childhood landscape, but seem to attach more easily to qualities suggested having innate significance. The stress-recovery process within the garden therapy seems to be supported, hastened and deepened because of a multisensory change in awareness when contact with nature is combined with therapeutic interventions. Different psycho-physiological processes are discussed as well as the importance of self-chosen places in the garden based on present mood and the significance of the interaction between symbolic and concrete activities. The garden, the caregivers, and the group of participants together make up an arena which combines structure with freedom of action, in which the participants get the chance to regulate their needs and desires. Two hypotheses are presented, which might contribute to filling some current gaps in knowledge regarding the potential benefits of human interactions with nature.
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| 10. |
- Adler, Karl
(författare)
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Digital soil mapping and portable X-ray fluorescence prediction of cadmium, copper and zinc concentrations as decision support for crop production
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Trace element concentrations in agricultural soil are important for crop production. Certain trace elements, e.g. copper (Cu) and zinc (Zn), are essential for crops to complete their life cycle. Other trace elements, e.g. cadmium (Cd), can be harmful to crops or the end-consumer. Hence, it is important to have maps of soil concentrations of trace elements or methods for determining concentrations in soil samples. This thesis investigated the possibility of predicting trace element concentrations (Zn, Cu, Cd) in soil samples using portable X-ray fluorescence (PXRF) measurements. It also examined usefulness of digital soil mapping (DSM) to create maps of Cu and Cd concentrations in agricultural topsoil in Sweden.Portable X-ray fluorescence models were validated at national and farm level. Predicted Zn concentrations were found to be comparable to those obtained in conventional laboratory analysis, while predicted Cd and Cu concentrations were less accurate. The most accurate PXRF models were created using non-linear machine learning algorithms, e.g. random forest.Digital soil mapping of Cd concentrations in Skåne County, combined with data from grain sampling, revealed that low Cd concentrations in winter wheat grain were associated with predicted low concentrations in soil. The map could thus be used to identify arable soils suitable for producing winter wheat for products with strict quality criteria, e.g. baby food. Digital soil mapping of Cu concentrations at national level revealed that 47% of arable soils are highly likely not at risk of Cu deficiency. Covariate importance analysis indicated importance of airborne gamma radiation measurement data in DSM of Cu and Cd concentrations.
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