Microbiome composition of the spermosphere and the rhizosphere of wild and modern bean accessions grown in an agricultural and a native soil from Colombia was characterized by metagenomics and... Show moreMicrobiome composition of the spermosphere and the rhizosphere of wild and modern bean accessions grown in an agricultural and a native soil from Colombia was characterized by metagenomics and cultivation-dependent approaches. A higher relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, was observed in the rhizosphere of wild accessions while an increase in relative abundance of Actinobacteria and Proteobacteria was observed in the rhizosphere of modern accessions. These divergences associated with differences in specific root length (SRL). Using 16S-rDNA data from other studies revealed that also wild relatives of other crop plant species presented higher relative abundance of Bacteroidetes. Additionally, bean accessions were grown in a native and an agricultural soil from Colombian. The transition of common bean from a native to an agricultural soil led to a gain of rhizobacterial diversity and to a stronger bean genotype-dependent effect on microbiome assembly. In addition, during seed imbibition and germination, significant differences were detected between the spermosphere microbiomes of wild and modern bean accessions. A domestication effect on microbiome assembly already at this early developmental stage was evidenced. The research presented in this thesis showed that domestication of common bean had a significant effect on the composition of the microbiome. Show less
This thesis investigates the effects of genetic modification of the starch quality in potato on the structure and function of the soil fungal community via changes in root-exudates and litter... Show moreThis thesis investigates the effects of genetic modification of the starch quality in potato on the structure and function of the soil fungal community via changes in root-exudates and litter composition, and compares the observed differences between the GM- and its parental variety in the context of the __normal__ variation effected by conventionally produced cultivars. In order to study the fungal community composition and functionality, an integrated approach of molecular fingerprinting methods and measurements of fungal enzymes involved in degradation of organic matter in the soil was employed. In field experiments the effect of soil type, season and plant growth stage on rhizosphere fungi were evaluated and in the greenhouse experiments stable isotopes were employed to monitor carbon flow from the plant to rhizosphere microbes and a decomposer experiment was designed to investigate the faith of the potatoes and leaves possibly left into the soil. The detailed greenhouse studies revealed differences between GM- and its parental variety. The field studies, however, confirmed that these differences are transient in field conditions and that fungi in the potato rhizosphere are affected more by soil type, sampling year, plant growth stage and cultivar type than the genetic modification. Show less
Plants are attacked by a variety of (micro)organisms. In order to cope with potential attackers many plants synthesize a diversity of repellent, deterrent and/or toxic compounds. Pyrrolizidine... Show morePlants are attacked by a variety of (micro)organisms. In order to cope with potential attackers many plants synthesize a diversity of repellent, deterrent and/or toxic compounds. Pyrrolizidine alkaloids (PAs) are a well-known class of defense compounds, abundantly found in species of Senecio and Jacobaea. The objectives of the study were to acquire knowledge on the PA composition of plants and its interaction with soil-borne microorganisms. In order to do so, a more sensitive, PA-analysing method was applied, which allowed us to distinguish between PAs in tertiary amine and N-oxide form. The tertiary PA form is known to have a more negative effect on generalist insects. Our study clearly showed that high levels of tertiary PAs occur in Jacobaea vulgaris and not caused by an artefact as suggested in previous studies. Green-house experiments showed that the PA composition below- and aboveground was significantly aff ected by both soil-type and soil-inoculum. The inoculum-induced PA composition aboveground did affect thrips resistance for one J. vulgaris genotype. Experiments also showed that the fungal community did depend on the PA composition of the plant while this had less or no effect on bacterial and mycorrhizal communities in roots and rhizosphere soil. Show less
Rising atmospheric CO2 levels are predicted to have major consequences upon carbon cycle feedbacks and the overall functioning of terrestrial ecosystems. Photosynthetic activity and the structure... Show moreRising atmospheric CO2 levels are predicted to have major consequences upon carbon cycle feedbacks and the overall functioning of terrestrial ecosystems. Photosynthetic activity and the structure of terrestrial macrophytes is expected to change, but it remains uncertain how this will affect soil-borne communities dependent on plant-derived carbon, and their feedbacks on ecosystem function. Our main objective is to assess the impact of increased atmospheric carbon dioxide on microbial community dynamics in the rhizosphere. Using a controlled growth system, we examined the short-term and long-term impact of elevated atmospheric CO2 on soil-borne microbial communities by comparing belowground community responses associated with plants grown under ambient versus double ambient CO2 environments. Results on the structure and dynamics of broad and specific microbial groups provided insight into the plant-microbe interactions of the r hizosphere under elevated CO2. We also showed that the specific microbial groups are affected by elevated CO2 and demonstrate that presumably rhizo-competent bacteria and fungi are most highly affected by increased atmospheric CO2. These patterns were consistent with observed changes in the density of antibiotic production genes as well as changes in exudation patterns. The results demonstrate that elevated CO2 influenced different parts of the soil microbial community, but that the effects depend on the plant species and soil type. Pulse labelling studies demonstrates that elevated atmospheric CO2 increases translocation of plant-fixed carbon, via arbuscular mycorrhizal fungi (AMF), and that distinct microbial populations incorporate plant-derived carbon under different levels of atmospheric CO2. As opposed to simply increasing the activity of soil-borne microbes resident at ambient CO2 conditions, elevated atmospheric CO2 clearly selects for opportunistic plant-associated microbial communities, with a shift in dominant AMF species, as well as rhizosphere bacterial and fungal populations. These experiments also showed that AMF are the main conduit in the transfer of carbon between plants and soil. The microbial carbon dynamic model derived from our results provides a general framework for reappraising our view of carbon flow paths in soils and their effects on soil biodiversity under elevated atmospheric CO2 concentration. Show less
