Soil is a home for an unbelievable diversity and abundance of microbial life that is essential for supporting life on our planet. Microorganisms living in soil take part in cleaning our water,... Show moreSoil is a home for an unbelievable diversity and abundance of microbial life that is essential for supporting life on our planet. Microorganisms living in soil take part in cleaning our water, degrading toxic compounds and recycling nutrients, and last but not least, they are essential partners to plants. Through their roots, plants release a mix of secretions to attract microorganisms, creating a remarkable environment called the rhizosphere. The rhizosphere is populated by microbes who often provide beneficial services to plants, like nutrient acquisition, growth promotion and protection against diseases. Modern agriculture suffers from losses caused by crop diseases, and a common way of controlling diseases is using pesticides. Pesticides often have a negative impact on the environment, and disease-causing agents (pathogens), can become resistant with time. One of the possible solutions to this problem is based on soil microbial communities. Due to the activity of their microbiome, some soils possess a natural capacity to protect plants against diseases. These soils are called disease suppressive soils, and the investigation of the microbial mechanisms leading to the natural protection of crops is the topic of this thesis. In our work we used a common pathogen of cereals, fungus Fusarium culmorum, and wheat, to first, identify suppressive soils able to protect this plant from the pathogen, and, investigate the mechanisms of protection using e.g. sequencing and mass spectrometry. During our project we identified potential microbes, genes and metabolites involved in soil disease suppressiveness. Moreover, we evaluated the impact of microplastic on the soil disease suppressiveness. Show less
Acidobacteria is a widely distributed phylum but their functional roles in ecosystem processes are still largely elusive. The Granulicella genus belongs to the class Acidobacteriia and is known to... Show moreAcidobacteria is a widely distributed phylum but their functional roles in ecosystem processes are still largely elusive. The Granulicella genus belongs to the class Acidobacteriia and is known to produce copious amount of Extracellular Polymeric Substances (EPS), which are fundamental for microbial life. The major goal of my thesis was to investigate and understand the metabolism of Granulicella sp. strains WH15 and 5B5, and the functions and environmental fate of EPS of Granulicella sp. WH15 (WH15EPS). Optimization of carbon concentration and manganese in culture medium allowed our strains, especially WH15, to grow faster in laboratory conditions, producing extractable amounts of EPS. Using the Stable Isotope Probing technique, we observed the incorporation of WH15EPS by Singulisphaera and its connections to other Planctomycetes and Acidobacteria, which were not reported before. In addition, our results showed, in the genomes of the microbes which incorporated WH15EPS, a large diversity of glycoside hydrolase with biotechnological potential and a high number of unclassified microorganisms that could be targeted for future studies. The data presented in this thesis establish a solid fundamental basis for more mechanistic studies of Acidobacteria and other uncultivated microbes. Show less
The use of N fertilizers has increased worldwide in the past century. While this increased input of N has increased food productivity, it has also contributed to decreases in biodiversity, soil... Show moreThe use of N fertilizers has increased worldwide in the past century. While this increased input of N has increased food productivity, it has also contributed to decreases in biodiversity, soil quality and environmental health, including increases in greenhouse gas emissions. These emissions in agricultural soils are largely carried out by the soil microbiome, or the microorganisms living in the soil and transforming N fertilizers to different forms. Here, the overall research aim was to gain detailed insight into the effects of nitrogen fertilizer schemes, including long term fertilization, on soil microbial communities. To do this, I applied next-generation sequencing technology and associated bioinformatics analyses to field experiments in the Netherlands and in Brazil. Show less
Soil biodiversity is huge and determines largely the functioning of terrestrial ecosystems both at the ‘macro’ and the ‘micro’ level. Despite the general acceptance of the large impact of land use... Show moreSoil biodiversity is huge and determines largely the functioning of terrestrial ecosystems both at the ‘macro’ and the ‘micro’ level. Despite the general acceptance of the large impact of land use and other human activities on species loss in terrestrial ecosystems, their effects on microbial species reduction and the consequences are largely unknown. A major reason is the scarcity of experimental approaches to assess the relevance of soil microbial diversity for the functioning of soil ecosystems. The main goal of the study described in this thesis was to obtain better understanding of the diversity, structuring and functioning of bacterial communities in soil and and rhizosphere. With that purpose, we initially applied the rather old dilution approach to manipulate the diversity of microbial communities in soil by inoculation and subsequent incubation of more or less diluted soil suspensions in pre-sterilized soils. Show less
