Microbial community analysis in soil (rhizosphere) and the marine (plastisphere) environment in function of plant health and biofilm formation

In this thesis, high-throughput sequencing methods were used to study microbial communities in two environments: the plant’s rhizosphere and on plastic debris. To prevent plant diseases and maintain a good crop productivity, crop cultivation often relies on high pesticide and fertilizer uses. There is a great interest in reducing this high use, and the effect of application of specific environment-friendly substrate amendments, such as biochar and chitin, to the soil or substrate is studied in this respect. These amendments can have a direct effect on the micro-organisms in the rhizosphere, the narrow zone of soil surrounding the plant root. This shift in rhizosphere microbiome should be directed towards beneficial micro-organisms such as plant-growth promotors and biocontrol agents. Micro-organisms in the ocean are less-extensively studied compared to a soil environment. Nonetheless they can reach high numbers, especially when they can attach to substrates, and perform similar crucial roles as for soil environments. With an expected amount of 8 million tons entering our marine ecosystem yearly, the major contaminator of our oceans and seas is probably plastic. The microbial colonization of plastic debris in the marine environment, also referred to as “the plastisphere”, has been studied since the seventies, but the dynamics of this colonization and impact on plastic degradation, the marine ecosystem and animal and human health is currently poorly understood.In the first part of this thesis, the effect of biochar and chitin on the rhizosphere microbiome in relation to crop growth, disease development or survival of human pathogens is studied. We showed that in nutrient-limiting conditions, biochar was able to change the physicochemical properties of soil and substrates and induced major changes in the bacterial composition of strawberry plants, redirecting the rhizosphere community towards a higher relative abundance of plant-growth promoters and biocontrol agents. No effect of biochar addition to peat was seen on the fungal composition of the strawberry rhizosphere. Both the increase in nutrient stock and the shift in bacterial community composition could be related to an increase in strawberry crop growth, a higher strawberry yield and an increase in resistance towards the fungal pathogen Botrytis cinerea. In addition, this aboveground infection also affected the rhizosphere bacterial community. This research indicates that upon biochar incorporation in peat, plants recruit rhizosphere bacteria that may help them in their defense and plant growth promotion.In contrast, chitin addition to potting soil altered both the bacterial and fungal community composition of the lettuce rhizosphere, redirecting the microbiome towards higher abundances of chitin-degraders and plant growth promotors. These effects were correlated with an increase in lettuce growth and a reduction in the survival of Salmonella enterica on the leaves. Especially the consumption of contaminated leafy vegetables, such as lettuce, can be problematic for human health and reported to be the cause of S. enterica outbreaks. The use of chitin can thus be tested further as an interesting supplementary strategy for sustainable control of this zoonotic pathogen in the food chain. In the second part of this thesis, the major contributors and dynamics of the bacterial and fungal colonization of marine plastic debris located at the seafloor in the Belgian part of the North Sea were studied. We showed that environmental properties, plastic-related properties and biofilm formation stages are probably the most important factors influencing the bacterial colonization on plastic. Dependent on the environment, this bacterial biofilm formation can go through progressive temporal stages, reaching a more or less stable community after a few months. In addition, we studied for the first time the fungal community on plastic debris, which was also quite diverse for different plastics, even when they were located at the same site. This microbial colonization could have major influences on the marine ecosystem. We showed that compared to seawater and sediment, other bacterial groups were attached on plastic, indicating that plastic could serve as a transport vector for micro-organisms to other environments. In contrast, the microbial colonization could also be beneficial in terms of biodegradation. Despite plastic-degradation has not been shown in this study, a Mycobacterium species was identified which is probably able to degrade the pigments of beach-located resin pellets, indicating that biodegradation of plastic-related chemicals is possible. The use of high-throughput sequencing techniques made it possible to give insight in the microbial community composition. Here we focussed mainly on taxonomic identification using amplicon sequencing, but already a first step was taken towards functional annotations using shotgun metagenomics in function of chitinase detection. Future studies should elaborate more on this also including e.g. shotgun metagenomics, metatranscriptomics and stable-isotope probing in order to identify specific biochar-, chitin- and even plastic-metabolizers and related functions