Bringing soil fungi into action: Options for forward-looking agriculture

Intensively managed agricultural production of food and fiber does often coincide with negative side-effects such as environmental pollution and soil degradation. The integration of ecology-based agricultural practices has a promising perspective to bring agriculture to a more sustainable level. Many studies point at the importance of re-integrating traditional agricultural practices, such as the use of organic amendments and crop diversification (intercropping, wider crop rotations, cover crops). Other lines of research explore the possibilities of soil inoculation with microbial strains as biofertilizers and biopesticides. Arable soils harbor a diverse community of saprotrophic fungi, however their biomass and activity is mostly limited. This is due to intensive management practices, such as the use of synthetic rather than organic fertilizers, use of chemical pesticides and mechanical disturbances of soils. Having an active community of saprotrophic fungi is essential for soil functioning, as can be seen in natural and semi-natural ecosystems. In this Ph.D. thesis study, I explore options for boosting the biomass of saprotrophic fungi in arable soils. I also test the impact of stimulation of saprotrophic fungi on plants and other soil microbial inhabitants, including bacteria, pathogenic- and mycorrhizal fungi.

Saprotrophic soil fungi can respond to organic inputs both in the form of dead plant parts (litter) and rhizodeposits derived from living roots. Therefore, two possible approaches were examined for the stimulation of saprotrophic fungi in arable soil, namely the addition of exogenous organic substrates and the modification of root exudate composition.

In a series of pot experiments, organic materials of varying quality and origin were amended into arable soil, to test the response of fungi in terms of biomass and community composition (Chapter 2). Based on a first screening, paper pulp and beech wood sawdust amendment resulted in a rapid increase in ascomycete saprotrophic fungi (mainly Sordariomycetes), which persisted for a period of at least two months. Using the same setup, I further tested the effect of wood sawdusts from distinct tree species, alone or in combination with mineral nitrogen. The fungus-stimulating effect of wood sawdust amendment was also tested in four arable soils with different soil characteristics. The results revealed that saprotrophic fungal communities of arable soils retain a good ability to respond to wood sawdust of deciduous trees, but not to sawdust of coniferous tree species. Combination of sawdust with mineral nitrogen resulted in extra stimulation of saprotrophic fungi.

The aim of Chapter 3 was to test the effect of phenolic root exudates on the biomass and community composition of rhizosphere fungi. To this end, an artificial rhizosphere model system was established. It allowed to introduce artificial exudate mixtures via diffusion into the soil, thereby simulating root exudation. In this way, phenolic acids were added both alone and in combination with a mixture of primary root exudate metabolites. Phenolic acids were applied at a rate consistent with the levels found for phenolic acids deposited in soils (0.02 - 0.2 mg g-1 soil). Phenolic acids had little effect on the total fungal biomass in the simulated rhizosphere. The same result was obtained in a follow-up experiment, where rhizosphere fungal biomass was measured for Arabidopsis thaliana mutants with an altered composition of phenolic root exudates. This indicates that selecting crop varieties for a higher exudation of phenolic acids is not a promising strategy for promoting saprotrophic fungi in the rhizosphere of crop plants. This study also showed that phenolic acids promote specific root-infecting fungi (Fusarium, Fusicolla and Trichoderma) in the simulated rhizosphere. Consequently, this indicates phenolic root exudates as potential modulators of rhizosphere and root fungal communities.

The composition and activity of microbes in bulk soil has a strong influence on the assembly of microbial communities in the rhizosphere and roots. Having established that wood sawdust amendment causes an effective stimulation of saprotrophic fungi in arable soil, Chapter 4 showed how this affects the biomass, activity and composition of microbial communities associated with crop seedlings. 13CO2-pulse labelling of carrot seedlings grown in sawdust-amended and control soil revealed that sawdust-stimulated fungi in soil can extend into the rhizosphere and actively consume plant-derived carbon. The total bacterial abundance and active uptake of root exudates was not affected by sawdust addition, while AMF abundance and activity were promoted. The analysis of rhizosphere and root-associated communities using DNA(-SIP) illustrated that Sordariomycetes, Glomeromycetes, Bacteroidia and Rhizobiales increased in relative abundance. Based on sequencing data, the sub-community of potential pathogenic fungi did not increase relative to the total fungal community. Hence, the conditioning of arable soil with sawdust promotes a higher activity of saprotrophic fungi in the rhizosphere, thereby steering root-associated microbial communities.

After individuating fungus-stimulating organic amendments (Chapter 2), assessing their ability to stimulate rhizosphere-competent fungi and describing their effects on bacteria (Chapter 4), I studied if the stimulation of saprotrophic fungi by woody materials and paper pulp can be used to control Rhizoctonia solani, one of the most widespread causal agents of soil-borne plant diseases (Chapter 5). To this end, a R. solani isolate was exposed to woody materials and paper pulp in a Petri dish assay. This showed that paper pulp is a highly suitable substrate for the growth of R. solani, while its performance was lower on sawdusts, but varied according to tree species identity. This was followed by two bioassays performed with an arable soil naturally infected by R. solani, where I planted seeds of a red beet variety which is  susceptible to this pathogen. The bioassays showed that oak and elder wood resulted in a consistent improved control of disease. In addition, paper pulp caused a short-term, transient stimulation of R. solani, which coincided with a poor performance of beets sown immediately after amendment. An interval of two weeks or longer between paper pulp addition and sowing resulted in disease suppression. These results point at the importance of timing of organic amendments relative to sowing, as a factor affecting the efficacy of disease-suppressing soil treatments.

Overall, this thesis provides information on how cellulose-rich organic amendments and phenolic root exudates affect the abundance and composition of saprotrophic fungi, bacteria and soil-borne pathogenic fungi in arable soils and in the rhizosphere of crops. Based on these results, I depict a promising perspective for the use of cellulose-rich materials as a tool to promote sustainable biocontrol via managing microbial communities and microbial interactions in arable soils. In addition, a possible role of phenolic root exudates in modulating the recruitment of root-infecting fungi is indicated.