The use of composts and nature management residues in horticultural substrates: a microbiome perspective

The Belgian horticultural sector faces a major challenge to reduce the use of environmental unfriendly products in the sector, including peat in horticultural substrates as well as chemical plant protection products (PPPs). Due to changing regulations, the public opinion, and Flemish and European policies, there is an urgent need to find alternatives for peat and chemical PPPs in the horticultural sector. To reduce the use of peat and chemical PPPs in horticulture, the replacement of peat in horticultural substrates with a more sustainable alternative in which beneficial microorganisms thrive would be a good solution. Good candidates in the search for these sustainable, bio-active peat alternatives are composts and management residues. Previous studies have already shown the potential of compost and management residues as peat alternatives in horticultural substrates. But despite their importance in terms of plant growth and health, the microbiological characteristics of these peat alternatives have, not received much attention. Our current understanding of the microbial communities in sustainable peat alternatives and their role in plant growth and health is still limited. In this thesis, we therefore aimed at contributing to the understanding of microbial communities in the sustainable peat alternatives for horticultural substrates, composts and management residues, and to elucidate their role in plant growth and health. In addition, we aimed to study the potential of different approaches to modify the microbial communities in composts and management residues in order to optimize plant growth and health in horticultural substrates. Composts and management residues are considered to have beneficial microbiological characteristics compared to peat-based substrates. Studies comparing microbiological characteristics of these three types of biomass are, however, lacking. Therefore, in Chapter 2, we compared the microbiological characteristics of composts and management residues with peat-based substrates with a focus on their use as peat replacers and additional benefits such as plant growth promotion and disease suppression. All subtypes of composts and management residues could be considered as suitable peat replacers from a microbiological point of view. Moreover, several subtypes of composts and management residues showed additional benefits compared to peat-based substrates regarding their microbiological characteristics. Based on our findings, we assumed that several subtypes of composts, including green composts, VFG composts, and woody composts, and subtypes of management residues, including grass clippings, chopped heath, and woody fractions of composts, have the potential to promote plant growth and disease suppression in horticultural substrates. Based on their microbiological characteristics (Chapter 2), we assumed that management residues, such as chopped heath and soft rush, may have a positive effect on disease suppression. However, besides the horticultural substrate, fertilization also has an important effect on the microbiome and accordingly disease suppression. Therefore, in Chapter 3, we studied the effect of nature management residues in horticultural substrates on disease suppression, taking fertilization into account. Moreover, we elucidated the link between disease suppression in horticultural substrates based on management residues and the rhizosphere microbiome. Disease suppression in sustainable horticultural substrates based on management residues was dependent on the fertilization regime, indicating the importance to include fertilization in future studies focusing on disease suppression in horticultural substrates. Moreover, disease suppression in sustainable horticultural substrates could be linked to the rhizosphere microbiome. A rhizosphere microbiome composition diverging from that of peat-based substrates was most favorable for disease suppression. In addition, several bacterial and fungal taxa were identified that were correlated with disease suppression. As plant growth and health is greatly affected by the rhizosphere microbiome (Chapter 3), there is a large interest to modify the rhizosphere microbiome in order to optimize plant growth and health. In Chapter 4 and 5 we determined if the microbiological characteristics of composts and management residues can be modified using different approaches. In Chapter 4, we investigated the effect of treatments that are used to optimize chemical properties of composts and nature management residues for a better fit in horticultural substrates on microbiological characteristics. Treatments to optimize chemical properties of composts and management residues, such as maturation, acidification, blending and sieving, had a limited effect on the microbiome of compost and management residues. The initial microbial composition of composts and management residues was more important than maturation or further optimization treatments to determine bacterial and fungal community composition. However, within each batch of compost, maturation and blending seemed to have a positive effect on the microbiological characteristics, and may therefore be used to induce a limited shift in the microbiome in order to optimize plant growth and health. In Chapter 5, we investigated the effect of artificial root exudates on the rhizosphere microbiome and plant growth in compost-based horticultural substrates. Artificially adding root exudate solutions to the rhizosphere may therefore be a promising approach to modify the rhizosphere microbiome in order to benefit plant growth and health. Artificial root exudates modified the microbial community composition and increased metabolic diversity and enzyme activity in horticultural substrates based on compost. The ability to steer the microbial activity and microbial community composition in horticultural substrates using artificial root exudates provides an interesting perspective for further research. However, no positive effects on plant growth were observed. High concentrations of artificial root exudates resulted in lower root development in peat-based and compost-based substrates which could be linked to the increased activity of urease and alkaline phosphatase in response to the addition of artificial root exudates. In addition, high concentrations of artificial root exudates caused plant stress in peat-based substrates. Taken together, this research shows the potential of composts and management residues as peat replacers from a microbiological point of view. Moreover, this thesis emphasizes the importance of fertilization and the role of the rhizosphere microbiome in disease suppression in horticultural substrates based on management residues. In addition, this thesis elucidates the potential of fertilization and artificial root exudates to modify the rhizosphere microbiome in horticultural substrates and to, potentially, optimize plant growth and/or health. Based on these findings, recommendations can be made for further research and the valorization of composts and management residues in the horticultural sector.