The horticultural sector faces significant challenges driven by the increasing demand for residue-free and environmentally sustainable produced plants. A key factor in addressing these challenges is the rhizosphere microbiome, which plays a crucial role in managing root-borne pathogens in horticultural substrates. This review explores the role of the rhizosphere microbiome in root pathogen suppression, highlighting specific microorganisms that contribute to disease control. We also identify key gaps in our understanding of the microbiome's involvement in root disease suppression within horticultural substrates. Furthermore, we propose four strategies to enhance biological control of root diseases by manipulating the rhizosphere microbiome: (1) the use of peat alternatives, (2) microbial inoculation, (3) the application of artificial root exudates, and (4) tailored fertilization. Particular emphasis is placed on the inoculation of peat alternatives with Trichoderma spp. as an effective approach for improving root disease management in horticultural systems.

The extensive use of peat in horticultural substrates raises significant environmental concerns due to its unsustainable extraction and limited availability. To address these challenges, this research explores sustainable alternatives by evaluating the impact of various peat-free and peat-reduced substrates on plant growth, while also assessing the potential benefits of microbial interventions. The study is conducted within the framework of the ToPGa collaborative project, which aims to promote sustainable horticultural practices by developing peat-reduced production systems. Initial trials tested bacterial inoculations, both in consortia and as single strains, showing improved plant growth in peat-free substrates compared to controls. Building on these results, subsequent experiments incorporated Schizophyllum commune and arbuscular mycorrhizal fungi (AMF) into substrates containing 50% and 30% peat, respectively. These beneficial microorganisms, known for their plant growth-promoting properties, demonstrated a significant increase in the growth of Petunia hybrida cv. “Mitchell.” Preliminary findings highlight the potential of beneficial microbial consortia to gradually reduce peat usage without compromising plant performance. Furthermore, microbial inoculations help mitigate common issues associated with peat-free substrates, such as nitrogen immobilization, thus maintaining productivity and supporting healthy plant development. The study also addresses the challenge of nitrogen immobilization by stabilizing the nitrogen cycle through the introduction of beneficial nitrogen-fixing bacteria and mycorrhizal fungi. This research underscores the importance of plant-microbe interactions in creating eco-friendly cultivation systems by improving the performance of peat-reduced substrates through microbial interventions and also providing a viable pathway toward reducing reliance on peat.

As the availability of chemical plant protection products decreases, there are less opportunities for curative treatments of plant diseases, such as Pythium, Fusarium and Phytophthora. As a consequence, the prevention of diseases are becoming increasingly important. Microorganisms can suppress the growth or establishments of pathogens in the root zone. This natural process is called disease suppression. However, growing media may lack a symbiotic microbial community for disease suppression. Many growing media have a low microbial diversity compared to soils at the start of plant growth and the microorganisms present may not contribute to disease suppression. The current redesign of growing media by renewable alternatives form an opportunity to include microbiology based solutions to increase the resilience against diseases. Here, we will discuss current and future research needs to optimize the microbiology of growing media to improve resilience against pathogens in soilless cultivation systems.  

Growing media support a range of microbial activity with by-products in gaseous form as well as aqueous solution. This will be affected by moisture, nutrient supply from fertilizer content, and storage conditions such as temperature. Growing media is commonly stored in plastic-wrapped bales prior to use, which is likely to restrict air exchange and aerobic microbial activity. Gas composition was measured using FTIR in bales of bedding mixture, both 6-months old and fresh from production, stored outside from October 2022. Both bales showed variation with height in temperature, physico-chemical properties, and gas composition. The older bale contained reduced oxygen (19 % near top to 11 % near bottom) and an accumulation of carbon dioxide (2 % near top to 10 % near bottom). In comparison, two days after delivery, the fresher material contained less oxygen (7.4 % near top to 1.1 % near bottom) and more CO2 (15.2 % near top to 19.6 % near bottom). In addition, a high concentration of nitrous oxide (N2O) was found, especially in the newly produced bale. A further time series was measured on a bale produced in February 2024 and stored outside for 12 weeks. A peak in nitrous oxide, sulphides, and methane, was observed after 4 weeks, declining over the following weeks. These gases result from biological activity following a standard environmental redox sequence. When oxygen becomes limiting, nitrogen species will be reduced, converting biologically available nitrates to nitrous oxide and nitrogen gas, then sulphates to hydrogen sulphide, and available carbon to methane. Possible implications of these biological processes include a loss of fertiliser nitrogen and potential production of compounds harmful to plant growth. Further studies should focus on managing storage conditions to optimise usability of the finished product.

Green compost is a potentially useful component of peat free growing media blends. It is often underutilised due to issues with chemical composition (e.g. EC), nutrient lock up, potential pathogens and microbial stability of the material. Dynamic respirometry, measuring evolved CO₂, is an established method in the UK composting industry to characterise the stability of green compost and has been demonstrated as more reliable for highly unstable materials than the standard OUR test. Microbial stability of growing media components is often reported, however, the interaction effect when these materials are blended is not currently well understood. Stability results for a range of PAS100 certified green composts tested alone are presented. Further testing with one of the green composts mixed with a wood fibre is also presented. Both the wood fibre and the green compost used in the blend demonstrated relatively high stability individually. When blended together the CO₂ production was higher than the prediction based on a simple addition of CO₂ production from the individual components. This indicates there is an interaction between the component parts within a blend resulting in reduced stability. The interaction effect could be due to an inoculation effect of the green compost on the relatively sterile wood fibre. Further work is required on these interaction effects when adding novel growing media components to blends, however, dynamic respirometry is a useful tool for studying microbial stability of growing media components and blends at a bulk scale.