The demand for ecologically cultivated fruits is growing each year, but the yields in organic farming are still lower than the yields in conventional farming. Moreover plant pathogens are a serious threat in organic fruit production and the assortment of conventional pesticides is limited in organic farming. The European Commission has established regulations that state which types of bioproducts can be used in organic farming. Appropriately chosen biopreparations might be a solution to this problem. Biopreparations are products used to inhibit the growth of pathogenic fungi or bacteria, stimulate plants growth and enhance plant nutrient uptake. They can be composed of plant growth promoting bacteria and fungi, plant extracts or animals-derived compounds. The second category of bioproducts useful for enhancing yield and nutrient uptake are biostimulants. They can be composed of microorganisms, protein hydrolysates, seaweed extracts and other substances. Bacteria, fungi and yeasts are used in biocontrol of plant pathogens and in enhancing plants growth by producing hormone-like substances and reducing symptoms of environmental stress caused by weather or soil factors such as drought or low nutrient availability.

The number of raspberry plants dying from a sudden outbreak of gray mold, verticillium wilt, anthracnosis, and phytophthora infection has increased in recent times, leading to crop failure. The plants suffer tissue collapse and black roots, symptoms similar to a Botrytis–Verticillium–Colletotrichum–Phytophthora disease complex. A sizeable number of fungal isolates were acquired from the root and rhizosphere samples of wild raspberries from different locations. Subsequent in vitro tests revealed that a core consortium of 11 isolates of selected Trichoderma spp. was the most essential element for reducing in phytopathogen expansion. For this purpose, isolates were characterized by the efficiency of their antagonistic properties against Botrytis, Verticillium, Colletotrichum and Phytophthora isolates and with hydrolytic properties accelerating the decomposition of organic matter in the soil and thus making nutrients available to plants. Prebiotic additive supplementation with a mixture of adonitol, arabitol, erythritol, mannitol, sorbitol, and adenosine was proven in a laboratory experiment to be efficient in stimulating the growth of Trichoderma isolates. Through an in vivo pathosystem experiment, different raspberry naturalization-protection strategies (root inoculations and watering with native Trichoderma isolates, applied separately or simultaneously) were tested under controlled phytotron conditions. The experimental application of phytopathogens attenuated raspberry plant and soil properties, while Trichoderma consortium incorporation exhibited a certain trend of improving these features in terms of a short-term response, depending on the pathosystem and naturalization strategy. What is more, a laboratory-scale development of a biopreparation for the naturalization of the raspberry rhizosphere based on the Trichoderma consortium was proposed in the context of two application scenarios. The first was a ready-to-use formulation to be introduced while planting (pellets, gel). The second was a variant to be applied with naturalizing watering (soluble powder).

The threat caused by plants fungal and fungal-like pathogens is a serious problem in the organic farming of soft fruits. The European Commission regulations prohibit some commercially available chemical plant protection products, and instead recommend the use of natural methods for improving the microbial soil status and thus increasing resistance to biotic stresses caused by phytopathogens. The solution to this problem may be biopreparations based on, e.g., bacteria, especially those isolated from native local environments. To select proper bacterial candidates for biopreparation, research was provided to preliminarily ensure that those isolates are able not only to inhibit the growth of pathogens, but also to be metabolically effective. In the presented research sixty-five isolates were acquired and identified. Potentially pathogenic isolates were excluded from further research, and beneficial bacterial isolates were tested against the following plant pathogens: Botrytis spp., Colletotrichum spp., Phytophthora spp., and Verticillium spp. The eight most effective antagonists belonging to Arthrobacter, Bacillus, Pseudomonas, and Rhodococcus genera were subjected to metabolic and enzymatic analyses and a resistance to chemical stress survey, indicating to their potential as components of biopreparations for agroecology.

The current study focuses on the optimization of bacterial growing medium composition, including the carbon and nitrogen source in different concentrations, the pH value of the medium and the temperature. Optimization was performed for four environmental bacterial isolates belonging to the genera Arthrobacter, Pseudomonas and Rhodococcus, which were previously obtained from wild raspberries. These bacteria proved to be potent antagonists against certain fungal and fungal-like plant pathogens. Furthermore, three preservation methods and three sample preparation techniques were evaluated. In addition, a prebiotic supplementary blend based on previous research was tested. The research included a pot experiment to estimate the influence of bacterial cultures on the growth of plant shoots and roots, on the soil enzymatic activity and the content of macronutrients, minerals and nitrogen in the soil depending on the naturalization strategy. The best carbon and nitrogen source were chosen. The addition of a supplementary blend resulted in the increased growth of two bacterial isolates. Bacterial inoculum applied to the roots and watering resulted in increased shoot mass in objects infected with plant pathogens, although in plants without the pathogen infection, bacterial inoculum resulted in the decreased mass of plants. Naturalization strategy should be matched to the pathogens present at plantations.

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Apple bull’s eye rot (BER), caused by Neofabraea representatives, is a major challenge for apple production. This study aimed to identify microbial antagonists capable of suppressing Neofabraea by leveraging soil microorganisms from six distinct apple orchard land management systems. Key...