Both mycorrhizal and Trichoderma spp. fungi are known for antagonistic effects against certain biological pathogens causing apple replant disease (ARD). The aim of this study was to assess the effectiveness of the bioinoculants based on endomycorrhizal and Trichoderma spp. fungi on the biological properties of soil as well as the parameters of the apple tree growths in a fruit tree nursery under replantation conditions. A two-year experiment was conducted on Jonagold apple trees grafted on to M.9 rootstock in western Poland. The trees were planted in the replant soil—from areas used for the production of apple trees, and in the crop rotation soil, that had not been used for nursery purposes before. A mycorrhizal inoculum and preparations containing Trichoderma spp. fungi were applied to the replant soil. Biological properties of the soil and the growth of the aerial and underground parts of the apple trees were assessed. The enzymatic (dehydrogenases and protease) and respiratory activity of the replant soil was significantly lower than that of the crop rotation soil. The apple trees grew worse when exposed to the ARD conditions. The effectiveness of applied bioinoculants in mitigating the effects of replantation in the nursery were shown. Both the treatment mycorrhization and the application of bioinoculants containing Trichoderma spp. increased the respiratory and enzymatic activity of the replant soil. The growth of the root system and the aerial parts of the trees (including leaves) was much better after the combined use of both types of fungi than in the replant soil that had not received the fungal treatment.

The imbalance of the soil microbiome is a primary indicator of ARD (apple replant disease). Biofumigation is a treatment that enables the restoration of microbiome balance. This study involved an analysis of the taxonomic and functional diversity of bacterial communities in replanted soil (ARD), in replanted soils with forecrops of French marigold (Tagetes patula L.), white mustard (Sinapis alba), and oilseed radish (Raphanus sativus var. oleifera), and in agricultural soil. The biofumigation treatment with phytosanitary plants changed the structure and abundance of the replanted soil microbiome in a fruit tree nursery. The count of operational taxonomic units (OTU) of the Proteobacteria, Bacteroidota, Patescibacteria, Chloroflexi, and Verrucomicrobiota phyla increased, whereas the count of the Firmicutes, Acidobacteriota, and Actinobacteriota phyla decreased. Biofumigation caused an increase in the content of some dominant bacterial genera, such as Flavobacterium, Massila, Sphingomonas, Arenimonas, and Devosia, in the replanted soil. Their presence in the soil may improve the growth of plants, induce their systemic resistance, and thus improve the production properties of soil with ARD. The research results led to the conclusion that the use of phytosanitary plants in nursery production can be an effective alternative to the chemical fumigation of soil.

Apple replant disease (ARD) may cause significant losses both in commercial orchards and in fruit tree nurseries. The negative effects of ARD may be limited by using biofumigation. The aim of the study was to assess the influence of this treatment on the biological properties of replanted soil in a tree nursery. In two-year experiment, apple trees of the ‘Golden Delicious’ cultivar were used. The trees were planted into soil from two sites. The soil from one site had not been used in a nursery before (crop rotation soil). The other soil had been used for the production of apple trees (replanted soil). Three species of plants were used in the replanted soil as a forecrop: French marigold (Tagetes patula), white mustard (Sinapis alba), and oilseed radish (Raphanus sativus var. oleifera). The following parameters were assessed in the experiment: the enzyme and respiratory activity of the soil, the total count of bacteria, fungi, oomycetes and actinobacteria in the soil, as well as the count and species composition of soil nematodes. The vegetative growth parameters of the apple trees were also assessed. The biological properties of the replanted soil were worse than those of the crop rotation soil. In the replanted soil, the organic matter content, enzyme and respiratory activity as well as the count of soil microorganisms were lower. The biofumigants, used as a forecrop on the replanted soil, significantly increased its enzyme activity and respiratory activity. Dehydrogenase activity increased more than twofold. Growth parameters of the trees were significantly improved. The height of the trees increased by more than 50%, and the leaf area, weight and total length of side shoots were higher as well. The density of nematodes in the replanted soil after biofumigation was significantly reduced, with a larger reduction in the marigold fumigated soil. Eight of the eleven nematode species were completely reduced in the first year after biofumigation treatment.

How soil is used affects its production characteristics in the future. Under ARD (Apple Replant Disease) conditions, replanted soil’s physical, chemical and biological properties deteriorate. Their improvement is possible through, for example, increasing the content of organic matter in the soil. The study aimed to assess the effect of two organic additives for replanted soil on its physical, chemical and biological properties, as well as on the vegetative growth of apple trees of the ‘Gala Schniga SchniCo(s)’ cultivar grafted on M.9 rootstock. The experiment was performed in 2021, in western Poland, on a nursery farm. The trees were planted in pots filled with soil from two stations: soil previously used for the production of apple trees (replanted soil) and nursery material (agricultural soil) unused for production so far. To fertilise it, three different portions of biocarbon and Carbomat Eco soil conditioner were added to the replanted soil. The experiment showed that apple trees grown on replanted soil had fewer side shoots, a smaller leaf area and a lower mass of leaves than those grown on agricultural soil. Furthermore, supplementation of replanted soil with organic additives caused a significant increase in its enzymatic activity and respiration, increased the rate of photosynthesis and improved several parameters determining the strength of vegetative growth in apple trees.

In a long-term monoculture with fruit trees and tree nurseries, it is necessary to regenerate the soil due to the risk of apple replant disease (ARD). The occurrence of ARD is manifested in the structure of the mycobiome. The assumption of our experiment was that the use of oil radish (Raphanus sativus var. oleifera), white mustard (Sinapis alba), and marigold (Tagetes patula L.) as phytosanitary plants for biofumigation would provide crops with nutrients, improve soil physicochemical properties, and influence the diversity of microbiota, including fungal networks, towards a beneficial mycobiome. Metagenomic analysis of fungal populations based on the hypervariable ITS1 region was used for assessing changes in the soil mycobiome. It showed that biofumigation, mainly with a forecrop of marigold (Tagetes patula L.) (R3), caused an improvement in soil physicochemical properties (bulk density and humus) and the highest increase in the abundance of operational taxonomic units (OTUs) of the Fungi kingdom, which was similar to that of agriculturally undegraded soils, and amounted to 54.37%. In this variant of the experiment, the most OTUs were identified at the phylum level, for Ascomycota (39.82%) and Mortierellomycota beneficial fungi (7.73%). There were no such dependencies in the soils replanted with forecrops of oilseed radish (Raphanus sativus var. oleifera) and white mustard (Sinapis alba). Biofumigation with marigold and oil radish contributed to a reduction in the genus Fusarium, which contains several significant plant-pathogenic species. The percentages of operational taxonomic units (OTUs) of Fusarium spp. decreased from 1.57% to 0.17% and 0.47%, respectively.