The damage caused by soil-borne diseases in Cunninghamia lanceolata (Lamb.) Hook (Cupressaceae), commonly called the Chinese fir, has become increasingly severe in China in recent years. Due to the strong seasonal dependence of the occurrence and severity of these diseases, the ecological processes influencing changes in the composition and function of the plant microbiome during different seasons of pathogen infection have been rarely studied. This study compared the seasonal variations in soil physicochemical properties between the rhizosphere soils of healthy and diseased C. lanceolata in major production areas in China. It further explored the effects of root rot on the composition, structure, and ecological functions of rhizosphere microorganisms. The results demonstrated that seasonal variations significantly influenced the physicochemical properties and microbial composition of the rhizosphere soil in C. lanceolata affected by root rot. Microbiome analysis further confirmed that, within the same season, healthy C. lanceolata contained a greater abundance of ecologically beneficial microbial taxa in the rhizosphere soil compared to diseased trees. These microorganisms may function as bioprotectants. This study enhances our understanding of the structural and functional changes in the rhizosphere soil microbiome associated with soil-borne diseases and provides potential ecological management strategies to improve plant resistance to root rot.

Root rot disease is a significant constraint to sweet cherry production in the highlands of southwest China, causing substantial yield losses. While the disease is prevalent, the complex interplay of climate, topography, soil, and management practices on its development remains poorly understood. To address this knowledge gap, a field survey encompassing 95 field sites was conducted to assess disease incidence (DI) and canopy damage index (CDI). Our results showed that the average DI and CDI were 27.04 and 20.52%, respectively. DI and CDI were influenced by management practices: they both increased with the number of planting years and were lower with Cerasus szechuanica rootstock and composted animal manures compared with Da-qingye rootstock and uncomposted animal manures. Climatic and topographic factors also played an important role in observing higher DI at higher altitudes and shady slopes (P < 0.05). Moreover, both DI and CDI demonstrated positive correlations with the aridity index and sunshine duration and negative correlations with mean annual temperature and mean annual precipitation (P < 0.05). Soil properties, including moisture content, bulk density, pH, and sand content, were positively associated with DI and CDI, while clay content and available potassium exhibited negative correlation. The present study emphasizes the combined impact of multiple factors on root rot disease in sweet cherry, with management practices and soil properties having a more decisive effect than climate and topography. These findings provide crucial insights for developing effective disease management strategies.

Root rot is a general term for soil-borne diseases that cause the necrosis and decay of underground plant parts. It has a wide host range and occurs in various types of plants, including crops, horticultural crops and medicinal plants. Due to the fact that medicinal plants generally have a long growth cycle and are primarily the root and rhizome herbs. This results in root rot causing more serious damage in medicinal plant cultivation than in other plants. Infected medicinal plants have shrivel or yellowed leaves, rotting rhizomes, and even death of the entire plant, resulting in a sharp decline in yield or even total crop failure, but also seriously reduce the commercial specifications and effective ingredient content of medicinal plants. The pathogens of root rot are complex and diverse, and Fusarium fungi have been reported as the most widespread pathogen. With the expansion of medicinal plant cultivation, root rot has occurred frequently in many medicinal plants such as Araliaceae, Fabaceae, Ranunculaceae, and Solanaceae and other medicinal plants. This article reviews recent research progress on root rot in medicinal plants, covering various aspects such as disease characteristics, occurrence, pathogen species, damage to medicinal plants, disease mechanisms, control measures, and genetic factors. The aim is to provide reference for better control of root rot of medicinal plants.

From 2016 to 2019, 128 organic and conventional spring and winter pea fields in Germany were surveyed to determine the effects of cropping history and pedo-climatic conditions on pea root health, the diversity of Fusarium and Didymella communities and their collective effect on pea yield. Roots generally appeared healthy or showed minor disease symptoms despite the frequent occurrence of 4 Didymella and 14 Fusarium species. Soil pH interacted with the occurrence of the Fusarium oxysporum species complex (FOSC) and F. tricinctum that correlated with reduced or increased soil pH values, respectively. While legumes in the cropping history or reduced time between legumes correlated with occurrence of D. pinodella and to a lesser degree with the members of the F. solani species complex (FSSC), the reverse was true at least in organic spring peas for F. redolens. Only in conventional systems increased root infections with F. redolens and the FSSC were linked to root rot incidence whereas yields negatively correlated with the FOSC and positively with F. tricinctum isolation frequencies. Overall, this study shows that pea root rot pathobiome is rather stable and that the damage caused is mostly due to the interaction with environmental conditions.

Armillaria is a soil-borne genus of basidiomycetes whose species can cause stem and root rot in woody plants. The effects of plant-pathogenic Armillaria species are well known in forests, but are underestimated in urban areas, where cases causing damage to trees and shrubs in green spaces have been steadily increasing in Switzerland since the 1980s. In this study, we present a simple, rapid, and cost-effective protocol for high-throughput diagnostics of the two primary pathogens A. mellea and A. ostoyae based on partial PCR amplification of the RPB2 gene. The specificity and sensitivity of the presented duplex PCR-I and single-plex PCR-II were evaluated using different methods: (i) testing both PCRs on tree pathogenic or soil-borne fungi of genera other than Armillaria, (ii) using dilution series of Armillaria-DNA to determine a minimum detection limit, and (iii) sequencing the selected RPB2 region to verify the primer sequences and positions. The utility of PCR-I and PCR-II as a high-throughput method was successfully tested on 65 DNA samples of Armillaria from Switzerland. Finally, an uninvolved person compared both classical methods, pairing test and sequencing, with PCR-I and PCR-II in a blind test. This study provides a reliable and alternative protocol for the rapid diagnosis of A. mellea and A. ostoyae causing root rot of woody plants.

Introduction The phenomenon in which the damage of plant diseases is suppressed by continuous cropping is defined as suppressiveness and the development of suppressive soils and key beneficial microorganisms have been identified through various previous studies. However, no studies have been conducted on microbial communities related to disease occurrence before the initial occurrence of diseases in crop monoculture.Methods We aimed to investigate the ecological modifications of pathogen population density in soil, disease occurrence rate, and microbiota community shifting during ginseng monoculture to better understand the tripartite social relationships in the monoculture system. To achieve the study's objectives, a long-term monoculture of ginseng was established. The microbial diversity and community structure were analyzed using high-throughput sequencing, and the pathogen population density and disease occurrence rate were determined using qPCR and observation.Results and discussion The results showed that the initial rhizosphere bacterial community of ginseng had already collapsed before the development of the root rot disease. The study also identified the crucial role of soil-borne pathogens in causing disease and the loss of initial keystone taxa populations in the early stages of monoculture. Our study revealed a novel aspect of soil microbiota dynamics during ginseng monoculture, with seven distinct microbes (Beijerinckiaceae, Comamonadaceae, Devosiaceae, Rhizobiaceae, Sphingobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae) participating in soil nitrogen metabolism as an 'initial community' that regulates root rot disease through nutritional competition. The findings contribute to ecological research on disease-suppressiveness soil, disease management, and sustainable agriculture.

Soilborne fungal pathogens that cause root rot, wilting and dying are the most important problems in pistachio production. The purpose of this study was to examine, isolate, and diagnose the pathogens from diseased pistachio trees in orchards and nurseries located in southeastern Turkey. Fungi isolated from the pistachio trees were identified by morphology and the sequences of the internal transcribed spacer (ITS) region and translation elongation factor-1 alpha (TEF-1 alpha). Fusarium solani, Fusarium oxysporum, Fusarium brachygibbosum, Fusarium chlamydosporum and Macrophomina phaseolina were the most important fungi causing root rot, wilting and decline of pistachio trees. Pathogenicity studies showed that all of the fungi identified can colonize and damage the vascular tissues of a sapling and cause substantial lesions and vascular discolourations. This study provides the first evidence of wilting due to the root and crown rot in pistachio trees in Siirt province of Turkey caused by some Fusarium species, especially F. solani, F. oxysporum, F. chlamydosporum, F. brachygibbosum and M. phaseolina. Finally, the research enabled the identification of some fungal pathogens that are seriously harming pistachio trees in southeastern Turkey.

Soybean (Glycine max [L.] Merr.) is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2), and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN-susceptible soybean 'Williams 82'. Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.

Root rot is a soil-borne disease primarily caused by fungi. The malady not only decrease the ability of absorbing water and nutrients, but also severely threat agricultural productivity. Recently, a new family member of twodimensional (2D) transition metal carbide materials, MXene (Ti3C2Tx), has gained much interest as a promising approach to control fungi. However, the efficient use and mechanism of MXene in protecting plant against pathogenic fungus are still rarely reported. Here, the synthesized MXene were first characterized by the atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic light scattering (DLS), transmission electron microscopy (TEM) and X-ray photoelectron spectra (XPS). MXene application in soil obviously enhanced the root rot disease resistance of T. grandis. Soil microbial community analysis indicated that the abundance of Fusasium genus was decreased by 68.32% after MXene treatment. Further, MXene specially affected the permeability of Fusarium solani via damaging their cell membranes, thereby causing the disintegration and cell death of F. solani. In addition, MXene nanoflakes could transport into roots through T. grandis root air space, which resulted in the accumulation of lignin in roots via enhancing the expression and activities of lignin biosynthesis-related genes in T. grandis roots. Taken together, our finding pioneers comprehensive insights into the antifungal mechanism of MXene against F. solani and the efficiency use of MXene in protecting plant against pathogenic fungus, which will prompt the rapid development of nanotechnology in sustainable forestry.

Root rot is a damaging disease caused by various pathogenic fungi including, Fusarium spp., Rhizoctonia spp., and especially oomycetes. This disease poses significant challenges to food crop production worldwide. Pythium and Phytophthora, most species of these genera, are fungus-like pathogens that can grow and expand in diverse agroecosystems, inflicting severe damage to the root systems of numerous food crops, including cereals, vegetables, and legumes. Multiple factors contribute to the proliferation of root rot, including temperature, soil moisture levels, and the existence of vulnerable host plants. Based on a wide range of scientific literature, this paper examines the impact of the disease on plant safety, emphasizing the substantial yield losses and economic harm faced by farmers worldwide. The paper provides also a comprehensive overview of the global prevalence, impact, and management strategies associated with root rot infections. A special highlight is directed at symptoms, infection process, and pathogenicity mechanisms employed by Pythium and Phytophthora species, with a particular case of olive root rot caused by these two pathogens. Additionally, detection strategies of pathogenic oomycetes are discussed as well, from conventional to recent tools that are employed now in the plant pathology field. Finally, various preventive and management strategies are provided in this work. These include cultural practices, chemical control measures, and biological control agents, from bacteria to antagonistic fungi with a special focus on the use of Trichoderma spp. strains, and host resistance breeding. The limitations and challenges associated with these strategies, such as the emergence of resistant strains and environmental concerns, are also addressed. In conclusion, this review helps to understand the biology, pathogenicity, and management options for these pathogens, which is crucial for developing sustainable solutions to mitigate the impact of root rot, ensuring food security, and raising sustainable agriculture in the face of this significant challenge.