Characterization of Bacillus amyloliquefaciens BA-4 and its biocontrol potential against Fusarium-related apple replant disease

Apple replant disease (ARD), caused by Fusarium pathogens, is a formidable threat to the renewal of apple varieties in China, necessitating the development of effective and sustainable control strategies. In this study, the bacterial strain BA-4 was isolated from the rhizosphere soil of healthy apple trees in a replanted orchard, demonstrating a broad-spectrum antifungal activity against five crucial apple fungal pathogens. Based on its morphology, physiological and biochemical traits, utilization of carbon sources, and Gram stain, strain BA-4 was tentatively identified as Bacillus amyloliquefaciens. Phylogenetic analysis using 16S rDNA and gyrB genes conclusively identified BA-4 as B. amyloliquefaciens. In-depth investigations into B. amyloliquefaciens BA-4 revealed that the strain possesses the capacity to could secrete cell wall degrading enzymes (protease and cellulase), produce molecules analogous to indole-3-acetic acid (IAA) and siderophores, and solubilize phosphorus and potassium. The diverse attributes observed in B. amyloliquefaciens BA-4 underscore its potential as a versatile microorganism with multifaceted benefits for both plant well-being and soil fertility. The extracellular metabolites produced by BA-4 displayed a robust inhibitory effect on Fusarium hyphal growth and spore germination, inducing irregular swelling, atrophy, and abnormal branching of fungal hyphae. In greenhouse experiments, BA-4 markedly reduced the disease index of Fusarium-related ARD, exhibiting protective and therapeutic efficiencies exceeding 80% and 50%, respectively. Moreover, BA-4 demonstrated plant-promoting abilities on both bean and Malus robusta Rehd. (MR) seedlings, leading to increased plant height and primary root length. Field experiments further validated the biocontrol effectiveness of BA-4, demonstrating its ability to mitigate ARD symptoms in MR seedlings with a notable 33.34% reduction in mortality rate and improved biomass. Additionally, BA-4 demonstrates robust and stable colonization capabilities in apple rhizosphere soil, particularly within the 10-20 cm soil layer, which indicates that it has long-term effectiveness potential in field conditions. Overall, B. amyloliquefaciens BA-4 emerges as a promising biocontrol agent with broad-spectrum antagonistic capabilities, positive effects on plant growth, and strong colonization abilities for the sustainable management of ARD in apple cultivation.

(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation

The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.

The root-lesion nematode, Pratylenchus penetrans, affects early growth and physiology of grafted M.9, G.41 and G.935 apple rootstocks similarly under field microplot conditions

The root-lesion nematode, Pratylenchus penetrans, is a ubiquitous parasite of roots of temperate fruit trees. It affects early growth of trees replanted into former orchard sites where populations have built up, and may contribute to decline complexes of older trees. Most British Columbia, Canada apple acreage is planted with M.9 rootstock, but growers are increasingly considering Geneva-series rootstocks such as G.41 and G.935. Among these rootstocks, responses to P. penetrans, specifically, are poorly known. To compare the resistance and tolerance to P. penetrans of G.41, G.935 and M.9 rootstocks ('Ambrosia' scion), a field microplot experiment was established in spring of 2020 at the Summerland Research and Development Centre. The experimental design was a 2 x 3 factorial combination of: P. penetrans inoculation (+/-) and rootstock (G.41, G.935, M.9), with 20 replicate microplots of each of the six treatment combinations arranged in a randomized complete block design. The P. penetrans inoculum was 5400 nematodes per microplot (54 P. penetrans L-1 soil), which is below commonly accepted damage thresholds. Though P. penetrans population densities were lower for the G.41 rootstock by the end of the 2021 growing season, the effects of P. penetrans were similar among rootstocks. In the establishment year (2020), P. penetrans caused significant reductions in aboveground growth. In 2021, shoot growth and root weight were reduced by P. penetrans. The nematode also reduced rates of leaf gas exchange and stem water potential. These data suggest that while G.41 and G.935 may have other horticultural benefits over M.9, they are equally susceptible to P. penetrans at the early stages of tree growth.

Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils

The tree fruit industry in Nova Scotia, Canada, is dominated by the apple (Malus domestica) sector. However, the sector is faced with numerous challenges, including apple replant disease (ARD), which is a well-known problem in areas with intensive apple cultivation. A study was performed using 16S rRNA/18S rRNA and 16S rRNA/ITS2 amplicon sequencing to assess soil- and root-associated microbiomes, respectively, from mature apple orchards and soil microbiomes alone from uncultivated soil. The results indicated significant (p < 0.05) differences in soil microbial community structure and composition between uncultivated soil and cultivated apple orchard soil. We identified an increase in the number of potential pathogens in the orchard soil compared to uncultivated soil. At the same time, we detected a significant (p < 0.05) increase in relative abundances of several potential plant-growth-promoting or biocontrol microorganisms and non-fungal eukaryotes capable of promoting the proliferation of bacterial biocontrol agents in orchard soils. Additionally, the apple roots accumulated several potential PGP bacteria from Proteobacteria and Actinobacteria phyla, while the relative abundances of fungal taxa with the potential to contribute to ARD, such as Nectriaceae and plant pathogenic Fusarium spp., were decreased in the apple root microbiome compared to the soil microbiome. The results suggest that the health of a mature apple tree can be ascribed to a complex interaction between potential pathogenic and plant growth-promoting microorganisms in the soil and on apple roots.

malus domestica MR5, the Causative Agent of Apple Replant Disease

Apple replant disease (ARD) caused by the fungal pathogen Fusarium proliferatum f. sp. malus domestica (Fpmd) MR5 brings annual losses to apple production within China. However, the genomic information of the pathogen is not yet available. Here, we obtained the whole-genome sequence of the highly virulent Fpmd MR5 using the Illumina PE150 platform. The genome size was 42.76 Mb and consisted of 9,047 genes. The GC content was 48.80%, and several genes potentially associated with pathogenicity were identified, such as carbohydrate-active enzymes, secreted proteins, and secondary metabolite gene clusters. There were 260 specific virulence factor genes, mainly related to fungal vegetative growth and the production of cell wall-degrading enzymes. These data will aid future studies investigating host-pathogen interactions and help us develop suitable disease management strategies.

Effect on microbial communities in apple orchard soil when exposed short-term to climate change abiotic factors and different orchard management practices

AIM

We assessed the effect of exposing apple orchard soil to different temperatures and CO2 levels on the resident microbiome of soils from a conventionally managed and an organically managed apple orchard. The key difference between these two orchards was that synthetic fertilizers and pesticides are routinely used in the former one.

METHODS AND RESULTS

To investigate the effect of CO2 and temperature, soil samples from each site at two depths were exposed to either elevated temperature (29°C) at either 5000 or 10 000 ppm for five weeks or control conditions (25°C + 400 ppm). Both bacterial and fungal communities were profiled with amplicon-sequencing. The differences between the two orchards were the most significant factor affecting the bacterial and fungal communities, contributing to 53.7-14.0% of the variance in Bray-Curtis β diversity, respectively. Elevated CO2 concentration and increased temperature affected organic orchard microbial diversity more than the conventionally managed orchard. A number of candidate beneficial and pathogenic microorganisms had differential abundances when temperature and CO2 were elevated, but their effect on the plant is unclear.

CONCLUSIONS

This study has highlighted that microbial communities in bulk soils are most significantly influenced by crop management practices compared to the climate conditions used in the study. The studied climate conditions had a more limited effect on microbial community diversity in conventionally managed soil samples than in organically managed soils.

Exogenous Dopamine and MdTyDC Overexpression Enhance Apple Resistance to Fusarium solani

Fusarium solani, one of the main pathogenic fungi involved in apple replant disease (ARD), is a serious threat to apple growth and development. Dopamine and tyrosine decarboxylase (TyDC), a key enzyme in the dopamine synthesis pathway, have been reported to play an active role in plant responses to biotic and abiotic stresses, but little is known about the functions of dopamine and Malus domestica TyDC (MdTyDC) in the interaction between F. solani and apple roots. In this study, seedlings treated with exogenous dopamine and apple plants overexpressing MdTyDC were inoculated with F. solani; both treatments reduced the root system damage caused by F. solani. After inoculation with F. solani, exogenous dopamine increased dopamine content in the seedlings; alleviated the inhibition of biomass accumulation; increased root metabolic activity, photosynthetic efficiency, and antioxidant enzyme activities; reduced reactive oxygen species accumulation; and upregulated the expression of genes encoding chitinase, β-1,3-glucanase, and pathogenesis-related proteins. Similar results were observed in MdTyDC-overexpressing apple plants. In addition, the overexpression of MdTyDC increased tyramine content and the deposition of cell wall-bound amines in roots. Overall, our results reveal that exogenous dopamine and overexpression of MdTyDC enhance apple resistance to F. solani, which is an important application for the prevention of ARD.

malus domestica Causing Apple Replant Disease in China

Apple replant disease (ARD) is the most serious threat facing the apple industry globally. ARD is mainly manifested as decreased plant growth, serious root rot disease, and considerable yield loss. Microbial factors are the dominant factors leading to the occurrence of ARD. Research on soil-borne pathogenic fungi leading to the occurrence of ARD in China is limited. In the present study, we selected 16 replanting orchards from the Northwest Loess region and around the Bohai Gulf. Diseased roots and rhizosphere soil from healthy apple trees and trees showing ARD symptoms were sampled at random. High-throughput sequencing was used to study the fungal communities in the rhizosphere soil, which showed that the composition of the rhizosphere soil fungal community of ARD-symptomatic and healthy apple trees was different. Nectriaceae at the family level and Fusarium at the genus level dominated the rhizosphere soil fungal community in the two regions, while for healthy apple trees, the relative abundance of Mortierella, Minimedusa, Tetracladium, and Chaetomium was higher. Tissue separation and serial dilution were used to separate fungi, and a total of 89 genera and 219 species were obtained, most of which were Fusarium. Fusarium was further confirmed to be the most abundant pathogen species leading to the occurrence of ARD in China through pathogenicity assays. A pathogenicity assay was carried out by the dip-and-cut technique using different host plants. It was found that Fusarium MR5 showed strong aggressiveness to apple rootstocks. Diseased seedlings specifically exhibited chlorosis of the leaves, browning from the edge of the leaf, followed by rolling and yellowing of the leaves, resulting in wilting and eventually death. Strain MR5 was preliminarily identified as F. proliferatum according to the morphological and cultural characteristics. A maximum likelihood analysis of identities based on six gene sequence (ITS, TUB2, IGS, mtSSU, RPB2, and the TEF gene) alignments between the MR5 strain and other strains showed 99 to 100% homology with F. proliferatum. Based on our test results, strain MR5 was identified as F. proliferatum f. sp. malus domestica, which is of great significance for finding new measures to control ARD in China.

Controlled-Release Diammonium Phosphate Alleviates Apple Replant Disease: An Integrated Analysis of Soil Properties, Plant Growth, and the Soil Microbiome

Exogenous application of nitrogen (N) and phosphate (P) has been demonstrated to alleviate apple replant disease (ARD). Yet, the effect of controlled-release diammonium phosphate (C-DAP), which continuously supply N and P for ARD control, is still poorly understood. Applying C-DAP markedly alleviated the typical symptoms of ARD. C-DAP maintained soil N and P at relatively high and stable levels during the entire growth period of the replanted seedlings, thus, limiting the copy number of the four key pathogenic Fusarium species that cause ARD. Particularly, continuously supplying N and P by C-DAP established a higher fungal diversity than that of conventional diammonium phosphate and induced the fungal community to be more similar to fumigated soil. The positive effect of C-DAP originated from the synergistic effects of regulating microorganisms and enhancing the resistance of the plant caused by a continuous nutrient supply. These findings provide a new perspective in the management of soil-borne diseases.

The Phlorizin-Degrading Bacillus licheniformis XNRB-3 Mediates Soil Microorganisms to Alleviate Apple Replant Disease

In this study, an endophytic phlorizin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and how it alleviates the pathogen pressure via changes in soil microbiomes were studied. The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect on Fusarium oxysporum reached the highest of 66.11%. The fermentation broth can also protect the roots of the plants from Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and indirectly affecting the growth of pathogens. The secreted antimicrobial substances were identified using gas chromatography-mass spectrometry (GC-MS) technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate promoted root development of Arabidopsis plants. Strain XNRB-3 has multifarious plant growth promoting traits and antagonistic potential. In pot and field experiments, the addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] was also significantly enhanced. It also reduced the abundance of four species of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as the soil enzyme activity. The above results indicated that B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent.

Homologous Cloning of Potassium Channel Genes From the Superior Apple Rootstock Line 12-2, Which is Tolerant to Apple Replant Disease

Potassium channels are important ion channels that are responsible for the absorption of potassium in the plant nutrient uptake system. In this study, we used homologous molecular cloning to obtain 8 K⁺ channel genes from the superior apple rootstock line 12-2 (self-named): MsAKT1-1, MsKAT3-2, MsKAT1-3, MsK2P3-4, MsK2P3-5, MsK2P5-6, MsK2P3-7, and MsK2P3-8. Their lengths varied from 942 bp (MsK2P5-6) to 2625 bp (MsAKT1-1), and the number of encoded amino acids varied from 314 (MsK2P5-6) to 874 (MsAKT1-1). Subcellular localization predictions showed that MsAKT1-1, MsKAT3-2, and MsKAT1-3 were localized on the plasma membrane, and MsK2P3-4, MsK2P3-5, MsK2P5-6, MsK2P3-7, and MsK2P3-8 were localized on the vacuole and plasma membrane. The 8 K⁺ channel proteins contained α helices, extended strands, β turns, and random coils. MsKAT1-3 had four transmembrane structures, MsKAT3-2 had six, and the other six K⁺ channel genes had five. Protein structure domain analysis showed that MsAKT1-1 contained nine protein domains, followed by MsKAT3-2 with four, MsKAT1-3 with three, and the other five two-pore domain K⁺ channel proteins with two. Semi-quantitative RT-PCR detection of the K⁺ channel genes showed that their expression levels were high in roots. qRT-PCR analysis showed that the relative expression levels of the 8 genes changed after exposure to ARD stress. The above results provide a theoretical basis for further research on the functions of potassium channel genes in 12-2 and a scientific basis for the breeding of ARD-resistant rootstock.

Isolation, Identification, and Antibacterial Mechanisms of Bacillus amyloliquefaciens QSB-6 and Its Effect on Plant Roots

Apple replant disease (ARD) is a common problem in major apple planting areas, and biological factors play a leading role in its etiology. Here, we isolated the bacterial strain QSB-6 from the rhizosphere soil of healthy apple trees in a replanted orchard using the serial dilution method. Strain QSB-6 was provisionally identified as Bacillus amyloliquefaciens based on its morphology, physiological and biochemical characteristics, carbon source utilization, and chemical sensitivity. Maximum likelihood analysis based on four gene sequences [16S ribosomal RNA gene (16S rDNA), DNA gyrase subunit A (gyrA), DNA gyrase subunit B (gyrB), and RNA polymerase subunit B (rpoB)] from QSB-6 and other strains indicated that it had 100% homology with B. amyloliquefaciens, thereby confirming its identification. Flat standoff tests showed that strain QSB-6 had a strong inhibitory effect on Fusarium proliferatum, Fusarium solani, Fusarium verticillioides, Fusarium oxysporum, Alternaria alternata, Aspergillus flavus, Phoma sp., Valsa mali, Rhizoctonia solani, Penicillium brasilianum, and Albifimbria verrucaria, and it had broad-spectrum antibacterial characteristics. Extracellular metabolites from strain QSB-6 showed a strong inhibitory effect on Fusarium hyphal growth and spore germination, causing irregular swelling, atrophy, rupture, and cytoplasmic leakage of fungal hyphae. Analysis of its metabolites showed that 1,2-benzenedicarboxylic acid and benzeneacetic acid, 3- hydroxy-, methyl ester had good inhibitory effects on Fusarium, and increased the length of primary roots and the number of lateral roots of Arabidopsis thaliana plantlet. Pot experiments demonstrated that a QSB-6 bacterial fertilizer treatment (T2) significantly improved the growth of Malus hupehensis Rehd. seedlings. It increased root length, surface area, tips, and forks, respiration rate, protective enzyme activities, and the number of soil bacteria while reducing the number of soil fungi. Fermentation broth from strain QSB-6 effectively prevented root damage from Fusarium. terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) assays showed that the T2 treatment significantly reduced the abundance of Fusarium in the soil and altered the soil fungal community structure. In summary, B. amyloliquefaciens QSB-6 has a good inhibitory effect on Fusarium in the soil and can significantly promote plant root growth. It has great potential as a biological control agent against ARD.

Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design

Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible 'M26' apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.

[Effects of dazomet fumigation on growth, biological characteristics of Malus hupehensis seedlings and soil environment]

In this study, we examined the effects of dazomet fumigation with different concentrations (0, 0.1, 0.2, 0.4 g·kg^-1) on the microbial characteristics of continuous cropping soil and growth of Malus hupehensis seedling in greenhouse and open-field pot. The results showed that all the treatment of dazomet fumigation could promote the growth of M. hupehensis seedlings in continuous cropping soil, with 0.2 g·kg^-1 treatment showing the strongest effect. Compared to the control, plant height, stem diameter, dry weight of M. hupehensis seedlings in 0.2 g·kg^-1 dazomet fumigation were increased by 192.9% and 91.8%, 72.8% and 60.1%, 196.8% and 195.0%, 138.5% and 130.7%, respectively in greenhouse and open-field. The root related indices (root length, root area, root volume, root respiration rate) were significantly promoted. The activities of SOD, POD, CAT in roots were increased by 114.6% and 118.5%, 123.5% and 107.6%, 164.6% and 175.6% respectively compared with the control, whereas the content of malondialdehyde was significantly lowered. Soil bacterial content, fungal content, copy number of Fusarium oxysporum gene and soil enzyme activity were significantly decreased with the increasing dazomet concentrations. In conclusion, 0.2 g·kg^-1 dazomet fumigation could increase the biomass of M. hupehensis seedlings in continuous cropping, improve soil environment, and effectively alleviate the continuous cropping obstacle. Therefore, 0.2 g ·kg^-1 dazomet fumigation could be given priority during the reconstruction of old apple orchards.

[Effects of residual apple fermentation products on continuous cropping soil environment and the growth of Malus hupehensis Rehd. Seedlings]

Effects of fermented apple products on the growth of continuous cropping Malus hupehensis Rehd. seedlings and soil environment were examined in a pot experiment to provide theoretical basis for apple replant disease. There were four treatments, the replanted soil (control, CK), sterilized replant soil (T₁), replanted soil applied with apple fermentation products (T₂), and replanted soil applied with sterilized apple fermentation products (T₃). The results showed that T₁, T₂ and T₃ significantly promoted seedlings growth, with better performance of T₁ and T₂. T₁ increased root respiration rate, plant height, ground diameter, fresh weight, and dry weight by 107.3%, 50.6%, 42.4%, 171.7%, 225.3%, while T₃ increased them by 104.4%, 50.6%, 42.3%, 171.8%, 225.5%, respectively over CK. T₂ and T₃ increased the activities of nutrient conversion-related enzymes in continuous cropping soil. T₂ increased the activities of catalase, urease, neutral phosphatase and sucrase by 44.5%, 169.5%, 23.4%, 169.3%, while T₃ increased them by 23.7%, 72.6%, 1.5%, 121.5%, respectively. Catalase and sucrase activities under T₁ treatment did not differ from that in CK, whereas their urease and neutral phosphatase activities were reduced by 40.8% and 41.6%, respectively. The contents of ammonium, nitrate, available phosphorus and available potassium in T₂ soil were increased by 18.6%, 50.6%, 14.0% and 36.7% respectively. T₃ only increased the content of available nitrogen, with ammonium and nitrate being increased by 7.0% and 23.6% respectively. The content of available nutrients of T₁ decreased compared with CK. T₁ and T₂ significantly reduced the abundance of actinomycetes and fungi in soil and increased that of bacteria. The abundance of bacteria, actinomycetes and fungi in T₃ treatment were all significantly decreased. Results of real-time fluorescence quantitative PCR analysis showed that the gene copies of Fusarium proliferaturn, F. moniliforme, F. solani and F. oxysporum in T₁, T₂ and T₃ were ecreased to different degrees. Apple fermented product could inhibit soil pathogen in replanted orchard soil, improve soil environment, and promote seedling growth, which could be used to alleviate the apple replant disease.

The mitigation effects of exogenous melatonin on replant disease in apple

Melatonin mediates many physiological processes in plants. The problem of apple replant disease is unsolved. Our study objectives were to evaluate the regulatory effect of melatonin on plant resistance to this challenge and investigate the preliminary mechanism by which melatonin helps alleviate the effects of this disease. Two-year-old trees of "Fuji" apple (Malus domestica), grafted onto rootstock M.26, were grown in "replant" soil for 6 months in the absence or presence of a 200 μmol/L melatonin supplement. The addition of melatonin to the soil significantly increased the rates of plant growth and net photosynthesis and chlorophyll concentrations under replant conditions. This molecule elevated the levels of K in leaves and roots and enhanced the activity of soil enzymes. Such supplementation also changed the composition of the bacterial and fungal communities in the soil. We concluded that the application of melatonin to a replant soil can protect their chloroplasts from oxidative damage and release the apple root from membrane damage, and also lead to increased soil enzyme activity and soil quality while altering the composition of bacterial and fungal communities. These changes can then promote seedling growth, stimulate photosynthesis, and elevate K levels, thereby alleviating the effects of apple replant disease.

Free-Living Nematodes Together With Associated Microbes Play an Essential Role in Apple Replant Disease

Apple replant disease (ARD) is a severe problem in apple production worldwide. It is caused by a complex of soil biota, leading to small discolorated roots, as well as increased biosynthesis of phytoalexins, total phenolic compounds and antioxidants. We sampled soil from randomized field plots with either apple trees affected by ARD, which were five times replanted every second year, or with healthy trees growing in plots, which had a grass cover during this period. We investigated the contribution of nematodes to ARD by dissecting the soil biota from plots infested with ARD and non-infested control plots into a nematode and a microbe fraction. Nematode communities significantly differed between ARD and control soil as revealed by high-throughput sequencing of 18S rRNA genes. Plant-parasitic nematodes were too low in abundance to explain root damage, and did not significantly differ between ARD and control soil. Their separate and synergistic effect on ARD symptoms of susceptible M26 apple rootstocks was analyzed 4 and 8 weeks after inoculation in three greenhouse experiments. Inoculants were either nematodes from ARD plots (N_ARD), N_ARD plus microbes from ARD plots (M_ARD), N_ARD plus microbes from control plots (M_Con), nematodes from control plots N_Con plus M_ARD, N_Con plus M_Con, M_ARD, or M_Con, or non-inoculated control. In all three experiments, the combination N_ARD plus M_ARD had the strongest adverse effect on the plants, with respect to growth parameters of shoots and roots, total phenolic compounds and phytoalexins in roots, and antioxidants in leaves. N_ARD also induced ARD but less than N_ARD plus M_ARD. N_ARD plus M_Con had delayed effects on the plants compared to N_ARD plus M_ARD, suggesting that detrimental nematode-microbe interactions built up with time. Effects of M_ARD or N_Con plus M_ARD were minor or not distinguishable from those of M_Con or non-inoculated control. Overall, the source of the inoculated nematodes -ARD or control soil- and the interaction between ARD nematodes and microbes were highly significant factors determining ARD. In conclusion, exploring the associations of nematodes and microbes in ARD soils will give the chance to unravel the etiology of ARD.

Impaired defense reactions in apple replant disease-affected roots of Malus domestica 'M26'

A soil- and site-dependent complex of diverse microbial populations causes apple replant disease (ARD), which leads to economic losses for tree nurseries and apple producers due to reduced plant growth and diminished fruit yields. Soil fumigation has been widely used to mitigate ARD, but the application of these chemicals is restricted in the European Union. Hence, other counteractions have to be developed. Genomics-based breeding may be used to select ARD-tolerant genotypes; however, molecular responses of ARD are not well understood. Recent studies revealed that biotic stress-associated genes involved in typical defense reactions are activated but do not result in an adequate response to ARD. The objective of this study was to analyze selected responsive genes in a time-course experiment to test for expression kinetics. Cultivating the ARD-susceptible apple rootstock 'M26' on ARD-affected soil resulted in significantly reduced growth as early as 7 days after planting. Genes involved in phytoalexin biosynthesis were upregulated in ARD samples as early as 3 days after planting and reached up to 26-fold changes at Day 10, which resulted in high amounts of 3-hydroxy-5-methoxybiphenyl, aucuparin, noraucuparin, 2-hydroxy-4-methoxydibenzofuran, 2'-hydroxyaucuparin and noreriobofuran. For the first time, these phytoalexins were detected, identified and quantified in apple roots. The lack of a sufficient defense response may be due to impaired sequestration and/or exudation of the potentially cytotoxic phytoalexins and perturbed formation of reactive oxygen species, leading to root damage in ARD soils. The findings provide a basis for comparative studies of the defense processes in more ARD-tolerant rootstocks.

Effects of Soil Pre-Treatment with Basamid® Granules, Brassica juncea, Raphanus sativus, and Tagetes patula on Bacterial and Fungal Communities at Two Apple Replant Disease Sites

Nurseries producing apple and rose rootstock plants, apple orchards as well as rose production often experience replanting problems after several cultivations at the same site when a chemical soil disinfectant is not applied. The etiology of apple and rose replanting problems is most likely caused by soil-borne pathogen complex, defined as "replant disease (RD)". Symptoms typical of RD are reduced shoot and root growth, a smaller leaf area, a significant decrease in plant biomass, yield and fruit quality and a shorter life span. In our previous study, we showed that RD symptoms were reduced when apple rootstock M106 were grown in RD soils treated either with the soil fumigant Basamid or after biofumigation by incorporating Brassica juncea or Raphanus sativus or by growing Tagetes under field conditions compared to untreated control soil. The present study aimed at identifying potential bacterial and fungal taxa that were affected by different soil treatments and linking bacterial and fungal responders to plant performance. Miseq® Illumina® sequencing of 16S rRNA gene fragments (bacteria) and ITS regions (fungi) amplified from total community DNA extracted from soil samples taken 4 weeks after treatments were performed. Soil properties and culture history of the two RD sites greatly influenced soil microbiomes. Several bacterial genera were identified that significantly increased in treated soils such as Arthrobacter (R. sativus, both sites), Curtobacterium (Basamid, both sites), Terrimonas (Basamid and R. sativus, site A) and Ferruginibacter (B. juncea, site K and R. sativus, site A) that were also significantly and positively correlated with growth of apple M106 plants. Only few fungal genera, such as Podospora, Monographella and Mucor, were significantly promoted in soils treated with B. juncea and R. sativus (both sites). The least pronounced changes were recorded for bacterial as well as fungal communities in the RD soils planted with Tagetes. The detection of bacterial and fungal genera that were significantly increased in relative abundance in response to the treatments and that were positively correlated with plant growth suggests that management of the soil microbial community could contribute to overcome the apple RD encountered at affected sites.

Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis - contribution to improved aboveground apple plant growth?

Replant disease (RD) severely affects apple production in propagation tree nurseries and in fruit orchards worldwide. This study aimed to investigate the effects of soil disinfection treatments on plant growth and health in a biotest in two different RD soil types under greenhouse conditions and to link the plant growth status with the bacterial community composition at the time of plant sampling. In the biotest performed we observed that the aboveground growth of apple rootstock M26 plants after 8 weeks was improved in the two RD soils either treated at 50°C or with gamma irradiation compared to the untreated RD soils. Total community DNA was extracted from soil loosely adhering to the roots and quantitative real-time PCR revealed no pronounced differences in 16S rRNA gene copy numbers. 16S rRNA gene-based bacterial community analysis by denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing revealed significant differences in the bacterial community composition even after 8 weeks of plant growth. In both soils, the treatments affected different phyla but only the relative abundance of Acidobacteria was reduced by both treatments. The genera Streptomyces, Bacillus, Paenibacillus, and Sphingomonas had a higher relative abundance in both heat treated soils, whereas the relative abundance of Mucilaginibacter, Devosia, and Rhodanobacter was increased in the gamma-irradiated soils and only the genus Phenylobacterium was increased in both treatments. The increased abundance of genera with potentially beneficial bacteria, i.e., potential degraders of phenolic compounds might have contributed to the improved plant growth in both treatments.