Search

Soil organic matter and pores distribution within aggregates were studied using X-ray computed tomography (XCT; Nikon XT H 225ST and GE Phoenix L240) and advanced 2D/3D measurements by the digital Keyence VHX-6000 microscope (Japan). A new methodological approach with computed tomography involvement for studying the spatial arrangement of pores, porosity, and soil morphology is presented. Changes in studied parameters are documented along the transect of intensively used Haplic Chernozem. Soil disturbance due to erosion and colluvial soil profile formation is reported. Moreover, soil organic matter quality and aggregate stability were evaluated. Obtained results showed statistically significant differences between the control and eroded sites and between eroded and accumulated sites. The correlation coefficients were the highest for soil organic carbon (SOC) and humic substances CHS (r = 0.805) and CHS and CHA/CFA (r = 0.764). The highest porosity, aggregates stability and coefficients stability were confirmed on the eroded site. The computed tomography measurements also document the high disturbance of Haplic Chernozem on the control site and the newly formed profile of Colluvisol. Despite excellent complementary technique further research is necessary to improve micro-XCT resolution and capacity for the soil micromorphological study.

With a reduction in available chemical treatments, there is an increased interest in biological control of grapevine trunk diseases. Few studies have investigated the impact of introducing beneficial microorganisms in the rhizosphere on the existing indigenous soil microbiome. In this study, we explored the effect of two biocontrol agents (BCAs), Trichoderma atroviride SC1 (Ta SC1) (Vintec; Certis Belchim) and Bacillus subtilis PTA-271 (Bs PTA-271), on the grapevine rhizosphere bacterial and fungal microbiome as well as plant defense expression using high-throughput amplicon sequencing and quantitative real-time polymerase chain reaction (PCR), respectively. Additionally, we quantified both Ta SC1 and Bs PTA-271 in the rhizosphere over time using droplet digital PCR. The fungal microbiome was more affected by factors such as soil type, BCA treatment, and sampling time compared with the bacterial microbiome. Specifically, Ta SC1 application produced negative impacts on fungal diversity, whereas application of BCAs did not affect bacterial diversity. Interestingly, the survival and establishment of both BCAs showed opposite trends depending on the soil type, indicating that the physicochemical properties of soils have a role in BCA establishment. Fungal co-occurrence networks were less complex than bacterial networks but highly impacted by Ta SC1 application. Soils treated with Ta SC1 presented more complex and stable co-occurrence networks, with a higher number of positive correlations. Induced grapevine defenses also differed according to the soil, being more affected by BCA inoculation on sandy soil. The findings of this research emphasize the complex relationships among microorganisms in the rhizosphere and highlight the significance of taking into account various factors, such as soil type, sampling time, and BCA treatment, and their influence on the structure and dynamics of microbial communities.

Abstract Background Bacterial contamination poses a high risk to the successful establishment and maintenance of plant tissue cultures. The aim of this study was to identify the isolates representing the frequent bacterial contaminants of Prunus rootstock tissue cultures and to determine the most effective concentration of nanomaterials for Curtobacterium sp. strain A7_M15 elimination without a negative impact on explants. Results Six Curtobacterium sp. strains were isolated and identified, and the whole-genome sequence was obtained for strain A7_M15. Two nanocomposites, reduced graphene oxide–copper–silver and silver–selenium, with the highest bactericidal activity were selected for elimination of Curtobacterium sp. contamination in Gisela 5 rootstock tissue cultures. Both nanocomposites showed 100% inhibition of bacterial plaque formation on culture medium at concentrations of 100, 200 and 400 mg L-1 Ag (2 ×–8 × MBC). The quantity of Curtobacterium sp. on culture medium assessed using cfu enumeration was reduced by 92% and 74% in comparison to the positive control after treatment with reduced graphene oxide–silver–copper and silver–selenium at a concentration of 200 mg L-1 Ag, respectively. None of the tested concentrations resulted in a decrease in Curtobacterium sp. quantity in explants. Curtobacterium sp. was detected in donor Gisela 5 plants, indicating an endophytic character of this bacterium. The dry weight of explants was not negatively affected by the application of nanocomposites regardless of concentration, and no detrimental effect of either nanocomposite at 100 or 200 mg L-1 Ag on the surface covered by plants was observed. Conclusions Reduced graphene oxide–silver–copper and silver–selenium nanocomposites at 200 mg L-1 Ag effectively limited the Curtobacterium sp. presence in micropropagated Prunus rootstock without causing phytotoxicity; therefore, those treatments could be offered as prevention with a high activity against bacterial contamination in plant tissue cultures. Graphical Abstract

Abstract Graphene oxide (GO) synthesised by modified Tour’s method was decorated with copper and zinc nanoparticles (NPs) and simultaneously reduced by sodium borohydride to obtain a nanocomposite of reduced GO with copper and zinc NPs (rGO–Cu–Zn). The nanocomposite rGO–Cu–Zn was characterised by transmission electron microscopy (TEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The rGO–Cu–Zn was tested against Xanthomonas euvesicatoria (X. euvesicatoria), which attacks tomatoes and causes bacterial spots (BSs), and compared with the commercial product Champion 50 WG. Total bacterial growth inhibition was observed for the 1% rGO–Cu–Zn, whereas Champion 50 WG at the same concentration inhibited but did not eradicate all the bacterial colonies. To evaluate the negative effect of the rGO–Cu–Zn on the molecular level, the expression of the genes associated with the action of abiotic and biotic stress factors was analysed. Gene expression in the plants treated with 10% rGO–Cu–Zn did not exhibit a noticeable increase. Graphical Abstract

Abstract During a previous study on microfungi associated with clematis roots, Penicillium-like fungi were isolated and identified based on morphology. In this study, we subjected those strains to a detailed examination which led to the proposal of two taxonomic novelties, named Rasamsonia chlamydospora and Talaromyces clematidis. The first taxon is characterized by rough-walled mycelium, acerose to flask shaped phialides, cylindrical conidia and by production of chlamydospore-like structures. The four-loci-based phylogeny analysis delineated the taxon as a taxonomic novelty in Rasamsonia. Talaromyces clematidis is characterized by restricted growth on Czapek yeast extract agar, dichloran 18% glycerol agar and yeast extract sucrose agar, and production of yellow ascomata on oatmeal agar. Phylogenetic analyses placed this taxon as a taxonomic novelty in Talaromyces sect. Bacillispori. Both taxa are introduced here with detailed descriptions, photoplates and information on their phylogenetic relationship with related species.

ABSTRACT In this study, we investigated the impact of zinc oxide (ZnO) and zinc oxide nanoparticles (ZnONPs) on Escherichia coli. These compounds are commonly used as fertilizers and feed additives and may have unintended consequences on bacteria. We conducted phenotypic and multi-omics analyses of E. coli exposed to sub-lethal concentrations of ZnO and ZnONPs for 40 sub-culturings and 20 sub-culturings with zinc followed by 20 sub-culturings without zinc in an attempt to reverse zinc effects. An extended treatment with ZnO for 40 sub-culturings had the greatest impact leading to bacterial resistance to aminoglycosides, cephalosporins, and sulfonamides while the treatment with ZnONPs for 40 sub-culturings led to the elevated MIC to chloramphenicol only. Cells exposed to these treatments were thicker and had retarded growth in elevated temperatures. Importantly, zinc withdrawal reversed most phenotypic changes. Zinc exposure caused dramatic changes in cell transcripts and proteins with a role in antibiotic response, heat stress, growth regulation, cell shape, and biofilm formation. An extended zinc exposure led to overall major alterations in E. coli biology and resulted in multi-drug resistance.IMPORTANCEA long-term exposure of bacteria to zinc oxide and zinc oxide nanoparticles leads to major alterations in bacterial morphology and physiology. These included biochemical and physiological processes promoting the emergence of strains with multi-drug resistance and virulence traits. After the removal of zinc pressure, bacterial phenotype reversed back to the original state; however, certain changes at the genomic, transcriptomic, and proteomic level remained. Why is this important? The extensive and intensive use of supplements in animal feed effects the intestinal microbiota of livestock and this may negatively impact the health of animals and people. Therefore, it is crucial to understand and monitor the impact of feed supplements on intestinal microorganisms in order to adequately assess and prevent potential health risks.

Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.

Abstract Xanthomonas euvesicatoria (Xe) is of the genera Xanthomonas, which causes a bacterial spot disease that affects tomato and pepper plants, resulting in significant economic losses. Commonly used bactericides lead to pathogen resistance, environmental contamination and a current risk to human health. Herein, a nanocomposite consisting of Cu and Ag loaded onto reduced graphene oxide (rGO) was synthesized, characterized and tested. After confirmation of the antibacterial properties in vitro, nanocomposites at concentrations of 50 and 500 µg mL−1 were applied to protect tomato and pepper plants under controlled greenhouse conditions. The tomato and pepper plants indicated significantly lower disease severity when treated with the nanocomposite (15.6 and 16.7%, respectively) than when treated with the commercial copper-based bactericide Kocide® 2000. The nanocomposite was demonstrated as a high-efficiency biocide and has the potential for crop disease management with no phytotoxic effect. Graphical Abstract

Production from crops of pome, stone fruit, nut, berry fruit, citrus, grapevine, and olive is increasingly threatened by fungal trunk diseases (FTD). These diseases and the consequent production losses are major problems. Many fungi (including Botryosphaeriaceae, Calosphaeriaceae, Diaporthaceae, Diatrypaceae, Nectriaceae, Phaeomoniellaceae, Pleosporaceae, Togniniaceae, Valsaceae) infect host wood, mainly through wounds and subsequent colonization of woody tissues, causing symptoms such as cankers, gummosis, wood rotting, blight and dieback. Propagative plant material, seedlings and fruit play a significant role in pathogen spread. Several abiotic factors (e.g. shifts in cultural practices and climate change) are involved in the disease development. This paper reviews recent literature on FTD of fruit crops, particularly focusing on the European status of pathogen occurrence. Case studies are described related to diseases of apple, citrus, grapevine, berry, nut and stone fruit, and olive trees. Aspects related to epidemiology and the increase in disease incidence along with the future perspectives on the FTD research are also discussed.

The steadfast propensity to global warming has had a severe impact on overall viticulture. Given the observed increase in growing season temperatures in Europe (+1.7 °C from 1950 to 2004), between 2000 and 2049, it is assumed that temperatures for major wine regions will increase on average by about +0.42 °C per decade and will generally increase by +2.04 °C. Phenolic compound development is affected by environmental parameters such as ultraviolet (UV) radiation, sunlight, maximum and minimum temperatures, and grapevine water status. Proanthocyanidins, flavan-3-ol monomers, and other pigmented polymers are impacted by soil management and canopy handling strategies, as well as obtaining a microclimate around the developing bunch. This review, after a necessary summary of the synthesis of phenolic compounds in the berry (flavonoids and non-flavonoids) to let the lector delve into the topic, describes the impact of climate change and therefore of environmental factors on their accumulation and storage throughout ripening and harvesting. For example, high berry temperatures can reduce the total concentrations of skin anthocyanin; a 35 °C temperature entirely obstructed anthocyanin synthesis, and instead quercetin 3-glucoside could be enhanced with exposure to solar radiation. In addition, increments via water deficit in the relative abundance of methoxylated anthocyanins were also found. The vineyard management strategies to mitigate the degradation of phenolic compounds and preserve their concentration are also further discussed. Finally, it is believed that it is necessary today to establish an elastic and variable approach towards the single wine year, moving away from the concept of product standardization.

The seed-borne bacterium Xanthomonas campestris pv. campestris (Xcc) as a causal organism of black rot disease remains the most serious bacterial problem of agricultural production of cruciferous plants worldwide. The eradication of a primary inoculum originating in seeds is available, but no treatment is totally effective. With the threat of developing chemical resistance and increasing pressure for sustainable disease management, biocontrol methods represent one of the main strategies currently applied in agriculture. Natural antimicrobials, including essential oils, are promising tools in disease management with low risks of environmental pollution and impact on human health. Thyme and clove essential oils were demonstrated to be highly effective in Xanthomonas studies in vitro; therefore, their application in black rot control was evaluated in this study. From five phenolic substances originating from thyme and clove essential oils (carvacrol, eugenol, linalool, p-cymene and thymol), the most promising in vitro results were observed with carvacrol, for which 0.0195% led to the death of all Xcc cells in 30 min. Moreover, a synergistic antibacterial effect of carvacrol and thymol solutions decreased the minimal inhibition concentration to 0.0049% and 0.0195% for carvacrol and thymol, respectively. Using the quadruple bactericidal values, the complete elimination of Xcc from the surface of infested cabbage seeds was obtained for both carvacrol and thymol solutions and their combined mixture at 2 MIC value. The elimination of bacterial infection from germinated cabbage plants was observed for both plate counting and quantitative real-time PCR methods. We also evaluated the effect of the application of phenolic treatment on the seed germination and germinated plants. Our results suggest a high potential of the application of carvacrol and thymol in vegetable seed production, specifically for cabbage, thus representing a suitable alternative to cupric derivatives.

Phyllosticta ampelicida causes grapevine black rot, a potentially damaging disease for grape production. This paper reports the draft genome sequence of P. ampelicida PA1 Galicia CBS 148563, which is 30.55 Mb and encodes 10,691 predicted protein-coding genes. This is the first sequence genome assembly of P. ampelicida, and this information is a valuable resource to support genomic attributes for determining pathogenic behaviour and comparative genomic analyses of grapevine black rot fungi.

During a study of Botryosphaeriaceae species associated with grapevine trunk diseases in the Czech Republic, a collection of 22 Botryosphaeriaceae-like strains were isolated from four cultivars (Blaufränkisch, Pálava, Pinot Noir, and Welschriesling) in four distinct vineyards. Based on morphology and DNA sequence data (ITS, tub2, and tef), four species were identified: Botryosphaeria dothidea, Diplodia mutila, D. seriata, and Neofusicoccum parvum. These species are reported for the first time from grapevine in the Czech Republic. Relationships between vascular lesions and particular species were highlighted in this study. Diplodia seriata was the most frequently isolated species, present in all four sampled cultivars, while D. mutila was the least frequent, present only in ‘Pálava’. The cultivar Pinot Noir was the most tolerant host for Botryosphaeriaceae fungi.

Phytophthora castaneae, an oomycete pathogen causing root and trunk rot of different tree species in Asia, was shown to harbor a rich diversity of novel viruses from different families. Four P. castaneae isolates collected from Chamaecyparis hodginsii in a semi-natural montane forest site in Vietnam were investigated for viral presence by traditional and next-generation sequencing (NGS) techniques, i.e., double-stranded RNA (dsRNA) extraction and high-throughput sequencing (HTS) of small RNAs (sRNAs) and total RNA. Genome organization, sequence similarity, and phylogenetic analyses indicated that the viruses were related to members of the order Bunyavirales and families Endornaviridae, Megabirnaviridae, Narnaviridae, Totiviridae, and the proposed family “Fusagraviridae.” The study describes six novel viruses: Phytophthora castaneae RNA virus 1–5 (PcaRV1-5) and Phytophthora castaneae negative-stranded RNA virus 1 (PcaNSRV1). All six viruses were detected by sRNA sequencing, which demonstrates an active RNA interference (RNAi) system targeting viruses in P. castaneae. To our knowledge, this is the first report of viruses in P. castaneae and the whole Phytophthora major Clade 5, as well as of the activity of an RNAi mechanism targeting viral genomes among Clade 5 species. PcaRV1 is the first megabirnavirus described in oomycetes and the genus Phytophthora.

Tomato is the most consumed vegetable in the world. The tomato brown rugose fruit virus (ToBRFV) is an important destructive virus that damages tomatoes and peppers with significant economic impact. The detection and characterization of this important viral pathogen were evaluated at the molecular and morphological level. The viral isolate was purified and inoculated on tomato and pepper plants. Small RNAs were sequenced in both plants and the profiles were compared. The complete genome of the isolate was obtained, and microRNA (miRNA) profiles were unveiled by small RNA sequencing. Symptoms caused by the isolate were also described and the morphology of the isolate was observed by transmission electron microscopy. Our results contribute to further understanding of the role of miRNAs in ToBRFV pathogenesis, which may be crucial for understanding disease symptom development in tomatoes and peppers.

‘Candidatus Phytoplasma spp.’ are pathogenic bacteria that infect many plant species. ‘Candidatus Phytoplasma pyri’, one of the members of the 16SrX group causes pear decline disease that adversely affects pear crops. To describe the prevalence of ‘Ca. P. pyri’ genotypes in the Czech Republic, 143 pear samples were collected from 41 locations including commercial orchards as well as trees along roads. Phytoplasma was detected by PCR in 115 samples, and it was possible to determine imp gene genotype in 84 samples. The most frequent genotypes were A1, B1, and C, which were identified in 71% of phytoplasma positive samples. ‘Ca. P. pyri’ was present either alone or as a mix of two populations in 88% of genotyped samples, and in another 6% of samples it was found in a mixed infection with ‘Ca. Phytoplasma mali’. A sole infection with ‘Ca. Phytoplasma mali’ was observed in 6% of samples. As for symptoms, 19% of symptomatic samples were found to be phytoplasma negative, and 74% of asymptomatic samples proved to be phytoplasma positive; leaf roll was more often observed in phytoplasma positive samples, while leaf narrowing rather indicated the absence of phytoplasma. The mildest symptoms were observed in samples infected with ‘Ca. P. pyri’ of the A1 imp genotype.

The study overviews results of bacterial incidence in in vitro plant tissue cultures obtained from commercial laboratory dealing with plants micropropagation. For the exploration, the 454 pyrosequencing of the 16S rRNA gene was used. Three samples of plant in vitro cultures with visual bacterial contamination were subjected for identification of present bacteria. Eleven genera as Acinetobacter, Lactobacillus, Methylobacterium, Roseomonas, Microbacterium, Mycobacterium, Curtobacterium, Acidovorax, Magnetospirillum, Chryseobacterium and Ralstonia were detected. Obtained results confirmed the advantages of high‑throughput amplicon sequencing analysis for identification of bacterial communities in contaminated plant in vitro cultures what provides an important information for applying appropriate measures to eliminate bacterial contamination.

Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alpha-diversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.