Evaluation of kasugamycin for fire blight management, effect on nontarget bacteria, and assessment of kasugamycin resistance potential in Erwinia amylovora

Norfloxacin inhibited the growth, development and reproduction of Grapholita molesta by reducing the abundance of Enterobacteriaceae bacteria in the guts of larva and ovaries of female moth

While antibiotics are occasionally used in orchard bacterial disease management, their ecological impacts remain understudied. This investigation reveals significant sublethal effects of norfloxacin on the key fruit tree pest Grapholita molesta (oriental fruit moth). Our results showed that the antibiotic norfloxacin induced multiple developmental alterations by reducing the abundance of Enterobacteriaceae bacteria in the larval guts and adult ovaries: larval stage prolongation (+8.64 %), reduced pupal weight (-6.95 %), shortened adult period (-9.55 %), and impaired female fecundity with 24.77 % lower egg production and 16.57 % reduced egg hatchability. Our findings demonstrate that optimized antibiotic applications could simultaneously manage bacterial pathogens and suppress pest populations, providing dual agricultural benefits. This study proposes a novel integrated approach for orchard management through targeted antibiotic utilization.

Development and evaluation of an attenuated Avibacterium paragallinarum strain as a live vaccine candidate for infectious coryza

Avibacterium paragallinarum (Av. paragallinarum), the causative agent of infectious coryza, is a significant pathogen responsible for substantial economic losses in the poultry industry. Current preventive strategies rely primarily on inactivated vaccines, which have limitations such as vaccine failure and limited cross-protection between serotypes. This study aimed to develop an attenuated strain of Av. paragallinarum as a potential live vaccine candidate. Using the Tn5-Kan transposon, we constructed a transposon mutant library and identified a mutant strain, designated 2019/HB64-40, which harbored a disrupted ksgA gene encoding a critical enzyme involved in ribosomal RNA methylation. Compared with the wild-type strain, the 2019/HB64-40 strain presented significantly reduced biofilm formation, lower hemagglutination titres, and impaired growth. Pathogenicity assessments in chickens demonstrated that the mutant strain displayed significantly attenuated virulence, characterized by fewer clinical symptoms and reduced bacterial shedding. Furthermore, following challenge, all unimmunized chickens presented severe clinical signs of infectious coryza at 2 dpi, with symptoms beginning to ameliorate by 5 dpi, culminating in a mean clinical sign score of 2.1. In contrast, only one chicken (1/10) in the immunized group displayed mild facial swelling and nasal discharge, with a mean clinical sign score of 0.1. The immunized group receiving the 2019/HB64-40 strain demonstrated 90% immunoprotection, highlighting the potential of this attenuated strain as a live vaccine candidate. While cross-serotype protection was not evaluated, the results suggest effective homologous protection and colonization capacity, underscoring its promising application in the prevention and treatment of infectious coryza.

Whole genome sequences of eight Erwinia amylovora phages isolated from South Korea

The gram-negative Enterobacteriaceae Erwinia amylovora is the causative agent of fire blight. Herein, we announce the full genome sequencing and annotation of eight E. amylovora bacteriophages from apple and pear orchards in South Korea, which have remarkable similarity to Erwinia phages previously isolated from the Americas.

Comparison of Resistance Acquisition and Mechanisms in Erwinia amylovora against Agrochemicals Used for Fire Blight Control

Agrochemicals containing antibiotics are authorized to manage fire blight that has been occurring in Korea since 2015. The minimum inhibitory concentration (MIC) of each antibiotic against Erwinia amylovora, the causal pathogen of fire blight, has increased over the years due to the pathogen's frequent exposure to antibiotics, indicating the necessity to prepare for the emergence of antibiotic resistance. In this study, E. amylovora was exposed to stepwise increasing concentrations of eight different agrochemicals, each containing single or mixed antibiotics, and gene mutation and changes in MIC were assessed. Streptomycin and oxolinic acid induced an amino acid substitution in RpsL and GyrA, respectively, resulting in a rapid increase in MIC. Oxytetracycline initially induced amino acid substitutions or frameshifts in AcrR, followed by substitutions of 30S small ribosomal protein subunit S10 or AcrB, further increasing MIC. E. amylovora acquired resistance in the order of oxolinic acid, streptomycin, and oxytetracycline at varying exposure frequencies. Resistance acquisition was slower against agrochemicals containing mixed antibiotics than those with single antibiotics. However, gene mutations conferring antibiotic resistance emerged sequentially to both antibiotics in the mixed formulations. Results suggested that frequent application of mixed antibiotics could lead to the emergence of multidrug-resistant E. amylovora isolates. This study provided essential insights into preventing the emergence of antibiotic-resistant E. amylovora and understanding the underlying mechanisms of resistance acquisition.

Competition for nutrient niches within the apple blossom microbiota antagonizes the initiation of fire blight infection

Changes in the plant microbiota composition are intimately associated with the health of the plant, but factors controlling the microbial community in flowers are poorly understood. In this study, we used apple flowers and fire blight as a model system to investigate the effects of floral microbiota and microbial competition on disease development and suppression. To compare changes in microbial flora with the RNA expression patterns of plants, the flower samples were collected in three different flowering stages (Bud, Popcorn, and Full-bloom). Using advanced sequencing technology, we analyzed the data and conducted both in vitro and in vivo experiments to validate our findings. Our results show that the Erwinia amylovora use arabinogalactan, which is secreted on the flowers, for early colonization of apple flowers. Pantoea agglomerans was more competitive for arabinogalactan than E. amylovora. Additionally, P. agglomerans suppressed the expression of virulence factors of E. amylovora by using arabinose, which is a major component of arabinogalactan, which induces virulence gene expression. The present data provide new insights into developing control strategies for diverse plant diseases, including fire blight, by highlighting the importance of nutrients in disease development or suppression.

The Use and Impact of Antibiotics in Plant Agriculture: A Review

Growers have depended on the specificity and efficacy of streptomycin and oxytetracycline as a part of their plant disease arsenal since the middle of the 20th century. With climate change intensifying plant bacterial epidemics, the established success of these antibiotics remains threatened. Our strong reliance on certain antibiotics for devastating diseases eventually gave way to resistance development. Although antibiotics in plant agriculture equal to less than 0.5% of overall antibiotic use in the United States, it is still imperative for humans to continue to monitor usage, environmental residues, and resistance in bacterial populations. This review provides an overview of the history and use, resistance and mitigation, regulation, environmental impact, and economics of antibiotics in plant agriculture. Bacterial issues, such as the ongoing Huanglongbing (citrus greening) epidemic in Florida citrus production, may need antibiotics for adequate control. Therefore, preserving the efficacy of our current antibiotics by utilizing more targeted application methods, such as trunk injection, should be a major focus. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Bacterial Lipopeptides Are Effective against Pear Fire Blight

Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and conducted screenings to assess their ability to inhibit E. amylovora in vitro. Through biochemical tests and partial 16S rRNA gene sequencing, we identified two promising strains, Priestia megaterium strain H1 and Bacillus subtilis strain I2. These strains were then evaluated for their efficacy in biocontrol under controlled laboratory conditions, focusing on immature fruits and leaves. Remarkably, all selected antagonists exhibited the capability to reduce the severity of the disease on both fruit and leaves. P. megaterium strain H1 and B. subtilis strain I2 exhibited significant reductions in disease incidence on both immature fruits and leaves compared to the control. Specifically, on immature fruits, they achieved reductions of 53.39% and 44.76%, respectively, while on leaves, they demonstrated reductions of 59.55% and 55.53%, respectively. Furthermore, during the study, we detected the presence of lipopeptides, including surfactin, iturins, bacillomycin D, and fengycins, in the methanol extract obtained from these two antagonistic bacteria using thin-layer chromatography (TLC). Based on the results obtained, B. subtilis strain I2 and P. megaterium strain H1 exhibit considerable potential for controlling fire blight. However, further evaluation of their efficacy under natural field conditions is essential to validate their practicality as a biocontrol method.

What role do biocontrol agents with Mg2+ play in the fate of antibiotic resistome and pathogenic bacteria in the phyllosphere?

The contamination of the plant phyllosphere with antibiotics and antibiotic resistance genes (ARGs), caused by application of antibiotics, is a significant environmental issue in agricultural management. Alternatively, biocontrol agents are environmentally friendly and have attracted a lot of interest. However, the influence of biocontrol agents on the phyllosphere resistome remains unknown. In this study, we applied biocontrol agents to control the wildfire disease in the Solanaceae crops and investigated their effects on the resistome and the pathogen in the phyllosphere by using metagenomics. A total of 250 ARGs were detected from 15 samples, which showed a variation in distribution across treatments of biocontrol agents (BA), BA with Mg2+ (T1), BA with Mn2+ (T2), and kasugamycin (T3) and nontreated (CK). The results showed that the abundance of ARGs under the treatment of BA-Mg2+ was lower than that in the CK group. The abundance of cphA3 (carbapenem resistance), PME-1 (carbapenem resistance), tcr3 (tetracycline antibiotic resistance), and AAC (3)-VIIIa (aminoglycoside antibiotic resistance) in BA-Mg2+ was significantly higher than that in BA-Mn2+ (P < 0.05). The abundance of cphA3, PME_1, and tcr3 was significantly negatively related to the abundance of the phyllosphere pathogen Pseudomonas syringae (P < 0.05). We also found that the upstream and downstream regions of cphA3 were relatively conserved, in which rpl, rpm, and rps gene families were identified in most sequences (92%). The Ka/Ks of cphA3 was 0 in all observed sequences, indicating that under the action of purifying selection, nonsynonymous substitutions are often gradually eliminated in the population. Overall, this study clarifies the effect of biocontrol agents with Mg2+ on the distribution of the phyllosphere resistome and provides evolutionary insights into the biocontrol process.

IMPORTANCE

Our study applied metagenomics analysis to examine the impact of biocontrol agents (BAs) on the phyllosphere resistome and the pathogen. Irregular use of antibiotics has led to the escalating dissemination of antibiotic resistance genes (ARGs) in the environment. The majority of BA research has focused on the effect of monospecies on the plant disease control process, the role of the compound BA with nutrition elements in the phyllosphere disease, and the resistome is still unknown. We believe BAs are eco-friendly alternatives for antibiotics to combat the transfer of ARGs. Our results revealed that BA-Mg2+ had a lower relative abundance of ARGs compared to the CK group, and the phyllosphere pathogen Pseudomonas syringae was negatively related to three specific ARGs, cphA3, PME-1, and tcr3. These three genes also present different Ka/Ks. We believe that the identification of the distribution and evolution modes of ARGs further elucidates the ecological role and facilitates the development of BAs, which will attract general interest in this field.

Genome sequence of Erwinia amylovora bacteriophage Omen

We report the genome of Erwinia amylovora phage Omen, isolated from a Portuguese orchard. Omen has a genome size of 85,304 bp, belongs to the genus Kolesnikvirus (myovirus morphotype), and shares over 80% nucleotide identity with various Erwinia phage genomes.

Acidifying Spray Suspensions of Oxytetracycline and Kasugamycin Enhances Their Effectiveness for Fire Blight Control in Apple and Pear

The stability of the fire blight control material, oxytetracycline, in water is strongly affected by pH, increasing with increasing acidity. From 2017 to 2021, pear and apple orchard trials were conducted to evaluate if acidic amendments to oxytetracycline sprays improve fire blight control. Compared with the water-treated control, infection suppression after two bloom applications of an acidified commercial oxytetracycline formulation averaged 85.9 ± 0.4% compared with 72.2 ± 1.7% without an acidifier, but individual trials frequently had insufficient statistical power to separate among acidified and non-acidified antibiotic treatments. Across trials, a significant linear relationship was observed for regression of relative infection suppression from oxytetracycline (hydrochloride formulation) on spray tank pH. Similar relationships were observed for oxytetracycline (calcium complex formulation) and kasugamycin (P values were 0.055 and 0.069, respectively). Also based on regression, acidified oxytetracycline and kasugamycin suppressed epiphytic populations of Erwinia amylovora on flowers to a greater degree than the antibiotic only. As spray suspensions, commercial oxytetracycline formulations at label rate and amended with citric acid (1.2 g/liter) in well water had pH values near 3.4, but after spraying, the pH of flowers washed in deionized water (1 ml/flower) measured in a range of 5.2 to 5.5 compared with a pH range of 5.8 to 6.0 after a treatment of oxytetracycline only. In pear fruit finish trials, sprays acidified with citric acid-based materials had negligible effects on fruit russeting. Based on a serological assay, the detectable residual of oxytetracycline on apple foliage was increased by co-application with citric acid compared with a non-acidified control.

A Novel IncX Plasmid Mediates High-Level Oxytetracycline and Streptomycin Resistance in Erwinia amylovora from Commercial Pear Orchards in California

Isolates of the fire blight pathogen Erwinia amylovora with high-level resistance to oxytetracycline (minimal inhibitory concentration [MIC] > 100 μg/ml) and to streptomycin (MIC > 100 μg/ml) were recovered from four commercial pear orchards in California between 2018 and 2020. The two representative oxytetracycline- and streptomycin-resistant (OxyTcR-SmR) strains 32-10 and 33-1 were as virulent as the antibiotic susceptible strain 13-1 in causing blossom blight of pear and were recovered more than 50% of the time 7 days after co-inoculation to pear flowers with strain 13-1. In the field, inoculation of strain 32-10 to pear flowers that were pretreated with oxytetracycline at 200 μg/ml did not reduce disease compared with an untreated control. Four OxyTcR-SmR strains were subjected to draft genome sequencing to identify the genetic determinants of antibiotic resistance and their location. A 43.6-kb IncX plasmid, designated pX11-7, was detected in each of the four strains, and this plasmid encoded the tetracycline-resistance gene tetB and the streptomycin-resistance gene pair strAB within a large putatively mobile genetic element consisting of the transposon Tn10 that had inserted within the streptomycin-resistance transposon Tn6082. We also determined that pX11-7 was conjugative and was transferred at a rate that was 104 to 105 higher into an E. amylovora strain isolated in California compared with an E. amylovora strain that was isolated in Michigan. The occurrence of high levels of resistance to both oxytetracycline and streptomycin in E. amylovora strains from commercial pear orchards in California significantly limits the options for blossom blight management in these locations.

Applications of Germicidal Ultraviolet Light as a Tool for Fire Blight Management (Erwinia amylovora) in Apple Plantings

Nighttime applications of germicidal UV light (UV-C) have been used to suppress several fungal diseases of plants, but less is known of UV-C's potential to suppress bacterial plant pathogens. Fire blight of apple and pear, caused by the bacterium Erwinia amylovora, is difficult to suppress using cultural practices, antibiotics, and host resistance. We therefore investigated the potential of UV-C as an additional means to manage the disease. Laboratory assays confirmed that in vitro exposure of cultures E. amylovora to UV-C at doses ranging from 0 to 400 J/m2 in the absence of visible light was more than 200% as effective as cultures exposed to visible light after the same UV-C treatments. In a 2-year orchard study, we demonstrated that with only two nighttime applications of UV-C at 200 J/m2 made at bloom resulted in an incidence of blossom blight and shoot blight equivalent to the results viewed when antibiotic and biopesticide commercial standards were applied. In vitro dose-response studies indicated consistency in pathogen response to suppressive UV-C doses, including pathogen isolates that were resistant to streptomycin. Based on these results, UV-C may be useful in managing bacterial populations with antibiotic resistance. Concurrent measurements of host growth after UV-C applications indicated that the dose required to suppress E. amylovora had no significant (P > 0.05) effects on foliar growth, shoot extension, internode length, or fruit finish but substantially reduced epiphytic populations of E. amylovora on host tissues.

Erwinia amylovora Type III Secretion System Inhibitors Reduce Fire Blight Infection Under Field Conditions

Fire blight, caused by Erwinia amylovora, is an economically important disease in apples and pears worldwide. This pathogen relies on the type III secretion system (T3SS) to cause disease. Compounds that inhibit the function of the T3SS (T3SS inhibitors) have emerged as alternative strategies for bacterial plant disease management, as they block bacterial virulence without affecting growth, unlike traditional antibiotics. In this study, we investigated the mode of action of a T3SS inhibitor named TS108, a plant phenolic acid derivative, in E. amylovora. We showed that adding TS108 to an in vitro culture of E. amylovora repressed the expression of several T3SS regulon genes, including the master regulator gene hrpL. Further studies demonstrated that TS108 negatively regulates CsrB, a global regulatory small RNA, at the posttranscriptional level, resulting in a repression of hrpS, which encodes a key activator of hrpL. Additionally, TS108 has no impact on the expression of T3SS in Dickeya dadantii or Pseudomonas aeruginosa, suggesting that its inhibition of the E. amylovora T3SS is likely species specific. To better evaluate the performance of T3SS inhibitors in fire blight management, we conducted five independent field experiments in four states (Michigan, New York, Oregon, and Connecticut) from 2015 to 2022 and observed reductions in blossom blight incidence as high as 96.7% compared with untreated trees. In summary, the T3SS inhibitors exhibited good efficacy against fire blight.

On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective

Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.

Alanine-Dependent TCA Cycle Promotion Restores the Zhongshengmycin-Susceptibility in Xanthomonas oryzae

Xanthomonas oryzae pv. oryzicola (Xoo) is a plant pathogenic bacterium that can cause rice bacterial blight disease, which results in a severe reduction in rice production. Antimicrobial-dependent microbial controlling is a useful way to control the spread and outbreak of plant pathogenic bacteria. However, the abuse and long-term use of antimicrobials also cause microbial antimicrobial resistance. As far as known, the mechanism of antimicrobial resistance in agricultural plant pathogenic bacteria still lacks prospecting. In this study, we explore the mechanism of Zhongshengmycin (ZSM)-resistance in Xoo by GC-MS-based metabolomic analysis. The results showed that the down-regulation of the TCA cycle was characteristic of antimicrobial resistance in Xoo, which was further demonstrated by the reduction of activity and gene expression levels of key enzymes in the TCA cycle. Furthermore, alanine was proven to reverse the ZSM resistance in Xoo by accelerating the TCA cycle in vivo. Our results are essential for understanding the mechanisms of ZSM resistance in Xoo and may provide new strategies for controlling this agricultural plant pathogen at the metabolic level.

Copper-Based Compounds against Erwinia amylovora: Response Parameter Analysis and Suppression of Fire Blight in Apple

Fire blight, caused by Erwinia amylovora, is one of the major bacterial disease of apple and pear, causing enormous economic losses worldwide. Several control measures against E. amylovora have been reported till date, however, none of them have proved to be effective significantly against the pathogen. In this study, mechanisms of the copper-based control agents (CBCAs): copper oxychloride (COCHL), copper oxide (COX), copper hydroxide (CHY), copper sulfate basic (CSB), and tribasic copper sulfate (TCS) and their disease severity reduction efficacy against E. amylovora were analyzed. Bis-1,3-dibutylbarbituric acid trimethine oxonol, carboxyl fluorescein diacetate succinimidyl ester, and 5-cyano-2,3-ditolyl tetrazolium chloride staining were used to check the damage of membrane potential, cytoplasmic pHin, and respiration of CBCAs-treated E. amylovora, respectively. High disturbance in the membrane potential of E. amylovora was found under COX and COCHL treatments. Similarly, higher significant changes in the inner cytoplasmic pHin were observed under COX, COCHL, and TCS treatment. CHY and COCHL-treated E. amylovora showed a significant reduction in respiration. In vitro bioassay results revealed that CHY, CSB, and TCS at 2,000 ppm reduced the severity of fire blight both in pre- and post-treatment of CBCAs in immature apple fruits and seedlings. Overall, the most effective CBCAs against E. amylovora could be CHY at 2,000 ppm as its showed inhibition mechanisms and disease severity reduction.

Survey of Oxolinic Acid-Resistant Erwinia amylovora in Korean Apple and Pear Orchards, and the Fitness Impact of Constructed Mutants

Fire blight caused by Erwinia amylovora (Ea) is a devastating disease in apple and pear trees. Oxolinic acid (OA), a quinolone family antibiotic that inhibits DNA gyrase, has been employed to control fire blight in South Korea since 2015. The continuous use of this bactericide has resulted in the emergence of OA-resistant strains in bacterial pathogens in other countries. To investigate the occurrence of OA-resistant Ea strains in South Korea, we collected a total of 516 Ea isolates from diseased apple and pear trees in 2020-2021 and assessed their sensitivities to OA. We found that all isolates were susceptible to OA. To explore the possibility of emerging OA-resistant Ea by continuous application of OA, we exposed Ea stains to a range of OA concentrations and constructed OA-resistant mutant strains. Resistance was associated with mutations in the GyrA at codons 81 and 83, which result in glycine to cysteine and serine to arginine amino acid substitutions, respectively. The in vitro growth of the mutants in nutrient media and their virulence in immature apple fruits were lower than those of wild-type. Our results suggest that OA-resistance decreases the fitness of Ea. Future work should clarify the mechanisms by which OA-resistance decreases virulence of this plant pathogen. Continuous monitoring of OA-resistance in Ea is required to maintain the efficacy of this potent bactericide.

Multi-Omics Analysis Reveals that the Antimicrobial Kasugamycin Potential Targets Nitrate Reductase in Didymella segeticola to Achieve Control of Tea Leaf Spot

Because of the lack of effective disease management measures, tea leaf spot-caused by the fungal phytopathogen Didymella segeticola (syn. Phoma segeticola)-is an important foliar disease. The important and widely used agricultural antimicrobial kasugamycin (Ksg), produced by the Gram-positive bacterium Streptomyces kasugaensis, effects high levels of control against crop diseases. The results of this study indicated that Ksg could inhibit the growth of D. segeticola hyphae in vitro with a half-maximal effective concentration (EC₅₀) of 141.18 μg ml^-1. Meanwhile, the curative effect in vivo on the pathogen in detached tea leaves also demonstrated that Ksg induced some morphological changes in organelles, septa, and cell walls as observed by optical microscopy and by scanning and transmission electron microscopy. This may indicate that Ksg disturbs biosynthesis of key metabolites, inhibiting hyphal growth. Integrated transcriptomic, proteomic, and bioinformatic analyses revealed that differentially expressed genes or differentially expressed proteins in D. segeticola hyphae in response to Ksg exposure were involved with metabolic processes and biosynthesis of secondary metabolites. Molecular docking studies indicated that Ksg may target nitrate reductase (NR), and microscale thermophoresis assay showed greater affinity with NR, potentially disturbing nitrogen assimilation and subsequent metabolism. The results indicated that Ksg inhibits the pathogen of tea leaf spot, D. segeticola, possibly by binding to NR, disturbing fungal metabolism, and inducing subsequent changes in hyphal growth and development.

What is the impact of aminoglycoside exposure on soil and plant root-associated microbiota? A systematic review protocol

BACKGROUND

Aminoglycosides are potent bactericidal antibiotics naturally produced by soil microorganisms and are commonly used in agriculture. Exposure to these antibiotics has the potential to cause shifts in the microorganisms that impact plant health. The systematic review described in this protocol will compile and synthesize literature on soil and plant root-associated microbiota, with special attention to aminoglycoside exposure. The systematic review should provide insight into how the soil and plant microbiota are impacted by aminoglycoside exposure with specific attention to the changes in the overall species richness and diversity (microbial composition), changes of the resistome (i.e. the changes in the quantification of resistance genes), and maintenance of plant health through suppression of pathogenic bacteria. Moreover, the proposed contribution will provide comprehensive information about data available to guide future primary research studies. This systematic review protocol is based on the question, "What is the impact of aminoglycoside exposure on the soil and plant root-associated microbiota?".

METHODS

A boolean search of academic databases and specific websites will be used to identify research articles, conference presentations and grey literature meeting the search criteria. All search results will be compiled and duplicates removed before title and abstract screening. Two reviewers will screen all the included titles and abstracts using a set of predefined inclusion criteria. Full-texts of all titles and abstracts meeting the eligibility criteria will be screened independently by two reviewers. Inclusion criteria will describe the eligible soil and plant root-associated microbiome populations of interest and eligible aminoglycosides constituting our exposure. Study validity will be evaluated using the CEE Critical Appraisal Tool Version 0.2 (Prototype) to evaluate the risk of bias in publications. Data from studies with a low risk of bias will be extracted and compiled into a narrative synthesis and summarized into tables and figures. If sufficient evidence is available, findings will be used to perform a meta-analysis.

Proof of Concept for Shoot Blight and Fire Blight Canker Management with Postinfection Spray Applications of Prohexadione-Calcium and Acibenzolar-S-Methyl in Apple

To reduce the severity of shoot blight and prevent the resulting development of cankers on perennial apple wood, we evaluated eight fire blight postinfection spray programs of prohexadione-calcium (PCA) alone or with acibenzolar-S-methyl (ASM) over 2 years. On mature trees of cultivar Royal Court, a single application of the high PCA rate (247 mg/liter) at 2 to 3 days after inoculation resulted in 89.5 and 69.5% reduction of shoot blight severity after inoculation. Two applications of PCA 247 mg/liter 12 or 14 days apart, with the first one applied 2 to 3 days after inoculation, resulted in 78.8 and 74.5% reduction of shoot blight severity in both years. A 100% control of canker incidence on perennial wood from infected shoots in both years was achieved with a single application of PCA (247 mg/liter) applied at 2 or 3 days after the inoculation, and three applications of PCA (125 mg/liter) + ASM (25 mg/liter) 12 to 16 days apart reduced canker incidence by 83.5 and 69% in the 2 years. The other programs with lower PCA rates and frequencies of application reduced shoot blight severity 50.8 and 51.8% (PCA) and 62.6 to 72% and 59.3% (PCA + ASM) over 2 years, respectively. Reduction of canker incidence on wood by the other programs was 66.5% and 69 to 90.4% in the two years, respectively. As fire blight cankers lead to death of dwarf apple trees and serve as primary sources of inoculum, our effective PCA and PCA + ASM programs could serve as viable postinfection management options. These treatments can reduce or prevent canker development and thus significantly abate tree losses in high-density apple orchards after fire blight epidemics occur.

Investigating the Distribution of Strains of Erwinia amylovora and Streptomycin Resistance in Apple Orchards in New York Using Clustered Regularly Interspaced Short Palindromic Repeat Profiles: A 6-Year Follow-Up

Fire blight, caused by the bacterium Erwinia amylovora, is one of the most important diseases of apple. The antibiotic streptomycin is routinely used in the commercial apple industries of New York (NY) and New England to manage the disease. In 2002 and again, from 2011 to 2014, outbreaks of streptomycin resistance (SmR) were reported and investigated in NY. Motivated by new grower reports of control failures, we conducted a follow-up investigation of the distribution of SmR and E. amylovora strains for major apple production regions of NY over the last 6 years (2015 to 2020). Characterization of clustered regularly interspaced short palindromic repeat (CRISPR) profiles revealed that a few "cosmopolitan" strains were widely prevalent across regions, whereas many other "resident" strains were confined to one location. In addition, we uncovered novel CRISPR profile diversity in all investigated regions. SmR E. amylovora was detected only in a small area spanning two counties from 2017 to 2020 and was always associated with one CRISPR profile (41:23:38), which matched the profile of SmR E. amylovora, discovered in 2002. This suggests the original SmR E. amylovora was never fully eradicated and went undetected because of several seasons of low disease pressure in this region. Investigation of several representative isolates under controlled greenhouse conditions indicated significant differences in aggressiveness on 'Gala' apples. Potential implications of strain differences include the propensity of strains to become distributed across wide geographic regions and associated resistance management practices. Results from this work will directly influence sustainable fire blight management recommendations for commercial apple industries in NY state and other regions.

Impact of Soil Disinfestation on Fungal and Bacterial Communities in Soil With Cucumber Cultivation

Soil treatment with disinfectants has been used for controlling soilborne phytopathogens. Besides suppressing specific pathogens, how these disinfectants impact soil health, especially soil microbial communities, is yet to be systemically determined. The objectives of this study were to examine the effects of three representative disinfectants, including the dazomet fumigant, fenaminosulf fungicide, and kasugamycin antibiotic on chemical properties, enzymatic activities, and microbial communities in soil for cucumber cultivation. Results showed that 14 days after soil treatment with these chemicals, residual content of dazomet and kasugamycin quickly declined in soil and were undetectable, while fenaminosulf residues were found at 0.48 ± 0.01 mg/kg. Total nitrogen and total carbon increased in soil after dazomet treatment. Urease and sucrase activities were significantly restrained after disinfectant application. The disinfectants did not significantly change the taxon of predominant bacteria and fungi but altered the relative abundance and diversity of soil microbiome, as well as microbial interspecific relationships. Moreover, cucumber cultivation enhanced the overall soil microbial diversity and enzymatic activities, which diminished the difference of soil microbiome among four treatments. The difference in soil microbial diversity among the four treatments became smaller after planting cucumber. Thus, soil microbial communities were affected by soil disinfectants and gradually recovered by cucumber application.

Orchard Management and Landscape Context Mediate the Pear Floral Microbiome

Crop-associated microbiota are a key factor affecting host health and productivity. Most crops are grown within heterogeneous landscapes, and interactions between management practices and landscape context often affect plant and animal biodiversity in agroecosystems. However, whether these same factors typically affect crop-associated microbiota is less clear. Here, we assessed whether orchard management strategies and landscape context affected bacterial and fungal communities in pear (Pyrus communis) flowers. We found that bacteria and fungi responded differently to management schemes. Organically certified orchards had higher fungal diversity in flowers than conventional or bio-based integrated pest management (IPM) orchards, but organic orchards had the lowest bacterial diversity. Orchard management scheme also best predicted the distribution of several important bacterial and fungal genera that either cause or suppress disease; organic and bio-based IPM best explained the distributions of bacterial and fungal genera, respectively. Moreover, patterns of bacterial and fungal diversity were affected by interactions between management, landscape context, and climate. When examining the similarity of bacterial and fungal communities across sites, both abundance- and taxon-related turnovers were mediated primarily by orchard management scheme and landscape context and, specifically, the amount of land in cultivation. Our study reveals local- and landscape-level drivers of floral microbiome structure in a major fruit crop, providing insights that can inform microbiome management to promote host health and high-yielding quality fruit. IMPORTANCE Proper crop management during bloom is essential for producing disease-free tree fruit. Tree fruits are often grown in heterogeneous landscapes; however, few studies have assessed whether landscape context and crop management affect the floral microbiome, which plays a critical role in shaping plant health and disease tolerance. Such work is key for identification of tactics and/or contexts where beneficial microbes proliferate and pathogenic microbes are limited. Here, we characterize the floral microbiome of pear crops in Washington State, where major production occurs in intermountain valleys and basins with variable elevation and microclimates. Our results show that both local-level (crop management) and landscape-level (habitat types and climate) factors affect floral microbiota but in disparate ways for each kingdom. More broadly, these findings can potentially inform microbiome management in orchards for promotion of host health and high-quality yields.

Effect of Kasugamycin, Oxytetracycline, and Streptomycin on In-orchard Population Dynamics of Erwinia amylovora on Apple Flower Stigmas

We assessed the effect of three antibiotics (streptomycin, oxytetracycline, and kasugamycin) on populations of the fire blight pathogen Erwinia amylovora on apple flower stigmas during three field seasons. Application timing relative to E. amylovora presence on flower stigmas had little impact on population dynamics and subsequent disease incidence. Although E. amylovora populations on water-treated flowers increased to 10^6-7 cfu flower^-1 after 4 to 5 days during each experiment, the antibiotics streptomycin and kasugamycin caused statistically significant reductions in stigma populations by as many as 4 to 5 logs over a 4- to 5-day period during two of the three experiments. In contrast, the effect of oxytetracycline on E. amylovora populations on stigmas was more variable, with reductions in E. amylovora populations only observed during one of the three experiments. In agreement with the population data, the disease incidence was significantly higher for oxytetracycline-treated flowers compared with the other antibiotic treatments during 2 of 3 years. Statistical analyses of the effects of weather parameters on antibiotic activity revealed that solar radiation and temperature negatively impacted the activity of both kasugamycin and oxytetracycline. We further assessed the potential for photodegradation of formulated kasugamycin (Kasumin 2L) and found that Kasumin 2L was susceptible to degradation in vitro after exposure to a 16-h photoperiod of daily light integrals (DLIs) varying from 6 to 35 mol⋅m^-2⋅d^-1. We further determined that exposure to three consecutive 16-h photoperiods of DLIs of 23 or 35 mol⋅m^-2⋅d^-1 reduced the available concentration of Kasumin 2L (assessed using a bioassay) from 100 μg⋅ml^-1 to 10 to 20 μg⋅ml^-1. Our results correlate the superior blossom blight control efficacy of kasugamycin and streptomycin with significant population reductions in E. amylovora on apple flower stigmas but indicate that, similar to oxytetracycline, kasugamycin is vulnerable to photodegradation, which would suggest that further considerations are necessary when applying this antibiotic.

Innovation and Application of the Type III Secretion System Inhibitors in Plant Pathogenic Bacteria

Many Gram-negative pathogenic bacteria rely on a functional type III secretion system (T3SS), which injects multiple effector proteins into eukaryotic host cells, for their pathogenicity. Genetic studies conducted in different host-microbe pathosystems often revealed a sophisticated regulatory mechanism of their T3SSs, suggesting that the expression of T3SS is tightly controlled and constantly monitored by bacteria in response to the ever-changing host environment. Therefore, it is critical to understand the regulation of T3SS in pathogenic bacteria for successful disease management. This review focuses on a model plant pathogen, Dickeyadadantii, and summarizes the current knowledge of its T3SS regulation. We highlight the roles of several T3SS regulators that were recently discovered, including the transcriptional regulators: FlhDC, RpoS, and SlyA; the post-transcriptional regulators: PNPase, Hfq with its dependent sRNA ArcZ, and the RsmA/B system; and the bacterial second messenger cyclic-di-GMP (c-di-GMP). Homologs of these regulatory components have also been characterized in almost all major bacterial plant pathogens like Erwiniaamylovora, Pseudomonassyringae, Pectobacterium spp., Xanthomonas spp., and Ralstonia spp. The second half of this review shifts focus to an in-depth discussion of the innovation and development of T3SS inhibitors, small molecules that inhibit T3SSs, in the field of plant pathology. This includes T3SS inhibitors that are derived from plant phenolic compounds, plant coumarins, and salicylidene acylhydrazides. We also discuss their modes of action in bacteria and application for controlling plant diseases.

Development of a novel biological control agent targeting the phytopathogen Erwinia amylovora

Antibiotics are used extensively to control animal, plant, and human pathogens. They are sprayed on apple and pear orchards to control the bacterium Erwinia amylovora, the causative agent of fire blight. This phytopathogen is developing antibiotic resistance and alternatives either have less efficacy, are phytotoxic, or more management intensive. The objective of our study was to develop an effective biological control agent colonizing the host plant and competing with Erwinia amylovora. It must not be phytotoxic, have a wide spectrum of activity, and be unlikely to induce resistance in the pathogen. To this end, several bacterial isolates from various environmental samples were screened to identify suitable candidates that are antagonistic to E. amylovora. We sampled bacteria from the flowers, leaves, and soil from apple and pear orchards from the springtime bloom period until the summer. The most effective bacteria, including isolates of Pseudomonas poae, Paenibacillus polymyxa, Bacillus amyloliquefaciens and Pantoea agglomerans, were tested in vitro and in vivo and formulated into products containing both the live strains and their metabolites that were stable for at least 9 months. Trees treated with the product based on P. agglomerans NY60 had significantly less fire blight than the untreated control and were statistically not different from streptomycin-treated control trees. With P. agglomerans NY60, fire blight never extended beyond the central vein of the inoculated leaf. The fire blight median disease severity score, 10 days after inoculation, was up to 70% less severe on trees treated with P. agglomerans NY60 as compared to untreated controls.

Dissipation and dietary risk assessment of kasugamycin and saisentong in Chinese cabbage

A quick, easy, cheap, effective, rugged, and safe pretreatment method using dispersive solid-phase extraction was developed to quantify kasugamycin in Chinese cabbage samples by using ultra-performance liquid chromatography/tandem mass spectrometry. A pretreatment method involving precolumn transformation was utilized to determine the residue of saisentong in Chinese cabbage through high-performance liquid chromatography/ultraviolet detection. These methods were successfully applied through field trials to determine the contents of kasugamycin and saisentong in Chinese cabbage. The dissipation of kasugamycin and saisentong in Chinese cabbage followed first-order kinetics with a linear correlation coefficient of 0.9066-0.9731 at the 95% confidence level. The half-lives of kasugamycin and saisentong in Chinese cabbage were 1.8-2.0 and 2.2-3.8 days, respectively. Terminal residual levels of kasugamycin in Chinese cabbage were not detected 14 days after application. The dietary risk assessment of kasugamycin and saisentong in Chinese cabbage showed that their risk quotients were 0.93 and 2.58%, respectively, in the preharvest interval (PHI) of 14 days. Kasugamycin and saisentong in Chinese cabbage did not pose potential health hazards at PHI of 14 days. The maximum residue limits of kasugamycin and saisentong in Chinese cabbage were 0.02 and 0.36 mg/kg, respectively, and 14 days was the safe PHI.

Characterization and Genome Structure of Virulent Phage EspM4VN to Control Enterobacter sp. M4 Isolated From Plant Soft Rot

Enterobacter sp. M4 and other bacterial strains were isolated from plant soft rot disease. Virulent phages such as EspM4VN isolated from soil are trending biological controls for plant disease. This phage has an icosahedral head (100 nm in diameter), a neck, and a contractile sheath (100 nm long and 18 nm wide). It belongs to the Ackermannviridae family and resembles Shigella phage Ag3 and Dickeya phages JA15 and XF4. We report herein that EspM4VN was stable from 10°C to 50°C and pH 4 to 10 but deactivated at 70°C and pH 3 and 12. This phage formed clear plaques only on Enterobacter sp. M4 among tested bacterial strains. A one-step growth curve showed that the latent phase was 20 min, rise period was 10 min, and an average of 122 phage particles were released from each absorbed cell. We found the phage’s genome size was 160,766 bp and that it annotated 219 open reading frames. The genome organization of EspM4VN has high similarity with the Salmonella phage SKML-39; Dickeya phages Coodle, PP35, JA15, and Limestone; and Shigella phage Ag3. The phage EspM4VN has five tRNA species, four tail-spike proteins, and a thymidylate synthase. Phylogenetic analysis based on structural proteins and enzymes indicated that EspM4VN was identified as a member of the genus Agtrevirus, subfamily Aglimvirinae, family Ackermannviridae.

Discovery and Characterization of Low-Molecular Weight Inhibitors of Erwinia tracheiphila

Plant pathogenic bacteria in the genus Erwinia cause economically important diseases, including bacterial wilt of cucurbits caused by Erwinia tracheiphila. Conventional bactericides are insufficient to control this disease. Using high-throughput screening, 464 small molecules (SMs) with either cidal or static activity at 100 µM against a cucumber strain of E. tracheiphila were identified. Among them, 20 SMs (SM1 to SM20), composed of nine distinct chemical moiety structures, were cidal to multiple E. tracheiphila strains at 100 µM. These lead SMs had low toxicity to human cells and honey bees at 100 µM. No phytotoxicity was observed on melon plants at 100 µM, except when SM12 was either mixed with Silwet L-77 and foliar sprayed or when delivered through the roots. Lead SMs did not inhibit the growth of beneficial Pseudomonas and Enterobacter species but inhibited the growth of Bacillus species. Nineteen SMs were cidal to Xanthomonas cucurbitae and showed >50% growth inhibition against Pseudomonas syringae pv. lachrymans. In addition, 19 SMs were cidal or static against Erwinia amylovora in vitro. Five SMs demonstrated potential to suppress E. tracheiphila when foliar sprayed on melon plants at 2× the minimum bactericidal concentration. Thirteen SMs reduced Et load in melon plants when delivered via roots. Temperature and light did not affect the activity of SMs. In vitro cidal activity was observed after 3 to 10 h of exposure to these five SMs. Here, we report 19 SMs that provide chemical scaffolds for future development of bactericides against plant pathogenic bacterial species.

Management of Fire Blight Using Pre-bloom Application of Prohexadione-Calcium

Fire blight, a bacterial disease of rosaceous plants caused by Erwinia amylovora, is one of the most important diseases affecting commercial apple production worldwide. Antibiotics, applied at bloom to protect against blossom infection, are the most effective means of management but raise concern due to the potential for antibiotic resistance in both the pathogen population and nontarget organisms. In addition, most fire blight outbreaks in New York State often emerge in late June to July as shoot blight, calling into question the role of blossom infections and the antibiotic applications made to manage them. Prohexadione-calcium (PhCa) is a gibberellic acid inhibitor used post-bloom to control shoot vigor and to manage shoot blight. However, the magnitude of shoot blight management is directly related to the suppression of shoot growth, which is undesirable, especially in young orchards during establishment years. PhCa is believed to control shoot blight by thickening cell walls in cortical parenchyma, preventing invasion of host tissues by E. amylovora. We hypothesize that PhCa applied pre-bloom could similarly prevent invasion of blossom pedicels following infection, leading to reduced disease incidence. We evaluated novel pre-bloom PhCa programs for their effects on disease management (blossom and shoot blight) as well as their impact on shoot growth for three years in a mature 'Gala' orchard in New York. In all three years of the study, all PhCa programs resulted in less than 27% incidence (71% control) of blossom blight and less than 13% incidence (77% control) of shoot blight with minimal effect on tree growth. Inclusion of a biopesticide during bloom further reduced the incidence of blossom blight in one year of three. Using light microscopy, we found that cell walls in the cortical parenchyma of fruitlet pedicels on trees receiving pre-bloom PhCa applications were significantly thicker than those of untreated trees 40 days after full bloom and inoculation. Overall, we found that pre-bloom applications of PhCa had utility in reducing blossom blight and shoot blight with minimal impacts on tree growth. These pre-bloom programs would fit with standard production practices and may contribute toward the development of fire blight management programs without the use of antibiotics.

Etiology of Cyclocarya paliurus Anthracnose in Jiangsu Province, China

Cyclocarya paliurus is an extremely valuable and multifunctional tree species whose leaves have traditionally been used in used in medicine or as a medicinal tea in China. In recent years, anthracnose has been frequently observed on young leaves of C. paliurus in several nurseries located in Jiangsu Province, resulting in great yield and quality losses. To date, no information is available about the prevalence of C. paliurus anthracnose in China. The main purpose of the present study was to characterize the etiology of C. paliurus anthracnose. Phylogenetic analysis of the eight-loci concatenated dataset revealed that all 44 single-spore Colletotrichum isolates belonged to three species in the Colletotrichum gloeosporioides species complex, namely, Colletotrichum aenigma, Colletotrichum fructicola, and C. gloeosporioides sensu stricto. Phenotypic features, including the colony appearance and the morphology of conidia, appressoria, and ascospores, were consistent with the phylogenetic grouping. Virulence tests validated that the three Colletotrichum species could cause typical symptoms of anthracnose on C. paliurus leaves, similar to those observed in the field. The optimum mycelial growth temperature ranged from 25 to 30°C for all representative isolates, while C. gloeosporioides s. s. isolates exhibited greater tolerance to high temperature (40°C). Fungicide sensitivity assays indicated that all three Colletotrichum species were sensitive to tetramycin, which may be a potential alternative for the management of C. paliurus anthracnose. To our knowledge, this study provides the first report of C. aenigma, C. fructicola, and C. gloeosporioides s. s. causing C. paliurus anthracnose in China as well as in the world.

Managing Onion Thrips can Limit Bacterial Stalk and Leaf Necrosis in Michigan Onion Fields

Onion thrips (Thrips tabaci) is a major insect pest of onion and it has been identified as a likely vector of Pantoea agglomerans (bacterial stalk and leaf necrosis), a relatively new pathogen to Michigan's onion industry. Our objective was to develop an integrated insect and disease management program by examining the efficacy of bactericides and insecticides alone and in combination to limit bacterial stalk and leaf necrosis caused by P. agglomerans. We also examined the association of onion thrips and disease incidence in the field, because thrips are known to transmit this pathogen. In the pesticide trial, insecticides reduced both thrips abundance and bacterial stalk and leaf necrosis incidence whereas bactericides alone did not reduce disease severity. Positive correlations among thrips population density, numbers of thrips positive for P. agglomerans, and bacterial stalk and leaf necrosis incidence in onion fields were determined. This study suggests that onion thrips feeding can facilitate the development of bacterial stalk and leaf necrosis in Michigan's commercial onion fields, and results from the pesticide trials indicate that thrips feeding damage is positively correlated with disease incidence. Therefore, in order to reduce bacterial stalk and leaf necrosis incidence in onion, management efforts should include reducing onion thrips populations through the use of insecticides and other cultural practices.

Rapid identification of Erwinia amylovora and Pseudomonas syringae species and characterization of E. amylovora streptomycin resistance using quantitative PCR assays

Erwinia amylovora and Pseudomonas syringae are bacterial phytopathogens responsible for considerable yield losses in commercial pome fruit production. The pathogens, if left untreated, can compromise tree health and economically impact entire commercial fruit productions. Historically, the choice of effective control methods has been limited. The use of antibiotics was proposed as an effective control method. The identification of these pathogens and screening for the presence of antibiotic resistance is paramount in the adoption and implementation of disease control methods. Molecular tests have been developed and accepted for identification and characterization of these disease-causing organisms. We improved existing molecular tests by developing methods that are equal or superior in robustness for identifying E. amylovora or P. syringae while being faster to execute. In addition, the real-time PCR-based detection method for E. amylovora provided complementary information on the susceptibility or resistance to streptomycin of individual isolates. Finally, we describe a methodology and results that compare the aggressiveness of the different bacterial isolates on four apple cultivars. We show that bacterial isolates exhibit different behaviors when brought into contact with various apple varieties and that the hierarchical clustering of symptom severity indicates a population structure, suggesting a genetic basis for host cultivar specificity.

Antibiotic Resistance in Plant-Pathogenic Bacteria

Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases.

Loss-of-Function Mutations in the Dpp and Opp Permeases Render Erwinia amylovora Resistant to Kasugamycin and Blasticidin S

Extensive use of the antibiotic streptomycin to control fire blight disease of apples and pears, caused by the enterobacterial plant pathogen Erwinia amylovora, leads to the development of streptomycin-resistant strains in the United States and elsewhere. Kasugamycin (Ksg) has been permitted to be used as an alternative or replacement to control this serious bacterial disease. In this study, we investigated the role of two major peptide ATP-binding cassette transporter systems in E. amylovora, the dipeptide permease (Dpp) and oligopeptide permease (Opp), in conferring sensitivity to Ksg and blasticidin S (BcS). Minimum inhibitory concentration and spot dilution assays showed that the dpp deletion mutants exhibited slightly enhanced resistance to Ksg in rich medium, whereas the opp mutant exhibited slightly enhanced resistance to Ksg in minimal medium and BcS in rich medium. Deletion of both dpp and opp conferred a higher level of resistance to Ksg in both rich and minimal media, whereas deletion of opp alone was sufficient to confer high level of resistance to BcS in minimal medium. In addition, bioinformatic analysis combined with reverse transcription-quantitative polymerase chain reaction showed that the Rcs phosphorelay system negatively regulates opp expression and the rcsB mutant was more sensitive to both Ksg and BcS in minimal medium as compared with the wild type. An electrophoresis motility shift assay further confirmed the direct binding of the RcsA/RcsB proteins to the promoter region of the opp operon. However, neither the Dpp nor the Opp permeases contributed to disease progress on immature pears, hypersensitive response on tobacco leaves, or exopolysaccharide amylovoran production. These results suggested that Ksg and BcS employ the Dpp and Opp permeases to enter E. amylovora cells and the Dpp and Opp permeases act synergistically for illicit transport of antibiotics.

Persistence in Phytopathogenic Bacteria: Do We Know Enough?

Phytopathogenic bacteria affect a wide range of crops worldwide and have a negative impact in agriculture due to their associated economic losses and environmental impacts. Together with other biotic and abiotic stress factors, they pose a threat to global food production. Therefore, understanding bacterial survival strategies is an essential step toward the development of new strategies to control plant diseases. One mechanism used by bacteria to survive under stress conditions is the formation of persister cells. Persisters are a small fraction of phenotypic variants within an isogenic population that exhibits multidrug tolerance without undergoing genetic changes. They are dormant cells that survive treatment with antimicrobials by inactivating the metabolic functions that are disrupted by these compounds. They are thus responsible for the recalcitrance of many human diseases, and in the same way, they are thought to contribute to the survival of bacterial phytopathogens under a range of stresses they face in the environment. It is believed that persister cells of bacterial phytopathogens may lead to the reoccurrence of disease by recovering growth and recolonizing the host plant after the end of stress. However, compared to human pathogens, little is known about persister cells in phytopathogens, especially about their genetic regulation. In this review, we describe the overall knowledge on persister cells and their regulation in bacterial phytopathogens, focusing on their ability to survive stress conditions, to recover from dormancy and to maintain virulence.

Efficacy of Copper and New Bactericides for Managing Olive Knot in California

Baseline sensitivities were established for kasugamycin and oxytetracycline for 147 strains of Pseudomonas savastanoi pv. savastanoi collected from olive knots throughout California. Minimum inhibitory concentrations for ≥95% growth inhibition ranged from 1.86 to 11.52 and 0.13 to 0.40 µg/ml for kasugamycin and oxytetracycline, respectively. In copper sensitivity evaluations, 95.3% of the strains collected grew at concentrations of metallic copper equivalent (MCE) of <20 µg/ml, 2.7% grew at MCE between 20 and 30 µg/ml (moderately sensitive), and 2% grew at MCE of 150 µg/ml (resistant). Copper resistance was never reported previously in the olive knot pathogen, and pathogenicity studies confirmed a high virulence of the copper-resistant strains. In comparative field studies, kasugamycin at 200 µg/ml performed equally to the standard copper hydroxide treatment (MCE of 1,260 µg/ml) for reducing knot development on lateral wounds of Arbequina and Manzanillo olive inoculated with a copper-sensitive strain and was better than copper using a highly copper-resistant strain. Oxytetracycline at 200 µg/ml was not as effective as copper or kasugamycin but significantly reduced the disease as compared with the untreated control. Field studies on application timings of copper, kasugamycin, and copper-kasugamycin mixtures to inoculated wounds indicated that treatments within 24 h of inoculation resulted in higher disease control than applications at later times. In greenhouse trials, copper or copper-kasugamycin applied to wounds 7 days before inoculation persisted and reduced knot incidence by >50%. Our findings indicate that kasugamycin is an effective bactericide for controlling olive knot and that the time of any bactericide application after inoculation is critical in managing the disease.

Antibiotics do not affect the degradation of fungicides and enhance the mineralization of chlorpyrifos in biomixtures

The use of antibiotics in agriculture produces residues in wastewaters. The disposal of such wastewaters in biopurification systems (BPS) employed for the treatment of pesticides could result in the inhibition of the degrading capacity of the biomixtures used in the BPS. We assayed the effect of two commercial formulations of antibiotics used in agriculture, one containing kasugamycin (KSG) and the other oxytetracycline plus gentamicin (OTC+GTM), on the biomixture performance. Doses from 0.1mgkg^-1 to 1000mgkg^-1 of KSG increased the respiration of the biomixture, and low doses enhanced the mineralization rate of the insecticide ¹⁴C-chlorpyrifos. On the contrary, OTC+GTM depressed the respiration of the biomixture and the initial mineralization rate of ¹⁴C-chlorpyrifos; nonetheless, the antibiotics did not decrease overall mineralization values. The application of both formulations in the biomixture at a relevant concentration did not harm the removal of the fungicides carbendazim and metalaxyl, or their enhanced degradation; on the other hand, the biomixture was unable to dissipate tebuconazol or triadimenol, a result that was unchanged during the addition of the antibiotic formulations. These findings reveal that wastewater containing these antibiotics do not affect the performance of BPS. However, such a response may vary depending on the type of pesticide and microbial consortium in the biomixture.

Microbiological Examination of Erwinia amylovora Exopolysaccharide Ooze

Fire blight, caused by the pathogen Erwinia amylovora, is the most devastating bacterial disease of pome fruit in North America and worldwide. The primary method of dispersal for E. amylovora is through ooze, a mass of exopolysaccharides and bacterial cells that is exuded as droplets from infected host tissue. During the 2013 and 2014 field seasons, 317 ooze droplets were collected from field-inoculated apple trees. Populations of E. amylovora in ooze droplets were 10⁸ CFU/μl on average. Ooze droplets harboring larger (>10⁸ CFU/μl) cell populations were typically smaller in total volume and had darker coloring, such as orange, red, or dark red hues. Examination of apple host tissue at the site of emergence of ooze droplets using scanning electron microscopy revealed that ooze was not exuding through natural openings; instead, it was found on erumpent mounds and small (10-μm) tears in tissue. These observations suggested that E. amylovora-induced wounds in tissue provided the exit holes for ooze extrusion from the host. Analyses of E. amylovora populations in ooze droplets and within the stems from which ooze droplets emerged indicated that approximately 9% of the total bacterial population from infected stems is diverted to ooze. Gene expression analyses indicated that E. amylovora cells in stem sections located above ooze droplets and in ooze droplets were actively expressing critical pathogenicity genes such as hrpL, dspE, and amsK. Thus, our study identified ooze as a source of large, concentrated populations of E. amylovora that emerged from the host by rupturing host tissue. Because the cells in ooze droplets are expressing genes required for pathogenesis, they are already primed for infection should they be dispersed from ooze to new infection courts.

Bypassing rRNA methylation by RsmA/Dim1during ribosome maturation in the hyperthermophilic archaeon Nanoarchaeum equitans

In all free-living organisms a late-stage checkpoint in the biogenesis of the small ribosomal subunit involves rRNA modification by an RsmA/Dim1 methyltransferase. The hyperthermophilic archaeon Nanoarchaeum equitans, whose existence is confined to the surface of a second archaeon, Ignicoccus hospitalis, lacks an RsmA/Dim1 homolog. We demonstrate here that the I. hospitalis host possesses the homolog Igni_1059, which dimethylates the N6-positions of two invariant adenosines within helix 45 of 16S rRNA in a manner identical to other RsmA/Dim1 enzymes. However, Igni_1059 is not transferred from I. hospitalis to N. equitans across their fused cell membrane structures and the corresponding nucleotides in N. equitans 16S rRNA remain unmethylated. An alternative mechanism for ribosomal subunit maturation in N. equitans is suggested by sRNA interactions that span the redundant RsmA/Dim1 site to introduce 2΄-O-ribose methylations within helices 44 and 45 of the rRNA.

Effects of Consecutive Streptomycin and Kasugamycin Applications on Epiphytic Bacteria in the Apple Phyllosphere

Antibiotic applications are essential for fire blight management in the eastern United States. Recently, streptomycin-resistant Erwinia amylovora strains were found in New York. There are growing concerns that streptomycin resistance may develop from postbloom streptomycin applications in local orchards. Our goal was to investigate the impacts of increasing streptomycin and kasugamycin applications on bacterial epiphyte community composition and antibiotic resistance in the phyllosphere of 'Idared' apple plantings in 2014 and 2015. Rinsate samples from leaves treated with 0, 3, 5, and 10 applications of streptomycin and kasugamycin were collected to isolate, enumerate, and identify epiphytic bacterial species. The majority of isolated epiphytic bacteria were identified as Pantoea agglomerans and fluorescent Pseudomonas spp., whereas E. amylovora was rarely found. Overall, postbloom streptomycin use did not result in an increased recovery of streptomycin-resistant E. amylovora. However, other streptomycin-resistant epiphytes (P. agglomerans and Pseudomonas spp.) did increase with increasing streptomycin applications. Increasing kasugamycin applications reduced the overall number and percentage of streptomycin-resistant epiphytes in the phyllosphere, which has important implications regarding the use of kasugamycin in orchards where streptomycin resistance is a concern.

Fire Blight Symptomatic Shoots and the Presence of Erwinia amylovora in Asymptomatic Apple Budwood

Erwinia amylovora, the causal agent of fire blight, causes considerable economic losses in young apple plantings in New York on a yearly basis. Nurseries make efforts to only use clean budwood for propagation, which is essential, but E. amylovora may be present in trees that appear to have no apparent fire blight symptoms at the time of collection. We hypothesized that the use of infected budwood, especially by commercial nursery operations, could be the cause, in part, of fire blight outbreaks that often occur in young apple plantings in New York. Our goal was to investigate the presence of E. amylovora in asymptomatic budwood from nursery source plantings as it relates to trees with fire blight symptoms. From 2012 to 2015, apple budwood was collected from two commercial budwood source plantings of 'Gala' and 'Topaz' at increasing distances from visually symptomatic trees. From these collections, internal contents of apple buds were analyzed for the presence of E. amylovora. E. amylovora was detected in asymptomatic budwood in trees more than 20 m from trees with fire blight symptoms. In some seasons, there were significant (P ≤ 0.05) differences in the incidence of E. amylovora in asymptomatic budwood collected from symptomatic trees and those up to 20 m from them. In 2014 and 2015, the mean E. amylovora CFU per gram recovered from budwood in both the Gala and Topaz plantings were significantly lower in budwood collected 20 m from symptomatic trees. Further investigation of individual bud dissections revealed that E. amylovora was within the tissue beneath the bud scales containing the meristem. Results from the study highlight the shortcomings of current budwood collection practices and the need to better understand the factors that lead to the presence of E. amylovora in bud tissues to ensure the production of pathogen-free apple trees.

Bacterial disease management: challenges, experience, innovation and future prospects: Challenges in Bacterial Molecular Plant Pathology

Plant diseases caused by bacterial pathogens place major constraints on crop production and cause significant annual losses on a global scale. The attainment of consistent effective management of these diseases can be extremely difficult, and management potential is often affected by grower reliance on highly disease-susceptible cultivars because of consumer preferences, and by environmental conditions favouring pathogen development. New and emerging bacterial disease problems (e.g. zebra chip of potato) and established problems in new geographical regions (e.g. bacterial canker of kiwifruit in New Zealand) grab the headlines, but the list of bacterial disease problems with few effective management options is long. The ever-increasing global human population requires the continued stable production of a safe food supply with greater yields because of the shrinking areas of arable land. One major facet in the maintenance of the sustainability of crop production systems with predictable yields involves the identification and deployment of sustainable disease management solutions for bacterial diseases. In addition, the identification of novel management tactics has also come to the fore because of the increasing evolution of resistance to existing bactericides. A number of central research foci, involving basic research to identify critical pathogen targets for control, novel methodologies and methods of delivery, are emerging that will provide a strong basis for bacterial disease management into the future. Near-term solutions are desperately needed. Are there replacement materials for existing bactericides that can provide effective disease management under field conditions? Experience should inform the future. With prior knowledge of bactericide resistance issues evolving in pathogens, how will this affect the deployment of newer compounds and biological controls? Knowledge is critical. A comprehensive understanding of bacterial pathosystems is required to not only identify optimal targets in the pathogens, but also optimal seasonal timings for deployment. Host resistance to effectors must be exploited, carefully and correctly. Are there other candidate genes that could be targeted in transgenic approaches? How can new technologies (CRISPR, TALEN, etc.) be most effectively used to add sustainable disease resistance to existing commercially desirable plant cultivars? We need an insider's perspective on the management of systemic pathogens. In addition to host resistance or reduced sensitivity, are there other methods that can be used to target these pathogen groups? Biological systems are variable. Can biological control strategies be improved for bacterial disease management and be made more predictable in function? The answers to the research foci outlined above are not all available, as will become apparent in this article, but we are heading in the right direction. In this article, we summarize the contributions from past experiences in bacterial disease management, and also describe how advances in bacterial genetics, genomics and host-pathogen interactions are informing novel strategies in virulence inhibition and in host resistance. We also outline potential innovations that could be exploited as the pressures to maximize a safe and productive food supply continue to become more numerous and more complex.

Exploring Diversity and Origins of Streptomycin-Resistant Erwinia amylovora Isolates in New York Through CRISPR Spacer Arrays

Streptomycin is the most effective and widely used chemical control in the eastern United States for blossom blight of apple caused by Erwinia amylovora; however, resistance to this antibiotic has been a concern in New York since 2002. From 2011 to 2014, statewide collections of E. amylovora were conducted resulting in the isolation of streptomycin-resistant (SmR) E. amylovora from several commercial orchards. Further genetic analysis of isolates was necessary to understand the origins and the diversity of these bacteria. Clustered regularly interspaced short palindromic repeat (CRISPR) spacer sequencing was employed to explore the diversity and possible origins of New York SmR E. amylovora isolates. The spacer array CR1, CR2, and CR3 regions of 27 SmR E. amylovora isolates and 76 streptomycin-sensitive (SmS) E. amylovora isolates were amplified and subsequently sequenced, revealing 19 distinct CRISPR spacer profiles for New York isolates. The majority of SmR E. amylovora isolates had the same CRISPR profile as SmR E. amylovora isolates discovered in 2002. This may infer that eradication efforts in 2002 failed and the bacterial populations continued to spread throughout the state. Several CRISPR profiles for SmR E. amylovora were identical to SmS E. amylovora collected from the same orchards, leading to the hypothesis that resistance may be developing within New York. Profiles not unique to New York were identical to many isolates from the Midwestern, eastern, and western United States, implying that streptomycin resistance may be due to the introduction of SmR E. amylovora from other regions of the United States. The increased understanding as to how SmR E. amylovora isolates are introduced, evolve, or have become established afforded by CRISPR profiling has been useful for disease management and restricting the movement of streptomycin resistance in New York.

A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S

Fighting antibiotic resistance requires a deeper understanding of the genetic factors that determine the antibiotic susceptibility of bacteria. Here we describe a chemical-genomic screen in Escherichia coli K-12 that was designed to discover new aspects of antibiotic resistance by focusing on a set of 26 antibiotics and other stresses with poorly characterized mode-of-action and determinants of resistance. We show that the screen identifies new resistance determinants for these antibiotics including a common signature from two antimicrobials, kasugamycin and blasticidin S, used to treat crop diseases like rice blast and fire blight. Following this signature, we further investigated the mechanistic basis for susceptibility to kasugamycin and blasticidin S in E. coli using both genetic and biochemical approaches. We provide evidence that these compounds hijack an overlapping set of peptide ABC-importers to enter the bacterial cell. Loss of uptake may be an underappreciated mechanism for the development of kasugamycin resistance in bacterial plant pathogens.

Bacterial species differ in their susceptibility to antibiotics but the reason for these differences remains an open question. Understanding the genetic basis of antibiotic susceptibility will be critical for predicting the efficacy of new antibiotics and possibly finding new antibiotic targets. Here we report a large-scale study that connects bacterial genes to antibiotics, using a set of antibiotics that were chosen to include poorly characterized compounds. We discovered genes that confer resistance to a number of neglected antibiotics, expanding our knowledge of gene function and antibiotic resistance in Escherichia coli K-12. Starting from this large-scale screen, we then investigated how two antibiotics with a common history, kasugamycin and blasticidin S, enter bacterial cells. Both mimic naturally occurring nutrients to trick E. coli into actively bringing them inside. Kasugamycin is used to control microbes that cause agricultural diseases and mutations that reduce uptake like those we describe here may be an underappreciated factor in the development of resistance to kasugamycin.

Prevalence of Streptomycin-Resistant Erwinia amylovora in New York Apple Orchards

Resistance to streptomycin in Erwinia amylovora was first observed in the United States in the 1970s but was not found in New York until 2002, when streptomycin-resistant (SmR) E. amylovora was isolated from orchards in Wayne County. From 2011 to 2014, in total, 591 fire blight samples representing shoot blight, blossom blight, and rootstock blight were collected from 80 apple orchards in New York. From these samples, 1,280 isolates of E. amylovora were obtained and assessed for streptomycin resistance. In all, 34 SmR E. amylovora isolates were obtained from 19 individual commercial orchards. The majority of the resistant isolates were collected from orchards in Wayne County, and the remaining were from other counties in western New York. Of the 34 resistant isolates, 32 contained the streptomycin resistance gene pair strA/strB in the transposon Tn5393 on the nonconjugative plasmid pEA29. This determinant of streptomycin resistance has only been found in SmR E. amylovora isolates from Michigan and the SmR E. amylovora isolates discovered in Wayne County, NY in 2002. Currently, our data indicate that SmR E. amylovora is restricted to counties in western New York and is concentrated in the county with the original outbreak. Because the resistance is primarily present on the nonconjugative plasmid, it is possible that SmR has been present in Wayne County since the introduction in 2002, and has spread within and out of Wayne County to additional commercial growers over the past decade. However, research is still needed to provide in-depth understanding of the origin and spread of the newly discovered SmR E. amylovora to reduce the spread of streptomycin resistance into other apple-growing regions, and address the sustainability of streptomycin use for fire blight management in New York.

Fe2+ chelator proferrorosamine A: a gene cluster of Erwinia rhapontici P45 involved in its synthesis and its impact on growth of Erwinia amylovora CFBP1430

Proferrorosamine A (proFRA) is an iron (Fe2+) chelator produced by the opportunistic plant pathogen Erwinia rhapontici P45. To identify genes involved in proFRA synthesis, transposon mutagenesis was performed. The identified 9.3 kb gene cluster, comprising seven genes, designated rosA-rosG, encodes proteins that are involved in proFRA synthesis. Based on gene homologies, a biosynthetic pathway model for proFRA is proposed. To obtain a better understanding of the effect of proFRA on non-proFRA producing bacteria, E. rhapontici P45 was co-cultured with Erwinia amylovora CFBP1430, a fire-blight-causing plant pathogen. E. rhapontici P45, but not corresponding proFRA-negative mutants, led to a pink coloration of E. amylovora CFBP1430 colonies on King's B agar, indicating accumulation of the proFRA-iron complex ferrorosamine, and growth inhibition in vitro. By saturating proFRA-containing extracts with Fe2+, the inhibitory effect was neutralized, suggesting that the iron-chelating capability of proFRA is responsible for the growth inhibition of E. amylovora CFBP1430.

16S rRNA methyltransferase KsgA contributes to oxidative stress resistance and virulence in Staphylococcus aureus

We previously reported that the rRNA methyltransferases RsmI and RsmH, which are responsible for cytidine dimethylation at position 1402 of 16S rRNA in the decoding center of the ribosome, contribute to Staphylococcus aureus virulence. Here we evaluated other 16S rRNA methyltransferases, including KsgA (RsmA), RsmB/F, RsmC, RsmD, RsmE, and RsmG. Knockout of KsgA, which methylates two adjacent adenosines at positions 1518 and 1519 of 16S rRNA in the intersubunit bridge of the ribosome, attenuated the S. aureus killing ability against silkworms. The ksgA knockout strain was sensitive to oxidative stress and had a lower survival rate in murine macrophages than the parent strain. The ksgA knockout strain exhibited decreased translational fidelity in oxidative stress conditions. Administration of N-acetyl-l-cysteine, a free-radical scavenger, restored the killing ability of the ksgA knockout strain against silkworms. These findings suggest that the methyl-modifications of 16S rRNA by KsgA contribute to maintain ribosome function under oxidative conditions and thus to S. aureus virulence.

Characterization of Streptomycin Resistance in Isolates of Erwinia amylovora in California

In surveys from 2006 to 2014, streptomycin resistance in Erwinia amylovora from pear-growing areas in California declined from very high incidence in 2006 and 2007 to very low incidence in 2013 and 2014. The majority of resistant strains were designated as moderately resistant-low (MR-L), and were almost exclusively found in Sacramento County, whereas highly resistant (HR) strains were only recovered in Sutter-Yuba and San Joaquin counties. Resistance of HR strains was associated with a mutation in codon 43 of the chromosomal rpsL gene that results in a change from lysine to arginine, the same mutation that was originally reported for resistant strains from California in the mid-1970s. MR-L strains were found to harbor the strA-strB streptomycin resistance genes on transposon Tn5393a. This transposon lacks insertion sequence IS1133 that provides a promoter for efficient expression of strA-strB, resulting in lower minimum inhibitory concentrations of MR-L strains compared with those from other locations that harbor strA-strB on Tn5393::IS1133. In contrast to previously described plasmid-mediated resistance where Tn5393 is inserted in pEa34, or pEA29, Tn5393a in MR-L strains was located on plasmid pEU30. This plasmid was first described in E. amylovora from the western United States but was not associated with streptomycin resistance determinants previously. We hypothesize that Tn5393a was introduced into an E. amylovora strain carrying pEU30 and transposed into that plasmid. This hypothesis was supported by clustered regularly interspaced short palindromic repeat (CRISPR) sequence analysis that showed that two MR-L strains share the same CRISPR1 pattern as a streptomycin-sensitive strain. With current low resistance levels in California growing regions, streptomycin could be successfully used again, but applications per season should be limited and the antibiotic should be mixed and rotated with different modes of action.