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

Elucidating the mechanism of resistance to anthracnose in litchi leaves through transcriptome analysis

BACKGROUND

Litchi, an important tropical fruit, is severely affected by anthracnose disease. However, the mechanism of its disease resistance response remains unknown, and resistant accession genetic resources and resistance-related genes have not yet been identified.

RESULTS

In this study, 82 accessions of litchi were evaluated for resistance to Colletotrichum gloeosporioides, and the accessions 'Haiken 5' and 'Nongmei 5 hao' were identified as resistant and susceptible, respectively. Leaves from these two accessions were inoculated with C. gloeosporioides and collected at 6 and 24 h for use as materials for transcriptome analysis. Analyses of the differentially expressed genes (DEGs) between the accessions and their controls, which were inoculated with potato dextrose agar medium, revealed that the resistant accession presented more DEGs with smaller changes in magnitude, whereas the susceptible accession presented fewer DEGs with greater changes in magnitude. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed, and phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, and plant-pathogen interactions were identified as common pathways. Chitinase activity, oxidoreductase activity, aminoglycan and glucosamine-containing compounds, and cell wall metabolic processes also participated in the defence reaction. Salicylic acid signalling in litchi leaves contributed to resistance to C. gloeosporioides. Short Time-series Expression Miner (STEM) and weighted correlation network analysis (WGCNA) were also employed to evaluate the gene expression trends and identify highly correlated genes.

CONCLUSION

Litchi accessions presented different resistance responses to anthracnose disease. Small changes in the expression levels of critical resistance-related genes were sufficient to produce the defence reaction. Calcium ion regulatory mechanisms and transcription factors have been preliminarily identified as contributors to disease resistance. Multiple pathways and molecular processes participate in the defence response. These results identify candidate genes and pathways involved in litchi plant defence against anthracnose.

Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies

This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.

Systematic review and meta-analysis of antimicrobial resistant bacteria in free-ranging wild mammals

BACKGROUND

Bacterial antimicrobial resistance is a significant global threat to public health, closely linked to the misuse of antimicrobials in human and veterinary medicine, aquaculture, and agriculture. The consequences of antimicrobial resistance overcome species boundaries and require a holistic approach for mitigation actions. The study of antimicrobial resistance in wildlife is thus increasingly relevant to understand the spread of antimicrobial resistance in the environment and the animal community, as well as to investigate the role of wildlife either as a carrier, reservoir, spillover, or indicator of antimicrobial resistance. The aim of this study is to describe the prevalence and type of antimicrobial resistance in bacterial isolates from wild mammals through systematic review and meta-analysis of the available literature, following the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) guidelines.

RESULTS

Out of 5052 collected documents, 3795 were screened, and finally 139 studies on antimicrobial resistance in free-ranging wild mammals were included in the meta-analysis. The studies covered 37 countries, mostly European. The Enterobacterales Escherichia coli and Salmonella spp., as well as Campylobacter spp., were the most frequently targeted bacterial species, mainly in the Artiodactyla order and specifically in the Suidae and Cervidae families. Low to moderate prevalences of antimicrobial resistance were found in all the continents, countries, bacteria, host taxa, and antimicrobials included in the meta-analysis, even for critically important antimicrobials as defined by the World Health Organisation, with higher values in Africa and Asia, in carnivores, and in animal species with high adaptability to diverse habitats.

CONCLUSION

This meta-analysis showed that antimicrobial resistance in wild mammals is widespread and variable according to taxonomy, trophic source, and geographic location. The meta-analysis highlighted methodological gaps that need to be addressed to improve the interpretation and conclusions obtained from the data. Genetic analyses on antimicrobial resistance and population ecological data should be included in future analysis to achieve a standardised methodology and overcome current limitations. To date, wildlife appears to be an environmental indicator of antimicrobial resistance and should be included in antimicrobial resistance surveillance plans not only because this sentinel role but also to monitor potential spill-back to livestock and/or humans.

Effects of Temperature on Resistance to Streptomycin in Xanthomonas arboricola pv. pruni

Xanthomonas arboricola pv. pruni (Xap) causes the shot hole disease of stone fruits and almonds. This bacterium is a damaging, widespread pathogen distributed across the major stone fruit producing regions of the world. To control shot hole disease, antibiotics such as streptomycin are mainly used. However, as concerns about antibiotic resistance increase, many restrictions are placed on the use of antibiotics. Additionally, it has been reported that the rise in temperature due to climate change affects disease occurrence and ecology. Therefore, in this study, we determined the minimum inhibitory concentration (MIC) of streptomycin for Xap at an optimal growth temperature of 28°C and investigated the changes in MIC and the occurrence frequency of resistant bacteria at 10°C, 25°C and 30°C. The results of this study showed that the MIC was 30 µg/ml at 28°C. In addition, when the change in streptomycin resistance concentration due to temperature was confirmed, we found that the resistance concentration decreased to 10 µg/ml at 30°C. When the occurrence of resistance according to concentration and temperature conditions was investigated, the occurrence frequency of resistant strains was found to be the highest at 50 µg/ml. In the case of temperature, the occurrence frequency of resistant strains was confirmed to be high at 30°C. These results provide basic data for further reducing the problem of antibiotic resistance by suggesting the possibility of changes in the occurrence of streptomycin-resistant strains depending on the antibiotic treatment environment.

The Antimicrobial Effects of Coffee and By-Products and Their Potential Applications in Healthcare and Agricultural Sectors: A State-of-Art Review

Coffee is one of the most consumed beverages around the world. Its production is dominated by the species Coffea arabica and Coffea canephora. However, the coffee elaboration process leads to generating a significant amount of waste, which arises in various stages of coffee bean processing and is rich in natural bioactive compounds such as phenolic compounds and alkaloids. Particularly, chlorogenic and caffeic acids have a high antimicrobial potential and have been demonstrated to be effective against bacteria and viruses of healthcare and food relevance, including multi-resistant pathogens. However, the production and accumulation of coffee waste have a negative environmental impact since they can contaminate the surrounding environment due to the presence of organic molecules such as caffeine and tannins. In this context, exploiting natural resources as a source of compounds with the antimicrobial potential of, for example, the bioactive compounds obtained from coffee, has been evaluated in previous works. This review aims to summarize the current knowledge on the antimicrobial properties of coffee and its by-products and their potential application in the healthcare sector and disease control in agricultural crops, with particular emphasis on improving sustainability and efficiency in agriculture through making use of waste, which carries high importance in today's society.

Lactic acid bacteria: A sustainable solution against phytopathogenic agents

Biological control agents (BCAs) are beneficial living organisms used in plant protection to control pathogens sustainably. Lactic acid bacteria (LAB) have gained attention in biopesticides due to their safety as recognized by the Food and Drug Administration. These bacteria possess antifungal properties, demonstrating inhibitory effects through nutrient competition or the production of antimicrobial metabolites. Numerous Lactobacillus species have shown the ability to inhibit pathogenic microorganisms, primarily through acid production. The organic acids secreted by LAB reduce the pH of the medium, creating a hostile environment for microorganisms. These organic acids are a primary inhibition mechanism of LAB. This article reviews several studies on LAB as BCAs, focusing on their inhibition modes. Additionally, it discusses the limitations and future challenges of using LAB to control phytopathogens for sustainable agriculture.

Activity of Streptomyces globosus OPF-9 against the important pathogen Alternaria longipes and biocontrol mechanisms revealed by multi-omic analyses

Plant diseases caused by fungal pathogens represent main threats to the yield and quality of agricultural products, and Alternaria longipes is one of the most important pathogens in agricultural systems. Biological control is becoming increasingly prevalent in the management of plant diseases due to its environmental compatibility and sustainability. In the present study, a bacterial strain, designated as OPF-9, was shown to effectively inhibit the pathogen A. longipes, which was identified as Streptomyces globosus. The culture conditions for OPF-9 were optimized through a stepwise approach and the fermentation broth acquired displayed an excellent inhibitory activity against A. longipes in vitro and in vivo. Further investigations suggested that the fermentation broth exhibited strong stability under a range of adverse environmental conditions. To reveal the molecular bases of OPF-9 in inhibiting pathogens, the whole-genome sequencing and assembly were conducted on this strain. It showed that the genome size of OPF-9 was 7.668 Mb, containing a chromosome and two plasmids. Multiple clusters of secondary metabolite synthesis genes were identified by genome annotation analysis. In addition, the fermentation broth of strain OPF-9 was analyzed by LC-MS/MS non-target metabolomic assay and the activity of potential antifungal substances was determined. Among the five compounds evaluated, pyrogallol displayed the most pronounced inhibitory activity against A. longipes, which was found to effectively inhibit the mycelial growth of this pathogen. Overall, this study reported, for the first time, a strain of S. globosus that effectively inhibits A. longipes and revealed the underlying biocontrol mechanisms by genomic and metabolomic analyses.

The underground world of plant disease: Rhizosphere dysbiosis reduces above-ground plant resistance to bacterial leaf spot and alters plant transcriptome

Just as the human gut microbiome is colonized by a variety of microbes, so too is the rhizosphere of plants. An imbalance in this microbial community, known as dysbiosis, can have a negative impact on plant health. This study sought to explore the effect of rhizosphere dysbiosis on the health of tomato plants (Solanum lycopersicum L.), using them and the foliar bacterial spot pathogen Xanthomonas perforans as model organisms. The rhizospheres of 3-week-old tomato plants were treated with either streptomycin or water as a control, and then spray-inoculated with X. perforans after 24 h. Half of the plants that were treated with both streptomycin and X. perforans received soil microbiome transplants from uninfected plant donors 48 h after the streptomycin was applied. The plants treated with streptomycin showed a 26% increase in disease severity compared to those that did not receive the antibiotic. However, the plants that received the soil microbiome transplant exhibited an intermediate level of disease severity. The antibiotic-treated plants demonstrated a reduced abundance of rhizobacterial taxa such as Cyanobacteria from the genus Cylindrospermum. They also showed a down-regulation of genes related to plant primary and secondary metabolism, and an up-regulation of plant defence genes associated with induced systemic resistance. This study highlights the vital role that beneficial rhizosphere microbes play in disease resistance, even against foliar pathogens.

Towards Pathogen-Free Coconut Germplasm Exchange

Coconut (Cocos nucifera L.) is an important palm species that serves as the mainstay of several industries and contributes to the livelihoods of millions of smallholder farmers. International exchange of coconut germplasm has been undertaken for several decades to facilitate the conservation of selected varieties within global genebanks and for the distribution to farmers and scientists. In vitro systems are a convenient and an efficient method for the exchange of coconut germplasm. However, it is possible that these tissue culture systems can transfer lethal pathogens causing a threat to the importing countries. In this review, the following topics are discussed: the major disease-causing agents of concern, the various tissues that could be used for coconut germplasm exchange, and the techniques available for the detection and elimination of disease-causing agents from various transmission systems. Additionally, the lack of clear, science-backed guidelines to facilitate the exchange of in vitro coconut materials is raised, along with recommendations for future studies to ensure the safe movement of coconut germplasm without biosecurity risks.

Transposons Carrying the aacC2e Aminoglycoside and blaTEM Beta-Lactam Resistance Genes in Acinetobacter

This study examines the genetic contexts and evolutionary steps responsible for the formation of the widely spread transposon Tn6925 carrying blaTEM and aacC2e, which confers resistance to beta-lactam and aminoglycoside antibiotics in Gram-negative bacteria. The blaTEM-1 and aacC2e genes were found in several transposons. They were first observed within an IS26 bounded 3.7 kb transposon (Tn6925) on several Acinetobacter baumannii plasmids located within a 4.7 kb dif module. Truncated and expanded variations of Tn6925 were found across other A. baumannii plasmids, as well as in other Gram-negative bacteria (including Vibrio cholerae). Moreover, blaTEM-1 and aacC2e were in much larger resistance-heavy transposons including the ISAba1-bounded 24.6 kb (here called Tn6927), found in an A. baumannii chromosome. A novel ISKpn12-bounded transposon was also observed to contain blaTEM and aacC2e which was found interrupting Tn5393 along with an IS26 pseudo-compound transposon to form a 24.9 kb resistance island in an Acinetobacter pittii plasmid. Multiple mobile genetic elements are involved in the formation of transposon structures that circulate blaTEM and aacC2e. Among these, IS26 and ISAba1 appear to have played a major role in the formation and spread of these elements in the Acinetobacter species.

NMR Metabolite Profiling for the Characterization of Vessalico Garlic Ecotype and Bioactivity against Xanthomonas campestris pv. campestris

The Italian garlic ecotype "Vessalico" possesses distinct characteristics compared to its French parent cultivars Messidor and Messidrôme, used for sowing, as well as other ecotypes in neighboring regions. However, due to the lack of a standardized seed supply method and cultivation protocol among farmers in the Vessalico area, a need to identify garlic products that align with the Vessalico ecotype arises. In this study, an NMR-based approach followed by multivariate analysis to analyze the chemical composition of Vessalico garlic sourced from 17 different farms, along with its two French parent cultivars, was employed. Self-organizing maps allowed to identify a homogeneous subset of representative samples of the Vessalico ecotype. Through the OPLS-DA model, the most discriminant metabolites based on values of VIP (Variable Influence on Projections) were selected. Among them, S-allylcysteine emerged as a potential marker for distinguishing the Vessalico garlic from the French parent cultivars by NMR screening. Additionally, to promote sustainable agricultural practices, the potential of Vessalico garlic extracts and its main components as agrochemicals against Xanthomonas campestris pv. campestris, responsible for black rot disease, was explored. The crude extract exhibited a MIC of 125 μg/mL, and allicin demonstrated the highest activity among the tested compounds (MIC value of 31.25 μg/mL).

Antibiotic Resistance in Plant Pathogenic Bacteria: Recent Data and Environmental Impact of Unchecked Use and the Potential of Biocontrol Agents as an Eco-Friendly Alternative

The economic impact of phytopathogenic bacteria on agriculture is staggering, costing billions of US dollars globally. Pseudomonas syringae is the top most phytopathogenic bacteria, having more than 60 pathovars, which cause bacteria speck in tomatoes, halo blight in beans, and so on. Although antibiotics or a combination of antibiotics are used to manage infectious diseases in plants, they are employed far less in agriculture compared to human and animal populations. Moreover, the majority of antibiotics used in plants are immediately washed away, leading to environmental damage to ecosystems and food chains. Due to the serious risk of antibiotic resistance (AR) and the potential for environmental contamination with antibiotic residues and resistance genes, the use of unchecked antibiotics against phytopathogenic bacteria is not advisable. Despite the significant concern regarding AR in the world today, there are inadequate and outdated data on the AR of phytopathogenic bacteria. This review presents recent AR data on plant pathogenic bacteria (PPB), along with their environmental impact. In light of these findings, we suggest the use of biocontrol agents as a sustainable, eco-friendly, and effective alternative to controlling phytopathogenic bacteria.

The Antibacterial Effect of Selected Essential Oils and Their Bioactive Constituents on Pseudomonas savastanoi pv. savastanoi: Phytotoxic Properties and Potential for Future Olive Disease Control

Plant pathogenic bacteria pose a significant threat to olive cultivation, leading to substantial economic losses and reduced yield. The efficacy of antimicrobial agents against these pathogens is of great interest for sustainable disease management strategies. As such, the management of olive knot disease is one of the major challenges in olive protection. In the presented study, through a series of in vitro assays, we investigated the antimicrobial effect of six essential oils (EOs) and their most concentrated constituents against causative agent of olive knot disease-Pseudomonas savastanoi pv. savastanoi, highlighting the high potential of Origanum compactum EO and its constituent carvacrol. Carvacrol exhibited the highest potential for practical application, demonstrating membrane disruption as its mechanism of action even at the lowest concentration. The bactericidal effect of antimicrobials was confirmed in a time-kill assay, where concentrations of MIC, 2× MIC, and 4× MIC were evaluated. Some of the applied treatments resulted in inhibition equal or higher than copper-based treatment. Additionally, we assessed the phytotoxicity of carvacrol by foliar application on olive cv. Leccino. The appearance of phytotoxic injuries majorly occurred on the young leaves of olive plants, with the highest proportion of damaged canopy observed when the 2× MIC concentration was applied. Due to its great efficiency against P. savastanoi pv. savastanoi in vitro, these findings highlight the potential of carvacrol as a molecule of interest for the development of environmentally friendly biopesticides. This study also contributes to the advancement of disease management practices in olive cultivation, leading to enhanced crop protection.