Antimicrobial Activity Against Phytopathogens and Inhibitory Activity on Solanine in Potatoes of the Endophytic Bacteria Isolated From Potato Tubers

Transcriptome analysis unravels the biocontrol mechanism of Serratia plymuthica A30 against potato soft rot caused by Dickeya solani

Endophytic bacterium Serratia plymuthica A30 was identified as a superior biocontrol agent due to its effective colonization of potato tuber, tolerance to cold conditions, and strong inhibitory action against various soft rot pathogens, including Dickeya solani. We characterized transcriptome changes in potato tubers inoculated with S. plymuthica A30, D. solani, or both at the early and the late phases of interaction. At the early phase and in the absence of the pathogen, A30 influenced the microbial recognition system to initiate plant priming. In the presence of the pathogen alongside biocontrol strain, defense signaling was highly stimulated, characterized by the induction of genes involved in the detoxification system, reinforcement of cell wall structure, and production of antimicrobial metabolites, highlighting A30's role in enhancing the host resistance against pathogen attack. This A30-induced resistance relied on the early activation of jasmonic acid signaling and its production in tubers, while defense signaling mediated by salicylic acid was suppressed. In the late phase, A30 actively interferes with plant immunity by inhibiting stress- and defense-related genes expression. Simultaneously, the genes involved in cell wall remodeling and indole-3-acetic acid signaling were activated, thereby enhancing cell wall remodeling to establish symbiotic relationship with the host. The endophytic colonization of A30 coincided with the induction of genes involved in the biosynthesis and signaling of ethylene and abscisic acid, while downregulating those related to gibberellic acid and cytokinin. This combination suggested fitness benefits for potato tubers by preserving dormancy, and delaying sprouting, which affects durability of tubers during storage. This study contributes valuable insights into the tripartite interaction among S. plymuthica A30, D. solani, and potato tubers, facilitating the development of biocontrol system for soft rot pathogens under storage conditions.

Time-Course Responses of Apple Leaf Endophytes to the Infection of Gymnosporangium yamadae

Apple rust, caused by Gymnosporangium yamadae, poses a significant challenge to apple production. Prior studies have underscored the pivotal role played by endophytic microbial communities, intimately linked with the host, in influencing plant diseases and their pathogenic outcomes. The objective of this study is to scrutinize alternations in endophytic microbial communities within apple leaves at different stages of apple rust using high-throughput sequencing technology. The findings revealed a discernible pattern characterized by an initial increase and subsequent decrease in the alpha diversity of microbial communities in diseased leaves. A microbial co-occurrence network analysis revealed that the complexity of the bacterial community in diseased leaves diminished initially and then rebounded during the progression of the disease. Additionally, employing the PICRUSt2 platform, this study provided preliminary insights into the functions of microbial communities at specific disease timepoints. During the spermogonial stage, endophytic bacteria particularly exhibited heightened activity in genetic information processing, metabolism, and environmental information processing pathways. Endophytic fungi also significantly enriched a large number of metabolic pathways during the spermogonial stage and aecial stage, exhibiting abnormally active life activities. These findings establish a foundation for comprehending the role of host endophytes in the interaction between pathogens and hosts. Furthermore, they offer valuable insights for the development and exploitation of plant endophytic resources, thereby contributing to enhanced strategies for managing apple rust.

Efficacy of 2,4-Di-tert-butylphenol in Reducing Ralstonia solanacearum Virulence: Insights into the Underlying Mechanisms

Ralstonia solanacearum can induce severe wilt disease in vital crops. Therefore, there is an urgent need to develop novel antifungal solutions. The natural compound 2,4-di-tert-butylphenol (2,4-DTBP) exhibits diverse physiological activities and affects soil function. However, its specific impact on the R. solanacearum remains unclear. Here, we investigated the antimicrobial potential of 2,4-DTBP. The results demonstrated that 2,4-DTBP effectively inhibited its growth and altered morphology. In addition, it substantially impeded biofilm formation, motility, and exopolysaccharide secretion. Transcriptomic analysis revealed that 2,4-DTBP inhibited energy production and membrane transport. Additionally, 2,4-DTBP hindered the growth by interfering with the membrane permeability, reactive oxygen species (ROS) production, and electrolyte leakage. Concomitantly, this led to a significant reduction in pathogenicity, as evidenced by the biomass of R. solanacearum in the invaded roots. Overall, our data strongly support the potential utility of 2,4-DTBP as a potent antibacterial agent capable of effectively preventing the onset of bacterial wilt caused by R. solanacearum.

Streptomyces as a promising biological control agents for plant pathogens

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa

The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.

Antimicrobial activity and comparative metabolomic analysis of Priestia megaterium strains derived from potato and dendrobium

The growth of endophytic bacteria is influenced by the host plants and their secondary metabolites and activities. In this study, P. megaterium P-NA14 and P. megaterium D-HT207 were isolated from potato tuber and dendrobium stem respectively. They were both identified as Priestia megaterium. The antimicrobial activities and metabolites of both strains were explored. For antimicrobial activities, results showed that P. megaterium P-NA14 exhibited a stronger inhibition effect on the pathogen of dendrobium, while P. megaterium D-HT207 exhibited a stronger inhibition effect on the pathogen of potato. The supernatant of P. megaterium P-NA14 showed an inhibition effect only on Staphylococcus aureus, while the sediment of P. megaterium D-HT207 showed an inhibition effect only on Escherichia coli. For metabolomic analysis, the content of L-phenylalanine in P. megaterium P-NA14 was higher than that of P. megaterium D-HT207, and several key downstream metabolites of L-phenylalanine were associated with inhibition of S. aureus including tyrosine, capsaicin, etc. Therefore, we speculated that the different antimicrobial activities between P. megaterium P-NA14 and P. megaterium D-HT207 were possibly related to the content of L-phenylalanine and its metabolites. This study preliminarily explored why the same strains isolated from different hosts exhibit different activities from the perspective of metabolomics.

Evaluation of the biocontrol activity of Frateuria defendens-derived metabolites against mollicutes

Frateuria defendens is a candidate biocontrol agent that has been shown to reduce phytoplasma-related disease symptoms in grapevines and periwinkle plants. While a crude filtrate prepared from F. defendens can inhibit mollicute growth, the specific growth parameters for this bacterium, necessary to enhance this protective inhibitory response, remain unknown. Moreover, the separation of filtrate preparations from bacterial cells via centrifugation and filtration is laborious and time-consuming. As such, the present study was conducted to define the optimal growth conditions associated with maximal inhibitory activity of F. defendens and to establish a better approach to separating these bacterial cells from their secreted metabolites. To conduct these analyses, F. defendens was cultured in a range of media types, while associated inhibitory effects were tested in vitro using Spiroplasma melliferum as a model mollicute bacterium, and in planta using phytoplasma-infected periwinkle plantlets. These analyses revealed F. defendens growth patterns change based upon media composition, with filtrates prepared from a specific rich medium (S-medium) exhibiting beneficial activities, including the inhibition of S. melliferum and enhanced plant growth. When F. defendens cells were grown within semi-permeable, membrane-coated Small Bioreactor Platform (SBP) capsules, they could be more readily separated from the secreted metabolite fraction, obviating the need for filtration and/or centrifugation. This study is the first to have reported the use of SBP capsules to separate bacterial cells from their secreted metabolites under sterile conditions while retaining the ability of these metabolites to inhibit S. melliferum growth and to benefit the host plant. The results highlight promising new approaches to the effective biocontrol of phytoplasma-driven diseases in grapevines and other economically important plant species.

A multifunctional enzyme portfolio for α-chaconine and α-solanine degradation in the Phthorimaea operculella gut bacterium Glutamicibacter halophytocola S2 encoded in a trisaccharide utilization locus

Steroidal glycoalkaloids (SGAs) are secondary metabolites commonly found in members of the family Solanaceae, including potatoes, and are toxic to pests and humans. The predominant SGAs in potato are α-chaconine and α-solanine. We previously reported that Glutamicibacter halophytocola S2, a gut bacterium of the pest Phthorimaea operculella (potato tuber moth), can degrade α-chaconine and α-solanine in potatoes, which can improve the fitness of P. operculella to feed on potatoes with a high content of toxic SGAs. Glutamicibacter halophytocola S2 harbored a gene cluster containing three deglycosylase genes-GE000599, GE000600, and GE000601-that were predicted encode α-rhamnosidase (RhaA), β-glucosidase (GluA), and β-galactosidase (GalA). However, there is limited information is available on the enzyme activities of the three enzymes expressed by this gene cluster and how they degrade the major toxic α-chaconine and α-solanine. In the current study, each enzyme of this gene cluster was produced by a prokaryotic expression approach and the activity of the recombinant enzymes for their target substrate and α-chaconine and α-solanine were evaluated by EPOCH microplate spectrophotometer and liquid chromatography mass spectrometry (LC-MS). The three enzymes had multifunctional activities, with RhaA and GluA could hydrolyze α-rhamnose, β-glucose, and β-galactose, while GalA can hydrolyze β-glucose and β-galactose. The degradation of α-chaconine and α-solanine was consistent with the results of the enzyme activity assays. The final product solanidine could be generated by adding RhaA or GluA alone. In conclusion, this study characterized the multifunctional activity and specific degradation pathway of these three enzymes in G. halophytocola S2. The three multifunctional enzymes have high glycosidic hydrolysis activity and clear gene sequence information, which help facilitates understanding the detoxification mechanism of insect gut microbes. The enzymes have a broad application potential and may be valuable in the removal of toxic SGAs from for potato food consumption.

Integrated Analysis of Transcriptome and Metabolome Reveals the Mechanism of Chlorine Dioxide Repressed Potato (Solanum tuberosum L.) Tuber Sprouting

Sprouting is an irreversible deterioration of potato quality, which not only causes loss in their commercial value but also produces harmful toxins. As a popular disinfectant, ClO2 can inhibit the sprouting of potato tubers. Using transcriptomic and metabolomic approaches to understand the repressive mechanism of ClO2 in potato sprouting is yet to be reported. Sequencing the transcriptome and metabolome of potatoes treated with ClO2 in this study revealed a total of 3,119 differentially expressed genes, with 1,247 and 1,872 genes showing down- and upregulated expression, respectively. The majority of the downregulated genes were associated with plant hormone signal transduction, whereas upregulated differential genes were associated primarily with biological processes, such as phenylpropanoid biosynthesis and the mitogen-activated protein kinase (MAPK) signaling pathway. Metabonomic assays identified a total of 932 metabolites, with 33 and 52 metabolites being down- and upregulated, respectively. Downregulated metabolites were mostly alkaloids, amino acids, and their derivatives, whereas upregulated metabolites were composed mainly of flavonoids and coumarins. Integrated transcriptomic and metabolomic analyses showed that many different metabolites were regulated by several different genes, forming a complex regulatory network. These results provide new insights for understanding the mechanism of ClO2-mediated repression of potato sprouting.

Analysis of Endophytic Bacterial Diversity From Different Dendrobium Stems and Discovery of an Endophyte Produced Dendrobine-Type Sesquiterpenoid Alkaloids

As the unique component of Dendrobium, dendrobine-type sesquiterpenoid alkaloids (DSAs) possess a variety of medicinal properties. It has been well documented that plant endophytes can in vitro synthesize secondary metabolites identical or similar to metabolites produced by their host plants. This study aimed to investigate the composition and distribution of endophytic bacteria of Dendrobium stems by Illumina MiSeq platform sequencing and cultivation-dependent methods and then to assess the potential for endophytic bacteria to produce DSAs. Results indicated that it was necessary to combine both cultivation-dependent and cultivation-independent methods to analyze the community structure of endophytic bacterial in plants comprehensively. The length of the Dendrobium stems influenced the endophytic bacterial community. The diversity and richness of endophytic bacteria in group J10_15cm of stems were the highest, which showed a significant difference from the other stem groups. However, there was no certain connection between the diversity and richness of endophytic bacteria and the content of dendrobine. It was most likely due to the influence of several specific endophytic bacteria genera, such as Sphingomonas and Rhodococcus. Athelia rolfsii, Myrothecium roridum, as pathogenic fungi, and Pectobacterium carotovorum subsp. actinidiae, as pathogenic bacteria of Dendrobium, were used to determine the antimicrobial activities. In these assays, six strains belonging to five genera showed antimicrobial activity against at least two phytopathogens. The strain BL-YJ10_15-29 (Paracoccus pueri THG-N2.35, 98.98%) showed the best antimicrobial activity against the three phytopathogens. In addition, 2 DSAs (6-hydroxydendrobine and nobilonine) were identified in the fermentation supernatant of the strain CM-YJ10_15-44 (Pseudomonas protegens CHA0, 99.24%), whereas the whole-genome analysis results further demonstrated that the precursors of the two DSAs [geranyl-PP and (E, E)-famesyl-PP] were synthesized mainly through the methyl-D-erythritol 4-phosphate pathway in this strain. This study provides new insight into the studies on the biosynthesis of DSAs and provides potential biocontrol bacteria.