Search Results (66)

Microorganisms in their natural ecological niches are constantly challenged by other inhabitants. Antagonisms exhibited by interacting microbial species are directed towards survival and increasing of their fitness. The Soft Rot Pectobacteriaceae (SRP) is a good model to study these complex microbial interactions. Along with being present in various environments, SRPs are often transferred between environments, allowing the bacteria to encounter members of other species. In this study, we investigated interactions between Dickeya solani, a representative of SRPs and a causative agent of potato soft rot, and Bacillus subtilis, which is known to be a potent producer of secondary metabolites mediating antibiosis. We have found that the soil isolate B. subtilis MB73/2 not only suppresses in vitro soft-rotting of infected potato tubers but is also able to cause directional, coordinated escape of natural isolates D. solani IFB0102 and IPO2222. While this coordinated movement of D. solani depends on surfactin produced by B. subtilis MB73/2, we show that both Dickeya strains exhibit different antagonistic interaction phenotypes toward the competing Bacillus. We prove that this antagonism depends on a single nucleotide polymorphism in one of transcriptional regulators of D. solani belonging to the LysR family. Full article

The immune response triggered when plant cell surface receptors recognize pathogen-associated molecular patterns (PAMPs) is known as PAMP-triggered immunity (PTI). Several studies have demonstrated that extracellular plant ferredoxin-like protein (PFLP) can enhance PTI signaling, thereby conferring resistance to bacterial diseases in various plants. The C-terminal casein kinase II (CK2) phosphorylation region of PFLP is essential for strengthening PTI. However, whether phosphorylation at this site directly enhances PTI signaling and consequently increases plant disease resistance remains unclear. To investigate this, site-directed mutagenesis was used to generate PFLPT90A, a non-phosphorylatable mutant, and PFLPT90D, a phospho-mimetic mutant, for functional analysis. Based on the experimental results, none of the recombinant proteins were able to enhance the hypersensitive response induced by the HrpN protein or increase resistance to the soft rot pathogen Pectobacterium carotovorum subsp. carotovorum ECC17. These findings suggest that phosphorylation at the T90 residue might be essential for PFLP-mediated enhancement of plant immune responses, implying that this post-translational modification is likely required for its disease resistance function in planta. To further explore the relationship between PFLP phosphorylation and endogenous CK2, the Arabidopsis insertion mutant cka2 and the complemented line CKA2R were analyzed under treatment with flg22_Pst from Pseudomonas syringae pv. tomato. The effects of PFLP on the hypersensitive response, rapid oxidative burst, callose deposition, and susceptibility to soft rot confirmed that CK2 is required for these immune responses. Furthermore, expression analysis of PTI-related genes FRK1 and WRKY22/29 in the mitogen-activated protein kinase (MAPK) signaling pathway demonstrated that CK2 is necessary for PFLP to enhance flg22_Pst-induced immune signaling. Taken together, these findings suggest that PFLP enhances A. thaliana resistance to bacterial soft rot primarily by promoting the MAPK signaling pathway triggered by PAMP recognition, with CK2-mediated phosphorylation being essential for its function. Full article

Potato early dying disease complex (PED) leads to premature senescence and rapid decline in potato plants. Unlike potato wilt caused solely by Verticillium species, PED symptoms are more severe due to the synergistic effects of multiple pathogens, including root-lesion nematodes, fungi such as Colletotrichum and Fusarium, and soft-rot bacteria. To investigate the microbiome responsible for PED, soil and stem samples from healthy-looking and symptomatic plants were analyzed using amplicon-targeted next-generation sequencing (Illumina MiSeq and PacBio technologies). Samples were collected from four locations in New Brunswick, Canada from fields previously rotated with barley or oat. Comparative analysis of the bacterial, fungal, and eukaryotic diversity in soil samples showed minimal differences, with only bacterial alpha diversity influenced by the plant health status. Verticillium dahliae was abundant in all soil samples, and its abundance was significantly higher in the stems of diseased plants. Additional fungal species implicated in PED, including Plectosphaerella cucumerina, Colletotrichum coccodes, Botrytis sp., and Alternaria alternata, were also identified in the stems. This study highlights the complex, plant-associated microbial interactions underlying PED and provides a foundation for microbiome-informed disease management strategies. Full article

Bacterial soft rot causes major crop losses annually and can be caused by several species from multiple genera. These bacteria have a broad host range and often infect produce through contact with soil. The main genera causing bacterial soft rot are Pectobacterium and Dickeya, both of which have widespread geographical distribution. Because of many recent renaming and reclassifications of bacteria causing soft rot, identification and characterization of the causative agents can be challenging. In this work, we surveyed commercially available produce exhibiting typical soft rot symptoms, isolating pectinolytic bacteria and characterizing them genetically and phenotypically. We found that in our sampling, many samples were from the genus Pectobacterium; however, other genera were also capable of eliciting symptoms in potatoes, including an isolate from the genus Chryseobacterium. Genomic analyses revealed that many of the Pectobacterium isolates collected share prophages not found in other soft rot species, suggesting a potential role for these prophages in the evolution or fitness of these isolates. Our Chryseobacterium isolate was most similar to C. scophthalmum, a fish pathogen, suggesting that this isolate may be a crossover pathogen. Full article

This study explores the biocontrol potential of Pediococcus sp. M21F004, a lactic acid bacteria (LAB) isolated from marine environments, against several bacterial and fungal phytopathogens. Out of 50 marine bacterial isolates, Pediococcus sp. M21F004 was selected for its exceptional antimicrobial activity. The strain, isolated from the intestine of a starry flounder, was identified as Pediococcus sp. Gas chromatography–mass spectrometry (GC-MS) analysis revealed that oleic acid (OA) is a key antimicrobial compound produced by Pediococcus sp. M21F004. In vitro assays showed that the culture broth (CB) of Pediococcus sp. M21F004, as well as OA, exhibited significant inhibitory effects against pathogens such as Fusarium oxysporum, Clarireedia homoeocarpa, and Pectobacterium carotovorum subsp. carotovorum. In vivo tests on cucumber Fusarium wilt, creeping bentgrass dollar spot, tomato bacterial wilt, and kimchi cabbage soft rot further demonstrated the strain’s efficacy in reducing disease severity. Moreover, OA had the highest control value of 74% against tomato bacterial wilt, followed by 64.1% against cucumber fusarium wilt, 42.5% against kimchi cabbage soft rot, and 16.5% against creeping bentgrass dollar spot. These findings suggest that Pediococcus sp. M21F004 and its metabolite OA offer promising alternatives to chemical pesticides, contributing to sustainable plant disease management by promoting resistance induction and providing an eco-friendly approach to agriculture. Full article

Pectobacterium brasiliense is a bacterial phytopathogen that causes soft and black rot and actively spreads worldwide. Our study is the first development of immunoassays for detecting P. brasiliense. We immunized rabbits and obtained serum with an extremely high titer (1:10⁸). Isolated polyclonal antibodies were tested by enzyme-linked immunosorbent assay (ELISA) using 18 closely related strains and 5 non-related bacterial pathogens. No cross-reactivity was found concerning the tested pathogens. The ELISA of P. brasiliense was developed in a double-antibody sandwich format with a detection limit of 1.5 × 10⁴ cells/mL. A lateral flow immunoassay (LFIA) for P. brasiliense was also developed in a double-antibody sandwich format with a detection limit of 1 × 10⁵ cells/mL. The results of P. brasiliense cells testing with LFIA in plant matrix showed a high correlation (R² = 0.932) between concentrations of added and revealed cells. When testing potato seed material, ELISA and LFIA confirmed 75 and 66% of positive samples according to real-time PCR, respectively. For negative samples, ELISA showed 84% coincidence, and LFIA coincided with PCR for 89% of samples. Thus, the developed immunoassays can be used to evaluate plant material in poorly equipped conditions or under field testing. Full article

When a plant is infected by a pathogen, endogenous immune responses are initiated. When the initiation of these defense responses is induced by a pathogen-associated molecular pattern (PAMP) of a pathogen, it is called PAMP-triggered immunity (PTI). Previous studies have shown that Bacillus amyloliquefaciens PMB05 can enhance PTI signals and improve disease control of bacterial soft rot and wilt in Arabidopsis thaliana. In the context of controlling bacterial wilt disease, the involvement of a mitogen-activated protein kinase (MAPK) signaling pathway has been established. Nevertheless, it remains unclear whether this pathway is also required for B. amyloliquefaciens PMB05 in controlling bacterial soft rot. In this study, A. thaliana ecotype Columbia (Col-0) and its mutants on a MAPK pathway-related pathway were used as a model and established that the ability of B. amyloliquefaciens PMB05 to control soft rot requires the participation of the MAPK pathway. Moreover, the enhancement of disease resistance by PMB05 is highly correlated with the activation of reactive oxygen species generation and stomata closure, rather than callose deposition. The spray inoculation method was used to illustrate that PMB05 can enhance stomatal closure, thereby restricting invasion by the soft rot bacterium. This control mechanism has also been demonstrated to require the activation of the MAPK pathway. This study demonstrates that B. amyloliquefaciens PMB05 can accelerate stomata closure via the activation of the MAPK pathway during PTI, thereby reducing pathogen invasion and achieving disease resistance against bacterial soft rot. Full article

Dickeya dadantii is a common pathogen of bacterial soft rot on a wide range of plants, including several crops. In this study, we present the complete genome sequence of the D. dadantii type strain DSM18020^T. The genome was assembled using PacBio technology, resulting in a 4,997,541 bp circular chromosome with a G+C content of 56.5%. Our sequence analyses predicted 4277 protein-encoding genes, including several associated with known bacterial virulence factors and secondary metabolites. Comparative genomics analysis between Dickeya revealed that the category of ‘metabolism’ is the most important in both the core and accessory genomes, while the category of ‘information storage and processing’ is the most dominant in unique genomes. These findings will not only help us to understand the pathogenic mechanisms of D. dadantii DSM18020^T, but also provide us with useful information for new control strategies against this phytopathogen. Full article

This review focuses on the pivotal role microscopy has played in diagnosing the type(s) of microbial attacks present in waterlogged ancient wooden objects, and to understand the nature and extent of deterioration of such objects. The microscopic journey began with the application of light microscopy (LM) to examine the deterioration of waterlogged woods, notably foundation piles supporting historic buildings, progressing into the use of high-resolution imaging tools (SEM and TEM) and techniques. Although bacteria were implicated in the deterioration of foundation piles, confirmation that bacteria can indeed degrade wood in its native state came when decaying wood from natural environments was examined using electron microscopy, particularly TEM, which enabled bacterial association with cell wall regions undergoing degradation to be clearly resolved. The information base has been a catalyst, stimulating numerous studies in the past three decades or so to understand the nature of microbial degradation of waterlogged archaeological wood more precisely, combining LM, SEM, and TEM with high-resolution chemical analytical methods, including chemical microscopy. The emerging information is aiding targeted developments towards a more effective conservation of ancient wooden objects as they begin to be uncovered from burial and waterlogging environments. Full article

The competitive colonization of bacteria on similar ecological niches has a significant impact during their establishment. The synthesis speeds of different chemical classes of molecules during early competitive colonization can reduce the number of competitors through metabolic effects. In this work, we demonstrate for the first time that Kosakonia cowanii Cp1 previously isolated from the seeds of Capsicum pubescens R. P. produced volatile organic compounds (VOCs) during competitive colonization against Pectobacterium aroidearum SM2, affecting soft rot symptoms in serrano chili (Capsicum annuum L.). The pathogen P. aroidearum SM2 was isolated from the fruits of C. annuum var. Serrano with soft rot symptoms. The genome of the SM2 strain carries a 5,037,920 bp chromosome with 51.46% G + C content and 4925 predicted protein-coding genes. It presents 12 genes encoding plant-cell-wall-degrading enzymes (PCDEWs), 139 genes involved in five types of secretion systems, and 16 genes related to invasion motility. Pathogenic essays showed soft rot symptoms in the fruits of C. annuum L., Solanum lycopersicum, and Physalis philadelphica and the tubers of Solanum tuberosum. During the growth phases of K. cowanii Cp1, a mix of VOCs was identified by means of HS-SPME-GC-MS. Of these compounds, 2,5-dimethyl-pyrazine showed bactericidal effects and synergy with acetoin during the competitive colonization of K. cowanii Cp1 to completely reduce soft rot symptoms. This work provides novel evidence grounding a better understanding of bacterial interactions during competitive colonization on plant tissue, where VOC synthesis is essential and has a high potential capacity to control pathogenic microorganisms in agricultural systems. Full article

Diseases that occur in silkworms include soft rot, hardening disease, digestive diseases, and sepsis. However, research on the causes of bacterial diseases occurring in silkworms and the resulting changes in the microbial community is lacking. Therefore, we examined the morphological characteristics of sepsis and changes in the microbial community between silkworms that exhibit a unique odor and healthy silkworms; thus, we established a relationship between disease-causing microorganisms and sepsis. After producing a 16S rRNA amplicon library for samples showing sepsis, we obtained information on the microbial community present in silkworms using next-generation sequencing. Compared to that in healthy silkworms, in silkworms with sepsis, the abundance of the Firmicutes phylum was significantly reduced, while that of Proteobacteria was increased. Serratia sp. was dominant in silkworms with sepsis. After bacterial isolation, identification, and reinfection through the oral cavity, we confirmed this organism as the disease-causing agent; its mortality rate was 1.8 times higher than that caused by Serratia marcescens. In summary, we identified a new causative bacterium of silkworm sepsis through microbial community analysis and confirmed that the microbial community balance was disrupted by the aberrant proliferation of certain bacteria. Full article

Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the “disease triangle” and is directly connected with a particular plant–pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant’s natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions. Full article

Pectobacterium brasiliense (Pbr) has caused significant economic losses in major vegetable production areas in Northern China by causing bacterial soft rot in cash crops such as potatoes and cucumbers. This study aimed to establish a PMA-qPCR detection method for Pbr by screening specific and sensitive primers based on the glu gene and the conserved region of the 23S rRNA gene. Based on the optimized PMA pretreatment conditions, a standard curve was designed and constructed for PMA-qPCR detection (y = −3.391x + 36.28; R² = 0.99). The amplification efficiency reached 97%, and the lowest detection limit of viable cells was approximately 2 × 10² CFU·mL⁻¹. The feasibility of the PMA-qPCR method was confirmed through a manually simulated viable/dead cell assay under various concentrations. The analysis of potato tubers and cucumber seeds revealed that nine naturally collected seed samples contained a range from 10² to 10⁴ CFU·g⁻¹ viable Pbr bacteria. Furthermore, the system effectively identified changes in the number of pathogenic bacteria in cucumber and potato leaves affected by soft rot throughout the disease period. Overall, the detection and prevention of bacterial soft rot caused by Pbr is crucial. Full article

While numerous studies have examined microbial attacks on waterlogged archaeological wood, limited information is available regarding microbial attacks in waterlogged tropical hardwoods submerged in marine environments. In this context, we explored microbial attacks in waterlogged archaeological rosewood (Dalbergia species), a tropical hardwood species that was submerged in the Yellow Sea for approximately 700 years, using various microscopic techniques and next-generation sequencing (NGS) methods. Based on morphological features, Type-I soft rot decay was identified as the main decay type. Most fibers in waterlogged archaeological rosewood studied were gelatinous (G) fibers of tension wood and the mode of soft rot decay differed from fibers without the G-layer. Differences in decay resistance between vessel/axial parenchyma cells and fibers were not obvious. Vestured- and simple pit membranes showed higher decay resistance than vessel and axial parenchyma cell walls, respectively. Microbial community analysis by NGS revealed the dominance of Ascomycota and Basidiomycota in the fungal community. Various bacterial communities were also identified, although no prominent signs of bacterial decay were noted. The identified bacterial communities markedly differed from those reported previously in terms of their composition and abundance. Together, our results offer detailed insights into the microbial types and communities responsible for degrading waterlogged archaeological rosewood, contributing to a better understanding of microbial attacks in tropical hardwoods exposed to marine environments. Full article

Quorum sensing (QS) is a communication mechanism used among microorganisms that regulate the population density and behavior by sensing the concentration of signaling molecules. Quorum quenching (QQ), a novel, eco-friendly, and efficient method for disease control, interferes with QS by disturbing the production and enzymatic degradation of signaling molecules, blocking communication among microorganisms, and thus has deep potential for use in plant disease control. Pectobacterium carotovorum can cause bacterial soft rot, resulting in yield reduction in a variety of crops worldwide, and can be mediated and regulated by the N-acyl homoserine lactones (AHLs), which are typical signaling molecules. In this study, a novel quenching strain of Pseudomonas multiresinivorans QL-9a was isolated and characterized, and it showed excellent degradation ability against AHLs, degrading 98.20% of N-(-3-oxohexanoyl)-L-homoserine lactone (OHHL) within 48 h. Based on the results of the gas chromatography–mass spectrometer (GC–MS) analysis, a possible pathway was proposed to decompose OHHL into fatty acids and homoserine lactone, in which AHL acylase was involved. Additionally, it has been demonstrated that the QL-9a strain and its crude enzyme are promising biocontrol agents that can considerably reduce the severity of the soft rot disease brought on by P. carotovorum, consequently preventing the maceration of a variety of host plant tissues. All of these results suggest promising applications of the QL-9a strain and its crude enzyme in the control of various plant diseases mediated by AHLs. Full article