A combination of a SEM technique and X-ray microanalysis for studying the spore germination process of Clostridium tyrobutyricum

Exploring boron applications in modern agriculture: Antifungal activities and mechanisms of phenylboronic acid derivatives

BACKGROUND

The unreasonable use of chemical fungicides causes common adverse consequences that not only affect the environment, but also cause resistance and resurgence problems of plant pathogens, which are extremely harmful to human health, the economy, and the environment. Based on the rich biological activities of boron-based compounds, 82 phenylboronic acid derivatives were selected and their antifungal activities against six agricultural plant pathogens were determined. Combined with transcriptomics tools, the mechanism of action of compound A49 (2-chloro-5-trifluoromethoxybenzeneboronic acid) against Botrytis cinerea Pers (B. cinerea) was studied.

RESULTS

The EC₅₀ values of compounds A24, A25, A30, A31, A36, A41, A49 and B23 against all six fungi were under 10 μg/mL. Compound A49 displayed significant activity against B. cinerea (EC₅₀  = 0.39 μg/mL), which was better than that of commercial fungicide boscalid (EC₅₀  = 0.55 μg/mL). A49 not only inhibited the germination of B. cinerea spores, but also caused abnormal cell morphology, loss of cell membrane integrity, enhanced cell membrane permeability, and accumulation of intracellular reactive oxygen species. Further findings showed that A49 reduced cellular antioxidant activity, and peroxidase and catalase activities. Transcriptomic results indicated that A49 could degrade intracellular redox processes and alter the metabolism of some amino acids. Meanwhile, A49 showed obvious activity in vivo and low cytotoxicity to mammal cells.

CONCLUSION

The boron-containing small molecule compounds had high efficiency and broad-spectrum antifungal activities against six plant pathogens, and are expected to be candidate compounds for a new class of antifungal drugs. © 2023 Society of Chemical Industry.

Microbacterium paulum sp. nov., isolated from microfiltered milk

A novel Gram-stain-positive, strictly aerobic, short rod-shaped bacterium, designated 2C^T, was isolated from freshly packaged microfiltered milk. This strain was able to grow within the NaCl concentration range of 0-5 % (w/v), temperature range of 8-37 °C (optimally at 30 °C) and at pH 6.0-10.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2C^T was closely related to species of the genus Microbacterium, with the highest sequence similarity (99.2 %) to Microbacterium lacticum DSM 20427^T as well as Microbacterium flavum DSM 18909^T (=YM18-098^T). The phylogenetic tree based on 16S rRNA genes showed that strain 2C^T clustered with M. flavum DSM 18909^T. However, the phylogenetic tree based on concatenated 16S rRNA and four housekeeping genes showed that strain 2C^T clustered with M. lacticum DSM 20427^T. Furthermore, the phylogenomic tree showed that strain 2C^T clustered with M. lacticum DSM 20427^T and M. flavum DSM 18909^T. The major respiratory quinones were MK-10, MK-11 and MK-12. The predominant cellular fatty acids were anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The polar lipid composition of strain 2C^T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified glycolipids and two unidentified lipids. The cell-wall peptidoglycan type was a variant of B1α {Gly} [l-Lys] d-Glu-l-Lys, with the amino acids lysine, glycine, alanine and glutamic acid. The whole-cell sugars consisted of galactose, glucose, ribose and minor amounts of rhamnose. In addition, strain 2C^T showed a glycolyl-type cell wall. The genomic DNA G+C content was 69.8mol%, while the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the closely related Microbacterium species were below the recognized thresholds of 95-96 % ANI and 70 % DDH for species definition. Based on the phenotypic and genotypic data, strain 2C^T (=LMG 32277^T=CECT 30329^T) is considered to represent a new species, for which the name Microbacterium paulum sp. nov. is proposed.

Colorimetric Point-of-Care Detection of Clostridium tyrobutyricum Spores in Milk Samples

Clostridium tyrobutyricum represents the main spoiling agent responsible for late blowing defects (LBD) in hard and semi-hard cheeses. Its spores are resistant to manufacturing procedures and can germinate during the long ripening process, causing the burst of the cheese paste with a consequent undesirable taste. The lower quality of blown cheeses leads to considerable financial losses for the producers. The early identification of spore contaminations in raw milk samples thus assumes a pivotal role in industrial quality control. Herein, we developed a point of care (POC) testing method for the sensitive detection of C. tyrobutyricum in milk samples, combining fast DNA extraction (with no purification steps) with a robust colorimetric loop-mediated isothermal amplification (LAMP) technique. Our approach allows for the sensitive and specific detection of C. tyrobutyricum spores (limit of detection, LoD: ~2 spores/mL), with the advantage of a clear naked-eye visualization of the results and a potential semi-quantitative discrimination of the contamination level. In addition, we demonstrated the feasibility of this strategy using a portable battery-operated device that allowed both DNA extraction and amplification steps, proving its potential for on-site quality control applications without the requirement of sophisticated instrumentation and trained personnel.

Phenotypic and Genotypic Investigation of Two Representative Strains of Microbacterium Species Isolated From Micro-Filtered Milk: Growth Capacity and Spoilage-Potential Assessment

The microbiota that spoil long-life micro-filtered milk generally includes species of the genus Microbacterium. The metabolic properties of this of microorganisms that could potentially modify the quality of micro-filtered milk are still unexplored when compared to better-known microorganisms, such as the spore-forming Bacillus and Paenibacillus spp., and Gram-negative contaminants, such as species of the genera Pseudomonas and Acinetobacter. In this preliminary study, two strains of Microbacterium (M. lacticum 18H and Microbacterium sp. 2C) isolated from micro-filtered milk were characterized in depth, both phenotypically and genotypically, to better understand their role in long-term milk spoilage. The study highlights the ability of these strains to produce high cell numbers and low acidification in micro-filtered milk under storage and shelf-life conditions. Phenotypic analyses of the two Microbacterium sp. isolates revealed that both strains have low proteolytic and lipolytic activity. In addition, they have the ability to form biofilms. This study aims to be a preliminary investigation of milk-adapted strains of the Microbacterium genus, which are able to grow to high cellular levels and perform slight but not negligible acidification that could pose a potential risk to the final quality of micro-filtered milk. Furthermore, M. lacticum 18H and Microbacterium sp. 2C were genotypically characterized in relation to the characteristics of interest in the milk environment. Some protein-encoding genes involved in lactose metabolism were found in the genomes, such as β-galactosidase, lactose permease, and L-lactate dehydrogenase. The phenotypically verified proteolytic ability was supported in the genomes by several genes that encode for proteases, peptidases, and peptide transferases.

Enterococcus faecalis and Vibrio harveyicolonize low-density polyethylene and biodegradable plastics under marine conditions

Conventional plastics and bioplastics are known to accumulate in aquatic ecosystems, emerging as new surfaces for biofilm formation and gene exchanges. On the other hand, the fate of non-conventional bioplastics in the marine environment is still unclear. In this study we have measured, by means of crystal violet test and scanning electron microscopy (SEM), the ability of two model bacteria, Vibrio harveyi and Enterococcus faecalis, to form biofilms on low-density polyethylene (PE), polylactic acid (PLA) and starch-based bioplastic (SBB) surfaces. Experiments were conducted in artificial sea water, incubating squares of 3 cm2 of the three plastics with the two model microorganisms and sampling overnight, and at 3 and 6 days. The presence of biofilms on plastic surfaces was detected from day one of incubation and SBB was the material with the highest biofilm formation. E. faecalis formed the thickest biofilm after 3 days with PLA and SBB, but did not remain stable, and after 6 days with PE. The maximum biofilm formation of V. harveyi was obtained overnight with SBB and PE, and after 3 days with PLA. Our data indicate that both plastic and bioplastics support the formation of biofilms of model pathogenic bacteria, highlighting potential concerns for human health.

A fluorescence in situ staining method for investigating spores and vegetative cells of Clostridia by confocal laser scanning microscopy and structured illuminated microscopy

Non-pathogenic spore-forming Clostridia are of increasing interest due to their application in biogas production and their capability to spoil different food products. The life cycle for Clostridium includes a spore stage that can assist in survival under environmentally stressful conditions, such as extremes of temperature or pH. Due to their size, spores can be investigated by a range of microscopic techniques, many of which involve sample pre-treatment. We have developed a quick, simple and non-destructive fluorescent staining procedure that allows a clear differentiation between spores and vegetative cells and effectively stains spores, allowing recovery and tracking in subsequent experiments. Hoechst 34580, Propidium iodide and wheat germ agglutinin WGA 488 were used in combination to stain four strains of Clostridia at different life cycle stages. Staining was conducted without drying the sample, preventing changes induced by dehydration and cells observed by confocal laser scanner microscopy or using a super-resolution microscope equipped with a 3D-structured illumination module. Dual staining with Hoechst/Propidium iodide differentiated spores from vegetative cells, provided information on the viability of cells and was successfully applied to follow spore production induced by heating. Super-resolution microscopy of spores probed by Hoechst 34580 also allowed chromatin to be visualised. Direct staining of a cheese specimen using Nile Red and Fast Green allowed in situ observation of spores within the cheese and their position within the cheese matrix. The proposed staining method has broad applicability and can potentially be applied to follow Clostridium spore behaviour in a range of different environments.

Effect of temperature on the microstructure of fat globules and the immunoglobulin-mediated interactions between fat and bacteria in natural raw milk creaming

Natural creaming of raw milk is the first step in production of Grana Padano and Parmigiano Reggiano Protected Denomination of Origin cheeses. This process decreases the fat content and plays an important role in the removal of clostridia species that may cause late-blowing defects in ripened cheeses. Partial coalescence of fat globules-that may influence fat behavior in cheese making and affect the microstructure of fat in the final cheese product-was observed at creaming temperatures higher than 22°C by confocal laser scanning microscopy. The widespread practice of heating of milk at 37°C before creaming at 8°C resulted in important changes in the size distribution of fat globules in raw milk, potentially altering the ability of fat to entrap clostridia spores. We investigated the role of immunoglobulin classes in both the clustering of fat globules and the agglutination of Clostridium tyrobutyricum to fat globules during creaming. Immunogold labeling and transmission electron microscopy showed that IgA and IgM but not IgG were involved in both clustering and agglutination. Both vegetative cells and spores were clearly shown to agglutinate to fat droplets, a process that was suppressed by thermal denaturation of the immunoglobulins. The debacterization of raw milk through natural creaming was improved by the addition of purified immunoglobulins. Overall, these findings provide not only a better understanding of the phenomena occurring during the natural creaming but also practical insights into how the process of creaming may be optimized in cheese production plants.

Microflora of processed cheese and the factors affecting it

The basic raw materials for the production of processed cheese are natural cheese which is treated by heat with the addition of emulsifying salts. From a point of view of the melting temperatures used (and the pH-value of the product), the course of processed cheese production can be considered "pasteurisation of cheese." During the melting process, the majority of vegetative forms of microorganisms, including bacteria of the family Enterobacteriaceae, are inactivated. The melting temperatures are not sufficient to kill the endospores, which survive the process but are often weakened. From a microbiological point of view, the biggest contamination problem of processed cheese is caused by gram-positive spore-forming rod-shaped bacteria of the genera Bacillus, Geobacillus, and Clostridium. Other factors affecting the shelf-life and quality of processed cheese are mainly the microbiological quality of the raw materials used, strict hygienic conditions during the manufacturing process as well as the type of packaging materials and storage conditions. The quality of processed cheese is not only dependent on the ingredients used but also on other parameters such as the value of water activity of the processed cheese, its pH-value, the presence of salts and emulsifying salts and the amount of fat in the product.

Rapid and reliable detection of bacterial endospores in environmental samples by diagnostic electron microscopy combined with X-ray microanalysis

Diagnostic negative staining electron microscopy is a front-line method for the rapid investigation of environmental and clinical samples in emergency situations caused by bioterrorism or outbreaks of an infectious disease. Spores of anthrax are one of the diagnostic targets in case of bioterrorism, because they have been used as a bio-weapon in the past and their production and transmission are rather simple. With negative staining electron microscopy bacterial spores can be identified based on their morphology at the single cell level. However, because of their particular density, no internal structures are visible which sometimes makes it difficult to distinguish spores from particles with a similar size and shape that are frequently present in environmental samples. Spores contain a high concentration of calcium ions besides other elements, which may allow a proper discrimination of spores from other suspicious particles. To investigate this hypothesis, negative staining electron microscopy, using either transmission or scanning electron microscopes, was combined with energy dispersive X-ray microanalysis, which reveals the element content of individual nanoparticles. A peak pattern consisting of calcium, sulphur and phosphorus was found as a typical signature within the X-ray spectrum of spores in various Clostridium and Bacillus species, including all strains of anthrax (Bacillus anthracis) tested. Moreover, spores could be reliably identified by this combined approach in environmental samples, like household products, soil or various presumed bioterrorist samples. In summary, the use of X-ray spectroscopy, either directly in the transmission electron microscope, or in a correlative approach by using scanning electron microscopy, improves the emergency diagnostics of suspicious environmental samples.

Array-based transcriptional analysis of Clostridium sporogenes UC9000 during germination, cell outgrowth and vegetative life

The members of the genus Clostridium, including the spore-forming anaerobic bacteria, have a complex and strictly regulated life cycle, but very little is known about the genetic pathways involved in the different stages of their life cycle. Clostridium sporogenes, a Gram-positive bacterium usually involved in food spoilage and frequently isolated from late blowing cheese, is genetically indistinguishable from the proteolytic Clostridium botulinum. As the non-neurotoxic counterpart, it is often used as an exemplar for the toxic subtypes. In this work, we performed a microscopic study combined with a custom array-based analysis of the C. sporogenes cycle, from dormant spores to the early stationary phase. We identified a total of 211 transcripts in spores, validating the hypothesis that mRNAs are abundant in spores and the pattern of mRNA expression is strikingly different from that present in growing cells. The spore transcripts included genes responsible for different life-sustaining functions, suggesting there was transcript entrapment or basic poly-functional gene activation for future steps. In addition, 3 h after the beginning of the germination process, 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appeared to be more active in terms of gene transcription and protein synthesis than the spore, and genes coding for germination and sporulation factors seemed to be expressed at this point. These results suggest that spores are not silent entities, and a broader knowledge of the genetic pathways involved in the Clostridium life cycle could provide a better understanding of pathogenic clostridia types.

Possible overestimation of surface disinfection efficiency by assessment methods based on liquid sampling procedures as demonstrated by in situ quantification of spore viability

The standard test methods used to assess the efficiency of a disinfectant applied to surfaces are often based on counting the microbial survivors sampled in a liquid, but total cell removal from surfaces is seldom achieved. One might therefore wonder whether evaluations of microbial survivors in liquid-sampled cells are representative of the levels of survivors in whole populations. The present study was thus designed to determine the "damaged/undamaged" status induced by a peracetic acid disinfection for Bacillus atrophaeus spores deposited on glass coupons directly on this substrate and to compare it to the status of spores collected in liquid by a sampling procedure. The method utilized to assess the viability of both surface-associated and liquid-sampled spores included fluorescence labeling with a combination of Syto 61 and Chemchrome V6 dyes and quantifications by analyzing the images acquired by confocal laser scanning microscopy. The principal result of the study was that the viability of spores sampled in the liquid was found to be poorer than that of surface-associated spores. For example, after 2 min of peracetic acid disinfection, less than 17% ± 5% of viable cells were detected among liquid-sampled cells compared to 79% ± 5% or 47% ± 4%, respectively, when the viability was evaluated on the surface after or without the sampling procedure. Moreover, assessments of the survivors collected in the liquid phase, evaluated using the microscopic method and standard plate counts, were well correlated. Evaluations based on the determination of survivors among the liquid-sampled cells can thus overestimate the efficiency of surface disinfection procedures.