Bacillus Subtilis as an Excellent Microbial Treatment Agent for Environmental Pollution: A Review

The use of microorganisms in environmental biotreatment is gaining attention, particularly Bacillus subtilis (B. subtilis), recognized for its effectiveness in wastewater treatment and soil remediation. Its success stems from its diverse biological activities and adaptability, which improve environmental quality and ecological balance. This paper reviews the remediation capabilities and mechanisms of B. subtilis, focusing on its applications in water purification and soil pollution management. B. subtilis facilitates pollutant degradation and adsorption through enzyme production, organic acids, unique cell wall properties, and interactions with other microorganisms. The article addresses current challenges and future directions, emphasizing the need for enhanced cultivation, screening, and genetic engineering of functional strains. Understanding the interactions of these strains with other microorganisms and studying their ecological and toxicological impacts are essential for optimizing microbial remediation, providing both theoretical and practical foundations for bioremediation efforts.

Response surface methodology to optimize the Bacillus subtilis var. sojae semen praeparatum liquid fermentation process for the production of fibrinolytic enzyme

Previously, during the Sojae Semen Praeparatum (SSP, Dandouchi in China) concoction process, three types of fibrinolytic enzyme-producing bacteria were screened and identified: Bacillus subtilis, Stenotrophomonas maltophilia and Micrococcus. The fibrin plate approach was used to measure the fibrinolytic enzyme activity of pure fermentation broth, it was found that fibrinolytic enzyme produced by Stenotrophomonas maltophilia has the highest enzyme activity, followed by Bacillus subtilis and Micrococcus is the lowest. In this study, in order to improve enzyme activity and yield, the response surface method was used to optimize the fermentation conditions, including 6 factors such as nitrogen source, carbon source, initial pH, inoculum amount, loading volume and fermentation temperature. Then, the results showed that: the optional fermentation temperature was determined as 28 ℃, 6% inoculum amount, 30.42 h fermentation time and 20 mL of loading volume in 100 mL erlenmeyer flask. Ultimately, under optimal fermentation conditions, enzyme activity produced by Bacillus subtilis var. SSP was 360.82 IU/mL, which was an increase of 109.68% (1.10 folds) compared to before optimization.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-024-06051-8.

Regulatory Effects of RNA-Protein Interactions Revealed by Reporter Assays of Bacteria Grown on Solid Media

Reporter systems are widely used to study biomolecular interactions and processes in vivo, representing one of the basic tools used to characterize synthetic regulatory circuits. Here, we developed a method that enables the monitoring of RNA-protein interactions through a reporter system in bacteria with high temporal resolution. For this, we used a Real-Time Protein Expression Assay (RT-PEA) technology for real-time monitoring of a fluorescent reporter protein, while having bacteria growing on solid media. Experimental results were analyzed by fitting a three-variable Gompertz growth model. To validate the method, the interactions between a set of RNA sequences and the RNA-binding protein (RBP) Musashi-1 (MSI1) were evaluated, as well as the allosteric modulation of the interaction by a small molecule (oleic acid). This new approach proved to be suitable to quantitatively characterize RNA-RBP interactions, thereby expanding the toolbox to study molecular interactions in living bacteria, including allosteric modulation, with special relevance for systems that are not suitable to be studied in liquid media.

Effects of Aqua-Glycerol Uptake Facilitator Protein GlpF on Spore Germination of Bacillus subtilis

Killing spores is an important challenge for the development of the food industry. After germination, the resistance of spores disappears and they are more easily killed, which is currently the main strategy for their destruction. Therefore, study of the mechanism of spore germination is of great significance for improving methods of spore inactivation. Previous studies have shown that the hydration of the spore core region, accompanied by the disappearance of bacterial spore resistance, is a key step in the germination pathway of bacterial spores. However, the specific mechanism of this process has been studied very little. In this study, Bacillus subtilis PY79 was used as a model strain, and its single water glycerol channel protein (GlpF) was regarded as a starting point to explore the mechanism of water transport during spore germination. First, we constructed glpF mutants and overexpression strains and discovered that the deletion of glpF did not affect the growth of bacterial vegetative cells and spores. Further germination experiments on the spores of the glpF-deficient strain through detecting calcium dipicolinate and absorbance of spores showed that the germination rate of the mutant strain spores increased, while increasing the water activity did not affect the results caused by glpF deletion. Meanwhile, overexpressed glpF affected the permeability of the spore coat. Finally, when treating spores with ultra-high pressure, the spores lacking glpF were more likely to be inactivated. The above results have suggested that the glpF gene plays an important role in spore germination.

The NmpRSTU multi-component signaling system of Myxococcus xanthus regulates expression of an oxygen utilization regulon

Myxococcus xanthus has numerous two-component signaling systems (TCSs), many of which regulate the complex social behaviors of this soil bacterium. A subset of TCSs consists of NtrC-like response regulators (RRs) and their cognate histidine sensor kinases (SKs). We have previously demonstrated that a multi-component, phosphorelay TCS named NmpRSTU plays a role in M. xanthus social motility. NmpRSTU was discovered through a screen that identified mutations in nmp genes that restored Type-IV pili-dependent motility to a nonmotile strain. The Nmp pathway begins with the SK NmpU, which is predicted to be active in the presence of oxygen. NmpU phosphorylates another SK, NmpS, a hybrid kinase containing an RR domain and a HisKA-CA domain. These two kinases work in a reciprocal fashion: when NmpU is active, NmpS is inactive, and vice versa. Finally, the phosphorelay culminates in NmpS phosphorylating the NtrC-like RR NmpR. To better understand the role of NmpRSTU in M. xanthus physiology, we determined the NmpR regulon by combining in silico predictions of the NmpR consensus binding sequence with in vitro electromobility shift assays (EMSAs) and in vivo transcriptional reporters. We identified several NmpR-dependent, upregulated genes likely to be important in oxygen utilization. Additionally, we demonstrate NmpRSTU plays a role in fruiting body development, suggesting a role for oxygen sensing in this behavior. We propose that NmpRSTU senses oxygen-limiting conditions, and NmpR upregulates genes associated with optimal utilization of that oxygen. This may be necessary for M. xanthus physiology and behaviors in the highly dynamic soil where oxygen concentrations vary dramatically.

IMPORTANCE

Bacteria use two-component signaling systems (TCSs) to respond to a multitude of environmental signals and subsequently regulate complex cellular physiology and behaviors. Myxococcus xanthus is a ubiquitous soil bacterium that encodes numerous two-component systems to respond to the conditions of its soil environment and coordinate multicellular behaviors such as coordinated motility, microbial predation, fruiting body development, and sporulation. To better understand how this bacterium uses a two-component system that has been linked to the sensing of oxygen concentrations, NmpRSTU, we determined the gene regulatory network of this system. We identified several genes regulated by NmpR that are likely important in oxygen utilization and for the M. xanthus response to varied oxygen concentrations in the dynamic soil environment.

Recent progress in proteins regulating the germination of Bacillus subtilis spores

Bacterial spores can remain dormant for years, but they maintain the ability to recommence life through a process termed germination. Although spore germination has been reviewed many times, recent work has provided novel conceptual and molecular understandings of this important process. By using Bacillus subtilis as a model organism, here we thoroughly describe the signal transduction pathway and events that lead to spore germination, incorporating the latest findings on transcription and translation that are likely detected during germination. Then, we comprehensively review the proteins associated with germination and their respective functions. Notably, the typical germinant receptor GerA and the SpoVAF/FigP complex have been newly established as channels for ions release at early stage of germination. Moreover, given that germination is also affected by spore quality, such as molecular cargo, we collect the data about the proteins regulating sporulation to affect spore quality. Specifically, RocG-mediated glutamate catabolism during sporulation to ensure spore quality; GerE-regulated coat protein expression, and CotH-modified coat protein by phosphorylation to ensure normal coat assembly; and RNase Y-degraded RNA in newly released spores to promote dormancy. The latest progress in our understanding of these germination proteins provides valuable insights into the mechanism underlying germination.

Newly identified SpoVAF/FigP complex: the role in Bacillus subtilis spore germination at moderate high pressure and influencing factors

The SpoVAF/FigP complex, a newly identified dormant spore ion channel, has been shown to amplify the response of germinant receptors (GRs) to nutrient germinants. However, its contribution to high-pressure-induced germination remains unexplored. In this study, we discovered that the 5AF/FigP complex played an important role in the GR-dependent germination of Bacillus subtilis spores under moderate high pressure (MHP) by facilitating the release of ions, such as potassium (K+), a mechanism in parallel with its role in nutrient-induced germination. Despite its predicted function as an ion channel, the 5AF/FigP complex failed to be activated by MHP in the absence of GerA-type GRs. We quantitatively examined the factors that influence the 5AF/FigP complex's function in MHP-induced germination using modeling and fitting techniques. Our results indicated that the complex's amplification effect was both enhanced and accelerated as pressure levels increase from 50 to 200 MPa. However, raising the MHP treatment temperature from 22°C to 30°C only speeded up the complex's function without enhancing its effectiveness. Moreover, extreme conditions of higher pressure (300 MPa) and temperature (34°C-37°C) could diminish the complex's functionality. Additionally, the amplification effect was weakened in spores produced at both elevated and reduced sporulation temperatures. Taken together, our findings highlight the essential role of the 5AF/FigP complex in boosting the efficiency of MHP-induced germination. This revelation has enriched our understanding of the intricate mechanisms underlying GR-dependent germination in Bacillus spores, offering valuable insights that can be utilized to refine the germination-inactivation strategies within the food industry.

IMPORTANCE

High-pressure-induced spore germination has been discovered for more than half a century, but the signal transduction pathway of the process still needs to be refined. In this study, for the first time, we revealed the role of the newly identified SpoVAF/FigP complex in high-pressure-induced spore germination, as well as the factors influencing its function in this process. The new findings in this work not only enhance the theoretical understanding of spore germination mechanisms under high pressure but also pave the way for developing novel strategies to inactivate spores during high-pressure food processing, a technology that is gaining popularity in the food industry as a promising non-thermal preservation method.

Effect of environmental stress factors on the expression of virulence genes and pathogenicity of lethal Bacillus cereus of bovine origin

Objective

Bacillus cereus (B. cereus) can be used as a probiotic or produce a variety of toxins that are pathogenic to humans and animals. Environmental stressors can affect the growth process of B. cereus and the expression of its virulence genes. Due to the limitations of methods such as pharmacological disinfection methods (there are limits to the use of antibiotics) and chemical disinfection methods (chemical methods may produce residues), attempts can be made to remove and reduce B. cereus infections through environmental stress factors.

Methods

In this study, the expression of four virulence genes (nheA, hblD, cytK, and entFM) of bovine-origin lethal B. cereus was investigated by qPCR under the effect of different environmental stressors. The extent of pathological damage to various organs of mice by B. cereus was observed by pathological sections.

Results

The results showed that high temperature could inhibit the expression of B. cereus virulence genes. Expression of B. cereus virulence genes was affected under the influence of pH. Different salt concentrations could make the B. cereus virulence genes show low expression. Under a single environmental stressors, nheA, hblD, cytK, and entFM had the lowest expression at 40°C, pH 8.0, and were lowly expressed at all salt concentrations except the control group. The action of multiple environmental stressors affect the expression of virulence genes. Under multiple environmental stressors, nheA, hblD and cytK were least expressed at a temperature of 40°C, pH 6.0, and salt concentration of 3.0%, and entFM was least expressed at a temperature of 20°C, pH 8.0, and salt concentration of 1.5%. Animal pathogenicity tests have shown that environmental stressors affect the virulence of B. cereus.

Conclusion

The level of virulence gene expression in B. cereus can be reduced by environmental stress factors, thus further reducing the risk of B. cereus to human health. This study provides some reference for the prevention and control of B. cereus disease.

Variation in heat resistance and biofilm formation of Bacillus cereus spores in various fermented soybean foods

This study investigated the heat resistance of Bacillus cereus spores (as well as spores in intact biofilm) in two types of Korean fermented soybean foods and presumed the potential key parameters (physicochemical and nutritional properties) associated with their heat resistance. For example, the D100°C-values of B. cereus ATCC 10987 and CH3 spores with strong heat resistance and prolific biofilm-forming capability were compared in various Jjigae-type (Cheonggukjang jjigae, Doenjang jjigae, and Gochujang jjigae) and Jang-type (Cheonggukjang, Doenjang, and Gochujang) foods commonly consumed in Korea. The D100°C-values of planktonic spores were significantly different depending on the type of food, that is, Jang and Jjigae. Compared with Jjigae-type foods, a higher heat resistance of B. cereus spores was found in Jang-type foods (particularly Doenjang and Gochujang) with low water activity and high salinity. In Jjigae-type foods, spore heat resistance showed a positive correlation with the pH of Jjigaes, indicating that an acidic environment weakens the spores. A negative correlation between the total fat content and spore heat resistance was found in Jjigae-type foods but not in Jang-type foods. Meanwhile, regarding the heat resistance of B. cereus spores in intact biofilm, the D100°C-values were significantly higher (up to 6.5-fold) than those of planktonic spores in all Jjigae-type foods. The slightly acidic pH and amount of carbohydrates are likely related to the large formation of extracellular polymeric substances and strong heat resistance of B. cereus spores in biofilm. This study may provide a comprehensive understanding of the relationship between the key parameters of foods and heat resistance of B. cereus spores with or without intact biofilm and methods to control their risks in different types of fermented soybean foods.

Optimization of the Cryoprotectants for Direct Vat Set Starters in Sichuan Paocai Using Response Surface Methodology

The quality of Sichuan paocai in natural fermentation is often inconsistent due to the complexity of its microbial community and environmental influences. To address this, dominant microbial strains were selectively inoculated to improve the product's quality and safety. However, vacuum freeze-drying, commonly used to prepare direct vat set (DVS) starters, can significantly damage strains due to freezing stress. This study aimed to optimize a freeze-drying protection system for Lactiplantibacillus plantarum and Bacillus subtilis to enhance their survival. Using response surface methodology, combinations of cryoprotectants were evaluated. A formulation comprising skim milk powder, glycerol, sucrose, and L-proline significantly improved strain viability after lyophilization, outperforming single cryoprotectants. Further investigation into storage conditions revealed that low temperatures (-20 °C) provided the best preservation for DVS starters. Furthermore, the optimized DVS starters demonstrated excellent fermentation performance in Sichuan paocai, enhancing its color, flavor, and sensory quality compared to natural fermentation. These findings offer a reliable freeze-drying protection strategy for survival and viability of L. plantarum and B. subtilis.

Applying machine learning and genetic algorithms accelerated for optimizing ethanol production

Corn straws can produce bioethanol via simultaneous saccharification and co-fermentation (SSCF). However, identifying optimal combinations of operating parameters from numerous possibilities through a cost-effective strategy to improve SSCF efficiency and yield remains challenging. The eXtreme Gradient Boost (XGB) and deep neural network (DNN) models were constructed to accurately predict ethanol yield from only five input variables, achieving >83 % accuracy. Subsequently, the XGB and the DNN models were merged with the genetic algorithm (GA) as the new optimization strategies. Experimental validation showed that the new strategy optimize the efficiency and yield of the SSCF ethanol production system quickly and accurately. Moreover, the potential optimization mechanism was investigated through the comprehensive interpretability analysis for XGB and the microbial ecology analysis. Enzyme Solution Volume (61.7 %) dominated, followed by time (12.9 %), substrate concentration (10.4 %), temperature (7.7 %), and inoculum volume (7.3 %). This efficient and accurate algorithm design strategy can significantly reduce the time required to optimize biochemical systems.

Training in modern statistical methodologies and software tools for the definition and analysis of (stochastic) quantitative microbial risk assessment models with relevant food products for the Italian and Spanish food supply chains

The fellowship, entitled 'Training in modern statistical methodologies and software tools for the definition and analysis of (stochastic) quantitative microbial risk assessment models with relevant food products for the Italian and Spanish food supply chains', was implemented at the Universidad Politécnica de Cartagena (UPCT), Spain. Supervised by Dr. Alberto Garre and Prof. Pablo S. Fernandez and coordinated by Dr. Virginia Filipello of the Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Italy, the fellowship aimed to provide hands-on training in quantitative microbial risk assessment (QMRA). The fellow benefited from UPCT's expertise in microbiological risk assessment, gaining knowledge of methodologies, terminologies and software tools essential for QMRA. The focus of the fellowship was on the risks associated with plant-based milk products, which are increasingly popular as sustainable alternatives to dairy milk. Despite the heat treatments these beverages undergo to ensure safety, risks persist, such as cross-contamination during post-processing or the survival of heat-resistant spores like Bacillus cereus. A recent European outbreak linked to contaminated oat milk underscored the importance of assessing these risks. The project was conducted in two phases: first, at UPCT's Food Microbiology Laboratory, where the fellow handled and characterised the thermal resistance of various B. cereus strains using a thermoresistometer; and second, through remote analysis of experimental data using risk analysis software tools. The fellow developed skills in microbiological techniques, such as spore preparation and thermal resistance evaluation, and became proficient in data analysis using the R programming language and the biorisk package. The fellowship culminated in the development of a QMRA model to estimate the likelihood of B. cereus-related foodborne illness from plant-based milks, considering different heat treatments and bacterial strains. The fellow's training covered all stages of risk assessment, including hazard identification, exposure assessment, hazard characterisation and risk characterisation, providing a comprehensive foundation for a career in food safety and microbial risk assessment.

Role of water activity on sporulation traits and resistance to 915 MHz microwave in the emetic type of Bacillus cereus on rice

The objective of this study is to investigate the influence of water activity on the sporulation of emetic strains of Bacillus cereus and the subsequent susceptibility of sporulated B. cereus to 915 MHz microwave treatment. Water activity levels were manipulated in the sporulation medium by adjusting glycerol concentrations to 0 %, 3 %, 7.5 %, and 10 %, resulting in corresponding water activities of 0.996, 0.981, 0.971, and 0.960, respectively and sporulated at 30℃. These changes in water activity were intended to simulate the variations in water activity that can occur during the cultivation and processing of rice, where B. cereus is commonly found. Sporulation rates increased with higher water activity, achieving over 90 % of total cells after 3, 5, 5, and 6 days of incubation at water activities of 0.996, 0.981, 0.971, and 0.960, respectively. Resistance to microwave treatment increased with higher water activity levels during sporulation. Microwave treatment for 5 min yielded a reduction of 3.03 log CFU/g at a water activity of 0.960 and 1.98 log CFU/g at 0.996 during sporulation. Lower water activity led to higher % dipicolinic acid (DPA) release during microwave treatment, as measured using a spectrometer, indicating greater membrane damage. To investigate the morphology of spores, transmission electron microscopy was used. Spores produced at lower water activity levels were observed to be enveloped by the mother cell, whereas those sporulated at higher water activity levels were distinct from the mother cell. Additionally, spores sporulated at higher water activity levels exhibited higher wet density in Percoll gradient. The levels of germination were also compared after sporulation under different water activity medium using L-alanine. The spores evolved under low water activity exhibited higher germination level compared to those from high water activity conditions. These findings suggested that water activity conditions during sporulation induce variations in morphology, density, germination level, and resistance to 915 MHz microwave. Our experimental results indicated that, even with the same sporulation percentage, there can be differences in the maturation stage, indicating that the level of 915 MHz microwave treatment should be adjusted according to the sporulation conditions of B. cereus.

Monitoring of Bacillus spore-forming dynamics through flow cytometry

The plate counting method is a traditional and widely accepted technique for live cell counting, often employed for Bacillus enumeration and spore forming rate calculations. However, this method requires at least 12 h to generate results, making it unsuitable for real-time monitoring of bacterial growth status and spore transformation rate. Bacillus thuringiensis crystals, produced during sporulation, are widely used as microbial pesticides, with high demand for industrial scale production. Variations in cultivation conditions and harvest timing during large-scale pore production of Bacillus thuringiensis significantly affect spore forming rate, impacting crystallization yield. Nevertheless, there is a lack of real-time monitoring methods for spore conversion rate. Flow cytometry (FCM), a well-established technique for single-cell analysis in eukaryotic cells, has been successfully applied in bacterial detection in environmental and food samples. In this study, we introduced a rapid flow cytometry-based method for determining spore forming rate of Bacillus thuringiensis, with two nucleic acid dyes, SYTO24 and LDS751. The method enables dynamic monitoring of spore, vegetative cell, and viable but non-culturable/dead cell proportions during the whole cultivation process, and spore forming rate could be gained within 30 min. Data of spore forming rate by FCM method is consistent with that by plate counting method, offering a faster and more efficient approach for assessing sporulation status in industrial Bacillus thuringiensis microbial pesticide production.

Influence of Sporulation Temperature on Germination and Growth of B. weihenstephanensis Strains in Specific Nutrients and in an Extended Shelf-Life Refrigerated Matrix Under Commercial Pasteurization and Storage Conditions

Extended shelf-life (ESL) refrigerated ready-to-eat foods are thermally pasteurized to ensure food safety and stability. However, surviving psychrotrophic Bacillus cereus spores can still pose a challenge. Studies predicting their behavior often overlook sporulation conditions. This study investigated the effect of sporulation temperature on germination of three Bacillus weihenstephanensis strains in specific nutrients (inosine and/or amino acids) with or without prior heat activation (80 °C, 10 min). Sporulation temperature variably affected germination, with stronger effects in moderately responsive strains and nutrients. Heat activation strongly stimulated germination, particularly in nutrients with poorer responses, mitigating differences induced by sporulation temperature. The influence of sporulation temperature on germination and growth in an ESL matrix at refrigeration temperatures (4 °C or 8 °C) in vacuum packaging after heat activation or commercial pasteurization (90 °C, 10 min) was also studied. The latter treatment increased germination rates of surviving spores; however, some strains suffered damage and lost viability upon germination at 4 °C but recovered and grew at 8 °C. These findings highlight the need to account for variability in spore recovery and outgrowth during quantitative risk assessments for psychrotrophic B. cereus in ESL foods.

Complex sporulation-specific expression of transcription termination factor Rho highlights its involvement in Bacillus subtilis cell differentiation

Termination factor Rho, responsible for the main factor-dependent pathway of transcription termination and the major inhibitor of antisense transcription, is an emerging regulator of various physiological processes in microorganisms. In Gram-positive bacterium Bacillus subtilis, Rho is involved in the control of cell adaptation to starvation and, in particular, in the control of sporulation, a complex differentiation program leading to the formation of a highly resistant dormant spore. While the initiation of sporulation requires a decrease in Rho protein levels during the transition to stationary phase, the mechanisms regulating the expression of rho gene throughout the cell cycle remain largely unknown. Here we show that a drop in the activity of the vegetative SigA-dependent rho promoter causes the inhibition of rho expression in stationary phase. However, after the initiation of sporulation, rho gene is specifically reactivated in two compartments of the sporulating cell using distinct mechanisms. In the mother cell, rho expression occurs by read-through transcription initiated at the SigH-dependent promoter of the distal spo0F gene. In the forespore, rho gene is transcribed from the intrinsic promoter recognized by the alternative sigma factor SigF. These regulatory elements ensure the activity of Rho during sporulation, which appears important for the proper formation of spores. We provide experimental evidence that disruption of the spatiotemporal expression of rho during sporulation affects the resistance properties of spores, their morphology, and the ability to return to vegetative growth under favorable growth conditions.

The megaplasmid pCER270 of Bacillus cereus emetic strain affects the timing of the sporulation process, spore resistance properties, and germination

The Bacillus cereus group includes closely related spore-forming Gram-positive bacteria. In this group, plasmids play a crucial role in species differentiation and are essential for pathogenesis and adaptation to ecological niches. The B. cereus emetic strains are characterized by the presence of the pCER270 megaplasmid, which encodes the non-ribosomal peptide synthetase for the production of cereulide, the emetic toxin. This plasmid carries several genes that may be involved in the sporulation process. Furthermore, a transcriptomic analysis has revealed that pCER270 influences the expression of chromosome genes, particularly under sporulation conditions. In this study, we investigated the role of pCER270 on spore properties in different species of the B. cereus group. We showed that pCER270 plays a role in spore wet heat resistance and germination, with varying degrees of impact depending on the genetic background. In addition, pCER270 ensures that sporulation occurs at the appropriate time by delaying the expression of sporulation genes. This regulation of sporulation timing is controlled by the pCER270-borne Rap-Phr system, which likely regulates the phosphorylation state of Spo0A. Acquisition of the pCER270 plasmid by new strains could give them an advantage in adapting to new environments and lead to the emergence of new pathogenic strains.

IMPORTANCE

The acquisition of new mobile genetic elements, such as plasmids, is essential for the pathogenesis and adaptation of bacteria belonging to the Bacillus cereus group. This can confer new phenotypic traits and beneficial functions that enable bacteria to adapt to changing environments and colonize new ecological niches. Emetic B. cereus strains cause food poisoning linked to the production of cereulide, the emetic toxin whose synthesis is due to the presence of plasmid pCER270. In the environment, cereulide provides a competitive advantage in producing bacteria against various competitors or predators. This study demonstrates that pCER270 also regulates the sporulation process, resulting in spores with improved heat resistance and germination capacity. The transfer of plasmid pCER270 among different strains of the B. cereus group may enhance their adaptation to new environments. This raises the question of the emergence of new pathogenic strains, which could pose a serious threat to human health.

Alanine and glutamate catabolism collaborate to ensure the success of Bacillus subtilis sporulation

Sporulation as a typical bacterial differentiation process has been studied for decades. However, two crucial aspects of sporulation, (i) the energy sources supporting the process, and (ii) the maintenance of spore dormancy throughout sporulation, are scarcely explored. Here, we reported the crucial role of RocG-mediated glutamate catabolism in regulating mother cell lysis, a critical step for sporulation completion of Bacillus subtilis, likely by providing energy metabolite ATP. Notably, rocG overexpression resulted in an excessive ATP accumulation in sporulating cells, leading to adverse effects on future spore properties, e.g. increased germination efficiency, reduced DPA content, and lowered heat resistance. Additionally, we revealed that Ald-mediated alanine metabolism was highly related to the inhibition of premature germination and the maintenance of spore dormancy during sporulation, which might be achieved by decreasing the typical germinant L-alanine concentration in sporulating environment. Our data inferred that sporulation of B. subtilis was a highly orchestrated biological process requiring a delicate balance in diverse metabolic pathways, hence ensuring both the completion of sporulation and production of high-quality spores.

Potential risk of biofilm-forming Bacillus cereus group in fresh-cut lettuce production chain

Bacillus cereus and Bacillus thuringiensis, which belong to the B. cereus group, are widely distributed in nature and can cause food poisoning symptoms. In this study, we collected 131 isolates belonging to the B. cereus group, comprising 124B. cereus and seven B. thuringiensis isolates, from fresh-cut lettuce production chain and investigated their potential risk by analyzing genotypic (enterotoxin and emetic toxin gene profiles) and phenotypic (antibiotic susceptibility, sporulation, and biofilm formation) characteristics. Enterotoxin genes were present only in B. cereus, whereas the emetic toxin gene was not detected in any of the B. cereus isolates. All isolates were susceptible to vancomycin, which is a last resort for treating B. cereus group infection symptoms, but generally resistant to β-lactam antimicrobials, and had the ability to form spores (at an average sporulation rate of 24.6 %) and biofilms at 30 °C. Isolates that formed strong biofilms at 30 °C had a superior possibility of forming a dense biofilm by proliferating at 10 °C compared to other isolates. Additionally, confocal laser scanning microscopy (CLSM) images revealed a notable presence of spores within the submerged biofilm formed at 10 °C, and the strengthened attachment of biofilm inner cells to the substrate was further revealed through biofilm structure parameters analysis. Collectively, our study revealed the prevalence and contamination levels of B. cereus and B. thuringiensis at fresh-cut lettuce production chain and investigated their genotypic and phenotypic characteristics, aiming to provide valuable insights for the development of potential risk management strategies to ensure food safety, especially along the cold chain.

Pilot-scale production of Bacillus subtilis MSCL 897 spore biomass and antifungal secondary metabolites in a low-cost medium

OBJECTIVES

Bacillus subtilis is a plant growth promoting bacterium (PGPB) that acts as a microbial fertilizer and biocontrol agent, providing benefits such as boosting crop productivity and improving nutrient content. It is able to produce secondary metabolites and endospores simultaneously, enhancing its ability to survive in unfavorable conditions and eliminate competing microorganisms. Optimizing cultivation methods to produce B. subtilis MSCL 897 spores on an industrial scale, requires a suitable medium, typically made from food industry by-products, and optimal temperature and pH levels to achieve high vegetative cell and spore densities with maximum productivity.

RESULTS

This research demonstrates successful pilot-scale (100 L bioreactor) production of a biocontrol agent B. subtilis with good spore yields (1.5 × 109 spores mL-1) and a high degree of sporulation (>80%) using a low-cost cultivation medium. Culture samples showed excellent antifungal activity (1.6-2.3 cm) against several phytopathogenic fungi. An improved methodology for inoculum preparation was investigated to ensure an optimal seed culture state prior to inoculation, promoting process batch-to-batch repeatability. Increasing the molasses concentration in the medium and operating the process in fed-batch mode with additional molasses feed, did not improve the overall spore yield, hence, process operation in batch mode with 10 g molasses L-1 is preferred. Results also showed that the product quality was not significantly impacted for up to 12 months of storage at room temperature.

CONCLUSION

An economically-feasible process for B. subtilis-based biocontrol agent production was successfully developed at the pilot scale.

Regulation of late-acting operons by three transcription factors and a CRISPR-Cas component during Myxococcus xanthus development

Upon starvation, rod-shaped Myxococcus xanthus bacteria form mounds and then differentiate into round, stress-resistant spores. Little is known about the regulation of late-acting operons important for spore formation. C-signaling has been proposed to activate FruA, which binds DNA cooperatively with MrpC to stimulate transcription of developmental genes. We report that this model can explain regulation of the fadIJ operon involved in spore metabolism, but not that of the spore coat biogenesis operons exoA-I, exoL-P, and nfsA-H. Rather, a mutation in fruA increased the transcript levels from these operons early in development, suggesting negative regulation by FruA, and a mutation in mrpC affected transcript levels from each operon differently. FruA bound to all four promoter regions in vitro, but strikingly each promoter region was unique in terms of whether or not MrpC and/or the DNA-binding domain of Nla6 bound, and in terms of cooperative binding. Furthermore, the DevI component of a CRISPR-Cas system is a negative regulator of all four operons, based on transcript measurements. Our results demonstrate complex regulation of sporulation genes by three transcription factors and a CRISPR-Cas component, which we propose produces spores suited to withstand starvation and environmental insults.

Impact of sporulation temperature on germination of Bacillus subtilis spores under optimal and adverse environmental conditions

Bacillus subtilis spores are important food spoilage agents and are occasionally involved in food poisoning. In foods that are not processed with intense heat, such bacterial spores are controlled by a combination of different hurdles, such as refrigeration, acidification, and low water activity (aw), which inhibit or delay germination and/or growth. Sporulation temperature has long been regarded as a relevant factor for the assessment of germination in chemically defined media, but little is known about its impact on food preservation environments. In this study, we compared germination dynamics of B. subtilis spores produced at optimal temperature (37 °C) with others incubated at suboptimal (20 °C) and supraoptimal (43 °C) temperatures in a variety of nutrients (rich-growth medium, L-alanine, L-valine, and AGFK) under optimal conditions as well as under food-related stresses (low aw, pH, and temperature). Spores produced at 20 °C had a lower germination rate and efficiency than those incubated at 37 °C in all the nutrients, while those sporulated at 43 °C displayed a higher germination rate and/or efficiency in response to rich-growth medium and mostly to L-alanine and AGFK under optimal environmental conditions. However, differences in germination induced by changes in sporulation temperature decreased when spores were activated by heat, mainly due to the greater benefit of heat for spores produced at 20 °C and 37 °C than at 43 °C, especially in AGFK. Non-heat-activated spores produced at 43 °C still displayed superior germination fitness under certain stresses that had considerably impaired the germination of the other two populations, such as reduced temperature and aw. Moreover, they presented lower temperature and pH boundaries for the inhibition of germination in rich-growth medium, while requiring a higher NaCl concentration threshold compared to spores obtained at optimal and suboptimal temperature. Sporulation temperature is therefore a relevant source of variability in spore germination that should be taken into account for the accurate prediction of spore behaviour under variable food preservation conditions with the aim of improving food safety and stability.

Transcriptomics integrated with metabolomics reveal the competitive relationship between co-cultured Trichoderma asperellum HG1 and Bacillus subtilis Tpb55

Microbial co-culture has proven to be an effective way to improve the ability of microorganisms to biocontrol. However, the interactive mechanisms of co-cultural microbes, especially between fungi and bacteria, have rarely been studied. By comparative analysis of morphology, transcriptomics and metabolomics, the interactive mechanisms of a sequential co-culture system of Trichoderma asperellum HG1 and Bacillus subtilis Tpb55 was explored in this study. The results revealed that co- culture has no significant effect on the growth and cell morphology of the two strains, but lead to mycelium wrinkling of HG1. RNA-seq analysis showed that co-culture significantly upregulated the HG1 genes concerning amino acid degradation and metabolism, proteolysis, resisting environmental stress, cell homeostasis, glycolysis, the glyoxylate cycle, and the citric acid (TCA) cycle, while Tpb55 genes related to cell homeostasis, spore formation and membrane fluidization were significantly upregulated, but genes associating to TCA, glycolytic cycles and fatty acid β-oxidation were significantly downregulated. Metabolomic results revealed that some amino acids related to energy metabolism were significantly altered in HG1, whereas palmitic acid, which is related to cell membrane functions, was upregulated in Tpb55. These results indicated that HG1 could interfere with carbon metabolism and cell membrane fluidity, but accelerate spore formation of Tpb55. Biophysical assays further convinced that co-culture could decrease ATP content and inhibit ATPase activity in HG1, and could promote spore formation and reduce the cell membrane fluidity of Tpb55. In addition, co-culture also accelerated the production of intracellular anti-oomycete compound octhilinone. The above results indicate that HG1 and Tpb55 are mainly in a competitive relationship in the co culture system. These findings provide new insights for understanding the interaction mechanism between co cultured microbes.

Mechanism of deltamethrin biodegradation by Brevibacillus parabrevis BCP-09 with proteomic methods

Ester-containing deltamethrin pesticides are widely used in farmland and have inevitable side effects on the biosphere and human health. Microbia have been used for efficient degradation of deltamethrin, but the related mechanism and enzyme characteristics have not been elucidated. In this study, a species Brevibacillus parabrevis BCP-09 could degrade up to 75 mg L-1 deltamethrin with a degradation efficiency of 95.41%. Proteomic and genomic methods were used to explore its degradation mechanism. Enzymes belonged to hydrolases, oxidases and aromatic compound degrading enzymes were expressed enhanced and might participate in the deltamethrin degradtion. RT-PCR experiment and enzyme activity analysis verified the degradation of deltamethrin by bacterial protein. Additionally, the formation of endospores can help strain BCP-09 resist the toxicity of deltamethrin and enhance its degradation. This study supplies a scientific evidence for the application of Brevibacillus parabrevis BCP-09 in the bioremediation of environmental pollution and enriches the resources of deltamethrin-biodegradable proteins.

Effects of spore purity on the wet heat resistance of Clostridium perfringens, Bacillus cereus and Bacillus subtilis spores

Heat resistance of spores of Clostridium perfringens 8238 (Hobbs Serotype 2), Bacillus cereus NCTC 11143 (4810/72), and Bacillus subtilis PS533, an isogenic derivative of strain PS832 (a 168 strain) was determined in ground beef at 95 °C. Spore purification was by centrifugation and washing with sterile distilled water (dH2O), followed by sonication and then Histodenz centrifugation for B. subtilis and C. perfringens, and centrifugation and washing with sterile dH2O followed by Histodenz centrifugation for B. cereus. Bags containing inoculated beef samples were submerged in a temperature-controlled water bath and held at 95 °C for predetermined lengths of time. Surviving spore populations were enumerated by plating on mannitol egg yolk polymyxin agar (MYP) agar plates for B. cereus and B. subtilis, and on tryptose-sulfite-cycloserine agar (TSC) agar plates for C. perfringens. Survivor curves were fitted to linear, linear with tail, and Weibull models using the USDA Integrated Pathogen Modeling Program (IPMP) 2013 software. The Weibull model provided a relatively better fit to the data since the root mean square error (RMSE), mean square error (MSE), sum of squared errors (SSE), and Akaike information criterion (AIC) values were lower than the values obtained using the linear or the linear with tail models. Additionally, the Weibull model accurately predicted the observed D-values at 95 °C for the three spore-formers since the accuracy factor (Af) values ranged from 1.03 to 1.08 and the bias factor (Bf) values were either 1.00 or 1.01. Times at 95 °C to achieve a 3-log reduction decreased from 206 min for C. perfringens spores purified with water washes alone to 191 min with water washes followed by sonication and Histodenz centrifugation, from 7.9 min for B. cereus spores purified with water washes alone to 1.4 min with water washes followed by Histodenz centrifugation, and from 20.6 min for B. subtilis spores purified with water washes alone to 6.7 min for water washes followed by sonication and Histodenz centrifugation. Thermal-death-time values reported in this study will assist food processors to design thermal processes to guard against bacterial spores in cooked foods. In addition, clearly spore purity is an additional factor in spore wet heat resistance, although the cause of this effect is not clear.

Selective purification and rapid quantitative detection of spores using a "stepped" magnetic flow device

A study on the inactivation and germination mechanism of spores is very important in the application of spores, as such high-purity spores are the basis of related research. However, spores and vegetative cells of bacteria often coexist, and it is difficult to separate them. In this study, a magnetic flow device for the purification of spores in the culture medium system was developed based on a "stepped" structure with a magnetic force that could absorb vegetative cells with magnetic nanoparticles. The operation process was as follows: first, vancomycin functionalized nanoparticles were used to prepare Van-Fe3O4 NPs, which were then combined with vegetative cells to form a magnetic conjugate. Subsequently, the magnetic conjugate (vegetative cells) flowed through the "stepped" magnetic flow device and was adsorbed. Meanwhile, the spores moved through the channel and were collected. The achieved purity of the collected spores was more than 95%. Further, the number of the obtained spores was quickly quantified using Raman spectroscopy. The entire purification and quantitative process can be completed within 30 min and the limit of detection was 5 CFU mL-1. This study showed outstanding spore purification ability and provided a new method for purification and rapid quantitative detection of spores.

Arabinose Plays an Important Role in Regulating the Growth and Sporulation of Bacillus subtilis NCD-2

A microbial fungicide developed from Bacillus subtilis NCD-2 has been registered for suppressing verticillium wilt in crops in China. Spores are the main ingredient of this fungicide and play a crucial role in suppressing plant disease. Therefore, increasing the number of spores of strain NCD-2 during fermentation is important for reducing the cost of the fungicide. In this study, five kinds of carbon sources were found to promote the metabolism of strain NCD-2 revealed via Biolog Phenotype MicroArray (PM) technology. L-arabinose showed the strongest ability to promote the growth and sporulation of strain NCD-2. L-arabinose increased the bacterial concentration and the sporulation efficiency of strain NCD-2 by 2.04 times and 1.99 times compared with D-glucose, respectively. Moreover, L-arabinose significantly decreased the autolysis of strain NCD-2. Genes associated with arabinose metabolism, sporulation, spore resistance to heat, and spore coat formation were significantly up-regulated, and genes associated with sporulation-delaying protein were significantly down-regulated under L-arabinose treatment. The deletion of msmX, which is involved in arabinose transport in the Bacillus genus, decreased growth and sporulation by 53.71% and 86.46% compared with wild-type strain NCD-2, respectively. Complementing the mutant strain by importing an intact msmX gene restored the strain's growth and sporulation.

A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Microorganisms are ubiquitously distributed in nature and usually appear as biofilms attached to a variety of surfaces. Here, we report the development of a thick biofilm in the drain pipe of several standard laboratory ice machines, and we describe and characterise, through culture-dependent and -independent techniques, the composition of this oligotrophic microbial community. By using culturomics, 25 different microbial strains were isolated and taxonomically identified. The 16S rRNA high-throughput sequencing analysis revealed that Bacteroidota and Proteobacteria were the most abundant bacterial phyla in the sample, followed by Acidobacteriota and Planctomycetota, while ITS high-throughput sequencing uncovered the fungal community was clearly dominated by the presence of a yet-unidentified genus from the Didymellaceae family. Alpha and beta diversity comparisons of the ice machine microbial community against that of other similar cold oligotrophic and/or artificial environments revealed a low similarity between samples, highlighting the ice machine could be considered a cold and oligotrophic niche with a unique selective pressure for colonisation of particular microorganisms. The recovery and analysis of high-quality metagenome-assembled genomes (MAGs) yielded a strikingly high rate of new species. The functional profiling of the metagenome sequences uncovered the presence of proteins involved in extracellular polymeric substance (EPS) and fimbriae biosynthesis and also allowed us to detect the key proteins involved in the cold adaptation mechanisms and oligotrophic metabolic pathways. The metabolic functions in the recovered MAGs confirmed that all MAGs have the genes involved in psychrophilic protein biosynthesis. In addition, the highest number of genes for EPS biosynthesis was presented in MAGs associated with the genus Sphingomonas, which was also recovered by culture-based method. Further, the MAGs with the highest potential gene number for oligotrophic protein production were closely affiliated with the genera Chryseoglobus and Mycobacterium. Our results reveal the surprising potential of a cold oligotrophic microecosystem within a machine as a source of new microbial taxa and provide the scientific community with clues about which microorganisms are able to colonise this ecological niche and what physiological mechanisms they develop. These results pave the way to understand how and why certain microorganisms can colonise similar anthropogenic environments.

Comparative study on the impact of equally stressful environmental sporulation conditions on thermal inactivation kinetics of B. subtilis spores

Control of bacterial spores continues to be one of the main challenges for the food industry due to their wide dissemination and extremely high resistance to processing methods. Furthermore, the large variability in heat resistance in spores that contaminate foods makes it difficult to establish general processing conditions. Such heterogeneity not only derives from inherent differences among species and strains, but also from differences in sporulation environments that are generally ignored in spores encountered in foods. We evaluated heat inactivation kinetics and the thermodependency of resistance parameters in B. subtilis 168 spores sporulated at adverse temperatures, water activity (aw), and pH, applying an experimental approach that allowed us to quantitatively compare the impact of each condition. Reduction of incubation temperature from the optimal temperature dramatically reduced thermal resistance, and it was the most influential factor, especially at the highest treatment temperatures. These spores were also more sensitive to chemicals presumably acting in the inner membrane. Reducing sporulation aw increased heat resistance, although the magnitude of that effect depended on the solute and the treatment temperature. Thus, changes in sporulation environments varied 3D100°C values up to 10.4-fold and z values up to 1.7-fold, highlighting the relevance of taking such a source of variability into account when setting heat processing conditions. UV-C treatment and sodium hypochlorite efficiently inactivated all spore populations, including heat-resistant ones produced at low aw.

The fermented product of high-yield surfactin strain Bacillus subtilis LYS1 improves the growth performance and intestinal villi morphology in broilers

This study aimed to select Bacillus spp. for surfactin production by solid-state fermentation and to investigate the physiochemical characterizations of the fermented product (FP) and its effect on growth performance, carcass trait, intestinal morphology, and clinical blood biochemistry of broilers. Accordingly, the correlations between the functional components of FP and the growth performance of broilers are elucidated. Four hundred eighty 1-day-old Ross 308 broiler chicks were randomly assigned to dietary supplementation of 2.5% fish meal, 2.5% unfermented product, or 2.5% FP produced by Bacillus subtilis LYS1 (LYS1), Bacillus amyloliquefaciens Da16, B. subtilis Lo6 (Lo6), B. subtilis NSN7, B. subtilis subsp. natto N21, or B. subtilis N12. Each treatment had 6 replicates. The experimental period was 5 wk. Results showed that the Lo6 showed the highest protease activity among all fermented groups. The LYS1 showed the highest surfactin yields (10.69 mg/g) among all fermented groups (P < 0.05). The weight gain (WG), feed conversion ratio (FCR), and production efficiency factor (PEF) of LYS1 group were significantly better than unfermented group at 0 to 3 and 0 to 5-wk-old (P < 0.05). The Bacillus-like counts and surfactin content of FP were moderately correlated to WG (0.7 > r > 0.3), FCR (-0.3 > r > -0.7), and PEF (0.7 > r > 0.3) at 0 to 3 and 0 to 5-wk-old (P < 0.05). The protease activity of FP was moderately correlated to WG (0.7 > r > 0.3), FCR (-0.3 > r > -0.7), and PEF (0.7 > r > 0.3) at 0 to 3-wk-old (P < 0.05). The villus height to crypt depth ratio in duodenum and jejunum of fish meal group and LYS1 group were higher than unfermented group (P < 0.05). In conclusion, LYS1 shows the highest surfactin yields. Diets supplemented with 2.5% LYS1 FP can improve the growth performance and the development of intestinal villi in broilers. Moreover, this study proves that the surfactin content, Bacillus-like counts, and protease activity of FP show a correlation to the growth performance of broilers.

Endospore production of Bacillus spp. for industrial use

The increased occurrence of antibiotic resistance and the harmful use of pesticides are a major problem of modern times. A ban on the use of antibiotics as growth promoters in animal breeding has put a focus on the probiotics market. Probiotic food supplements are versatile and show promising results in animal and human nutrition. Chemical pesticides can be substituted by biopesticides, which are very effective against various pests in plants due to increased research. What these fields have in common is the use of spore-forming bacteria. The endospore-forming Bacillus spp. belonging to this group offer an effective solution to the aforementioned problems. Therefore, the biotechnological production of sufficient qualities of such endospores has become an innovative and financially viable field of research. In this review, the production of different Bacillus spp. endospores will be reviewed. For this purpose, the media compositions, cultivation conditions and bioprocess optimization methods of the last 20 years are presented and reflected.

Bioprocess development for endospore production by Bacillus coagulans using an optimized chemically defined medium

Bacillus coagulans is a promising probiotic, because it combines probiotic properties of Lactobacillus and the ability of Bacillus to form endospores. Due to this hybrid relationship, cultivation of this organism is challenging. As the probiotics market continues to grow, there is a new focus on the production of these microorganisms. In this work, a strain-specific bioprocess for B. coagulans was developed to support growth on one hand and ensure sporulation on the other hand. This circumstance is not trivial, since these two metabolic states are contrary. The developed bioprocess uses a modified chemically defined medium which was further investigated in a one-factor-at-a-time assay after adaptation. A transfer from the shake flask to the bioreactor was successfully demonstrated in the scope of this work. The investigated process parameters included temperature, agitation and pH-control. Especially the pH-control improved the sporulation in the bioreactor when compared to shake flasks. The bioprocess resulted in a sporulation efficiency of 80%-90%. This corresponds to a sevenfold increase in sporulation efficiency due to a transfer to the bioreactor with pH-control. Additionally, a design of experiment (DoE) was conducted to test the robustness of the bioprocess. This experiment validated the beforementioned sporulation efficiency for the developed bioprocess. Afterwards the bioprocess was then scaled up from a 1 L scale to a 10 L bioreactor scale. A comparable sporulation efficiency of 80% as in the small scale was achieved. The developed bioprocess facilitates the upscaling and application to an industrial scale, and can thus help meet the increasing market for probiotics.

Sporulation conditions influence the surface and adhesion properties of Bacillus subtilis spores

Spore-forming bacteria of the Bacillus subtilis group are responsible for recurrent contamination of processing lines in the food industry which can lead to food spoilage. The persistence of B. subtilis would be due to the high resistance of spores to extreme environmental condition and their propensity to contaminate surfaces. While it is well known that sporulation conditions modulate spore resistance properties, little is known about their effect on surface and adhesion properties. Here, we studied the impact of 13 sporulation conditions on the surface and adhesion properties of B. subtilis 168 spores. We showed that Ca2+ or Mg2+ depletion, lower oxygen availability, acidic pH as well as oxidative stresses during sporulation lead to the release of more hydrophobic and adherent spores. The consequences of these sporulation conditions on crust composition in carbohydrates and proteins were also evaluated. The crust glycans of spores produced in a sporulation medium depleted in Ca2+ or Mg2+ or oxygen-limited conditions were impaired and contained lower amounts of rhamnose and legionaminic acid. In addition, we showed that lower oxygen availability or addition of hydrogen peroxide during sporulation decreases the relative amount of two crust proteins (CgeA and CotY) and the changes observed in these conditions could be due to transcriptional repression of genes involved in crust synthesis in late stationary phase. The fact that sporulation conditions affect the ease with which spores can contaminate surfaces could explain the frequent and recurrent presence of B. subtilis spores in food processing lines.

Spore-forming properties and enhanced oxygen tolerance of butyrate-producing Anaerostipes spp

OBJECTIVES

Butyrate producing bacteria are promising candidates for next-generation probiotics. However, they are extremely sensitive to oxygen, which is a significant obstacle to their inclusion in food matrices in a viable form. The present study characterized the spore-forming properties and stress tolerance of human gut butyrate-producing Anaerostipes spp.

METHODS

Spore formation properties in six species of Anaerostipes spp. were studied by in vitro and in silico tests.

RESULTS

Spores were observed from the cells of three species using microscopic analyses, while the remaining three did not form spores under the tested conditions. Spore-forming properties were confirmed by an ethanol treatment. The spores of Anaerostipes caccae were tolerant to oxygen and survived for 15 weeks under atmospheric conditions. Spores tolerated heat stress at 70 °C, but not at 80 °C. An in silico analysis of the conservation of potential sporulation signature genes revealed that the majority of human gut butyrate-producing bacteria were classified as potential spore formers. Comparative genomics revealed that three spore-forming Anaerostipes spp. specifically possessed the spore formation-related genes of bkdR, sodA, and splB, which may be key genes for different sporulation properties in Anaerostipes spp.

CONCLUSIONS

The present study demonstrated the enhanced stress tolerance of butyrate producing Anaerostipes spp. for future probiotic application. Presence of specific gene(s) are possibly keys for sporulation in Anaerostipes spp.

Bacterial molecular machinery in the Martian cryosphere conditions

The exploration of Mars is one of the main objectives of space missions since the red planet is considered to be, or was in the past, potentially habitable. Although the surface of Mars is now dry and arid, abundant research suggests that water covered Mars billions of years ago. Recently, the existence of liquid water in subglacial lakes has been postulated below the South pole of Mars. Until now, experiments have been carried out on the survival of microorganisms in Martian surface conditions, but it remains unknown how their adaptation mechanisms would be in the Martian cryosphere. In this work, two bacterial species (Bacillus subtilis and Curtobacterium flacumfaciens) were subjected to a simulated Martian environment during 24 h using a planetary chamber. Afterward, the molecular machinery of both species was studied to investigate how they had been modified. Proteomes, the entire set of proteins expressed by each bacterium under Earth (named standard) conditions and Martian conditions, were compared using proteomic techniques. To establish this evaluation, both the expression levels of each protein, and the variation in their distribution within the different functional categories were considered. The results showed that these bacterial species followed a different strategy. The Bacillus subtilis resistance approach consisted of improving its stress response, membrane bioenergetics, degradation of biomolecules; and to a lesser extent, increasing its mobility and the formation of biofilms or resistance endospores. On the contrary, enduring strategy of Curtobacterium flacumfaciens comprised of strengthening the cell envelope, trying to protect cells from the extracellular environment. These results are especially important due to their implications for planetary protection, missions to Mars and sample return since contamination by microorganisms would invalidate the results of these investigations.

Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages

Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.

Assessment of calcium hypochlorite for Bacillus anthracis spore surface's decontamination

Contamination with microorganisms occurs in laboratories but is also of high concern in the context of bioterrorism. Decontamination is a cornerstone that promotes good laboratory practices and occupational health and safety. Among the most resistant structures formed by microorganisms are spores, produced notably by Clostridium and Bacillus species. Here, we compared six products containing four different molecules (hydrogen peroxide, peracetic acid, sodium and calcium hypochlorite) on B. anthracis Sterne spores. We first selected the most efficient product based on its activity against spore suspensions using French and European standards. Four products showed sporicidal activity, of which only two did so in a time frame consistent with good laboratory practices. Then, we tested one of these two products under laboratory conditions on fully virulent B. anthracis spores, during common use and after contamination through a spill of a highly concentrated spore suspension. We, thus, robustly validated a decontaminant based on calcium hypochlorite not only on its ability to kill spores but also on its effectiveness under laboratory conditions. At the end, we were able to assure a complete disinfection in 1 min after spillover and in 2 min for common use.

New Thoughts on an Old Topic: Secrets of Bacterial Spore Resistance Slowly Being Revealed

The quest for bacterial survival is exemplified by spores formed by some Firmicutes members. They turn up everywhere one looks, and their ubiquity reflects adaptations to the stresses bacteria face. Spores are impactful in public health, food safety, and biowarfare. Heat resistance is the hallmark of spores and is countered principally by a mineralized gel-like protoplast, termed the spore core, with reduced water which minimizes macromolecular movement/denaturation/aggregation. Dry heat, however, introduces mutations into spore DNA. Spores have countermeasures to extreme conditions that are multifactorial, but the fact that spore DNA is in a crystalline-like nucleoid in the spore core, likely due to DNA saturation with small acid-soluble spore proteins (SASPs), suggests that reduced macromolecular motion is also critical in spore dry heat resistance. SASPs are also central in the radiation resistance characteristic of spores, where the contributions of four spore features-SASP; Ca2+, with pyridine-2,6-dicarboxylic acid (CaDPA); photoproduct lyase; and low water content-minimize DNA damage. Notably, the spore environment steers UV photochemistry toward a product that germinated spores can repair without significant mutagenesis. This resistance extends to chemicals and macromolecules that could damage spores. Macromolecules are excluded by the spore coat which impedes the passage of moieties of ≥10 kDa. Additionally, damaging chemicals may be degraded or neutralized by coat enzymes/proteins. However, the principal protective mechanism here is the inner membrane, a compressed structure lacking lipid fluidity and presenting a barrier to the diffusion of chemicals into the spore core; SASP saturation of DNA also protects against genotoxic chemicals. Spores are also resistant to other stresses, including high pressure and abrasion. Regardless, overarching mechanisms associated with resistance seem to revolve around reduced molecular motion, a fine balance between rigidity and flexibility, and perhaps efficient repair.

The analysis of the function, diversity, and evolution of the Bacillus phage genome

BACKGROUND

Phages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representative Bacillus prophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds of Bacillus phages.

RESULTS

We obtained the following conclusions: First, Bacillus phages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact on Bacillus populations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, the Bacillus phage genome showed diversity, with a clear genome boundary between Bacillus prophages and Bacillus lytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of the Bacillus phage, resulting in low genome similarity between the Bacillus phages. Finally, the lysis module played an important influence on the process of Bacillus phage cross-species infestation.

CONCLUSIONS

This study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host in Bacillus phages.

Early Growth Patterns of Bacillus cereus on Potato Substrate in the Presence of Low Densities of Black Soldier Fly Larvae

Bacillus cereus is a common and ubiquitous bacterium that can cause foodborne illnesses in humans and other animals. Common methods of contact between foodborne pathogens and their victims include exposure through contaminated food or food containment products. Using larvae of black soldier flies, Hermetia illucens, for biological conversion of wastes into components of animal feeds is a rapidly growing technology. However, contamination of larval biomass with pathogenic microorganisms may challenge its use on an industrial scale. We conducted laboratory experiments to test the effects of the black soldier fly larvae developing on simulated potato waste substrate on B. cereus abundance. We observed a general increase in the number of colony-forming units and concentration of hblD - gene when the larvae were present in the substrate, although the effect was modulated by larval densities and time since inoculation. It is possible that starch breakdown by black soldier fly larvae may provide a beneficial environment for B. cereus. Our results differ from the suppression in the presence by black soldier fly larvae reported for several other bacterial species and highlight the importance of taking proper food safety measures when using this technology.

Effects of sporulation conditions on the growth, germination, and resistance of Clostridium perfringens spores

Clostridium perfringens can form metabolically dormant spores that can survive in meat preservation processes and cause food spoilage and human disease upon germination and outgrowth. The characteristics of spores in food products are closely related to the sporulation environment. To control or inactivate C. perfringens spores in food industry, the effects of sporulation conditions on the spores characteristics should be examined. This study aimed to investigate the effects of temperature (T), pH, and water activity (a_w) on the growth, germination, and wet-heat resistance of C. perfringens C1 spores isolated from food product. The results showed that C. perfringens C1 spores produced at T = 37 °C, pH = 8, and a_w = 0.997 had the highest sporulation rate and germination efficiency and lowest wet-heat resistance. A further increase in pH and sporulation temperature reduced the spore counts and germination efficiency, but enhanced spores' wet-heat resistance. By using air-drying method and Raman spectroscopy analysis, the water content, composition, and levels of calcium dipicolinic acid, proteins, and nucleic acids in spores produced under different sporulation conditions were determined. The results obtained revealed that sporulation conditions should be carefully considered during food production and processing, thus providing a novel insight into prevention and control of spores in food industry.

Accurate identification of living Bacillus spores using laser tweezers Raman spectroscopy and deep learning

Accurately, rapidly, and noninvasively identifying Bacillus spores can greatly contribute to controlling a plenty of infectious diseases. Laser tweezers Raman spectroscopy (LTRS) has confirmed to be a powerful tool for studying Bacillus spores at a single cell level. In this study, we constructed a single-cell Raman spectra dataset of living Bacillus spores and utilized deep learning approach to accurately, nondestructively identify Bacillus spores. The trained convolutional neural network (CNN) could efficiently extract tiny Raman spectra features of five spore species, and provide a prediction accuracy of specie identification as high as 100 %. Moreover, the spectral feature differences in three Raman bands at 660, 826, and 1017 cm^-1 were confirmed to mostly contribute to producing such high prediction accuracy. In addition, optimal CNN model was employed to monitor and identify sporulation process at different metabolic phases in one growth cycle. The obtained average prediction accuracy of metabolic phase identification was approximately 88 %. It can be foreseen that, LTRS combined with CNN approach have great potential for accurately identifying spore species and metabolic phases at a single cell level, and can be gradually extended to perform identification for many unculturable bacteria growing in soil, water, and food.

Comparison of one-step with two-step production of Bacillus atrophaeus spores for use as bioindicators

The production method of spores significantly influences the resistance of spores used as bioindicators (BI) in the validation of sterilization of packaging material surfaces in aseptic food manufacturing. Therefore, the standardization of the spore production method represents an important and desirable goal in industrial BI production to ensure reliable validation test results. Previously, we recommended a two-step production approach for submerged spore production, in which the cultivation phase to obtain high cell mass was separate from the sporulation phase. In this work, a one-step manufacturing process was investigated to reduce production complexity and facilitate standardization of spore production. It was found that one-step BI production is technically possible but at the expense of spore yield. The two-step manufacturing process can realize almost 10-fold higher spore yields.

Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-forming Bacillus spp

Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.

Glutamate catabolism during sporulation determines the success of the future spore germination

Bacterial spores can preserve cellular dormancy for years, but still hold the remarkable ability to revive and recommence life. This cellular awakening begins with a rapid and irreversible event termed germination; however, the metabolic determinants required for its success have been hardly explored. Here, we show that at the onset of the process of sporulation, the metabolic enzyme RocG catabolizes glutamate, facilitating ATP production in the spore progenitor cell, and subsequently influencing the eventual spore ATP reservoir. Mutants displaying low RocG levels generate low ATP-containing spores that exhibit severe germination deficiency. Importantly, this phenotype could be complemented by expressing RocG at a specific window of time during the initiation of sporulation. Thus, we propose that despite its low abundance in dormant spores, ATP energizes spore germination, and its production, fueled by RocG, is coupled with the initial developmental phase of spore formation.

Lactobacillus rhamnosus GR-1 attenuates foodborne Bacillus cereus-induced NLRP3 inflammasome activity in bovine mammary epithelial cells by protecting intercellular tight junctions

Background

Bacillus cereus is an important pathogen that causes human food poisoning, specifically diarrhea and vomiting. B. cereus can also induce mastitis in dairy cows and has a strong survival ability in milk, as it cannot be inactivated by high-temperature short-time pasteurization. Therefore, B. cereus can enter the market through pasteurized milk and other dairy products, imposing enormous hidden dangers on food safety and human health.

Results

In this study, B. cereus 2101 (BC) was isolated from milk samples of cows with mastitis. BC grew rapidly with strong hemolysis, making it difficult to prevent mastitis and ensure food security. MAC-T cells were treated with BC and/or Lactobacillus rhamnosus GR-1 (LGR-1). Pretreatment with LGR-1 protected the integrity of tight junctions and the expression of zonula occludens-1 (ZO-1) and occludin destroyed by BC. Furthermore, LGR-1 pretreatment reduced the expression of NOD-like receptor family member pyrin domain-containing protein 3 (NLRP3), caspase recruitment and activation domain (ASC), Caspase-1 p20, gasdermin D (GSDMD) p30, inflammatory factors (interleukin (IL)-1β and IL-18), and cell death induced by BC. Moreover, LGR-1 pretreatment reduced NLRP3 inflammasome activity and increased expressions of ZO-1 and occludin induced by lipopolysaccharides (LPS) + ATP stimulation. MAC-T cells were transfected with NLRP3 siRNA or MCC950 and/or treated with BC and/or LGR-1. NLRP3-siRNA transfection and MCC950 attenuated BC-induced NLRP3 inflammasome activity. Expression of inflammatory cytokines and cell death suggested that the inflammatory pathway might play an important role in the induction of the NLRP3 inflammasome by BC and the protection of LGR-1.

Conclusions

These results suggest that LGR-1 might be a probiotic alternative to antibiotics and could be administered to prevent mastitis in dairy cows, thus ensuring food security.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00752-w.

Effects of pulsed near infrared light (NIR) on Bacillus subtilis spores

In this study, we develop a characterization of bacterial spore resistance to NIR pulsed light under modalities traditionally used in multiphoton microscopy. Energy dose and laser power are both key parameters in spore and bacterial cell inactivation. Surprisingly, spores and vegetative cells seem to show a similar sensitivity to pulsed NIR, spores being only 2-fold more resistant than their vegetative counterparts. This work enables us to eliminate certain hypotheses concerning the main driver of spore inactivation processes. Our findings suggest that damage leading to inactivation is mainly caused by photochemical reactions characterized by multiple possible pathways, including DNA damage or oxidation processes.

Changes in the Spore Proteome of Bacillus cereus in Response to Introduction of Plasmids

Fluorescent fusion proteins were expressed in Bacillus cereus to visualize the germinosome by introducing a plasmid that carries fluorescent fusion proteins of germinant receptor GerR subunits or germinosome scaffold protein GerD. The effects of plasmid insertion and recombinant protein expression on the spore proteome were investigated. Proteomic analysis showed that overexpression of the target proteins had negligible effects on the spore proteome. However, plasmid-bearing spores displayed dramatic abundance changes in spore proteins involved in signaling and metabolism. Our findings indicate that the introduction of a plasmid alone alters the spore protein composition dramatically, with 993 proteins significantly down-regulated and 415 proteins significantly up-regulated among 3323 identified proteins. This shows that empty vector controls are more appropriate to compare proteome changes due to plasmid-encoded genes than is the wild-type strain, when using plasmid-based genetic tools. Therefore, researchers should keep in mind that molecular cloning techniques can alter more than their intended targets in a biological system, and interpret results with this in mind.

Acetoin production from lignocellulosic biomass hydrolysates with a modular metabolic engineering system in Bacillus subtilis

Background

Acetoin (AC) is a vital platform chemical widely used in food, pharmaceutical and chemical industries. With increasing concern over non-renewable resources and environmental issues, using low-cost biomass for acetoin production by microbial fermentation is undoubtedly a promising strategy.

Results

This work reduces the disadvantages of Bacillus subtilis during fermentation by regulating genes involved in spore formation and autolysis. Then, optimizing intracellular redox homeostasis through Rex protein mitigated the detrimental effects of NADH produced by the glycolytic metabolic pathway on the process of AC production. Subsequently, multiple pathways that compete with AC production are blocked to optimize carbon flux allocation. Finally, the population cell density-induced promoter was used to enhance the AC synthesis pathway. Fermentation was carried out in a 5-L bioreactor using bagasse lignocellulosic hydrolysate, resulting in a final titer of 64.3 g/L, which was 89.5% of the theoretical yield.

Conclusions

The recombinant strain BSMAY-4-PsrfA provides an economical and efficient strategy for large-scale industrial production of acetoin.