Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments

Effective role and mechanism of scrap iron filings in controlling hydrogen sulfide production in septic tanks

Long-term anaerobic conditions in septic tanks exacerbate the release of hazardous gases, such as hydrogen sulfide (H2S), which degrades urban air quality. While traditional iron salt addition effectively inhibits H2S production, its large-scale application imposes economic burdens and challenges for low-carbon emission reduction. To address this issue, this study proposes the use of scrap iron filings (SIFs) as a source of Fe2+ and Fe3+ ions and evaluates their efficacy in sulfide control through a long-term laboratory-scale septic tank reactor. Experimental results demonstrated that the addition of SIFs reduced the average concentration of dissolved sulfides by 45.6 % and gaseous H2S by 92.6 %. Microbial community analysis of septic tank sediments revealed a significant decrease in sulfate-reducing bacteria (SRB) and an increase in sulfur-oxidizing bacteria (SOB), indicating that SIFs influence microbial activity by suppressing sulfide generation while enhancing sulfide oxidation. Furthermore, the addition of SIFs slightly increased the carbon-to-nitrogen (C/N) and carbon-to-phosphorus (C/P) ratios in the effluent, potentially improving subsequent nitrogen and phosphorus removal in wastewater treatment. These findings suggest a promising strategy for reducing hydrogen sulfide emissions and corrosion in septic tanks.

The effect of combination of root exudates substances on stimulation of Bacillus spores' germination

Root exudates play a crucial role in the rhizosphere by influencing the growth and activity of plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis. Previous studies have shown that most Bacillus spores can germinate in the rhizosphere while remain dormant in the soil. Understanding the relationship between specific components of root exudates and spore germination could provide valuable insights into how plants alter the ratio of spores in the rhizosphere through root exudates. In this study, we observed that Bacillus spore germination was induced by root exudates from maize (Fengtian) and two cucumber varieties (9930 and Jinchun 4). Maize root exudates induced spore germination at a significantly higher rate compared to cucumber exudates. We identified L-valine, β-alanine, xylose, glucose, and asparagine as key germination-inducing compounds in the exudates. Notably, when these compounds were combined, spore germination rates increased to over 80 %. We found that the maize-specific root exudate asparagine significantly enhanced the spore germination inducing ability of other germinants even at low concentrations. Furthermore, our results indicate that the GerA receptor specifically recognizes amino acids, while GerB and GerK work cooperatively to sense sugars and amides. These findings provide new insights into plant-microbe interactions and could inform the development of more effective Bacillus-based biofertilizers, improving their application in sustainable agriculture.

Amino Acids From Root Exudates Induce Bacillus Spore Germination to Enhance Root Colonisation and Plant Growth Promotion

Strains of Bacillus species, plant growth-promoting rhizobacteria, have been commercialised as biofertilisers; they are ideal for this because these species form spores that can be stored stably for a long time. However, for these spores to exert their full beneficial effects, they must germinate. The specific germination signals in the rhizosphere, particularly those from plant root exudates, remain largely unknown. Here, we investigated the germination signals from different growth states of cucumber (Cucumis sativus) for spores of Bacillus velezensis SQR9 and Bacillus subtilis NCIB 3610. We identified the corresponding germination receptors and compared them biochemically between the Bacillus species. Larger plants better stimulated spore germination. Five amino acids-L-isoleucine, L-ornithine, L-valine, L-serine and β-alanine were-identified as spore germination signals. Combined application of a mixture of these amino acids with bacterial spores markedly enhanced the cucumber growth-promoting properties of B. velezensis SQR9. The germination receptor for these amino acids was GerA in both Bacillus species. Differences in spore germination efficiency between B. subtilis and B. velezensis may be attributable to variations in the GerA ligand-recognition sites. Expression of GerA from B. subtilis NCIB 3610 in B. velezensis SQR9 enhanced the spore germination rate of the latter. Our study highlights the pivotal role of amino acids in regulating spore germination of Bacillus and subsequent plant root colonisation, emphasising their potential to enhance the efficacy of Bacillus-based biofertilisers. Engineering of germination receptors is a promising approach to enhance the spore germination efficiency of biofertiliser strains.

Prevalence of spore-forming bacteria in plant-based raw materials used for plant-based milk alternatives

Plant-based milk alternatives can be produced from a variety of raw materials. The microbial load of the used raw materials can vary greatly, affecting the heating parameters necessary for reducing the microbial load. In this study, plant-based raw materials for producing oat-, almond-, pea-, and rice-based drinks were examined for their microbial load. In this context, flours, flakes, protein isolates, and syrups were tested. The microbiological tests included i) the mesophilic viable cell count (mVCC), ii) the thermophilic viable cell count (tVCC), iii) the mesophilic spore count (mSC), and iv) the thermophilic spore count (tSC). Pure cultures were isolated from each sample, and bacterial species were identified using 16S rRNA gene analysis. The plant-based raw materials (oat, almond, pea and rice) showed wide variations in the viable cell and spore count, ranging from 1 to 8.5 log10 CFU/g. Most of the raw materials contained a high proportion of spores in the viable cell count. Despite previous ultra-high temperature treatment (UHT treatment), the oat and rice syrups showed spore levels of 1 to 4 log10 CFU/g. In total, 435 bacterial isolates were classified with the most frequent species belonging to the genus Bacillus. Among these, B. licheniformis, B. subtilis, and B. tequilensis were the most prevalent. However, other species such as B. cereus, B. amyloliquefaciens, P. etheri, and G. stearothermophilus were also present. Based on the initial spore load of the raw materials, the required effect of the heat treatment B* can be calculated to ensure a commercially sterile plant-based drink. For an average mesophilic bacterial load of oat flours with 5 log10 CFU/g, a 12 log10 reduction is required and for a higher contamination with 9 log10 CFU/g a 16 log10 reduction is already necessary.

Enhancing Photocatalytic and Antibacterial Properties Through a Synergistic Approach in ZnS-CuSe Nanocomposites

This study introduces a novel single-step sonochemical synthesis method for producing pure ZnS and CuSe. It offers a comprehensive report on the fabrication of ZnS─CuSe nanocomposites with varying compositions (90, 70, and 50% ZnS combined with 10, 30, and 50% CuSe), denoted as CZ-1, CZ-2, and CZ-3, via a wet-chemical method. Comprehensive characterization was conducted to assess phase purity, structural integrity, composition, detection of free radicals, and optical properties. The results revealed that the average crystallite sizes of ZnS and CuSe were 46.91 and 20.31 nm, respectively. Morphological analysis showed CuSe formed nanoflakes, whereas ZnS appeared as nanoparticles. Optical properties revealed a red shift in absorption spectra and a decrease in band gap with increasing CuSe concentration. Electrons in the CBM (conduction band minimum) can be captured by •O2 to produce large amounts of •O2- and •OH radicals, formed via •O2- →H2O2 →•OH. DFT calculations support these findings, offering insights into how CuSe affects the electronic structure of ZnS. Among the materials, CZ-3 showed superior photocatalytic activity, achieving 98% degradation of methylene blue (MB) dye and effective inhibition of B. subtilis and P. aeruginosa under visible light irradiation.

Bacterial Spore Inactivation Technology in Solid Foods: A Review

In response to physiological stress, some bacterial strains have the ability to produce spores that are able to resist conventional food heating processes and even more extreme environmental factors. Dormant spores can germinate and return to their vegetative state during food preservation, leading to food spoilage, or safety issues that pose a risk to human health. Thus, spore inactivation technology is gaining more and more attention. Several techniques have been used in liquid foods to efficiently inactivate spores, including novel thermal and nonthermal treatments. However, solid foods have unique characteristics that make it challenging to achieve the same spore inactivation effect as in previous liquid food studies. Therefore, exploring the effectiveness of spore inactivation techniques in solid foods is of great significance, and clarifying the mechanism for deactivating spore through related techniques is informative in enhancing the effectiveness of spore deactivation in solid foods. This article reviews the practical applications of spore inactivation technology in solid foods.

Genome sequence of Bacillus sp. strain BAU-SS-2023, isolated from nasal swab of cattle in Bangladesh

We report the genome sequence of the Bacillus sp. strain BAU-SS-2023, isolated from nasal swabs of cattle in Bangladesh. The strain was isolated using brain heart infusion (BHI) broth and blood agar media. The genome was 9,162,285 bp, 32.4% G+C content, 9,145 coding sequences, 6 rRNAs, 73 tRNAs, and 9 noncoding RNAs.

Nasal delivery of killed Bacillus subtilis spores protects against influenza, RSV and SARS-CoV-2

Introduction

Spores of the bacterium Bacillus subtilis (B. subtilis) have been shown to carry a number of properties potentially beneficial for vaccination. Firstly, as vehicles enabling mucosal delivery of heterologous antigens and secondly, as stimulators of innate immunity. Here, we have examined the specificity of protection conferred by the spore-induced innate response, focusing on influenza H1N1, respiratory syncytial virus (RSV), and coronavirus-2 (SARS-CoV-2) infections.

Methods

In vivo viral challenge murine models were used to assess the prophylactic anti-viral effects of B. subtilis spores delivered by intranasal instilling, using an optimised three-dose regimen. Multiple nasal boosting doses following intramuscular priming with SARS-CoV-2 spike protein was also tested for the capability of spores on enhancing the efficacy of parenteral vaccination. To determine the impact of spores on immune cell trafficking to lungs, we used intravascular staining to characterise cellular participants in spore-dosed pulmonary compartments (airway and lung parenchyma) before and after viral challenge.

Results

We found that mice pre-treated with spores developed resistance to all three pathogens and, in each case, exhibited a significant improvement in both survival rate and disease severity. Intranasal spore dosing expanded alveolar macrophages and induced recruitment of leukocyte populations, providing a cellular mechanism for the protection. Most importantly, virus-induced inflammatory leukocyte infiltration was attenuated in spore-treated lungs, which may alleviate the associated collateral tissue damage that leads to the development of severe conditions. Remarkably, spores were able to promote the induction of tissue-resident memory T cells, and, when administered following an intramuscular prime with SARS-CoV-2 spike protein, increased the levels of anti-spike IgA and IgG in the lung and serum.

Conclusions

Taken together, our results show that Bacillus spores are able to regulate both innate and adaptive immunity, providing heterologous protection against a variety of important respiratory viruses of high global disease burden.

Probiotic Potential of Bacillus sp. 62A Isolated from a Marine Extreme Environment

Antimicrobial resistance is an important health concern globally, and probiotics are considered an alternative to minimize it. The present study examined the in vitro probiotic characteristics and in vivo immunomodulatory potential of Bacillus sp. 62A - an extremophile bacterium. Bacillus sp. 62A was evaluated in vitro for its cytotoxicity, hemolytic activity, antibiotic susceptibility, and resistance to gastrointestinal conditions (bile salts, low pH, and intestinal adherence). Additionally, the immunomodulatory effect of Bacillus sp. 62A was studied in mice. The animals were supplemented daily with phosphate-buffered saline (control) and Bacillus sp. 62A at 1 × 108 colony forming units (CFU). Samples were taken on days 5 and 10. Isolated splenocytes were challenged with Escherichia coli for immunological analyses and immune-related gene expression. Serum and feces were collected for IgA and IgG determination. Bacillus sp. 62A did not show cytotoxicity, hemolytic activity, or resistance to antibiotics. Furthermore, the bacterium has autoaggregation and intestinal adhesion capacities and grows in the presence of bile salts and low pH. Bacillus supplementation in mice improved respiratory burst activity, nitric oxide production, and IL-1β and IL-6 gene expressions, mainly at 10 days. After E. coli challenge, Bacillus supplementation in mice induced an anti-inflammatory response through a decrease in immunological parameters and an increase in IL-10 gene expression. Moreover, serum IgA and IgG and fecal IgG augmented in supplemented mice. In conclusion, Bacillus sp. 62A has biosafe and immunomodulatory probiotic potential.

Inactivation Kinetics of Alicyclobacillus acidoterrestris Spores and Determination of Spore Germicidal Fluences Under UV-C Treatment

The aim of this study is to measure the UV-C inactivation kinetics and determine the fluences required for incremental inactivation of Alicyclobacillus acidoterrestris (AAT). Spores from five strains of AAT (ATCC 49025, DSM 2498, VF, SAC, and WAC) were suspended in clear phosphate-buffered saline (PBS) and individually treated with UV-C doses up to 100 mJ/cm2. A collimated beam device emitting UV-C at 254 nm (from a monochromatic low-pressure mercury lamp [LPM]) and at 268 nm (from UV light-emitting diodes [UV-LEDs]) was used for UV treatments. The log reduction from each treatment was plotted against the UV-C fluence. Curve fitting using the GInaFiT tool for Excel was attempted using both linear and nonlinear regression models. The goodness-of-fit and model performances, assessed using Akaike's Information Criterion and Bayesian Information Criterion, revealed that the Weibull model provided a better fit for the inactivation data and was thus used to determine UV-C doses required for 1-log inactivation and incremental log inactivation. Similar AAT spore inactivation efficacy was observed at both 254 and 268 nm. A UV-C dose of 100 mJ/cm2 at 254 nm inactivated >4-log CFU/mL, while at 268 nm, a 3.7-5.08-log CFU/mL reduction was observed for AAT strains ATCC 49025, DSM 2498, WAC, and VF. Among the five strains of AAT tested, spores of WAC demonstrated greater resistance, requiring UV-C doses of 2.76 mJ/cm2 and 100 mJ/cm2 for 1-log (D10-value) and 4-log inactivation at 254 nm, and 5.89 mJ/cm2 and >100 mJ/cm2 at 268 nm. In contrast, spores of SAC showed greater sensitivity, with UV-C doses of 1.87 mJ/cm2 and 47.92 mJ/cm2 required for 1-log and 4-log inactivation at 254 nm, and 6.20 mJ/cm2 and 44.61 mJ/cm2 at 268 nm. This study lays the foundation for designing a successful UV-based nonthermal pasteurization system.

Overview of endospore-forming bacteria in food: The road towards a harmonised method for the enumeration of their spores

Endospore-forming bacteria are an important challenge for the food industry due to their ubiquitous nature, widespread presence in the food chain and sophisticated survival mechanisms. An accurate method is needed that can provide insight into the quality of raw materials, predict spoilage potential and ensure food safety. A plethora of methods exist for the enumeration of spore-forming bacteria which vary among countries, industries and food producers. These methods describe a wide range of values in the key method parameters, such as heat treatment, growth medium, incubation time, and temperature. Consequently the results obtained can vary leading to misalignment and confusion. In addition, many of these methods are empirical and have not been validated. A harmonised international approach for the enumeration of spores is needed to provide consistent and reliable results on which to base food safety and quality decisions. A group of experts associated with the Internal Standardisation Organisation working group undertaking this task has identified the main endospore-forming bacterial species occurring in foods based on a wide selection of publications. Endospores are typically formed by bacteria belonging to twelve families originating from the Negativicutes, Bacilli and Clostridia classes, with the latter two being the most important for the food industry. This review will be used as a first step in method standardisation.

Effect of surfactants on inactivation of Bacillus subtilis spores by chlorine

Bacterial spores pose significant risks to human health, yet the inactivation of spores is challenging due to their unique structures and chemical compositions. This study investigated the synergistic effect between surfactants and chlorine on the inactivation kinetics of Bacillus subtilis spores. Two surfactants, cocamidopropyl betaine (CAPB) and cetyltrimethylammonium chloride (CTMA) were selected to investigate chlorine disinfection in absence and presence of surfactants. The concurrent presence of both chlorine and surfactant resulted in a moderate reduction in the lag-phases for spore inactivation and negligible increase in the second-order inactivation rate constants. In contrast, when the spores were pre-exposed to surfactants, the lag-phases decreased by about 50 % for both CAPB and CTMA, and the second-order inactivation rate constants during post-chlorination remained constant for CAPB but increased by a factor of 2.3 for CTMA, compared to the control group with phosphate buffer. This synergistic effect became more pronounced with longer surfactant pre-exposure times, reaching its maximum at 3-6 h. The observed synergistic effect suggests that surfactants can potentially enhance the permeability of the coat which is the outmost layer of B. subtilis spores and a primary barrier for chemical disinfectants. Tracing a group of B. subtilis spores sequentially treated with surfactant and chlorine by atomic force microscopy, a significant decrease in compressive stiffness of the spores was observed due to exposure to surfactants, indicating alterations in the coat by surfactants. The trend in reducing compressive stiffness aligned well with the decrease of lag-phases in inactivation kinetics. Furthermore, CTMA was found to inactivate B. subtilis spores through mechanisms different from chlorine. Chlorine primarily inactivated B. subtilis spores before damaging the inner membrane of the spores which plays a crucial role in protecting the genetic material stored in the core of the spores. In comparison, CTMA damaged 22 % of the inner membrane for an inactivation efficiency of 99 %. A synergistic effect in damaging the inner membrane was observed when applying CTMA and chlorine simultaneously instead of sequentially.

Programming Aliphatic Polyester Degradation by Engineered Bacterial Spores

Enzymatic degradation of plastics is a sustainable approach to address the growing issue of plastic accumulation. Here, we demonstrate the degradation of aliphatic polyesters using enzyme-displaying bacterial spores and the fabrication of self-degradable spore-containing plastics. The degradation proceeds without nutrient-dependent spore germination into living cells. Engineered spores completely degrade aliphatic polyesters into small molecules, retain activity through multiple cycles, and regain full activity through germination and sporulation. We also found that the interplay between the glass transition temperature and melting temperature of polyester substrates affects heterogeneous biocatalytic degradation by engineered spores. Directly incorporating spores into polyesters results in robust materials that are completely degradable. Our study offers a straightforward and sustainable biocatalytic approach to plastic degradation.

Uncovering the therapeutic potential of anti-tuberculoid agent Isoniazid in a model of microbial-driven Crohn's disease

AIMS

TNFα has long stood as a hallmark feature of both inflammatory bowel disease and arthritis with its therapeutic potential demonstrated in neutralizing monoclonal antibody treatments such as Infliximab. Due to the high global burden of latent Mycobacterium tuberculosis (TB) infections, prior to receiving anti-TNF therapy, patients testing positive for latent TB are given prophylactic treatment with anti-tuberculoid medications including the first described TB-selective antibiotic, Isoniazid. While this is common clinical practice to prevent the emergence of TB, little is known about whether Isoniazid modifies intestinal inflammation alone. The aim of this study, therefore, was to determine whether Isoniazid presents a novel TB-independent therapeutic option for the treatment of Crohn's disease (CD)-like ileitis and uncover new mechanisms predisposing the host to intestinal inflammation.

METHODS

The transgenic TNFΔARE mouse model of Crohn's-like terminal ileitis was used. The impact of Isoniazid administration (10 mg/kg/day dose in drinking water) on disease development was monitored between 8 and 12 weeks of age using a variety of behavioral and serological assays. Behavioral and motor functions were assessed using the LABORAS automated monitoring system while systemic and local tissue inflammation were determined at experimental termination using multiplex cytokine analysis. Whole-mount tissue immunofluorescence and fluorescent in situ hybridization were used to qualify changes within the host as well as the microbial compartment of the ileum and associated mesentery. Proposed cellular mechanisms of altered cytokine decay were performed on isolated primary splenocytes in vitro using selective pharmacological agents.

RESULTS

Compared to age-matched wild-type littermates, TNFΔARE mice display prominent progressive sickness behaviors from 8 through 12 weeks of age indicated by reduced movement, climbing, and rearing. Prophylactic administration of Isoniazid (10 mg/kg/day) is effectively able to protect TNFΔARE mice from this loss of function during the same period. Analysis revealed that Isoniazid was able to significantly reduce both systemic and intestinal inflammation compared to untreated vehicle controls impacting the epithelial colonization of known pathobiont segmented filamentous bacteria (SFB). Reduction in terminal ileal inflammation was also associated to the diminished formation of precursor-tertiary lymphoid organs within the associated ileal mesentery which were found to be associated with endospores derived SFB itself. Finally, we reveal that due to their genetic manipulation, TNFΔARE mice display accelerated posttranscriptional decay of IL-22 mRNA resulting in diminished IL-22 protein production and associated downstream antimicrobial peptide production.

CONCLUSIONS

Isoniazid protects against the development of intestinal and systemic inflammation in the TNFΔARE model of terminal ileitis by limiting the expansion of mucosal SFB and progression of the associated microbial-driven inflammation. This work highlights a possible mycobacterial-independent function of Isoniazid in limiting CD pathophysiology through limiting the mucosal establishment of pathobionts such as SFB and the association of such microbe-derived endospores linked to the formation of ectopic tertiary lymphoid organs seen commonly in patients.

Viability of microencapsulated species of Trichoderma as a strategy to optimize use in biological control

The increasing use of chemical fungicides without effective control of phytopathogens has led to the development of resistance in microorganisms. As a promising alternative, products formulated with Trichoderma have emerged for their sustainable and effective potential in integrated disease management. However, the predominant formulations do not offer the necessary protection against abiotic factors. In this study, we investigated Trichoderma species encapsulated in sodium alginate through storage viability experiments and their antagonistic potential. The viability and storage conditions of the capsules were evaluated by plating at 5, 15, 30, 45, 60, and 150 days after production, kept in dry or refrigerated environments. The antagonistic potential was determined by the culture pairing method using the phytopathogen Fusarium sp. The results demonstrated that it was possible to maintain the viability of the conidia, with no differences between storage environments. Additionally, the capsule provided UV protection to the conidia encapsulated species possess antagonistic potential, inhibiting 52.54% of Fusarium sp. growth. Consequently, encapsulation is an alternative formulation method that ensures the viability of Trichoderma conidia and optimizes its use in biological control.

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.

Ornithinibacillus xuwenensis sp. nov., A Novel Thermotolerant Bacterium Isolated from Mangrove Sediment

A Gram-stain positive, long-rod-shaped, motile, and aerobic bacterial strain, designated 16A2ET, was isolated from mangrove sediment sample. The 16S rRNA gene sequence similarity analysis indicated that strain 16A2ET exhibited high similarity to Ornithinibacillus contaminans CCUG 53201T (98.2%), Ornithinibacillus bavariensis WSBC 24001T (98.1%), and Ornithinibacillus scapharcae TW25T (97.7%). Strain 16A2ET grew within a temperature range of 20-50 °C (optimum 40 °C), a pH range of 6.0-9.0 (optimum pH 8.0), and in the presence of 0-10% (w/v) NaCl (optimum 1%). The genome size of strain 16A2ET is 3.60 Mbp, with a G + C content of 36.7%. The overall genome related index (OGRI) analyses revealed low average nucleotide identity (ANI < 75.9%), average amino acid identity (AAI < 77.5%), and digital DNA-DNA hybridization (dDDH < 19.8%) with other species in the genus Ornithinibacillus. Chemotaxonomic analyses revealed that the major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phospholipids, and an aminophospholipid. The predominant fatty acids were iso-C15:0, anteiso-C15:0, and anteiso-C17:0. The sole respiratory quinone was menaquinone-7 (MK-7), and the peptidoglycan amino acid type was determined to be A4β. Based on phenotypic and genotypic analyses, strain 16A2ET (= GDMCC 1.4379T = JCM 36753T) represents a novel species within the genus Ornithinibacillus, for which the name Ornithinibacillus xuwenensis sp. nov. is proposed.

Natural biomolecules for cell-interface engineering

Cell-interface engineering is a way to functionalize cells through direct or indirect self-assembly of functional materials around the cells, showing an enhancement to cell functions. Among the materials used in cell-interface engineering, natural biomolecules play pivotal roles in the study of biological interfaces, given that they have good advantages such as biocompatibility and rich functional groups. In this review, we summarize and overview the development of studies of natural biomolecules that have been used in cell-biointerface engineering and then review the five main types of biomolecules used in constructing biointerfaces, namely DNA polymers, amino acids, polyphenols, proteins and polysaccharides, to show their applications in green energy, biocatalysis, cell therapy and environmental protection and remediation. Lastly, the current prospects and challenges in this area are presented with potential solutions to solve these problems, which in turn benefits the design of next-generation cell engineering.

Foodborne spore-forming bacteria: Challenges and opportunities for their control through the food production chain

Foodborne spore-forming bacteria represent a significant challenge within the food production chain due to their widespread occurrence and resistance to various processing methods. In addition to their role in food spoilage, these bacteria exhibit pathogenic properties, posing risks to public health. A comprehensive understanding of the impact of unit operations along the food production continuum, from farm or field to fork, is essential for ensuring both the safety and quality of food products. This chapter explores the factors influencing the growth, inactivation, and persistence of these bacteria, as well as the challenges and opportunities for their control. The discussion encompasses preventive measures, control strategies at the farm and field levels, and processing operations, including both thermal and non-thermal methods. Post-processing controls, such as storage and distribution practices, are also addressed. Furthermore, consumer behavior, education, and lessons learned from past outbreaks and product recalls contribute to a broader understanding of how to manage spore-forming bacteria within the food production chain. By assessing and quantifying the effects of each processing step, it becomes possible to implement effective control measures, thereby ensuring microbiological safety and enhancing the quality of food products.

Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighbouring cells and sequester nutrients. This metabolite-mediated competition probably evolved in complex microbial communities in the presence of viral pathogens. We therefore hypothesized that microbes secrete natural products that make competitors sensitive to phage infection. We used a binary-interaction screen and chemical characterization to identify a secondary metabolite (coelichelin) produced by Streptomyces sp. that sensitizes its soil competitor Bacillus subtilis to phage infection in vitro. The siderophore coelichelin sensitized B. subtilis to a panel of lytic phages (SPO1, SP10, SP50, Goe2) via iron sequestration, which prevented the activation of B. subtilis Spo0A, the master regulator of the stationary phase and sporulation. Metabolomics analysis revealed that other bacterial natural products may also provide phage-mediated competitive advantages to their producers. Overall, this work reveals that synergy between natural products and phages can shape the outcomes of competition between microbes.

Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference

The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. Cutibacterium was the most abundant bacterium in palmar samples from Shanghai and Kunming, Psychrobacter in Chifeng samples, and Psychrobacillus in Urumqi samples. Additionally, Streptococcus and Staphylococcus were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.

The ionic liquid-assisted sample preparation method pTRUST allows sensitive proteome characterization of a variety of bacterial endospores to aid in the search for protein biomarkers

Bacterial endospores are ubiquitous and are responsible for various human infections. Recently, we reported that an ionic liquid (IL)-based sample preparation method (named pTRUST) facilitated highly efficient shotgun analysis of the Bacillus subtilis spore proteome in trace samples. In this study, we evaluated the efficiency and applicability of the pTRUST technology using three different spore preparations: one purified from the closely related subspecies B. subtilis natto and two from B. licheniformis and B. cereus. We showed that the pTRUST method allowed rapid solubilization and processing of all tested spore samples prepared for highly sensitive mass spectrometry (MS) analysis. Bioinformatics analysis using the BLAST program suggested that a set of 25 proteins commonly identified between the above three species and B. subtilis spores may be universal biomarkers among various bacterial species, including 43 spore-producing bacteria associated with industrial dairy processing environments and product spoilage. In contrast, the two identified proteins, D4FV94 in B. subtilis natto and Q737A2 in B. cereus, are likely species-specific biomarkers, because their orthologs are absent or rare in all organisms. The sensitivity and applicability of pTRUST, along with the putative protein biomarkers identified in this study, will facilitate a wide spectrum of spore research for biological and clinical applications.

Efficient Autoinducible Expression of Recombinant Proteins via the DegSU Quorum Sensing System in a Robust Bacillus subtilis

DegSU quorum sensing (QS) system enables autoinducible expression of recombinant proteins in Bacillus subtilis . However, insufficient promoter strength and a complex regulatory circuit limit its practical application. Here, the QS-responsive promoter PaprE was modified by core region mutation, upstream truncation, and addition of activating binding sites, yielding PE742 with a 118.3% increase in strength. A mathematical model was developed to accurately quantify the regulatory process from a comprehensive perspective. Guided by this model, the DegSU QS system was further optimized in a robust B. subtilis by knocking out competitive target genes sacB and amyE, operons pgs and srfA, introducing variants degUL113F and degQ36Hy, and increasing regulatory strength by 84.0%. A 52.5% increase in acetoin titer and a 65.9% increase in extracellular carboxypeptidase activity validated the industrial value of this study. Overall, this study addresses the limitations of the DegSU QS system in practical application and demonstrates its potential for high-level recombinant protein production.

Pivotal role of Helicobacter pylori virulence genes in pathogenicity and vaccine development

One of the most prevalent human infections is Helicobacter pylori (H. pylori), which affects more than half of the global population. Although H. pylori infections are widespread, only a minority of individuals develop severe gastroduodenal disorders. The global resistance of H. pylori to antibiotics has reached concerning levels, significantly impacting the effectiveness of treatment. Consequently, the development of vaccines targeting virulence factors may present a viable alternative for the treatment and prevention of H. pylori infections. This review aims to provide a comprehensive overview of the current understanding of H. pylori infection, with a particular focus on its virulence factors, pathophysiology, and vaccination strategies. This review discusses various virulence factors associated with H. pylori, such as cytotoxin-associated gene A (cagA), vacuolating cytotoxin gene (vacA), outer membrane proteins (OMPs), neutrophil-activated protein (NAP), urease (ure), and catalase. The development of vaccines based on these virulence characteristics is essential for controlling infection and ensuring long-lasting protection. Various vaccination strategies and formulations have been tested in animal models; however, their effectiveness and reproducibility in humans remain uncertain. Different types of vaccines, including vector-based vaccines, inactivated whole cells, genetically modified protein-based subunits, and multiepitope nucleic acid (DNA) vaccines, have been explored. While some vaccines have demonstrated promising results in murine models, only a limited number have been successfully tested in humans. This article provides a thorough evaluation of recent research on H. pylori virulence genes and vaccination methods, offering valuable insights for future strategies to address this global health challenge.

Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean

This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.

Bacterial Patterning: A Promising Biofabrication Technique

Bacterial patterning has emerged as a pivotal biofabrication technique in the biomedical field. In the past 2 decades, a diverse array of bacterial patterning approaches have been developed to enable the precise manipulation of the spatial distribution of bacterial patterns for various applications. Despite the significance of these advancements, there is a deficiency of review articles providing an overview of bacterial patterning technologies. In this mini-review, we systematically summarize the progress of bacterial patterning over the past 2 decades. This review commences with an elucidation of the definition and fundamental principles of bacterial patterning. Subsequently, we introduce the established bacterial patterning strategies, accompanied by discussions about the advantages and limitations of each approach. Furthermore, we showcase the biomedical applications of these strategies, highlighting their efficacy in spatial control of biofilms, biosensing, and biointervention. Finally, this mini-review is concluded with a summary and an outlook on future challenges and opportunities. It is anticipated that this mini-review can serve as a concise guide for those who are interested in this exciting and rapidly evolving research area.

A review of the potential impacts of coastal mosquito control programs on Australian Stingless Bees (Apidae, Meliponini)-likely exposure pathways and lessons learned from studies on honey bees

The impact of the programmatic use of larvicides for mosquito control on native stingless bees (e.g., Apidae, Meliponini) is a growing concern in Australia due to heightened conservation awareness and the growth of hobbyist stingless bee keeping. In Australia, the two most widely used mosquito larvicides are the bacterium Bacillus thuringiensis var. israelensis (Bti) and the insect hormone mimic methoprene (as S-methoprene). Each has a unique mode of action that could present a risk to stingless bees and other pollinators. Herein, we review the potential impacts of these larvicides on native Australian bees and conclude that their influence is mitigated by their low recommended field rates, poor environmental persistence, and the seasonal and intermittent nature of mosquito control applications. Moreover, evidence suggests that stingless bees may display a high physiological tolerance to Bti similar to that observed in honey bees (Apis mellifera), whose interactions with B. thuringiensis-based biopesticides are widely reported. In summary, neither Bti or methoprene is likely to pose a significant risk to the health of stingless bees or their nests. However, current knowledge is limited by regulatory testing requirements that only require the use of honey bees as toxicological models. To bridge this gap, we suggest that regulatory testing is expanded to include stingless bees and other nontarget insects. This is imperative for improving our understanding of the potential risks that these and other pesticides may pose to native pollinator conservation.

Revolutionary self-powered transducing mechanism for long-lasting and stable glucose monitoring: achieving selective and sensitive bacterial endospore germination in microengineered paper-based platforms

We introduce a groundbreaking proof-of-concept for a novel glucose monitoring transducing mechanism, marking the first demonstration of a spore-forming microbial whole-cell sensing platform. The approach uses selective and sensitive germination of Bacillus subtilis spores in response to glucose in potassium-rich bodily fluids such as sweat. As the rate of germination and the number of metabolically active germinating cells are directly proportional to glucose concentration, the electrogenic activity of these cells-manifested as electricity-serves as a self-powered transducing signal for glucose detection. Within a microengineered, paper-based microbial fuel cell (MFC), these electrical power outputs are measurable and can be visually displayed through a compact interface, providing real-time alerts. The dormant spores extend shelf-life, and the self-replicating bacteria ensure robustness. The MFC demonstrated a remarkable sensitivity of 2.246 µW·(log mM)-1·cm-2 to glucose concentrations ranging from 0.2 to 10 mM, with a notably lower limit of detection at ~0.07 mM. The sensor exhibited exceptional selectivity, accurately detecting glucose even in the presence of various interferents. Comparative analyses revealed that, unlike conventional enzymatic biosensors whose performance degrades significantly through time even when inactive, the spore-based MFC is stable for extended periods and promptly regains functionality when needed. This preliminary investigation indicates that the spore-forming microbial whole-cell sensing strategy holds considerable promise for efficient diabetes management and can be extended toward noninvasive wearable monitoring, overcoming critical challenges of current technologies and paving the way for advanced biosensing applications.

Visualization of Bacillus subtilis spore structure and germination using quick-freeze deep-etch electron microscopy

Bacterial spores, known for their complex and resilient structures, have been the focus of visualization using various methodologies. In this study, we applied quick-freeze and replica electron microscopy techniques, allowing observation of Bacillus subtilis spores in high-contrast and three-dimensional detail. This method facilitated visualization of the spore structure with enhanced resolution and provided new insights into the spores and their germination processes. We identified and described five distinct structures: (i) hair-like structures on the spore surface, (ii) spike formation on the surface of lysozyme-treated spores, (iii) the fractured appearance of the spore cortex during germination, (iv) potential connections between small vesicles and the core membrane and (v) the evolving surface structure of nascent vegetative cells during germination.

Engineering the cell wall reactive groups of Plant Growth Promoting Rhizobacteria by culture strategy for heavy metal removal

This research delved into the effects of nutrient limitation on the level of sporulation and the cadmium adsorption capacity of the bacterium Bacillus sp. isolated from the rhizosphere of endemic soils in the Region of Valparaiso, Chile. The bacteria were subjected to nitrogen limitation in fed-batch mode and were compared to bacteria grown in batch culture without nutrient limitation. The cultures were carried out in a 3 L bioreactor with an external nitrogen supply of ammonium at a flow of 0.123 L h-1. The specific maximum growth rate was 0.42 h-1 in batch and 0.45 h-1 in the exponential phase of the fed-batch. The analysis of sporulation did not show any significant difference between the biomass coming from the fed-batch and batch cultures. It was found that maximum cadmium adsorption capacity varied with culture strategy. The dry biomass grown without nutrient limitation exhibited a maximum adsorption capacity for cadmium of 65.0 mgCd g-1biomass. Conversely, the limited biomass achieved a lower cadmium adsorption capacity of approximately 36.0 mgCd g-1biomass. FTIR analysis showed that nitrogen limitation induced changes in the composition of the outer cell wall, specifically an increase of deacetlylated polysaccharides, reducing the relative amount of secondary amines and proteins from the peptidoglycan matrix. Amino groups from acetylated polysaccharides and proteins have been associated elsewhere with greater cadmium affinity, which could explain the poor results obtained with the nitrogen-restricted biomass. This study shows that new physiological states displaying different adsorption capabilities were effectively obtained by engineering the cell coverage of the bacteria using varying culture strategies. The fed-batch culture proved to be a valuable tool for studying PGPR strains for biosorption and other applications. Exploring diverse nutrient limitations and other pollutants in this bacterium and other members of the PGPR family offer great opportunities to tailor biosorption strategies based on specific conditions, ultimately contributing to sustainable environmental solutions.

Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation

Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.

Influences of Bacillus pumilus SA388 as an environmentally friendly antibiotic alternative on growth performance, blood biochemistry, immunology, cecal microbiota, and meat quality in broiler chickens

The widespread use of antibiotics causes the development of antibiotic-resistant bacterial strains, which have a severe impact on poultry productivity and human health. As a result, research is continuing to develop safe natural antibiotic alternatives. In the current study, Bacillus pumilus SA388 was isolated from the chicken feces and confirmed to be a probiotic. The selected strain was tested for its antimutagenic and antioxidant capabilities before being employed as a probiotic food supplement and antibiotic alternative. The effect of B. pumilus SA388 impact on broiler chickens' growth performance, gut microbiome, blood biochemical markers, immunological response, and meat quality was also studied. B. pumilus SA388 showed significant bactericidal activity against Streptococcus pyogenes, Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, Salmonella typhi, and Klebsiella pneumonia. A total of 200 chickens were used in the present study, divided equally among four experimental groups (ten birds per group with 5 replicates): group 1 (control, G1) received a basal diet without B. pumilus SA388, group 2 (G2) received a basal diet supplemented with 0.4 mg/kg of B. pumilus SA388, group 3 (G3) received a basal diet supplemented with 0.8 mg/kg of B. pumilus SA388, and group 4 (G4) received a basal diet supplemented with 1.6 mg/kg of B. pumilus SA388. Over 35 d, the B. pumilus SA388-supplemented groups outperformed the G1 in terms of body weight gain, performance index, and feed conversion ratio, with a preference for the G4 treatment. The levels of alanine aminotransferase (ALT), aspartate transaminase (AST), low-density lipoprotein (LDL), and total cholesterol decreased significantly (P < 0.05) with increasing B. pumilus SA388 dosages compared to the control G1 group. Dietary supplementation of B. pumilus SA388 at 1.6 mg/kg (G4) significantly (P < 0.05) resulted in improved lipid profile, immunological response, thyroid function, and gut microbiota compared to the control group (G1). Compared to the broilers in the control treatment (G1), the addition of B. pumilus SA388 to broilers in G4 significantly (P < 0.05) enhanced juiciness, tenderness, aroma, and taste. Adding B. pumilus SA388 to chicken feed at different doses significantly (P < 0.05) decreased average feed intake while increasing economic and relative efficiency measures. In conclusion, B. pumilus SA388 has been proven to be an effective antibiotic and nutritional supplement.

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.

Characterization and comparative genomic analysis of a marine Bacillus phage reveal a novel viral genus

Bacillus pumilus exhibits substantial economic significance, with its metabolism, adaptability, and ecological functions regulated by its bacteriophages. Here, we isolated and characterized a novel temperate phage vB_BpuM-ZY1 from B. pumilus derived from mangrove sediments by mitomycin C induction. Phage vB_BpuM-ZY1 is a typical myophage, which has an icosahedral head with a diameter of 43.34 ± 2.14 nm and a long contractible tail with a length of 238.58 ± 5.18 nm. Genomic analysis indicated that vB_BpuM-ZY1 encodes genes for lysogeny control, and its life cycle may be intricately regulated by multiple mechanisms. vB_BpuM-ZY1 was predicted to employ P2-like 5'-extended-cos packaging strategy. In addition, genome-wide phylogenetic tree and proteome tree analyses indicated that vB_BpuM-ZY1 belongs to the Peduoviridae family but forms a separate branch at a deeper taxonomic level. Particularly, the comparative genomic analysis showed that vB_BpuM-ZY1 has less than 70% intergenomic similarities with its most similar phages. Thus, we propose that vB_BpuM-ZY1 is a novel Bacillus phage belonging to a new genus under the Peduoviridae family. The protein-sharing network analysis identified 44 vB_BpuM-ZY1-related phages. Interestingly, these evolutionarily related myophages infect a broad range of hosts across different phyla, which may be explained by the high structural variations of the host recognition domain in their central spike proteins. Collectively, our study will contribute to our understanding of Bacillus phage diversity and Bacillus-phage interactions, as well as provide essential knowledge for the industrial application of B. pumilus.

IMPORTANCE

Although recent metagenomics research has obtained a wealth of phage genetic information, much of it is considered "dark matter" because of the lack of similarity with known sequences in the database. Therefore, the isolation and characterization of novel phages will help to interpret the vast unknown viral metagenome data and improve our understanding of phage diversity and phage-host interactions. Bacillus pumilus shows high economic relevance due to its wide applications in biotechnology, industry, biopharma, and environmental sectors. Since phages influence the abundance, metabolism, evolution, fitness, and ecological functions of bacteria through complex interactions, the significance of isolation and characterization of novel phages infecting B. pumilus is apparent. In this study, we isolated and characterized a B. pumilus phage belonging to a novel viral genus, which provides essential knowledge for phage biology as well as the industrial application of B. pumilus.

Transformation and degradation of tebuconazole and its metabolites in constructed wetlands with arbuscular mycorrhizal fungi colonization

Arbuscular mycorrhizal fungi (AMF) colonization has been used in constructed wetlands (CWs) to enhance treatment performance. However, its role in azole (fungicide) degradation and microbial community changes is not well understood. This study aims to explore the impact of AMF on the degradation of tebuconazole and its metabolites in CWs. Total organic carbon levels were consistently higher with the colonization of AMF (AMF+; 9.63- 16.37 mg/L) compared to without the colonization of AMF (AMF-; 8.79-14.48 mg/L) in CWs. Notably, tebuconazole removal was swift, occurring within one day in both treatments (p = 0.885), with removal efficiencies ranging from 94.10 % to 97.83 %. That's primarily due to rapid substrate absorption at the beginning, while degradation follows with a longer time. Four metabolites were reported in CWs first time: tebuconazole hydroxy, tebuconazole lactone, tebuconazole carboxy acid, and tebuconazole dechloro. AMF decreased the abundance of tebuconazole dechloro in the liquid phase, suggesting an inhibitory effect of AMF on dechlorination processes. Furthermore, tebuconazole carboxy acid and hydroxy were predominantly found in plant roots, with a higher abundance observed in AMF+ treatments. Metagenomic analysis highlighted an increasing abundance in bacterial community structure in favor of beneficial microorganisms (xanthomonadales, xanthomonadaceae, and lysobacter), along with a notable presence of functional genes like codA, NAD, and deaD in AMF+ treatments. These findings highlight the positive influence of AMF on tebuconazole stress resilience, microbial community modification, and the enhancement of bioremediation capabilities in CWs.

Air quality in a small city: criteria pollutants, volatile organic compounds, metals, and microbes

This work presents a year-long integral study of air quality parameters in Ciudad Real, a small city in the center of Spain, and its influence on the nearby national park, Las Tablas de Daimiel. The study covers meteorological parameters and criteria pollutants such as O3, NO, NO2, SO2, and PM10. Additionally, for each month, a 1-week campaign was performed sampling air in sorbent tubes with 8-h time resolution to analyze anthropogenic volatile organic compounds and the effects of seasons, daytime, and working-weekend days. During these campaigns, 24-h PM2.5 samples were also collected to measure the load of bacteria and fungi, as well as the trace concentrations of elements.The city and the national park NOx profiles showed that emissions from the town had a non-perceivable effect on the protected area. PM10 levels in Ciudad Real were influenced by Saharan intrusions, as was the national park; however, Ciudad Real had a higher contribution from anthropogenic sources. Ozone levels were lower in the city during the cold season due to the higher concentration of NOx and have not changed significantly in the last decade.The VOCs with higher average concentrations were toluene, m,p-xylene, benzene, methylene chloride, and o-xylene, with traffic being the main source of these pollutants in the city. For benzene and carbon tetrachloride levels, weak carcinogenic risks were estimated. In PM2.5, the most abundant metals were Na, Zn, Mg, Ca, Al, Fe, and K. The carcinogenic and non-carcinogenic risks estimated from the levels of the studied metals were negligible. Bacterial and fungal counts positively correlated with the concentration of PM2.5. Microbial community composition showed seasonal variability, with the dominance of human pathogenic bacteria which correlated with certain pollutants such as SO2. Bacillus and Cutibacterium were the most abundant genera.

Synergistic Interactions among Vacuum, Solar Heating, and UV Irradiation Enhance the Lethality of Interplanetary Space

A Planetary Atmospheric Chamber (PAC) was used to create simulations of interplanetary conditions to test the spore survival of three Bacillus spp. exposed to interacting conditions of vacuum (VAC), simulated solar heating (HEAT), and simulated solar ultraviolet irradiation (UV). Synergism was observed among the experimental factors for all three Bacillus spp. tested that suggested the increased lethality of HEAT and UV when concomitantly exposed to VAC. The most aggressive biocidal effects were observed for assays with VAC + HEAT + UV conditions run simultaneously over short time-steps. The results were used to predict the accumulation of extremely rapid Sterility Assurance Levels (SALs; def., -12 logs of bioburden reduction) measured in a few minutes to a few hours for external surfaces of interplanetary spacecraft. Furthermore, the results were extrapolated to predict that approx. 1 × 104 SAL exposures might be accumulated for external surfaces on the Europa Clipper spacecraft during a 3.5-year transit time between Venus (0.7 AU) and Mars (1.5 AU) during a series of Venus-Earth-Earth gravity assists (VEEGA trajectory) to Jovian space. The results are applicable to external spacecraft surfaces exposed to direct solar heating and UV irradiation during transits though the inner solar system.

Spore-forming bacteria in gelatin: Characterization, identification by 16S rRNA and MALDI-TOF mass spectrometry (MS), and presence of heat resistance and virulence genes

Gelatin, a versatile protein derived from collagen, is widely used in the food, pharmaceutical and medical sectors. However, bacterial contamination by spore-forming bacteria during gelatin processing represents a significant concern for product safety and quality. In this study, an investigation was carried out to explore the heat and chemical resistance, as well as the identification and characterization of spore-forming bacteria isolated from gelatin processing. The methodologies involved chemical resistance tests with drastic pH in microplates and thermal resistance tests in capillary tubes of various isolates obtained at different processing stages. In addition, phenotypic and genotypic analyses were carried out to characterize the most resistant isolates of spore-forming bacteria. The findings of this study revealed the presence of several species, including Bacillus cereus, Bacillus licheniformis, Bacillus sonorensis, Bacillus subtilis, Geobacillus stearothermophilus, and Clostridium sporogenes, with some isolates exhibiting remarkable chemical and heat resistances. In addition, a significant proportion of the most resistant isolates showed gelatinase activity (n = 19/21; 90.5 %) and the presence of heat resistance (n = 5/21; 23.8 %), and virulence genes (n = 11/21; 52.4 %). The results of this study suggest that interventions should be done in quality control practices and that process parameter adjustments and effective contamination reduction strategies should be implemented through gelatin processing.

Stochastic processes drive the dynamic assembly of bacterial communities in Salix matsudana afforested soils

Introduction

This study investigates the dynamic shifts in soil bacterial communities within a Salix matsudana afforested ecosystem transitioning from agricultural land. Understanding the temporal variability in bacterial diversity and community structures is crucial for informing forest management and conservation strategies, particularly in regions undergoing afforestation.

Methods

We employed high-throughput sequencing across three distinct months (August, September, and October) to analyze the temporal variability in bacterial community composition and diversity. Network analysis was utilized to identify keystone species and assess community stability under varying environmental conditions, including fluctuations in temperature and precipitation.

Results

We uncover significant temporal variability in bacterial diversity and community structures, which are closely tied to fluctuations in temperature and precipitation. Our findings reveal the abundance of the dominant bacterial phyla, such as Actinobacteria and Proteobacteria, which did not change overall, highlighting the stability and resilience of the microbial community across seasonal transitions. Notably, the increasing similarity in community composition from August to October indicates a reduction in species turnover, likely driven by more homogeneous environmental conditions. Through comprehensive network analysis, we identify the pivotal role of keystone species, particularly the human pathogen Nocardia, in maintaining community stability under reduced soil moisture. The observed variations in community connectivity underscore the microbial community's resilience and adaptability to seasonal shifts, with higher stability in August and October contrasting with the instability observed in September.

Discussion

These results underscore the complex interplay between stochastic and deterministic processes in bacterial community assembly, significantly shaped by prevailing environmental conditions. The insights gained from this research have far-reaching implications for forestry management and conservation strategies, particularly in regions undergoing similar afforestation efforts.

Anthrax in Humans, Animals, and the Environment and the One Health Strategies for Anthrax Control

Anthrax is a notorious disease of public health importance caused by Bacillus anthracis. The causative agent can also be used as a biological weapon. Spores of these bacteria can sustain extreme environmental conditions and remain viable in soil for decades. Domestic and wild ruminants are highly susceptible to this pathogen, which usually presents as a peracute to acute disease. In humans, cutaneous anthrax is frequent but pulmonary and enteric anthrax are more serious. Humans, animals, and the environment are all involved, making anthrax a perfect target for a One Health approach. The environment plays a key role in disease transmission. At a time when the One Health concept is not mere slogans, collaborative efforts of medical professionals, veterinarians, and environmental scientists will be valuable for the prevention and control of this disease. In this review, we discussed the transmission dynamics of anthrax in the environment, animals, and humans, as well as One Health strategies to control and prevent anthrax.

Perchlorate-tolerant bacterial strains isolated from the Mars-analog Qaidam Basin soils exposed to Earth's near space

Earth's lower near space of 20-40 km above sea level with polyextreme conditions serves as a unique Mars analog for astrobiological research to investigate the limits of life on Earth and planetary protection considerations for Mars exploration. In this study, we exposed Mars-like desert regolith to near space at a float altitude of ~35 km and isolated four bacterial strains after exposure. In addition to stress tolerance to extreme environmental stressors, these strains represent a remarkable tolerance to perchlorate that is widespread in present-day Martian soils. These extremophilic bacterial strains screened through near-space exposure could serve as promising candidates for future astrobiological research in space stations or in laboratory-based planetary simulation environments.

Identification and characterization of four Bacillus species from the intestine of hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), their antagonistic role on common pathogenic bacteria, and effects on intestinal health

As an alternative to the criticized antibiotics, probiotics have been adopted for their eco-friendly nature and ability to enhance host growth and immunity. Nevertheless, reports suggest ineffectiveness in commercially available probiotics since most are from non-fish sources; thus, this study was envisaged to isolate and characterize new Bacillus spp. from the gut of hybrid grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂) which could serve as potential probiotics. The isolation and characterization were performed based on their morphological and biochemical properties, and 16S rRNA sequencing homology analysis. A subsequent 30-day in vivo biosafety feeding trial was conducted to ascertain isolates' non-pathogenicity, as well as their effects on fish growth, and intestinal mucosal microvilli via scanning electron microscopy (SEM) analysis. Four Bacillus spp. strains, namely, B. velezensis strain PGSAK01 (accession number OQ726606), B. stercoris strain PGSAK05 (accession number OQ726607), B. velezensis strain PGSAK17 (accession number OQ726601), and B. subtilis strain PGSAK19 (accession number OQ726605), were identified and characterized in the current study. The strains showed promising probiotic properties such higher adhesion capability, higher thermotolerance, displaying higher survivability to 0.5 % bile, lower pH tolerance, γ-haemolytic activity, and multispecies characteristics. Among the 24 antibiotics tested, while all isolates showed susceptibility to 21, the PGSAK01 strain showed resistance to furazolidone antibiotics. None of the isolates showed possession of i) virulence factor genes encoding enterotoxigenic (hblA, hblC, hblD, nheA, nheB, and entFM) and emetic (cereulide synthetase gene, ces) genes, and ii) streptomycin resistance gene (vat c), ampicillin-resistant genes (mecA and bla), and vancomycin-resistant gene (van B). Nevertheless, the PGSAK01 and PGSAK17 strains showed possession of tek K, cat, and ant(4')-Ia (adenylyltransferase) (except the PGSAK01) resistant genes. All isolates displayed better antimicrobial effects against pathogenic bacteria Streptococcus agalactiae, S. iniae, Vibrio harveyi, and V. alginolyticus. The in vivo biosafety trial involved hybrid grouper fish being grouped into five (average weight 32 ± 0.94 g), namely, the group fed the basal diet void of isolate's supplementation (control), and the remaining four groups fed the basal diet with 1 × 108 CFU/g diet of individual strain PGSAK01, PGSAK05, PGSAK17, and PGSAK19 supplementation. At the end of the study, a significantly higher WGR, K (except the PGSAK01 group), VSI; lysozyme (except PGSAK01 group), total antioxidant activity, alkaline phosphatase, superoxide dismutase enzyme activities; highly dense intestinal mucosal villi (based on the scanning electron microscopy analysis); and significantly lower malondialdehyde levels were witnessed in the isolated treated groups compared to the control, supporting the results obtained in the auto-aggregation and cell-surface hydrophobicity test. This work's results have provided thought-provoking targets; thus, studies involving extensive genome sequencing and functional annotation analysis will be explored to offer unfathomable insights into their mechanisms of action and potential health benefits, further establishing the four Bacillus strains' (PGSAK01, PGSAK05, PGSAK17, and PGSAK19) potential role in probiotic fields and functional foods.

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.

A Model for Mechanical Stress Limited Bacterial Growth and Resporulation in Confinement

In this study, we propose a self-limiting growth model forBacillus subtilisspores confined within porous polyacrylamide (PA) hydrogels. We observed thatB. subtilisspores germinate into vegetative cells within the hydrogel matrix, forming spherical colonies. These colonies expand until the mechanical stress they exert on their environment surpasses the yield stress of the hydrogel, leading to formation of a nonpermeable layer that halts nutrient diffusion and forces the bacteria to resporulate. These novel observations suggest a model to explain why bacterial growth in confined environments and material interfaces may be limited, providing insight for natural phenomena and biotechnological applications involving bacterial encapsulation.

Oral probiotic administration attenuates postexercise inflammation in horses

Probiotics are commonly incorporated into equine diets to impart health and performance benefits; however, peer-reviewed evidence supporting their efficacy in horses is limited. Interestingly, bacteria from the Bacillus genus are gaining interest for their unique ability to impact metabolic, immune, and inflammatory pathways. The objective of this trial was to evaluate a selection of Bacilli for their role in altering the inflammatory response in horses to exercise. Eighteen horses were utilized in a randomized cross-over trial. Horses were randomly assigned to one of 6 starting treatments including a negative and positive control, and groups that received one of 4 probiotics (Bacillus coagulans GBI-30, 6086, Bacillus subtilis-1, Bacillus subtilis-2, or Bacillus amyloliquefaciens) top dressed to their daily ration at a rate of 8 billion CFU/d mixed into dried whey powder. All horses received a similar base diet of grass hay offered at 2.0% of bodyweight daily along with 4.54 kg of a commercially available textured horse feed. Each 3-wk phase of the trial consisted of a 2-wk dietary acclimation followed by a 1-wk exercise challenge and sample collection. Between phases, horses were offered only their base diet. On the day of exercise, horses were offered their 0700 ration and then subjected to a 2-h standardized exercise test. Blood samples were obtained prior to starting exercise and then again at 0, 2, 4, 6, 8, 24, 48, and 72-h postexercise. Horses in the positive control group were administered 0.23 mg/kg BW flunixin meglumine immediately following the 0-h sampling. Samples were analyzed for serum amyloid A (SAA), interleukin-6 (IL-6), and prostaglandin E2 (PGE2) concentrations. Data were evaluated via ANOVA using the MIXED procedure in SAS 9.4. Exercise-induced inflammation as evidenced by SAA, IL-6, and PGE2 increases postexercise. Horses consuming B. coagulans GBI-30, 6086 had reduced production of SAA, IL-6, and PGE2 compared to all other probiotic-fed groups and the negative control (P < 0.001). The positive control successfully ameliorated the postexercise inflammatory response. These data highlight the potential for B. coagulans GBI-30, 6086 to be incorporated into equine rations as a method to support optimal response to exercise or other inflammation-inducing challenges. Additional research is ongoing to elucidate the methodology by which these results occur.

Influence of phenotypic variation of Paenibacillus polymyxa E681 on growth promotion in cucumbers

The goal of the current study is to better understand how bacteria may adapt to survive under adverse environmental conditions by altering and improving their phenotypes. In this study, we report the consequences of phenotypic variation in Paenibacillus polymyxa E681 (E681), a plant growth-promoting rhizobacterium (PGPR), isolated from winter barley root that has a variety of advantageous effects on crop plants. In our previous study, two different types of bacterial cells in E681 were distinguished. We used the term F-type for the variant that doesn't produce endospores and B-type for the endospore-producing wild type. Under the circumstances of our experiment, the cucumber rhizosphere soil and the surface of the seeds produced phenotypic variance. On tryptic soy agar (TSA) plates, the B-type spontaneously converted into the F-type, but the reverse was not reversible. Intriguingly, the plant growth promotion test displayed that cucumber seedlings treated with F-type cells had characteristics resembling those of the untreated control. Whereas, growth promotion of cucumber seedlings treated with B-type depends on temperature conditions. In particular, an increased growth promotion was observed at a low temperature of 20°C. The phenotypic change from B-type to F-type did not occur at 20°C for 6 days in the growth curve analysis of E681, but it did occur on the fourth and second days at 30 and 37°C, respectively. Therefore, before using PGPR strains as a bacterial inoculant for sustainable agriculture, it is imperative to resolve phenotypic variance in these strains.

Characterization and genome mining of Bacillus subtilis BDSA1 isolated from river water in Bangladesh: A promising bacterium with diverse biotechnological applications

The metabolic versatility of Bacillus subtilis makes it useful for a wide range of applications in biotechnology, from bioremediation to industrially important metabolite production. Understanding the molecular attributes of the biocontrol characteristics of B. subtilis is necessary for its tailored use in the environment and industry. Therefore, the present study aimed to conduct phenotypic characterization and whole genome analysis of the B. subtilis BDSA1 isolated from polluted river water from Dhaka, Bangladesh to explore its biotechnological potential. The chromium reduction capacity at 100 ppm Cr (VI) showed that B. subtilis BDSA1 reduced 40 % of Cr (VI) within 24hrs at 37 °C. Exposure of this bacterium to 200 ppm cadmium resulted in 43 % adsorption following one week of incubation at 37 °C. Molecular detection of chrA and czcC gene confirmed chromium and cadmium resistance characteristics of BDSA1. The size of the genome of the B. subtilis BDSA1 was 4.2 Mb with 43.4 % GC content. Genome annotation detected the presence of numerous genes involved in the degradation of xenobiotics, resistance to abiotic stress, production of lytic enzymes, siderophore formation, and plant growth promotion. The assembled genome also carried chromium, cadmium, copper, and arsenic resistance-related genes, notably cadA, czcD, czrA, arsB etc. Genome mining revealed six biosynthetic gene clusters for bacillaene, bacillibacin, bacilysin, subtilosin, fengycin and surfactin. Importantly, BDSA1 was predicted to be non-pathogenic to humans and had only two acquired antimicrobial resistance genes. The pan-genome analysis showed the openness of the B. subtilis pan-genome. Our findings suggested that B. subtilis BDSA1 might be a promising candidate for diverse biotechnological uses.

Rapid evolutionary tuning of endospore quantity versus quality trade-off via a phase-variable contingency locus

The UV resistance of bacterial endospores is an important quality supporting their survival in inhospitable environments and therefore constitutes an essential driver of the ecological success of spore-forming bacteria. Nevertheless, the variability and evolvability of this trait are poorly understood. In this study, directed evolution and genetics approaches revealed that the Bacillus cereus pdaA gene (encoding the endospore-specific peptidoglycan-N-acetylmuramic acid deacetylase) serves as a contingency locus in which the expansion and contraction of short tandem repeats can readily compromise (PdaAOFF) or restore (PdaAON) the pdaA open reading frame. Compared with B. cereus populations in the PdaAON state, populations in the PdaAOFF state produced a lower yield of viable endospores but endowed them with vastly increased UV resistance. Moreover, selection pressures based on either quantity (i.e., yield of viable endospores) or quality (i.e., UV resistance of viable endospores) aspects could readily shift populations between PdaAON and PdaAOFF states, respectively. Bioinformatic analysis also revealed that pdaA homologs within the Bacillus and Clostridium genera are often equipped with several short tandem repeat regions, suggesting a wider implementation of the pdaA-mediated phase variability in other sporeformers as well. These results for the first time reveal (1) pdaA as a phase-variable contingency locus in the adaptive evolution of endospore properties and (2) bet-hedging between what appears to be a quantity versus quality trade-off in endospore crops.

Programming aliphatic polyester degradation by engineered bacterial spores

Enzymatic degradation of plastics is a sustainable approach to addressing the growing issue of plastic accumulation. The primary challenges for using enzymes as catalysts are issues with their stability and recyclability, further exacerbated by their costly production and delicate structures. Here, we demonstrate an approach that leverages engineered spores that display target enzymes in high density on their surface to catalyze aliphatic polyester degradation and create self-degradable materials. Engineered spores display recombinant enzymes on their surface, eliminating the need for costly purification processes. The intrinsic physical and biological characteristics of spores enable easy separation from the reaction mixture, repeated reuse, and renewal. Engineered spores displaying lipases completely degrade aliphatic polyesters and retain activity through four cycles, with full activity recovered through germination and sporulation. Directly incorporating spores into polyesters results in robust materials that are completely degradable. Our study offers a straightforward and sustainable biocatalytic approach to plastic degradation.