Advances in engineered Bacillus subtilis biofilms and spores, and their applications in bioremediation, biocatalysis, and biomaterials

First insights into the prevalence, genetic characteristics, and pathogenicity of Bacillus cereus from generations worldwide

Bacillus cereus, a global threat, is one of the major causes of toxin-induced foodborne diseases. However, a comprehensive assessment of the prevalence and characteristics of B. cereus worldwide is still lacking. Here, we applied whole-genome sequence analysis to 191 B. cereus collected in Africa, America, Asia, Europe, and Oceania from the 1900s to 2022, finding that CC142 dominated the global B. cereus clonal complex. The results provided direct evidence that B. cereus could spread through the food chain and intercontinentally. B. cereus from different generations worldwide showed coherence in the antibiotic-resistant gene and virulence and biofilm gene profiles, although with high genomic heterogeneity. The BCI-BCII-vanZF-fosB profiles and virulence and biofilm genes were detected at high rates, and we emphasized that B. cereus would pose a serious challenge to global public health and clinical treatment.IMPORTANCEThis study first emphasized the prevalence, genetic characteristics, and pathogenicity of Bacillus cereus worldwide from the 1900s to 2022 using whole-genome sequence analysis. The CC142 dominated the global Bacillus cereus clonal complex. Moreover, we revealed a close evolutionary relationship between the isolates from different sources. B. cereus isolates from different generations worldwide showed coherence in potential pathogenicity, although with high genomic heterogeneity. The BCI-BCII-vanZF-fosB profiles and virulence and biofilm genes were detected at high rates, and we emphasized that B. cereus would pose a serious challenge to global public health and clinical treatment.

Positive effects of molybdenum on the biomineralization process on the surface of low-alloy steel catalyzed by Bacillus subtilis

The adhesion of microorganisms and the subsequent formation of mineralized layers in biofilms are of great significance in inhibiting the corrosion of metal materials. In this work, we found that the adhesion and subsequent mineralization of Bacillus subtilis on the surface of low-alloy steel are influenced by the molybdenum in the material. The addition of molybdenum will lead to increased adhesion of B. subtilis on the material surface, and the subsequent biomineralization ability has also been improved. Through transcriptome and physiological and biochemical tests, we found that molybdenum can affect the chemotaxis, mobility and carbonic anhydrase secretion related genes of B. subtilis, and then affect the formation and mineralization of the biofilm of B. subtilis.

Toward Practical Applications of Engineered Living Materials with Advanced Fabrication Techniques

Engineered Living Materials (ELMs) are materials composed of or incorporating living cells as essential functional units. These materials can be created using bottom-up approaches, where engineered cells spontaneously form well-defined aggregates. Alternatively, top-down methods employ advanced materials science techniques to integrate cells with various kinds of materials, creating hybrids where cells and materials are intricately combined. ELMs blend synthetic biology with materials science, allowing for dynamic responses to environmental stimuli such as stress, pH, humidity, temperature, and light. These materials exhibit unique "living" properties, including self-healing, self-replication, and environmental adaptability, making them highly suitable for a wide range of applications in medicine, environmental conservation, and manufacturing. Their inherent biocompatibility and ability to undergo genetic modifications allow for customized functionalities and prolonged sustainability. This review highlights the transformative impact of ELMs over recent decades, particularly in healthcare and environmental protection. We discuss current preparation methods, including the use of endogenous and exogenous scaffolds, living assembly, 3D bioprinting, and electrospinning. Emphasis is placed on ongoing research and technological advancements necessary to enhance the safety, functionality, and practical applicability of ELMs in real-world contexts.

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.

Important role of Bacillus subtilis as a probiotic and vaccine carrier in animal health maintenance

Bacillus subtilis is a widespread Gram-positive facultative aerobic bacterium that is recognized as generally safe. It has shown significant application value and great development potential in the animal farming industry. As a probiotic, it is frequently used as a feed growth supplement to effectively replace antibiotics due to its favourable effects on regulating the intestinal flora, improving intestinal immunity, inhibiting harmful microorganisms, and secreting bioactive substances. Consequently, the gut health and disease resistance of farmed animals can be improved. Both vegetative and spore forms of B. subtilis have also been utilized as vaccine carriers for delivering the antigens of infectious pathogens for over a decade. Notably, its spore form is regarded as one of the most prospective for displaying heterologous antigens with high activity and stability. Previously published reviews have predominantly focused on the development and applications of B. subtilis spore surface display techniques. However, this review aims to summarize recent studies highlighting the important role of B. subtilis as a probiotic and vaccine carrier in maintaining animal health. Specifically, we focus on the beneficial effects and underlying mechanisms of B. subtilis in enhancing disease resistance among farmed animals as well as its potential application as mucosal vaccine carriers. It is anticipated that B. subtilis will assume an even more prominent role in promoting animal health with in-depth research on its characteristics and genetic manipulation tools.

Preparation of bacterial fertilizer from biogas residue after anaerobic co-digestion of kitchen waste and residual sludge

Azotobacter chroococcum and Bacillus subtilis were selected as fermentation strains, and biogas residue after anaerobic digestion of kitchen waste and residual sludge was used as fermentation substrate. A single factor optimization test was used to optimize the solid-state fermentation parameters of biogas residue with the number of viable bacteria and the number of spores as indexes. The results showed that the optimum inoculation conditions involved the following: 55% initial moisture content, 15% initial inoculation amount, 30 ℃, and 1:1 initial inoculation ratio for 13 days. Pot experiment showed that the prepared three kinds of bacterial fertilizers could not only effectively promote the growth of white clover, improve the composition of soil nutrients, but also change the structure of soil bacterial community, which is of great significance to the health of soil ecosystem in white clover.

Microbial degradation of the benzimidazole fungicide carbendazim by Bacillus velezensis HY-3479

Carbendazim (methyl benzimidazol-2-ylcarbamate: MBC) is a fungicide of the benzimidazole group that is widely used in the cultivation of pepper, ginseng, and many other crops. To remove the remnant carbendazim, many rhizobacteria are used as biodegradation agents. A bacterial strain of soil-isolated Bacillus velezensis HY-3479 was found to be capable of degrading MBC in M9 minimal medium supplemented with 250 mg/L carbendazim. The strain had a significantly higher degradation efficiency compared to the control strain Bacillus subtilis KACC 15590 in high-performance liquid chromatography (HPLC) analysis, and HY-3479 had the best degradation efficiency of 76.99% at 48 h. In gene expression analysis, upregulation of carbendazim-degrading genes (mheI, hdx) was observed in the strain. HY-3479 was able to use MBC as the sole source of carbon and nitrogen, but the addition of 12.5 mM NH4NO3 significantly increased the degradation efficiency. HPLC analysis showed that the degradation efficiency increased to 87.19% when NH4NO3 was added. Relative gene expression of mheI and hdx also increased for samples with NH4NO3 supplementation. The enzyme activity of the carbendazim-degrading enzyme and the 2-aminobenzimidazole-degrading enzyme was found to be highly present in the HY-3479 strain. It is the first reported B. velezensis strain to biodegrade carbendazim (MBC). The biodegradation activity of strain HY-3479 may be developed as a useful means for bioremediation and used as a potential microbial agent in sustainable agriculture.

Treatment of low-pH rubber wastewater using ureolytic bacteria and the production of calcium carbonate precipitate for soil stabilization

Rubber wastewater contains variable low pH with a high load of nutrients such as nitrogen, phosphorous, suspended solids, high biological oxygen demand (BOD), and chemical oxygen demand (COD). Ureolytic and biofilm-forming bacterial strains Bacillus sp. OS26, Bacillus cereus OS36, Lysinibacillus macroides ST13, and Burkholderia multivorans DF12 were isolated from rubber processing centres showed high urease activity. Microscopic analyses evaluated the structural organization of biofilm. Extracellular polymeric substances (EPS) matrix of the biofilm of the strains showed the higher abundance of polysaccharides and lipids which help in the attachment and absorption of nutrients. The functional groups of polysaccharides, proteins, and lipids present in EPS were revealed by ATR-FTIR and 1H NMR. A consortium composed of B. cereus OS36, L. macroides ST13, and B. multivorans DF12 showed the highest biofilm formation, and efficiently reduced 62% NH3, 72% total nitrogen, and 66% PO43-. This consortium also reduced 76% BOD, 61% COD, and 68% TDS. After bioremediation, the pH of the remediated wastewater increased to 11.19. To reduce the alkalinity of discharged wastewater, CaCl2 and urea were added for calcite reaction. The highest CaCO3 precipitate was obtained at 24.6 mM of CaCl2, 2% urea, and 0.0852 mM of nickel (Ni2+) as a co-factor which reduced the pH to 7.4. The elemental composition of CaCO3 precipitate was analyzed by SEM-EDX. XRD analysis of the bacterially-induced precipitate revealed a crystallinity index of 0.66. The resulting CaCO3 precipitate was used as soil stabilizer. The precipitate filled the void spaces of the treated soil, reduced the permeability by 80 times, and increased the compression by 8.56 times than untreated soil. Thus, CaCO3 precipitated by ureolytic and biofilm-forming bacterial consortium through ureolysis can be considered a promising approach for neutralization of rubber wastewater and soil stabilization.

Comparative negation of amphiphile production using nutrition factors: Amyloids versus biosurfactants

Microbial amphiphiles play an important role in environmental activities such as microbial signaling, bioremediation, and biofilm formation. Microorganisms rely on their unique characteristics of interfaces to carry out critical biological functions, which are helped by amphipathic biomolecules known as amphiphiles. Bacillus amyloids aid in cell adhesion and biofilm formation. Pseudomonas sp. are essential in biofilm development and are a vital survival strategy for many bacteria. Furthermore, Pseudomonas and Bacillus are well-known for their ability to produce biosurfactants with a range of applications, including bioremediation and removing biological pollutants from different environments. The study employed 31 different media types and a range of analytical techniques to assess the presence of amyloid proteins and the absence of biosurfactants in Bacillus licheniformis K125 (GQ850525.1) and Pseudomonas fluorescens CHA0. The presence of amyloid proteins was confirmed through Congo red and thioflavin T staining. The carefully constructed medium also efficiently inhibited the synthesis of biosurfactants by these bacteria. Additionally, surface tension measurements, emulsification index, thin-layer chromatography, and high-performance thin-layer chromatography analyses indicated the absence of biosurfactants in the tested media.

Enhanced exopolysaccharide production in gamma irradiated Bacillus subtilis: A biofilm-mediated strategy for ZnO nanoparticles removal

Biofilm-mediated strategy was studied for ZnO nanoparticle removal from aqueous media. Bacillus subtilis isolated from the soil rhizosphere was selected based on its high viscosity (133 Pa/s) of the cultivated culture and biofilm formation. The bacterium was exposed to gamma-irradiation to enhance EPS production along with its cultivation in EPS-producing media. The results show an increase in viscosity that reached 160 Pa/s at 2 kGy. EPS production increased from 4.45 to 7.95 mg/mL and the protein/carbohydrate ratio increased from 3 to 4.4 which reflects the stickiness of EPS. Thermal Gravimetric Analysis (TGA) showed 2 phase weight loss for gamma irradiated EPS and defined protein peaks when characterized using Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF). Native and gamma-irradiated Bacillus subtilis cells with their enhanced EPS were grown as a biofilm on sterile waste gauze fabric, Scanning Electron Microscopy (SEM) showed an increased biofilm attachment in gamma-irradiated samples. The latter was used for the removal of ZnO NP from aqueous media. Energy dispersive X-ray (EDX) mapping confirms that ZnO NPs were entrapped within the carbon and oxygen elements forming the biofilm with net intensities of 14.04, 1713, and 1190, respectively. The results confirm that biofilm-mediated strategy is effective in nanoparticles removal.

Antioxidants improve β-cypermethrin degradation by alleviating oxidative damage and increasing bioavailability by Bacillus cereus GW-01

Microbial degradation of pesticide residues has the potential to reduce their hazards to human and environmental health. However, in some cases, degradation can activate pesticides, making them more toxic to microbes. Here we report on the β-cypermethrin (β-CY) toxicity to Bacillus cereus GW-01, a recently described β-CY degrader, and effects of antioxidants on β-CY degradation. GW-01 exposed to β-CY negatively affected the growth rate. The highest maximum specific growth rate (μm) appeared at 25 mg/L β-CY. β-CY induced the oxidative stress in GW-01. The activities of superoxide dismutase (SOD), catalyse (CAT), and glutathione-S-transferase (GST) were significantly higher than that in control (p < 0.01); but they are decreased as growth phase pronged, which is contrary to the β-CY degradation by GW-01 cells obtaining from various growth phase. Ascorbic acid (Vc), tea polyphenols (TP), and adenosine monophosphate (AMP) improved the degradation through changing the physiological property of GW-01. TP and AMP prompted the expression of gene encoding β-CY degradation in GW-01, while Vc does the opposite. Biofilm formation was significantly inhibited by β-CY, while was significantly enhanced by certain concentrations of TP and AMP (p < 0.05); while cell surface hydrophobicity (CSH) was negatively associated with β-CY concentrations from 25 to 100 mg/L, and these 4 antioxidants all boosted the CSH. Cells grown with β-CY had lower levels of saturated fatty acids but increased levels of some unsaturated and branched fatty acids, and these antioxidants alleviated the FA composition changes and gene expression related with FA metabolism. We also mined transcriptome analyses at lag, logarithmic, and stationary phases, and found that β-CY induced oxidative stress. The objective of this study was to elaborate characteristics in relation to the microbial resistance of pesticide poisoning and the efficiency of pesticide degradation, and to provide a promising method for improving pesticide degradation by microbes.

"3-in-1" Hybrid Biocatalysts: Association of Yeast Cells Immobilized in a Sol-Gel Matrix for Determining Sewage Pollution

This study presents a novel ″3-in-1″ hybrid biocatalyst design that combines the individual efficiency of microorganisms while avoiding negative interactions between them. Yeast cells of Ogataea polymorpha VKM Y-2559, Blastobotrys adeninivorans VKM Y-2677, and Debaryomyces hansenii VKM Y-2482 were immobilized in an organosilicon material by using the sol-gel method, resulting in a hybrid biocatalyst. The catalytic activity of the immobilized microorganism mixture was evaluated by employing it as the bioreceptor element of a biosensor. Optical and scanning electron microscopies were used to examine the morphology of the biohybrid material. Elemental distribution analysis confirmed the encapsulation of yeast cells in a matrix composed of methyltriethoxysilane (MTES) and tetraethoxysilane (TEOS) (85 and 15 vol %, respectively). The resulting heterogeneous biocatalyst exhibited excellent performance in determining the biochemical oxygen demand (BOD) index in real surface water samples, with a sensitivity coefficient of 50 ± 3 × 10-3·min-1, a concentration range of 0.3-31 mg/L, long-term stability for 25 days, and a relative standard deviation of 3.8%. These findings demonstrate the potential of the developed hybrid biocatalyst for effective pollution monitoring and wastewater treatment applications.

The Transcription Factor CsgD Contributes to Engineered Escherichia coli Resistance by Regulating Biofilm Formation and Stress Responses

The high cell density, immobilization and stability of biofilms are ideal characteristics for bacteria in resisting antibiotic therapy. CsgD is a transcription activating factor that regulates the synthesis of curly fimbriae and cellulose in Escherichia coli, thereby enhancing bacterial adhesion and promoting biofilm formation. To investigate the role of CsgD in biofilm formation and stress resistance in bacteria, the csgD deletion mutant ΔcsgD was successfully constructed from the engineered strain E. coli BL21(DE3) using the CRISPR/Cas9 gene-editing system. The results demonstrated that the biofilm of ΔcsgD decreased by 70.07% (p < 0.05). Additionally, the mobility and adhesion of ΔcsgD were inhibited due to the decrease in curly fimbriae and extracellular polymeric substances. Furthermore, ΔcsgD exhibited a significantly decreased resistance to acid, alkali and osmotic stress conditions (p < 0.05). RNA-Seq results revealed 491 differentially expressed genes between the parent strain and ΔcsgD, with enrichment primarily observed in metabolism-related processes as well as cell membrane structure and catalytic activity categories. Moreover, CsgD influenced the expression of biofilm and stress response genes pgaA, motB, fimA, fimC, iraP, ompA, osmC, sufE and elaB, indicating that the CsgD participated in the resistance of E. coli by regulating the expression of biofilm and stress response. In brief, the transcription factor CsgD plays a key role in the stress resistance of E. coli, and is a potential target for treating and controlling biofilm.

Phenotypically complex living materials containing engineered cyanobacteria

The field of engineered living materials lies at the intersection of materials science and synthetic biology with the aim of developing materials that can sense and respond to the environment. In this study, we use 3D printing to fabricate a cyanobacterial biocomposite material capable of producing multiple functional outputs in response to an external chemical stimulus and demonstrate the advantages of utilizing additive manufacturing techniques in controlling the shape of the fabricated photosynthetic material. As an initial proof-of-concept, a synthetic riboswitch is used to regulate the expression of a yellow fluorescent protein reporter in Synechococcus elongatus PCC 7942 within a hydrogel matrix. Subsequently, a strain of S. elongatus is engineered to produce an oxidative laccase enzyme; when printed within a hydrogel matrix the responsive biomaterial can decolorize a common textile dye pollutant, indigo carmine, potentially serving as a tool in environmental bioremediation. Finally, cells are engineered for inducible cell death to eliminate their presence once their activity is no longer required, which is an important function for biocontainment and minimizing environmental impact. By integrating genetically engineered stimuli-responsive cyanobacteria in volumetric 3D-printed designs, we demonstrate programmable photosynthetic biocomposite materials capable of producing functional outputs including, but not limited to, bioremediation.

Plant Growth Promotion Using Bacillus cereus

Plant growth-promoting bacteria (PGPB) appear to be a sensible competitor to conventional fertilization, including mineral fertilizers and chemical plant protection products. Undoubtedly, one of the most interesting bacteria exhibiting plant-stimulating traits is, more widely known as a pathogen, Bacillus cereus. To date, several environmentally safe strains of B. cereus have been isolated and described, including B. cereus WSE01, MEN8, YL6, SA1, ALT1, ERBP, GGBSTD1, AK1, AR156, C1L, and T4S. These strains have been studied under growth chamber, greenhouse, and field conditions and have shown many significant traits, including indole-3-acetic acid (IAA) and aminocyclopropane-1-carboxylic acid (ACC) deaminase production or phosphate solubilization, which allows direct plant growth promotion. It includes an increase in biometrics traits, chemical element content (e.g., N, P, and K), and biologically active substances content or activity, e.g., antioxidant enzymes and total soluble sugar. Hence, B. cereus has supported the growth of plant species such as soybean, maize, rice, and wheat. Importantly, some B. cereus strains can also promote plant growth under abiotic stresses, including drought, salinity, and heavy metal pollution. In addition, B. cereus strains produced extracellular enzymes and antibiotic lipopeptides or triggered induced systemic resistance, which allows indirect stimulation of plant growth. As far as biocontrol is concerned, these PGPB can suppress the development of agriculturally important phytopathogens, including bacterial phytopathogens (e.g., Pseudomonas syringae, Pectobacterium carotovorum, and Ralstonia solanacearum), fungal phytopathogens (e.g., Fusarium oxysporum, Botrytis cinerea, and Rhizoctonia solani), and other phytopathogenic organisms (e.g., Meloidogyne incognita (Nematoda) and Plasmodiophora brassicae (Protozoa)). In conclusion, it should be noted that there are still few studies on the effectiveness of B. cereus under field conditions, particularly, there is a lack of comprehensive analyses comparing the PGP effects of B. cereus and mineral fertilizers, which should be reduced in favor of decreasing the use of mineral fertilizers. It is also worth mentioning that there are still very few studies on the impact of B. cereus on the indigenous microbiota and its persistence after application to soil. Further studies would help to understand the interactions between B. cereus and indigenous microbiota, subsequently contributing to increasing its effectiveness in promoting plant growth.

Development of a biofilm-forming bacterial consortium and quorum sensing molecules for the degradation of lignin-containing organic pollutants

The presence of lignin along with other pollutants makes effluent more complex when it is discharged from Pulp and paper mills. The present study investigates the use of biofilm-forming bacteria isolated from pulp paper mill effluent contaminated sites (PPMECSs) for lignin degradation. Isolated biofilm-forming and lignin-degrading bacteria were identified as Bacillus subtilis, Enterobacter cancerogenus, and Bacillus licheniformis by 16S rRNA gene sequencing. Thin liquid chromatography (TLC) analysis showed that the consortium of bacteria produced acyl-homoserine lactone (AHL) as quorum sensing molecules and extracellular polymeric substances (EPS) that protect the bacterial consortium under unfavorable conditions. The potential consortium was able to reduce lignin (900 ppm) by 73% after 8 days of incubation in a minimal salt medium containing kraft lignin and glucose at pH 7.0 and 37 °C as compared to individual strains. The degradation by-products were identified as amides, alcohols, and acids. The major organic pollutants in the effluent were reduced after treatment of the constructed consortium, thus confirming active biotransformation and biodegradation of the lignin. Microscopic examination also indicated the presence of lignin induced biofilm formation. Hence, the constructed biofilm-forming bacterial consortia based on quorum sensing offered a sustainable and effective solution to treat lignin-containing complex pollutants.

Water a major source of endocrine-disrupting chemicals: An overview on the occurrence, implications on human health and bioremediation strategies

Endocrine disrupting chemicals (EDCs) are toxic compounds that occur naturally or are the output of anthropogenic activities that negatively impact both humans and wildlife. A number of diseases are associated with these disruptors, including reproductive disorders, cardiovascular disorders, kidney disease, neurological disorders, autoimmune disorders, and cancer. Due to their integral role in pharmaceuticals and cosmetics, packaging companies, agro-industries, pesticides, and plasticizers, the scientific awareness on natural and artificial EDCs are increasing. As these xenobiotic compounds tend to bioaccumulate in body tissues and may also persist longer in the environment, the concentrations of these organic compounds may increase far from their original point of concentrations. Water remains as the major sources of how humans and animals are exposed to EDCs. However, these toxic compounds cannot be completely biodegraded nor bioremediated from the aqueous medium with conventional treatment strategies thereby requiring much more efficient strategies to combat EDC contamination. Recently, genetically engineered microorganism, genome editing, and the knowledge of protein and metabolic engineering has revolutionized the field of bioremediation thereby helping to breakdown EDCs effectively. This review shed lights on understanding the importance of aquatic mediums as a source of EDCs exposure. Furthermore, the review sheds light on the consequences of these EDCs on human health as well as highlights the importance of different remediation and bioremediation approaches. Particular attention is paid to the recent trends and perspectives in order to attain sustainable approaches to the bioremediation of EDCs. Additionally, rigorous restrictions to preclude the discharge of estrogenic chemicals into the environment should be followed in efforts to combat EDC pollution.

Steam explosion pretreatment coupling high-temperature short-time sterilization facilitating cellulose degradation and sporulation-regulatory gene expression in high-solid fermentation

Steam explosion coupling high-temperature short-time sterilization (SE-HTST) was exploited to modify cellulosic biomass medium properties and promote high-solid fermentation (HSF). Biomass characterization analysis showed that SE-HTST enlarged microstructural pores and cavities in solid media, providing more effective space for microbial growth. Meanwhile, SE-HTST helped to release glucose from the cellulose with 35.8 ± 4.5, 20.0 ± 2.3, and 12.3 ± 5.7 mg glucose/g dry medium at 24, 48, and 72 h of fermentation, which were 3.1, 2.3, and 1.5 times higher than that in medium from conventional thermal sterilization (CTS), respectively. SE-HTST increased the viable cell and spore number of Bacillus subtilis by 1.8 and 1.6 times at 72 h of fermentation compared to CTS. Moreover, the expressions of master transcriptional gene spo0A and the early sigma factors of sigF and sigE genes gradually increased in the SE-HTST medium, showing enhanced sporulation in HSF. Therefore, SE-HTST is an effective strategy for facilitating cellulose degradation, improving glucose nutrients in biomass medium, and promoting sporulation-regulatory gene expression during high-solid fermentation, which enhances the production of microbial ecological agents using B. subtilis significantly.

Biomaterials releasing drug responsively to promote wound healing via regulation of pathological microenvironment

Wound healing is characterized by complex, orchestrated, spatiotemporal dynamic processes. Recent findings demonstrated suitable local microenvironments were necessities for wound healing. Wound microenvironments include various biological, biochemical and physical factors, which are produced and regulated by endogenous biomediators, exogenous drugs, and external environment. Successful drug delivery to wound is complicated, and need to overcome the destroyed blood supply, persistent inflammation and enzymes, spatiotemporal requirements of special supplements, and easy deactivation of drugs. Triggered by various factors from wound microenvironment itself or external elements, stimuli-responsive biomaterials have tremendous advantages of precise drug delivery and release. Here, we discuss recent advances of stimuli-responsive biomaterials to regulate local microenvironments during wound healing, emphasizing on the design and application of different biomaterials which respond to wound biological/biochemical microenvironments (ROS, pH, enzymes, glucose and glutathione), physical microenvironments (mechanical force, temperature, light, ultrasound, magnetic and electric field), and the combination modes. Moreover, several novel promising drug carriers (microbiota, metal-organic frameworks and microneedles) are also discussed.

Microbial assemblage for solid waste bioremediation and valorization with an essence of bioengineering

Environmental solid waste bioremediation is a method of treating contaminated solid waste that involves changing ecological conditions to foster the growth of a broad spectrum of microorganisms and the destruction of the target contaminants. A wide range of microorganisms creates metabolites that may break down and change solid waste-based pollution to various value-added molecules. Diverse bioremediation technologies, their limitations, and the procedure involve recycling solid waste materials from the environment. The existing environmental solid waste disposal services are insufficient and must be upgraded with more lucrative recovery, recycling, and reuse technologies to decrease the enormous expenditures in treatment procedures. Bioremediation of solid waste eliminates the toxic components. It restores the site with the advent of potential microbial communities towards solid waste valorization utilizing agriculture solid waste, organic food waste, plastic solid waste, and multiple industrial solid wastes.Bioengineering on diverse ranges of microbial regimes has accelerated to provide extra momentum toward solid waste recycling and valorization. This approach increases the activity of bioremediating microbes in the commercial development of waste treatment techniques and increases the cost-effective valuable product generation. This framework facilitates collaboration between solid waste and utilities. It can aid in establishing a long-term management strategy for recycling development with the advent of a broad spectrum of potential microbial assemblages, increasing solid waste contamination tolerance efficiency and solid waste degradability. The current literature survey extensively summarises solid waste remediation valorization using a broad spectrum of microbial assemblages with special emphasis on bioengineering-based acceleration. This approach is to attain sustainable environmental management and value-added biomolecule generation.

Corncob biochar combined with Bacillus subtilis to reduce Cd availability in low Cd-contaminated soil

Soil contamination by heavy metals such as Cd can pose a risk to the environment and human health. However, Cd is difficult to immobilize at low concentration levels in soil. Individually, Bacillus subtilis and biochar have been shown to be inefficient at immobilizing Cd in soil. In this study, corncob biochar was generated at different pyrolysis temperatures (300 °C-550 °C), and the Cd immobilization efficiency and performance of corncob biochar loaded with B. subtilis (CB@B) and corncob biochar alone (CB) were evaluated in solutions and in soil. The characterization (SEM and FTIR) of CB generated at different pyrolysis temperatures and CB generated at different pyrolysis temperatures in CB@B (300 °C-550 °C) indicated that a superior pore structure and abundant O-functional groups were obtained at a pyrolysis temperature of 400 °C for both CB@B and CB. The X-ray diffraction and X-ray photoelectron spectroscopy results indicate that the formation of Cd compounds was associated with the positive combined biosorption effect of the bacteria and biochar, electronic adsorption, activity of the O-functional groups (C[double bond, length as m-dash]O, COOH, OH, and Si-O-Si), and complexation between extracellular substances and Cd²⁺. Adsorption experiments were conducted in a solution to assess the effects of various operating parameters such as the time, pH, and adsorbent dose. The 400 °C-CB@B and 400 °C-CB samples achieved the largest reductions in the Cd concentration at 81.21% and 5.70%, respectively. Then, CaCl₂ extraction experiments were conducted in soil, and using 0.25%-CB@B, a 55.21% decrease was realized in the Cd concentration after 56 days and a 16.71% increase was realized in soil pH to 8.38. No significant difference was observed in the CB-treated groups, among which 1.0%-CB achieved the largest reduction of 26.08% after 56 days and a 3.20% increase in the soil pH to 7.41. The Tessier sequential extraction method obtained similar trends. Overall, 400 °C-CB@B demonstrated outstanding immobilization efficiency and durability, indicating that it provided a safe and nutrient-rich habitat for B. subtilis to realize a synergistic effect for Cd immobilization.

Bioremediation of Endocrine Disrupting Chemicals- Advancements and Challenges

Endocrine Disrupting Chemicals (EDCs), major group of recalcitrant compounds, poses a serious threat to the health and future of millions of human beings, and other flora and fauna for years to come. A close analysis of various xenobiotics undermines the fact that EDC is structurally diverse chemical compounds generated as a part of anthropogenic advancements as well as part of their degradation. Regardless of such structural diversity, EDC is common in their ultimate drastic effect of impeding the proper functioning of the endocrinal system, basic physiologic systems, resulting in deregulated growth, malformations, and cancerous outcomes in animals as well as humans. The current review outlines an overview of various EDCs, their toxic effects on the ecosystem and its inhabitants. Conventional remediation methods such as physico-chemical methods and enzymatic approaches have been put into action as some form of mitigation measures. However, the last decade has seen the hunt for newer technologies and methodologies at an accelerated pace. Genetically engineered microbial degradation, gene editing strategies, metabolic and protein engineering, and in-silico predictive approaches - modern day's additions to our armamentarium in combating the EDCs are addressed. These additions have greater acceptance socially with lesser dissonance owing to reduced toxic by-products, lower health trepidations, better degradation, and ultimately the prevention of bioaccumulation. The positive impact of such new approaches on controlling the menace of EDCs has been outlaid. This review will shed light on sources of EDCs, their impact, significance, and the different remediation and bioremediation approaches, with a special emphasis on the recent trends and perspectives in using sustainable approaches for bioremediation of EDCs. Strict regulations to prevent the release of estrogenic chemicals to the ecosystem, adoption of combinatorial methods to remove EDC and prevalent use of bioremediation techniques should be followed in all future endeavors to combat EDC pollution. Moreover, the proper development, growth and functioning of future living forms relies on their non-exposure to EDCs, thus remediation of such chemicals present even in nano-concentrations should be addressed gravely.

Effects of drying strategies on sporulation and titer of microbial ecological agents with Bacillus subtilis

Drying operation is beneficial to the preservation and transportation of microbial ecological agents. In this study, drying kinetics and water distribution variations in solid biomass medium during hot air drying (HAD) and vacuum freeze drying (VFD) were systematically investigated. Meanwhile, the effects of different drying strategies on the sporulation of Bacillus subtilis and the titer of microbial ecological agents were compared. The results showed that both HAD and VFD induced rapid water removal from the solid biomass medium. VFD retained bound water and maintained the porous structure of the solid medium. Both HAD and VFD induced sporulation. The expression level of sporulation-regulatory genes spo0A, sigF, and sigE followed the order 80°C-HAD > 60°C-HAD > VFD. The spore number in the medium after 80°C-HAD drying for 6 h was 0.72 × 10¹⁰/g dry medium, which was 9.1 and 12.5% larger than that of the medium with 60°C-HAD and VFD, respectively. Therefore, 80°C-HAD is an effective drying strategy for promoting sporulation, which improves the titer of microbial ecological agents with B. subtilis.

Three-dimensional bioprinting: A cutting-edge tool for designing and fabricating engineered living materials

The design of engineered living materials (ELMs) is an emerging field developed from synthetic biology and materials science principles. ELMs are multi-scale bulk materials that combine the properties of self-healing and organism adaptability with the designed physicochemical or mechanical properties for functional applications in various fields, including therapy, electronics, and architecture. Among the many ELM design and manufacturing methods, three-dimensional (3D) bioprinting stands out for its precise control over the structure of the fabricated constructs and the spatial distribution of cells. In this review, we summarize the progress in the field, cell type and material selection, and the latest applications of 3D bioprinting to manufacture ELMs, as well as their advantages and limitations, hoping to deepen our understanding and provide new insights into ELM design. We believe that 3D bioprinting will become an important development direction and provide more contributions to this field.

The context matrix: Navigating biological complexity for advanced biodesign

Synthetic biology offers many solutions in healthcare, production, sensing and agriculture. However, the ability to rationally engineer synthetic biosystems with predictable and robust functionality remains a challenge. A major reason is the complex interplay between the synthetic genetic construct, its host, and the environment. Each of these contexts contains a number of input factors which together can create unpredictable behaviours in the engineered biosystem. It has become apparent that for the accurate assessment of these contextual effects a more holistic approach to design and characterisation is required. In this perspective article, we present the context matrix, a conceptual framework to categorise and explore these contexts and their net effect on the designed synthetic biosystem. We propose the use and community-development of the context matrix as an aid for experimental design that simplifies navigation through the complex design space in synthetic biology.

Biosurfactant from Bacillus subtilis DS03: Properties and Application in Cleaning Out Place System in a Pilot Sausages Processing

Biosurfactants (BS) are amphiphilic molecules that align at the interface reducing the surface tension. BS production is developed as an alternative to synthetic surfactants because they are biodegradable, with low toxicity and high specificity. BS are versatile, and this research proposes using a biosurfactant crude extract (BCE) as part of cleaning products. This paper reported the BCE production from Bacillus subtilis DS03 using a medium with molasses. The BCE product was characterized by different physical and chemical tests under a wide pH range, high temperatures, and emulsifying properties showing successful results. The water surface tension of 72 mN/m was reduced to 34 mN/m with BCE, achieving a critical micelle concentration at 24.66 ppm. BCE was also applied to polystyrene surface as pre-treatment to avoid microbial biofilm development, showing inhibition in more than 90% of Escherichia coli, Staphylococcus aureus, and Listeria monocytogenes above 2000 ppm BCE. The test continued using BCE as post-treatment to remove biofilms, reporting a significant reduction of 50.10% Escherichia coli, 55.77% Staphylococcus aureus, and 59.44% Listeria monocytogenes in a concentration higher than 250 ppm BCE. Finally, a comparison experiment was performed between sodium lauryl ether sulfate (SLES) and BCE (included in commercial formulation), reporting an efficient reduction with the mixtures. The results suggested that BCE is a promising ingredient for cleaning formulations with applications in industrial food applications.

Cecal Metabolomic Fingerprint of Unscathed Rats: Does It Reflect the Good Response to a Provocative Decompression?

On one side, decompression sickness (DCS) with neurological disorders lead to a reshuffle of the cecal metabolome of rats. On the other side, there is also a specific and different metabolomic signature in the cecum of a strain of DCS-resistant rats, that are not exposed to hyperbaric protocol. We decide to study a conventional strain of rats that resist to an accident-provoking hyperbaric exposure, and we hypothesize that the metabolomic signature put forward may correspond to a physiological response adapted to the stress induced by diving. The aim is to verify and characterize whether the cecal compounds of rats resistant to the provocative dive have a cecal metabolomic signature different from those who do not dive. 35 asymptomatic diver rats are selected to be compared to 21 rats non-exposed to the hyperbaric protocol. Because our aim is essentially to study the differences in the cecal metabolome associated with the hyperbaric exposure, about half of the rats are fed soy and the other half of maize in order to better rule out the effect of the diet itself. Lower levels of IL-1β and glutathione peroxidase (GPX) activity are registered in blood of diving rats. No blood cell mobilization is noted. Conventional and ChemRICH approaches help the metabolomic interpretation of the 185 chemical compounds analyzed in the cecal content. Statistical analysis show a panel of 102 compounds diet related. 19 are in common with the hyperbaric protocol effect. Expression of 25 compounds has changed in the cecal metabolome of rats resistant to the provocative dive suggesting an alteration of biliary acids metabolism, most likely through actions on gut microbiota. There seem to be also weak changes in allocations dedicated to various energy pathways, including hormonal reshuffle. Some of the metabolites may also have a role in regulating inflammation, while some may be consumed for the benefit of oxidative stress management.

Biofilm-mediated bioremediation is a powerful tool for the removal of environmental pollutants

Biofilm-mediated bioremediation is an attractive approach for the elimination of environmental pollutants, because of its wide adaptability, biomass, and excellent capacity to absorb, immobilize, or degrade contaminants. Biofilms are assemblages of individual or mixed microbial cells adhering to a living or non-living surface in an aqueous environment. Biofilm-forming microorganisms have excellent survival under exposure to harsh environmental stressors, can compete for nutrients, exhibit greater tolerance to pollutants compared to free-floating planktonic cells, and provide a protective environment for cells. Biofilm communities are thus capable of sorption and metabolization of organic pollutants and heavy metals through a well-controlled expression pattern of genes governed by quorum sensing. The involvement of quorum sensing and chemotaxis in biofilms can enhance the bioremediation kinetics with the help of signaling molecules, the transfer of genetic material, and metabolites. This review provides in-depth knowledge of the process of biofilm formation in microorganisms, their regulatory mechanisms of interaction, and their importance and application as powerful bioremediation agents in the biodegradation of environmental pollutants, including hydrocarbons, pesticides, and heavy metals.

Engineered Bacteria-Based Living Materials for Biotherapeutic Applications

Future advances in therapeutics demand the development of dynamic and intelligent living materials. The past static monofunctional materials shall be unable to meet the requirements of future medical development. Also, the demand for precision medicine has increased with the progressively developing human society. Therefore, engineered living materials (ELMs) are vitally important for biotherapeutic applications. These ELMs can be cells, microbes, biofilms, and spores, representing a new platform for treating intractable diseases. Synthetic biology plays a crucial role in the engineering of these living entities. Hence, in this review, the role of synthetic biology in designing and creating genetically engineered novel living materials, particularly bacteria, has been briefly summarized for diagnostic and targeted delivery. The main focus is to provide knowledge about the recent advances in engineered bacterial-based therapies, especially in the treatment of cancer, inflammatory bowel diseases, and infection. Microorganisms, particularly probiotics, have been engineered for synthetic living therapies. Furthermore, these programmable bacteria are designed to sense input signals and respond to disease-changing environments with multipronged therapeutic outputs. These ELMs will open a new path for the synthesis of regenerative medicines as they release therapeutics that provide in situ drug delivery with lower systemic effects. In last, the challenges being faced in this field and the future directions requiring breakthroughs have been discussed. Conclusively, the intent is to present the recent advances in research and biomedical applications of engineered bacteria-based therapies during the last 5 years, as a novel treatment for uncontrollable diseases.

Spores-on-a-chip: new frontiers for spore research

In recent years, microfluidic technologies have become widespread in biological science. However, the suitability of this technique for understanding different aspects of spore research has hardly been considered. Herein, we review recent developments in 'spores-on-a-chip' technologies, highlighting how they could be exploited to drive new frontiers in spore research.

Green biorefinery: Microalgae-bacteria microbiome on tolerance investigations in plants

Co-culture of microalgae and microorganisms, supported with the resulting synergistic effects, can be used for wastewater treatment, biomass production, agricultural applications and etc. Therefore, this study aimed to explore the role of Bacillus subtilis (B. subtilis) in tolerance against the harsh environment of seafood wastewater, at which these microalgal-bacterial flocs were formed by microalgae cultivation. In this present study, B. subtilis isolated from the cultivation medium of Chlorella vulgaris and exposed to different salinity (0.1-4% w/v sodium chloride) and various pH range to determine the tolerant ability and biofilm formation. Interestingly, this bacteria strain that isolated from microalgae cultivation medium showed the intense viability in the salt concentration exceeding up to 4% (w/v) NaCl but demonstrated the decrease in cell division as environmental culture undergoing over pH 10. Cell viability was recorded higher than 71% and 92% for B. subtilis inoculum in media with salt concentration greater than 20 gL^-1 and external pH 6.5-9, respectively. This showed that B. subtilis isolated from microalgal-bacteria cocultivation exhibited its tolerant ability to survive in the extremely harsh conditions and thus, mitigating the stresses due to salinity and pH.