Construction of recombinant Bacillus subtilis strains for polyhydroxyalkanoates synthesis

Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects

From its early identification by Christian Gottfried Ehrenberg to its current prominence in scientific research, Bacillus subtilis (B. subtilis) has emerged as a foundational model organism in microbiology. This comprehensive review delves deep into its genetic, physiological, and biochemical intricacies, revealing a sophisticated cellular blueprint. With the incorporation of advanced techniques such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 and integrative computational methodologies, the potential applications of B. subtilis span diverse sectors. These encompass its significant contributions to biotechnology, agriculture, and medical fields and its potential for aiding environmental cleanup efforts. Yet, as we move forward, we must grapple with concerns related to safety, ethics, and the practical implementation of our lab findings in everyday scenarios. As our understanding of B. subtilis deepens, it is evident that its contributions will be central to pioneering sustainable solutions for global challenges in the years to come.

De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain

BACKGROUND

Certain Bacillus species play a vital role in polyhydroxyalkanoate (PHA) production. However, most of these isolates did not properly identify to species level when scientifically had been reported.

RESULTS

From NGS analysis, 5719 genes were predicted in the de novo genome assembly. Based on genome annotation using RAST server, 5,527,513 bp sequences were predicted with 5679 bp number of protein-coding sequence. Its genome sequence contains 35.1% and 156 GC content and contigs, respectively. In RAST server analysis, subsystem (43%) and non-subsystem coverage (57%) were generated. Ortho Venn comparative genome analysis indicated that Bacillus sp. BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579 T (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579 T (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579 T (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579 T strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons.

CONCLUSIONS

This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.

Bacillus subtilis as a robust host for biochemical production utilizing biomass

Bacillus subtilis is regarded as a suitable host for biochemical production owing to its excellent growth and bioresource utilization characteristics. In addition, the distinct endogenous metabolic pathways and the suitability of the heterologous pathways have made B. subtilis a robust and promising host for producing biochemicals, such as: bioalcohols; bioorganic acids (lactic acids, α-ketoglutaric acid, and γ-aminobutyric acid); biopolymers (poly(γ-glutamic acid, polyhydroxyalkanoates (PHA), and polysaccharides and monosaccharides (N-acetylglucosamine, xylooligosaccharides, and hyaluronic acid)); and bioflocculants. Also for producing oligopeptides and functional peptides, owing to its efficient protein secretion system. Several metabolic and genetic engineering techniques, such as target gene overexpression and inactivation of bypass pathways, have led to the improvement in production titers and product selectivity. In this review article, recent progress in the utilization of robust B. subtilis-based host systems for biomass conversion and biochemical production has been highlighted, and the prospects of such host systems are suggested.

Processability and Degradability of PHA-Based Composites in Terrestrial Environments

In this work, composites based on poly(3-hydroxybutyrate-3-hydroxyvalerate) (PHB-HV) and waste wood sawdust (SD) fibers, a byproduct of the wood industry, were produced by melt extrusion and characterized in terms of processability, thermal stability, morphology, and mechanical properties in order to discriminate the formulations suitable for injection molding. Given their application in agriculture and/or plant nursery, the biodegradability of the optimized composites was investigated under controlled composting conditions in accordance with standard methods (ASTM D5338-98 and ISO 20200-2004). The optimized PHB-HV/SD composites were used for the production of pots by injection molding and their performance was qualitatively monitored in a plant nursery and underground for 14 months. This study presents a sustainable option of valuation of wood factory residues and lowering the production cost of PHB-HV-based compounds without affecting their mechanical properties, improving their impact resistance and biodegradability rates in terrestrial environments.

Integrated systems for biopolymers and bioenergy production from organic waste and by-products: a review of microbial processes

Recently, issues concerning the sustainable and harmless disposal of organic solid waste have generated interest in microbial biotechnologies aimed at converting waste materials into bioenergy and biomaterials, thus contributing to a reduction in economic dependence on fossil fuels. To valorize biomass, waste materials derived from agriculture, food processing factories, and municipal organic waste can be used to produce biopolymers, such as biohydrogen and biogas, through different microbial processes. In fact, different bacterial strains can synthesize biopolymers to convert waste materials into valuable intracellular (e.g., polyhydroxyalkanoates) and extracellular (e.g., exopolysaccharides) bioproducts, which are useful for biochemical production. In particular, large numbers of bacteria, including Alcaligenes eutrophus, Alcaligenes latus, Azotobacter vinelandii, Azotobacter chroococcum, Azotobacter beijerincki, methylotrophs, Pseudomonas spp., Bacillus spp., Rhizobium spp., Nocardia spp., and recombinant Escherichia coli, have been successfully used to produce polyhydroxyalkanoates on an industrial scale from different types of organic by-products. Therefore, the development of high-performance microbial strains and the use of by-products and waste as substrates could reasonably make the production costs of biodegradable polymers comparable to those required by petrochemical-derived plastics and promote their use. Many studies have reported use of the same organic substrates as alternative energy sources to produce biogas and biohydrogen through anaerobic digestion as well as dark and photofermentation processes under anaerobic conditions. Therefore, concurrently obtaining bioenergy and biopolymers at a reasonable cost through an integrated system is becoming feasible using by-products and waste as organic carbon sources. An overview of the suitable substrates and microbial strains used in low-cost polyhydroxyalkanoates for biohydrogen and biogas production is given. The possibility of creating a unique integrated system is discussed because it represents a new approach for simultaneously producing energy and biopolymers for the plastic industry using by-products and waste as organic carbon sources.

Microbial production of polyhydroxyalkanoates (PHAs) and its copolymers: A review of recent advancements

Traditional mineral oil based plastics are important commodity to enhance the comfort and quality of life but the accumulation of these plastics in the environment has become a major universal problem due to their low biodegradation. Solution to the plastic waste management includes incineration, recycling and landfill disposal methods. These processes are very time consuming and expensive. Biopolymers are important alternatives to the petroleum-based plastics due to environment friendly manufacturing processes, biodegradability and biocompatibility. Therefore use of novel biopolymers, such as polylactide, polysaccharides, aliphatic polyesters and polyhydroxyalkanoates is of interest. PHAs are biodegradable polyesters of hydroxyalkanoates (HA) produced from renewable resources by using microorganisms as intracellular carbon and energy storage compounds. Even though PHAs are promising candidate for biodegradable polymers, however, the production cost limit their application on an industrial scale. This article provides an overview of various substrates, microorganisms for the economical production of PHAs and its copolymers. Recent advances in PHAs to reduce the cost and to improve the performance of PHAs have also been discussed.

Isolation and Identification of Poly β-Hydroxybutyrate Over-Producing Bacteria and Optimization of Production Medium

Background:

Biodegradable polyesters are candidates for the development of environmental friendly plastics. Poly-β-hydroxybutyrate (PHB) is a type of polyester from the hydroxyalkanoates family, synthesized by bacteria as an intracellular material and accumulated as granules in the cytoplasm.

Objectives:

The aim of this study was to isolate Poly β-hydroxybutyrate over producing bacteria and optimize the production medium.

Materials and Methods:

A variety of PHB-accumulating bacterial strains were isolated from Kermanshah oil refinery sludge in Iran. Poly-β-hydroxybutyrate-producing bacterial strains were confirmed by the gas chromatography method. The strain with the highest rate of PHB production was selected. Use of sugar cane molasses, a by-product of the sugar refinery industry, was investigated for the production of PHB. Plackett-Burman statistical method was employed to obtain factors in cell growth and PHB production. Optimization by the Response Surface Method (RSM) was done via two carbon sources, glucose and molasses.

Results:

In the present study, 21 of 63 strains isolated from the refinery oil sludge produced PHB, seven of which were over producers. Poly-β-hydroxybutyrate production was analyzed by Sudan Black B staining, spectrophotometric and gas chromatography (GC) methods. The strain with the highest rate of PHB production was used to optimize the culture medium. Fifteen factors were analyzed in PHB production by the Plackett-Burman method to find the most effective factors. Five important factors were optimized by RSM. Molasses were used as a cheap source of carbon. The maximum PHB obtained from molasses was 6.62 g/L. The phenotypic and 16S rRNA biotyping tests led to the identification of the isolate as Bacillus coagulans.

Conclusions:

The results suggest that B. coagulans is a good candidate for the fermentative production of PHB.

Class IV polyhydroxyalkanoate (PHA) synthases and PHA-producing Bacillus

This review highlights the recent investigations of class IV polyhydroxyalkanoate (PHA) synthases, the newest classification of PHA synthases. Class IV synthases are prevalent in organisms of the Bacillus genus and are composed of a catalytic subunit PhaC (approximately 40 kDa), which has a PhaC box sequence ([GS]-X-C-X-[GA]-G) at the active site, and a second subunit PhaR (approximately 20 kDa). The representative PHA-producing Bacillus strains are Bacillus megaterium and Bacillus cereus; the nucleotide sequence of phaC and the genetic organization of the PHA biosynthesis gene locus are somewhat different between these two strains. It is generally considered that class IV synthases favor short-chain-length monomers such as 3-hydroxybutyrate (C4) and 3-hydroxyvalerate (C5) for polymerization, but can polymerize some unusual monomers as minor components. In Escherichia coli expressing PhaRC from B. cereus YB-4, the biosynthesized PHA undergoes synthase-catalyzed alcoholytic cleavage using endogenous and exogenous alcohols. This alcoholysis is thought to be shared among class IV synthases, and this reaction is useful not only for the regulation of PHA molecular weight but also for the modification of the PHA carboxy terminus. The novel properties of class IV synthases will open up the possibility for the design of new PHA materials.

Dark fermentative bioconversion of glycerol to hydrogen by Bacillus thuringiensis

Biodiesel manufacturing units discharge effluents rich in glycerol. The need is to convert crude glycerol (CG) into useful products such as hydrogen (H2). Under batch culture, Bacillusthuringiensis EGU45 adapted on pure glycerol (PG, 2% v/v) resulted in an H2 yield of 0.646 mol/mol glycerol consumed on minimal media (250 mL) supplemented with 1% ammonium nitrate at 37°C over 4 days. Here, H2 constituted 67% of the total biogas. Under continuous culture, at 2 days of hydraulic retention time, B. thuringiensis immobilized on ligno-cellulosic materials (banana leaves - BL, 10% v/v) resulted in a H2 yield of 0.386 mol/mol PG consumed. On CG, the maximal H2 yield of 0.393 mol/mol feed consumed was recorded. In brief, B. thuringiensis could transform CG, on limited resources - minimal medium with sodium nitrate, by immobilizing them on cheap and easily available biowaste, which makes it a suitable candidate for H2 production on a large scale.

Production of polyhydroxyalkanoates (PHAs) from waste materials and by-products by submerged and solid-state fermentation

Polyhydroxyalkanoates are biodegradable polymers produced by prokaryotic organisms from renewable resources. The production of PHAs by submerged fermentation processes has been intensively studied over the last 30 years. In recent years, alternative strategies have been proposed, such as the use of solid-state fermentation or the production of PHAs in transgenic plants. This paper gives an overview of submerged and solid-state fermentation processes used to produce PHAs from waste materials and by-products. The use of these low-cost raw materials has the potential to reduce PHA production costs, because the raw material costs contribute a significant part of production costs in traditional PHA production processes.

Bacillus subtilis as potential producer for polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by microbes to overcome environmental stress. Commercial production of PHAs is limited by the high cost of production compared to conventional plastics. Another hindrance is the brittle nature and low strength of polyhydroxybutyrate (PHB), the most widely studied PHA. The needs are to produce PHAs, which have better elastomeric properties suitable for biomedical applications, preferably from inexpensive renewable sources to reduce cost. Certain unique properties of Bacillus subtilis such as lack of the toxic lipo-polysaccharides, expression of self-lysing genes on completion of PHA biosynthetic process – for easy and timely recovery, usage of biowastes as feed enable it to compete as potential candidate for commercial production of PHA.

Polyhydroxyalkanoates in Gram-positive bacteria: insights from the genera Bacillus and Streptomyces

Gram-positive bacteria, notably Bacillus and Streptomyces, have been used extensively in industry. However, these microorganisms have not yet been exploited for the production of the biodegradable polymers, polyhydroxyalkanoates (PHAs). Although PHAs have many potential applications, the cost of production means that medical applications are currently the main area of use. Gram-negative bacteria, currently the only commercial source of PHAs, have lipopolysaccharides (LPS) which co-purify with the PHAs and cause immunogenic reactions. On the other hand, Gram- positive bacteria lack LPS, a positive feature which justifies intensive investigation into their production of PHAs. This review summarizes currently available knowledge on PHA production by Gram- positive bacteria especially Bacillus and Streptomyces. We hope that this will form the basis of further research into developing either or both as a source of PHAs for medical applications.