Development of an efficient electroporation method for rhizobacterial Bacillus mycoides strains

Construction of an efficient electroporation transformation system promotes the application of Targetron in wild-type Paenibacillus elgii 219

Paenibacillus species have attracted much attention as a promising cell factory that can yield a variety of bioactive peptides and functional exopolysaccharides. Improving the production capacity of Paenibacillus through genetic engineering is crucial for the development of bioactive natural products. This study systematically evaluated the effects of electroporation transformation parameters on the introduction of DNA into Paenibacillus elgii 219, which was isolated from soil and preserved in our lab. The transformation efficiency was improved to 1.25 × 106 transformants/μg DNA by optimizing factors including the growth and recovery media content, the growth stages of P. elgii 219, electric field strength, electroporation buffer composition, cell wall weakening, and DNA quality. The results represent the highest transformation efficiency reported thus far for Paenibacillus. This work further established a group II intron-based gene editing system suitable for P. elgii 219 for the first time. As expected, plasmid pDX4383 was successfully transferred into P. elgii 219, and a putative glycosyltransferase gene was deleted, thereby eliminating flocculent precipitation during fermentation. Taken together, this study demonstrates that the electroporation-mediated transformation of exogenous DNA combined with group II intron-based gene editing provides an effective approach for the genetic engineering of Paenibacillus bacteria.IMPORTANCEThe establishment of an efficient plasmid DNA transformation protocol for P. elgii 219 has established a robust foundation for further in-depth investigations into its physiological and metabolic processes. Additionally, the successful advancement of group II intron-mediated gene editing technology imbues P. elgii 219 with the potential to serve as a highly efficient cell factory. These accomplishments furnish novel perspectives and references for the exploration of other Paenibacillus species in environmental contexts and the development of their products with economic value.

Transformation of Gardnerella vaginalis with a Bifidobacterium-Escherichia coli shuttle vector plasmid

Gardnerella spp. significantly influence female reproductive health and are indicators of bacterial vaginosis, a common gynecological disorder. Lack of genetic tools for Gardnerella spp. is a hindrance to fully understanding their role in the vaginal microbiome, and no naturally occurring plasmids have yet been identified in these organisms. The aim of this study was to transform Gardnerella vaginalis and characterize transformants carrying Bifidobacterium-E. coli shuttle vector pKO403-lacZ'-Sp. G. vaginalis ATCC 49145 was selected for protocol development based on its high growth rate, lack of restriction activity, and susceptibility to spectinomycin. Low efficiency (~102 cfu/µg of plasmid DNA) but reproducible transformation was achieved. The expression of the spectinomycin resistance gene and the β-galactosidase gene of pKO403-lacZ'-Sp in G. vaginalis ATCC 49145 resulted in an increase in spectinomycin tolerance from 2 µg/mL (MIC) to >512 µg/mL, and an appreciable increase in β-galactosidase activity compared with the wild type. Plasmid copy number was determined to be ~3 per genome copy. Plasmid was lost rapidly in the absence of spectinomycin selection, with only ~5% of colony-forming units retaining the resistant phenotype after 24 h of growth without selection. These results demonstrate that G. vaginalis can be transformed by electroporation and that pKO403-lacZ'-Sp can be maintained and its genes expressed in this host, offering a starting point for the development of genetic tools for mechanistic studies of this important member of the vaginal microbiome.

IMPORTANCE

The healthy human vaginal microbiome is mainly dominated by Lactobacillus spp. An imbalance or shift in this population can lead to a gynecological disorder known as bacterial vaginosis (BV). In BV, there is a reduction in Lactobacillus spp. and an overgrowth of mixed anaerobes and facultative bacteria including Gardnerella spp. The reason for this increase in the Gardnerella population and associated changes in the vaginal microbiota composition is yet not understood, and a lack of genetic tools is one of the major barriers to performing mechanistic research to study the biology of these clinically significant organisms. The first step in developing genetic tools is introducing foreign DNA. In this study, we have developed a protocol for transformation and identified a plasmid that can be maintained in G. vaginalis.

Optimization of plasmid electrotransformation into Bacillus subtilis using an antibacterial peptide

Bacillus subtilis can potentially serve as an efficient expression host for biotechnology due to its ability to secrete extracellular proteins and enzymes directly into the culture medium. One of the important challenges in the biotechnology industry is to optimize the transformation conditions of B. subtilis bacteria. This study aims to provide a new method to optimize the transformation conditions and improve the transformation efficiency of B. subtilis WB600. To increase the transformation efficiency in B. subtilis, two methods of adding CM11 antibacterial peptides to the bacterial medium along with electroporation and optimizing the variables including the growth medium composition, time to adding CM11 peptide, electroporation voltage, recovery medium, and cell recovery time are used. The results of this study showed that the addition of antimicrobial peptides (AMPs) with a concentration of 2 μg/ml increases the transformation efficiency by 4 times compared to the absence of AMP in the bacterial medium. Additionally, the findings from our study indicated that the most optimal rate of transformation for B. subtilis was observed at a voltage of 7.5 kV/cm, with a recovery period of 12 h. With the optimized method, the transformation efficiency came up to 1.69 × 104 CFU/µg DNA. This improvement in transformation efficiency will be attributed to the research of expression of exogenous genes in B. subtilis, gene library construction for transformation of wild-type B. subtilis strains.

Highly Efficient Genetic Transformation Methods for the Marine Oleaginous Diatom Fistulifera solaris

The oleaginous diatom Fistulifera solaris is a promising producer of biofuel owing to the high content of the lipids. A genetic transformation technique by microparticle bombardment for this diatom was already established. However, the transformation efficiency was significantly lower than those of other diatoms. Devoting efforts to advance the genetic modifications of this diatom is crucial to unlock its full potential. In this study, we optimized the microparticle bombardment protocol, and newly established a multi-pulse electroporation protocol for this diatom. The nutrient-rich medium in the pre-culture stage played an essential role to increase the transformation efficiency of the bombardment method. On the other hand, use of the nutrient-rich medium in the electroporation experiments resulted in decreasing the efficiency because excess nutrient salts could hamper to establish the best conductivity condition. Adjustments on the number and voltage of the poring pulses were also critical to obtain the best balance between cell viability and efficient pore formation. Under the optimized conditions, the transformation efficiencies of microparticle bombardment and multi-pulse electroporation were 111 and 82 per 108 cells, respectively (37 and 27 times higher than the conventional bombardment method). With the aid of the optimized protocol, we successfully developed the transformant clone over-expressing the endogenous fat storage-inducing transmembrane protein (FIT)-like protein, which was previously found in the genome of the oleaginous diatom F. solaris and the oleaginous eustigmatophyte Nannochloropsis gaditana. This study provides powerful techniques to investigate and further enhance the metabolic functions of F. solaris by genetic engineering.

Efficient Electrotransformation of Bacillus thuringiensis for Gene Manipulation and Expression

Genetic manipulation of Bacillus spp., such as B. thuringiensis and B. cereus, is laborious and time consuming due to challenges in transformation of the plasmid DNA construct. Larger shuttle plasmids, such as pMAD, that are commonly used in markerless gene replacement are particularly difficult to transform into Bacillus spp. Here, we present robust protocols that work efficiently for the transformation of both small and large plasmid constructs into B. thuringiensis. Our protocols involve preparation of efficient electrocompetent Bacillus cells by cultivating the cells in the presence of a cell wall-weakening agent, followed by washing the cells with optimized solutions. The protocols further highlight the importance of using unmethylated plasmid DNA for the efficient transformation of B. thuringiensis. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of electrocompetent B. thuringiensis Basic Protocol 2: Transformation of B. thuringiensis.

Improving cadmium accumulation by Solanum nigrum L. via regulating rhizobacterial community and metabolic function with phosphate-solubilizing bacteria colonization

Soil cadmium (Cd) mobilized with phosphate-solubilizing bacteria (PSB), especially for strains effectively colonized in rhizosphere, is an important pathway for promoting its accumulation by Cd-hyperaccumulators. In this study, screened PSB strains, Acinetobacter pittii (AP) and Escherichia coli (EC), were used to evaluate their effects on Cd mobilization in rhizosphere, Cd accumulation by Solanum nigrum L., and rhizobacterial community and metabolic function under different colonization condition. Results indicated that AP or EC inoculated in soils significantly promoted plant growth, and simultaneously motivated Cd accumulation in S. nigrum L. by 119% and 88%, respectively, when compared with that of uninoculated treatment. Higher efficiency colonization of AP contributed to more organic acids (malic, l-proline, l-alanine, and γ-aminobutanoic) production in the rhizosphere soil and Cd accumulation by S. nigrum L., when compared with that of EC treatment. Taxonomic distribution and co-occurrence network analyses demonstrated that inoculation of AP or EC enriched dominant microbial taxa with plant growth promotion function and keystone taxa related to Cd mobilization in the rhizosphere soil, respectively. Inoculated strains up-regulated the expression of genes related to bacterial mobility, amino acid metabolism, and carbon metabolism among rhizobacterial community. Overall, this study provided a feasible method for soil Cd phytoremediation by promoting Cd mobilization with the enhancement of keystone taxa and organic acid secretion based on the high-efficiency colonization of PSB.

Electrotransformation of thermophilic bacterium Caldimonas manganoxidans

Caldimonas manganoxidans is a Gram-negative, thermophilic, bioplastic-producing bacterium that is a promising strain to overcome the drawbacks of existing bioplastic manufacturing methods. However, genetic manipulation of this species has not previously been studied. Here, we developed an optimized electrotransformation protocol for C. manganoxidans by screening conditions, including the bacterial growth phase, electroporation buffer, pulse strength, and recovery time. The optimized transformation protocol obtained (3.1 ± 0.78) × 10⁸ colony-forming units/μg DNA of plasmid pBBR1MCS-2. High transformation efficiency was observed when using plasmid DNA isolated from C. manganoxidans. The DNA methylases of Escherichia coli did not affect the transformation efficiency of C. manganoxidans. The electrotransformation technique proposed here will be beneficial for the genetic manipulation of thermophilic Caldimonas species.

Biomineralization of Cd2+ and inhibition on rhizobacterial Cd mobilization function by Bacillus Cereus to improve safety of maize grains

Reducing cadmium (Cd) bioavailability and rhizobacterial Cd mobilization functions in the rhizosphere via the inoculation of screened microbial inoculum is an environmental-friendly strategy to improve safety of crop grains. In this study, Bacillus Cereus, a model Cd resistant strain, was selected to explore its effects on Cd bioavailability and uptake, bacterial metabolic functions related to Cd mobilization. Results indicated that inoculation of Bacillus Cereus in maize roots of sand pot with water-soluble Cd (0.06-0.15 mg/kg) and soil pot with high Cd-contaminated soil (total Cd: 2.33 mg/kg; Cd extracted by NH₄NO₃: 38.6 μg/kg) could decrease water-soluble Cd ion concentration by 7.7-30.1% and Cd extracted with NH₄NO₃ solution by 7.8-22.5%, inducing Cd concentrations in maize grains reduced by 10.6-39.9% and 17.4-38.6%, respectively. Even for a single inoculation in soil, Cd concentration in maize grains still satisfy food safety requirements (Cd content: 0.1 mg/kg dry weight) due to its successful colonization on root surface of maize. Bacillus Cereus could enrich more plant growth promotion bacteria (PGPB) and down-regulate the expression of genes related to bacterial motility, membrane transports, carbon and nitrogen metabolism in the rhizosphere soil, decreasing Cd bioavailability in soil. Approximately 80% Cd²⁺ in media was transferred into intracellular, meanwhile Cd salts (sulfide and/or phosphate) were produced in Bacillus Cereus through biomineralization process. Overall, this study could provide a feasible method for improving safety of maize grains via the inoculation of Bacillus Cereus under Cd pollution.

Efficient electrotransformation of Rhodococcus ruber YYL with abundant extracellular polymeric substances via a cell wall-weakening strategy

Rhodococcus spp. have broad potential applications related to the degradation of organic contaminants and the transformation or synthesis of useful compounds. However, some Gram-positive bacteria are difficult to manipulate genetically due to low transformation efficiency. In this study, we investigated the effects of chemicals including glycine, isonicotinic acid hydrazide (INH), Tween 80 and penicillin G, as well as cell growth status, competent cell concentration, electroporation field strength, electroporation time and heat shock time, on the electrotransformation efficiency of the tetrahydrofuran-degrading bacterium Rhodococcus ruber YYL with low transformation efficiency. The highest electrotransformation efficiency was 1.60 × 106 CFU/µg DNA after parameter optimization. GmhD (D-glycero-D-manno-heptose 1-phosphate guanosyltransferase) gene, which is important in the biosynthesis of lipopolysaccharide, was deleted via the optimized electrotransformation method. Compared with wild-type strain, YYL ΔgmhD showed extremely high electrotransformation efficiency because the surface of it had no mushroom-like extracellular polymeric substances (EPS). In addition, the results showed that cell wall-weakening reagents might cause some translucent substances like EPS, to detach from the cells, increasing the electrotransformation efficiency of strain YYL. We propose that these results could provide a new strategy for unique bacteria that are rich in EPS, for which genetic manipulation systems are difficult to establish.

Factors and Conditions That Impact Electroporation of Clostridioides difficile Strains

Understanding the underlying biology of pathogens is essential to develop novel treatment options. To drive this understanding, genetic tools are essential. In recent years, the genetic toolbox available to Clostridioides difficile researchers has expanded significantly but still requires the conjugal transfer of DNA from a donor strain into C. difficile. Here we describe an electroporation-based transformation protocol that was effective at introducing existing genetic tools into different C. difficile strains.

An important risk factor for acquiring Clostridioides difficile infection is antibiotic use. Therefore, a detailed knowledge of the physiology and the virulence factors can help drive the development of new diagnostic tools and nonantibiotic therapeutic agents to combat these organisms. Several genetic systems are available to study C. difficile in the laboratory environment, and all rely on stably replicating or segregationally unstable plasmids. Currently, the transfer of plasmids into C. difficile can only be performed by conjugation using Escherichia coli or Bacillus subtilis as conjugal donors. Here we report a method to introduce plasmid DNA into C. difficile using electroporation and test factors that might contribute to higher transformation efficiencies: osmolyte used to stabilize weakened cells, DNA concentration, and recovery time postelectroporation. Depending on the C. difficile strain and plasmid used, this transformation protocol achieves between 20 and 200 colonies per microgram of DNA and is mostly influenced by the recovery time postelectroporation. Based on our findings, we recommend that each strain be tested for the optimum recovery time in each lab.

IMPORTANCE Understanding the underlying biology of pathogens is essential to develop novel treatment options. To drive this understanding, genetic tools are essential. In recent years, the genetic toolbox available to Clostridioides difficile researchers has expanded significantly but still requires the conjugal transfer of DNA from a donor strain into C. difficile. Here we describe an electroporation-based transformation protocol that was effective at introducing existing genetic tools into different C. difficile strains.

Rapid immobilization of viable Bacillus pseudomycoides in polyvinyl alcohol/glutaraldehyde hydrogel for biological treatment of municipal wastewater

A new approach for easy synthesis of Bacillus pseudomycoides immobilized polyvinyl alcohol (PVA)/glutaraldehyde (GA) hydrogel for application in a wastewater treatment system is reported. Optimization studies revealed that GA/PVA mass ratio of 0.03 and acidic pH of 2 were required for hydrogel synthesis and eventually for bacterial cell immobilization. The synthesized crosslinked matrix possessed a pore size suitable for microbial cell entrapment while maintaining cell accessibility to external environment for bioremediation. Possible crosslinking and bacterial cell immobilization in the hydrogel were evidenced by FTIR, XRD, and SEM studies, respectively. Further, the extent of crosslinking of GA with PVA was investigated and confirmed by transmittance and permeability experiments. The viability and proliferation of hydrogel embedded cells (after 25 days) was confirmed by confocal fluorescence microscopy which also indicated that acidic pH of polymer solution did not affect the immobilized live cells. B. pseudomycoides immobilized hydrogel were demonstrated to be effective for treatment of municipal wastewater and reduced biochemical oxygen demand (BOD), chemical oxygen demand (COD), and protein content below the recommended levels. Overall, the results from this bench-scale work show that employing bacteria-embedded PVA/GA hydrogel for the treatment of municipal wastewater yield promising results which should be further explored in pilot/field-scale studies.

Artificial transformation methodologies for improving the efficiency of plasmid DNA transformation and simplifying its use

The uptake of exogenous DNA materials through the cell membrane by bacteria, known as transformation, is essential for the genetic manipulation of bacteria and, thus, plays key roles in biotechnological and biological research. The efficiency of natural transformation is very low; therefore, various artificial transformation methods have been developed for simple and efficient bacterial transformation. The basic bacterial transformation method is based on chemical, physical, and electrical processes and other means to permeabilize the bacterial cell membrane to allow plasmid DNA uptake. With the introduction of novel chemicals, materials, and devices and the optimization of protocols, new transformation methods have become simpler, cheaper, and more reproducible for use in diverse bacterial species compared with conventional methods. In this review, artificial transformation methods have been classified according to the membrane-permeabilizing mechanisms employed by them. Their influential factors, transformation efficiency, advantages, disadvantages, and practical applications are briefly illustrated. Finally, physicochemical transformation as a new bacterial transformation technique has also been described.

Biofilm Formation and Synthesis of Antimicrobial Compounds by the Biocontrol Agent Bacillus velezensis QST713 in an Agaricus bisporus Compost Micromodel

Bacillus velezensis QST713 is widely used as a biological control agent for crop protection and disease suppression. This strain is used industrially in France for the protection of Agaricus bisporus against Trichoderma aggressivum f. europaeum, which causes green mold disease. The efficacy of this biocontrol process was evaluated in a previous study, yet the mode of its action has not been explored under production conditions. In order to decipher the underlying biocontrol mechanisms for effective biofilm formation by strain QST713 in the compost and for the involvement of antimicrobial compounds, we developed a simplified micromodel for the culture of A. bisporus during its early culture cycle. By using this micromodel system, we studied the transcriptional response of strain QST713 in the presence or absence of A. bisporus and/or T. aggressivum in axenic industrial compost. We report the overexpression of several genes of the biocontrol agent involved in biofilm formation in the compost compared to their expression during growth in broth compost extract either in the exponential growth phase (the epsC, blsA, and tapA genes) or in the stationary growth phase (the tapA gene), while a gene encoding a flagellar protein (hag) was underexpressed. We also report the overexpression of Bacillus velezensis QST713 genes related to surfactin (srfAA) and fengycin (fenA) production in the presence of the fungal pathogen in the compost.IMPORTANCE Biocontrol agents are increasingly used to replace chemical pesticides to prevent crop diseases. In the button mushroom field in France, the use of Bacillus velezensis QST713 as a biocontrol agent against the green mold Trichoderma aggressivum has been shown to be efficient. However, the biocontrol mechanisms effective in the Agaricus bisporus/Trichoderma aggressivum/Bacillus velezensis QST713 pathosystem are still unknown. Our paper focuses on the exploration of the bioprotection mechanisms of the biocontrol agent Bacillus velezensis QST713 during culture of the button mushroom (Agaricus bisporus) in a micromodel culture system to study the specific response of strain QST713 in the presence of T. aggressivum and/or A. bisporus.

An Improved Method of Preparing High Efficiency Transformation Escherichia coli with Both Plasmids and Larger DNA Fragments

The high-throughput, cost-efficient transformation systems determine the success of gene cloning and functional analysis. Among various factors that affect this transformation systems, the competence ability of target cells is one of the most important factors. We found antimicrobial peptides LFcin-B can increase the permeability of the cell membrane, and their lethal antibacterial properties can be inhibited by moderately high concentrations of Ca2+ and Mn2+. In this study, we established a convenient and rapid method (CRM) by adding small concentrations of (0.35 mg/L) and moderately high concentrations of MnCl2 (50 mM) and CaCl2 (30 mM) in transformation buffer. The transformation efficiency of E. coli cells (DH5α, JM109 and TOP10) prepared by CRM were comparable with electroporation for plasmid transformation (3.1 ± 0.3 × 109 cfu/µg). Unlike competent cells prepared using other chemical methods, those obtained using CRM method are extremely competent for receiving larger size DNA fragments (> 5000 bp) into plasmid vectors. The competent E. coli cells prepared by CRM method are particularly useful for most high-efficiency transformation experiments under normal laboratory conditions.

Exploring plant-microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR-Cas9 system

Bacillus subtilis HS3 and Bacillus mycoides EC18 are two rhizosphere-associated bacteria with plant growth-promoting activity. The CRISPR-Cas9 system was implemented to study various aspects of plant-microbe interaction mechanisms of these two environmental isolates. The results show that fengycin and surfactin are involved in the antifungal activity of B. subtilis HS3. Moreover, this strain emits several other volatile organic compounds than 2,3-butanediol, contributing to plant growth promotion. Confocal laser scanning microscopy observations of the GFP-labelled strain showed that HS3 selectively colonizes root hairs of grass (Lolium perenne) in a hydroponic system. For B. mycoides EC18, we found that the wild-type EC18 strain and a ΔasbA (petropectin-deficient) mutant, but not the ΔdhbB (bacillibactin-deficient) and ADKO (asbA and dhbB double knockout) mutants, can increase the plant biomass and total chlorophyll. All the mutant strains have a reduced colonization capability on Chinese cabbage (Brassica rapa) roots, at the root tip and root hair region compared with the wild-type strain. These results indicate that the siderophore, bacillibactin, is involved in the plant growth promoting activity and could affect the root colonization of B. mycoides. Collectively, the CRISPR-Cas9 system we developed for environmental isolates is broadly applicable and will facilitate deciphering the mechanisms of Bacillus-plant interactions. © 2018 The Authors.

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates

Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides, a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant–microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability in the two environments. Altogether, the presented transcriptome profiles provide highly improved insights into the life strategies of plant-associated endophytes and soil isolates of B. mycoides.