2,3-Butanediol production by the non-pathogenic bacterium Paenibacillus brasilensis

MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa

Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection. Paenibacillus polymyxa is a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of three P. polymyxa strains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging to P. polimixa species, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.

Microbial cell factories using Paenibacillus: status and perspectives

Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium Paenibacillus has been widely applied in: agriculture, medicine, industry, and environmental remediation. Paenibacillus species not only accelerate plant growth and degrade toxic substances in wastewater and soil but also produce industrially-relevant enzymes and antimicrobial peptides. Due to a lack of genetic manipulation tools and methods, exploitation of the bioresources of naturally isolated Paenibacillus species has long been limited. Genetic manipulation tools and methods continue to improve in Paenibacillus, such as shuttle plasmids, promoters, and genetic tools of CRISPR. Furthermore, genetic transformation systems develop gradually, including: penicillin-mediated transformation, electroporation, and magnesium amino acid-mediated transformation. As genetic manipulation methods of homologous recombination and CRISPR-mediated editing system have developed gradually, Paenibacillus has come to be regarded as a promising microbial chassis for biomanufacturing, expanding its application scope, such as: industrial enzymes, bioremediation and bioadsorption, surfactants, and antibacterial agents. In this review, we describe the applications of Paenibacillus bioproducts, and then discuss recent advances and future challenges in the development of genetic manipulation systems in this genus. This work highlights the potential of Paenibacillus as a new microbial chassis for mining bioresources.

Enzymes and pathways in microbial production of 2,3-butanediol and 3-acetoin isomers

2,3-Butanediol (BD) and acetoin (AC) are products of the non-oxidative metabolism of microorganisms, presenting industrial importance due to their wide range of applications and high market value. Their optical isomers have particular applications, justifying the efforts on the selective bioproduction. Each microorganism produces different isomer mixtures, as a consequence of having different butanediol dehydrogenase (BDH) enzymes. However, the whole scene of the isomer bioproduction, considering the several enzymes and conditions, has not been completely elucidated. Here we show the BDH classification as R, S or meso by bioinformatics analysis uncovering the details of the isomers production. The BDH was compared to diacetyl reductases (DAR) and the new enoyl reductases (ER). We observed that R-BDH is the most singular BDH, while meso and S-BDHs are similar and may be better distinguished through their stereo-selective triad. DAR and ER showed distinct stereo-triads from those described for BDHs, agreeing with kinetic data from the literature and our phylogenetic analysis. The ER family probably has meso-BDH like activity as already demonstrated for a single sequence from this group. These results are of great relevance, as they organize BD producing enzymes, to our known, never shown before in the literature. This review also brings attention to nontraditional enzymes/pathways that can be involved with BD/AC synthesis, as well as oxygen conditions that may lead to the differential production of their isomers. Together, this information can provide helpful orientation for future studies in the field of BD/AC biological production, thus contributing to achieve their production on an industrial scale.

Molecular characterization of Paenibacillus antarcticus IPAC21, a bioemulsifier producer isolated from Antarctic soil

Paenibacillus antarcticus IPAC21, an endospore-forming and bioemulsifier-producing strain, was isolated from King George Island, Antarctica. As psychrotolerant/psychrophilic bacteria can be considered promising sources for novel products such as bioactive compounds and other industrially relevant substances/compounds, the IPAC21 genome was sequenced using Illumina Hi-seq, and a search for genes related to the production of bioemulsifiers and other metabolic pathways was performed. The IPAC21 strain has a genome of 5,505,124 bp and a G + C content of 40.5%. Genes related to the biosynthesis of exopolysaccharides, such as the gene that encodes the extracellular enzyme levansucrase responsible for the synthesis of levan, the 2,3-butanediol pathway, PTS sugar transporters, cold-shock proteins, and chaperones were found in its genome. IPAC21 cell-free supernatants obtained after cell growth in trypticase soy broth at different temperatures were evaluated for bioemulsifier production by the emulsification index (EI) using hexadecane, kerosene and diesel. EI values higher than 50% were obtained using the three oil derivatives when IPAC21 was grown at 28°C. The bioemulsifier produced by P. antarcticus IPAC21 was stable at different NaCl concentrations, low temperatures and pH values, suggesting its potential use in lower and moderate temperature processes in the petroleum industry.

Current Advances in Microbial Production of Acetoin and 2,3-Butanediol by Bacillus spp

The growing need for industrial production of bio-based acetoin and 2,3-butanediol (2,3-BD) is due to both environmental concerns, and their widespread use in the food, pharmaceutical, and chemical industries. Acetoin is a common spice added to many foods, but also a valuable reagent in many chemical syntheses. Similarly, 2,3-BD is an indispensable chemical on the platform in the production of synthetic rubber, printing inks, perfumes, antifreeze, and fuel additives. This state-of-the-art review focuses on representatives of the genus Bacillus as prospective producers of acetoin and 2,3-BD. They have the following important advantages: non-pathogenic nature, unpretentiousness to growing conditions, and the ability to utilize a huge number of substrates (glucose, sucrose, starch, cellulose, and inulin hydrolysates), sugars from the composition of lignocellulose (cellobiose, mannose, galactose, xylose, and arabinose), as well as waste glycerol. In addition, these strains can be improved by genetic engineering, and are amenable to process optimization. Bacillus spp. are among the best acetoin producers. They also synthesize 2,3-BD in titer and yield comparable to those of the pathogenic producers. However, Bacillus spp. show relatively lower productivity, which can be increased in the course of challenging future research.

Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria

Obligate methanotrophic bacteria can utilize methane, an inexpensive carbon feedstock, as a sole energy and carbon substrate, thus are considered as the only nature-provided biocatalyst for sustainable biomanufacturing of fuels and chemicals from methane. To address the limitation of native C1 metabolism of obligate type I methanotrophs, we proposed a novel platform strain that can utilize methane and multi-carbon substrates, such as glycerol, simultaneously to boost growth rates and chemical production in Methylotuvimicrobium alcaliphilum 20Z. To demonstrate the uses of this concept, we reconstructed a 2,3-butanediol biosynthetic pathway and achieved a fourfold higher titer of 2,3-butanediol production by co-utilizing methane and glycerol compared with that of methanotrophic growth. In addition, we reported the creation of a methanotrophic biocatalyst for one-step bioconversion of methane to methanol in which glycerol was used for cell growth, and methane was mainly used for methanol production. After the deletion of genes encoding methanol dehydrogenase (MDH), 11.6 mM methanol was obtained after 72 h using living cells in the absence of any chemical inhibitors of MDH and exogenous NADH source. A further improvement of this bioconversion was attained by using resting cells with a significantly increased titre of 76 mM methanol after 3.5 h with the supply of 40 mM formate. The work presented here provides a novel framework for a variety of approaches in methane-based biomanufacturing.

Genetics and regulation of nitrogen fixation in Paenibacillus brasilensis PB24

Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N₂) present in the biosphere into biologically available forms of nitrogen. Paenibacillus brasilensis PB24 is a diazotrophic Gram-positive bacterium and is considered ecologically and industrially important because it is able to produce antimicrobial substances and 2,3-butanediol. However, the genetics and regulation of its nitrogen fixing (nif) genes have never been assessed so far. Therefore, the present study aimed to (i) identify the structural and regulatory genes related to BNF in the PB24 genome, (ii) perform comparative genomics analysis of the nif operon among different Paenibacillus species and (iii) study the expression of these genes in the presence and absence of NH₄. Strain PB24 showed a nif operon composed of nine genes (nifBHDKENXhesAV), with a conserved synteny (with small variations) among the Paenibacillus species evaluated. BNF regulatory genes, glnK and amtB (encoding GlnK signal transduction protein and AmtB transmembrane protein, respectively) and glnR and glnA genes (encoding the transcription factor GlnR and glutamine synthetase) were found in the PB24 genome. Primers were designed for qPCR amplification of the nitrogenase structural (nifH, nifD and nifK) and regulatory (glnA and amtB) BNF genes. The structural gene expression in PB24 was up- and downregulated in the absence and presence of NH₄, respectively. The gene expression levels indicated a GlnR-mediated repression of genes associated with ammonium import (amtBglnK) and BNF (nif genes). Additionally, the regulatory mechanism of GlnR in P. brasilensis PB24 differed from the other Paenibacillus evaluated, considering the different distribution of binding sites recognized by GlnR.

Paenibacillus brasilensis YS-1: A Potential Biocontrol Agent to Retard Xinyu Tangerine Senescence

The Xinyu tangerine (Citrus reticulata Blanco) is a non-climacteric fruit that is widely cultivated and consumed in China but highly susceptible to fungal infections. Antagonistic microorganisms can control postharvest diseases and extend the storage life of citrus fruits. However, little work has been done to investigate the effects of applying Paenibacillus brasilensis YS-1 by immersion to enhance the cold storability of Xinyu tangerines. Fruits were soaked with P. brasilensis YS-1 fermented filtrates for 10 min and in sterile water as the control. The decay incidence, weight loss, nutrient content, respiration rate, malondialdehyde (MDA) content, and defensive enzymes activities in citrus fruit were measured during cold storage at 5 ± 0.5 °C. The results showed that P. brasilensis YS-1 treatment significantly reduced postharvest decay and effectively maintained the nutritional quality compared to the control under cold storage. The weight loss, respiration rate, and MDA content were lower in P. brasilensis YS-1-treated fruits than the control fruits, indicating that P. brasilensis YS-1 treatment increased the activities of superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalnine ammonia-lyase (PAL). According to the results, a postharvest application of P. brasilensis YS-1 can control the postharvest decay and maintain fruit quality, as well as increase the defensive enzyme activity, so as to achieve the purpose of retarding postharvest senescence in citrus fruit.

Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis

The microbial production of chemicals and fuels from plant biomass offers a sustainable alternative to fossilized carbon but requires high rates and yields of bioproduct synthesis. Z. mobilis is a promising chassis microbe due to its high glycolytic rate in anaerobic conditions that are favorable for large-scale production. However, diverting flux from its robust ethanol fermentation pathway to nonnative pathways remains a major engineering hurdle. To enable controlled, high-yield synthesis of bioproducts, we implemented a central-carbon metabolism control-valve strategy using regulated, ectopic expression of pyruvate decarboxylase (Pdc) and deletion of chromosomal pdc. Metabolomic and genetic analyses revealed that glycolytic intermediates and NADH accumulate when Pdc is depleted and that Pdc is essential for anaerobic growth of Z. mobilis. Aerobically, all flux can be redirected to a 2,3-butanediol pathway for which respiration maintains redox balance. Anaerobically, flux can be redirected to redox-balanced lactate or isobutanol pathways with ≥65% overall yield from glucose. This strategy provides a promising path for future metabolic engineering of Z. mobilis.