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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. [ABSTRACT FROM AUTHOR]

We screened for bacteria that may facilitate the suppressive effect on Ralstonia pseudosolanacearum at temperatures < 30 °C after anaerobic soil disinfestation (ASD) with 1% v/v ethanol. Among 22 isolates grown anaerobically, we selected three that significantly suppressed R. pseudosolanacearum population after ASD at 25 °C. Based on the 16 S rRNA sequences, two isolates were inferred as Paenibacillus polymyxa and the other as Paenibacillus sp. Using qPCR primers designed for these strains, we found that all strains increased in the soil after ASD at 25 °C. After ASD with 1% v/v ethanol and with or without soil inoculation with these three strains in a concrete frame in the field at mean temperature of 26.3 °C, the R. pseudosolanacearum population was significantly lower in the inoculation treatment at a depth of 10 cm. These results suggest that these Paenibacillus strains have the potential to promote the ASD effect using 1% ethanol at low temperatures. [ABSTRACT FROM AUTHOR]

Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth–promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides. [ABSTRACT FROM AUTHOR]

A Gram-stain-positive, facultatively anaerobic, rod-shaped bacterium, designated JX-17T, was isolated from a soil sample collected in Jiangxi Province, PR China. Growth was observed at 15–48 °C (optimum 37 °C), at pH 5.0–9.0 (optimum pH 7.0) and with 0–6.0% (w/v) NaCl (optimum 1.0%). Strain JX-17T could degrade approximately 50% of 50 mg/L mesotrione within 2 days of incubation, but could not use mesotrione as sole carbon source for growth. Strain JX-17T showed less than 95.3% 16S rRNA gene sequence similarity with type strains of the genus Paenibacillus. In the phylogenetic tree based on 16S rRNA gene and genome sequences, strain JX-17T formed a distinct lineage within the genus Paenibacillus. The ANI values between JX-17T and the most closely related type strains P. lentus CMG1240T and P. farraposensis UY79T were 70.1% and 71.4%, respectively, and the dDDH values between them were 19.0% and 23.3%, respectively. The major cellular fatty acids were anteiso-C15:0, iso-C16:0, anteiso-C17:0 and C16:0, the predominant respiratory quinone was MK-7, the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, an aminophospholipid and a phosphatidylinositol. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid, and the DNA G + C content was 50.1 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain JX-17T represents a novel species within the genus Paenibacillus, for which the name Paenibacillus lacisoli sp. nov is proposed, with strain JX-17T (= GDMCC 1.3962T = KCTC 43568T) as the type strain. [ABSTRACT FROM AUTHOR]

In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in P. ternata tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in P. ternata tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as Stenotrophomonas, Pseudomonas, Mycobacterium, and Chryseomicrobium were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in P. ternata. The succinate content was positively correlated with the genera Brevundimonas, Ensifer, Nocardioides, and Paenibacillus, while it was negatively correlated with the genera Lentimicrobium, Anaerovorax, and Pajaroellobacter. These findings highlight the key role of endophytic bacteria in regulating the efficacy of P. ternata. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds. [ABSTRACT FROM AUTHOR]

Background: The β-galactosidase from Paenibacillus wynnii (β-gal-Pw) is a promising candidate for lactose hydrolysis in milk and dairy products, as it has a higher affinity for the substrate lactose (low KM value) compared to industrially used β-galactosidases and is not inhibited by the hydrolysis-generated product D-galactose. However, β-gal-Pw must firstly be produced cost-effectively for any potential industrial application. Accordingly, the yeast Komagataella phaffii was chosen to investigate its feasibility to recombinantly produce β-gal-Pw since it is approved for the regulated production of food enzymes. The aim of this study was to find the most suitable way to produce the β-gal-Pw in K. phaffii either extracellularly or intracellularly. Results: Firstly, 11 different signal peptides were tested for extracellular production of β-gal-Pw by K. phaffii under the control of the constitutive GAP promoter. None of the signal peptides resulted in a secretion of β-gal-Pw, indicating problems within the secretory pathway of this enzyme. Therefore, intracellular β-gal-Pw production was investigated using the GAP or methanol-inducible AOX1 promoter. A four-fold higher volumetric β-galactosidase activity of 7537 ± 66 µkatoNPGal/Lculture was achieved by the K. phaffii clone 27 using the AOX1 promoter in fed-batch bioreactor cultivations, compared to the clone 5 using the GAP promoter. However, a two-fold higher specific productivity of 3.14 ± 0.05 µkatoNPGal/gDCW/h was achieved when using the GAP promoter for β-gal-Pw production compared to the AOX1 promoter. After partial purification, a β-gal-Pw enzyme preparation with a total β-galactosidase activity of 3082 ± 98 µkatoNPGal was obtained from 1 L of recombinant K. phaffii culture (using AOX1 promoter). Conclusion: This study showed that the β-gal-Pw was produced intracellularly by K. phaffii, but the secretion was not achieved with the signal peptides chosen. Nevertheless, a straightforward approach to improve the intracellular β-gal-Pw production with K. phaffii by using either the GAP or AOX1 promoter in bioreactor cultivations was demonstrated, offering insights into alternative production methods for this enzyme. [ABSTRACT FROM AUTHOR]

Termites present a significant hazard to wooden structures, agriculture and urban environments. Termiticides are now required to meet more stringent environmental standards. Microbial metabolites with antitermitic properties are considered practical alternatives for termite control. Here, we report an antitermitic compound-producing endophytic bacterium HDZK-BYB36 isolated from the termite-resistant tree, Port-Orford-cedar (Chamaecyparis lawsoniana). The morphological, physio-biochemical, and 16S rDNA characteristics of the bacterium were investigated, as well as its antimicrobial and antitermitic activities. The antitermitic compounds from the strain HDZK-BYB36 were analyzed by GC-MS. Phylogenetic analyses revealed that HDZK-BYB36 was a subspecies of Paenibacillus aliginolyticus, sharing 98.72% identity with P. alginolyticus DSM 5050T. The HDZK-BYB36 demonstrated robust antimicrobial and termiticidal activities. It produced at least 4 antitermitic compounds, namely nootkatone, τ-muurolol, torreyol and α-cadinol, as determined by GC-MS analysis. The isolation of HDZK-BYB36 presents an effective and innovative resource for generating antitermitic compounds, providing a sustainable approach towards the prevention and control of termites. [ABSTRACT FROM AUTHOR]

Bacteria can solubilize phosphorus (P) through the secretion of low-molecular-weight organic acids and acidification. However, the genes involved in the production of these organic acids are poorly understood. The objectives of this study were to verify the calcium phosphate solubilization and the production of low-molecular-weight organic acids by diverse genera of phosphate solubilizing bacterial strains (PSBS); to identify the genes related to the synthesis of the organic acids in the genomes of these strains and; to evaluate growth and nutrient accumulation of maize plants inoculated with PSBS and fertilized with Bayóvar rock phosphate. Genomic DNA was extracted for strain identification and annotation of genes related to the organic acids production. A greenhouse experiment was performed with five strains plus 150 mg dm− 3 P2O5 as Bayóvar rock phosphate (BRP) to assess phosphate solubilization contribution to maize growth and nutrition. Paraburkholderia fungorum UFLA 04–21 and Pseudomonas anuradhapurensis UFPI B5-8A solubilized over 60% of Ca phosphate and produced high amounts of citric/maleic and gluconic acids in vitro, respectively. Eleven organic acids were identified in total, although not all strains produced all acids. Besides, enzymes related to the organic acids production were found in all bacterial genomes. Plants inoculated with strains UFPI B5-6 (Enterobacter bugandensis), UFPI B5-8A, and UFLA 03–10 (Paenibacillus peoriae) accumulated more biomass than the plants fertilized with BRP only. Strains UFLA 03–10 and UFPI B5-8A increased the accumulation of most macronutrients, including P. Collectively, the results show that PSBS can increase maize growth and nutrient accumulation based on Bayóvar rock phosphate fertilization. [ABSTRACT FROM AUTHOR]

Background/Objectives: Research-engaged academic institutions offer the opportunity to couple undergraduate education/citizen science projects with antimicrobial biodiscovery research. Several initiatives reflecting this ethos have been reported internationally (e.g., Small World, Tiny Earth, MicroMundo, Antibiotics Unearthed). These programs target soil habitats due to their high microbial diversity and promote initial screening with non-selective, nutrient media such as tryptic soy agar (TSA). However, evaluation of published outputs to date indicates that isolate recovery on TSA is consistently dominated by the genera Bacillus, Pseudomonas, and Paenibacillus. In this study, we evaluated the potential of soil extract agar to enhance soil isolate diversity and antibiosis induction outcomes in our undergraduate Antibiotics Unearthed research program. Methods: We comparatively screened 229 isolates from woodland and garden soil samples on both tryptic soy agar (TSA) and soil extract agar (SEA) for antimicrobial activity against a panel of clinically relevant microbial pathogens. Results: On one or both media, 15 isolates were found to produce zones of clearing against respective pathogens. 16S rRNA gene sequencing linked the isolates with three genera: Streptomyces (7), Paenibacillus (6), and Pseudomonas (2). Six of the Streptomyces isolates and one Pseudomonas demonstrated antimicrobial activity when screened on SEA, with no activity on TSA. Furthermore, incorporation of the known secondary metabolite inducer N acetyl-glucosamine (20 mM) into SEA media altered the pathogen inhibition profiles of 14 isolates and resulted in broad-spectrum activity of one Streptomyces isolate, not observed on SEA alone. In conclusion, SEA was found to expand the diversity of culturable isolates from soil and specifically enhanced the recovery of members of the genus Streptomyces. SEA was also found to be a superior media for antibiosis induction among Streptomyces isolates when compared to TSA. It was noted that Paenibacillus isolates' antibiosis induction demonstrated a strain-specific response with respect to the growth media used. Conclusions: The authors propose SEA inclusion of in soil screening protocols as a cost-effective, complementary strategy to greatly enhance outcomes in undergraduate/citizen science-engaged antimicrobial biodiscovery initiatives. [ABSTRACT FROM AUTHOR]

The aim of this study was to determine the effects of single and combined applications of plant-growth-promoting rhizobacteria (PGPR) bacteria on plant nutrition, biochemical content and fruit characteristics in Albion and Monterey strawberry cultivars. Bacillus subtilis OSU-142, Bacillus megaterium M3 and Paenibacillus polymyx were the PGPR used in the experiment. For each bacterial treatment, 10 mL of a 108 CFU mL−1 suspension was applied to the soil where Albion and Monterey cultivars were grown. PGPR bacteria were applied as single treatments and a mixture of equal amounts of these three bacterial species was applied as a mixed treatment. This study was carried out with a total of four different bacterial treatments and one control group. The highest fruit weight was obtained in the Monterey cultivar with 12.67 g in the Mix treatment and in the Albion cultivar with 11.79 g in the Bacillus megaterium M3 treatment. Regarding biochemical properties, Paenibacillus polymyxa was effective in influencing nutrient element content in fruits, while Bacillus subtilis OSU-142, Paenibacillus polymyxa and Bacillus megaterium M3 applications were more effective in leaf nutrient element content. It has been observed that the Mix treatment resulting from the combined use of bacteria, rather than their separate use, has a greater impact on fruit weight. Consequently, it has been understood that PGPR bacteria are potentially effective in improving the agronomic, pomological, and biochemical characteristics of strawberry cultivars and can be used in studies and breeding programs aimed at increasing strawberry yield and quality. [ABSTRACT FROM AUTHOR]

Introduction: The fungus Fusarium verticillioides significantly threatens maize crops in tropical soils. In light of this, biological control has emerged as a promising strategy to reduce fungicide costs and environmental risks. In this study, we aimed to test the antifungal activity of cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04) against F. verticillioides, thereby contributing to the development of effective biocontrol measures. Methods: The research employed a comprehensive approach. The antifungal activity of the bacterial strains was tested using cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04). The UPLC-MS evaluated the CFS to identify the main bioactive molecules involved in the inhibitory effect on F. verticillioides. Scanning electron microscopy (SEM) was used to assess the impact of CFS on spores and hyphae, and genome sequencing was conducted to identify the genes involved in biological control. These robustmethodologies ensure the reliability and validate our findings. Results: The CFS of the four strains demonstrated significant inhibition of fungal growth. The UPLC-MS analysis revealed the presence of lipopeptides with antifungal activity, including surfactin and fengycins A and B expressed by the three strains of Bacillus velezensis and iturin A expressed by strains LIS05 and IM14. For Paenibacillus ottowii, fusaricidins, ABCDE, and five previously unreported lipopeptides were detected. Scanning electron microscopy (SEM) showed that treatments with CFS led to significant distortion and breakage of the F. verticillioides hyphae, in addition to the formation of cavities in the membrane. Genome mining confirmed the presence of genes coding for the lipopeptides identified by UPLC-MS, including the gene for iturin in CTO2. Genomic sequencing revealed that CT02, IM14, and LIS05 belong to different strains of Bacillus velezensis, and LIS04 belongs to Paenibacillus ottowii, a species recently described. Discussion: The four bacterial strains, including three novel strains identified as Bacillus velezensis and one as the recently described species Paenibacillus ottowii, demonstrate significant potential as biocontrol agents for managing fungal disease. This finding underscores the novelty and potential impact of our research. [ABSTRACT FROM AUTHOR]

Due to their known mechanisms for biological control and plant growth promotion, Paenibacillus spp. are widely used in agriculture. However, the use of this microbial inoculant in Paenibacillus-based products and its potential benefits have received little attention. We describe the efficacy of Paenibacillus spp. in relation to crop development, biological control and bioremediation based on a study of researchers from around the world. In addition, this article addresses how Paenibacillus spp. produces beneficial metabolites. Agriculture will benefit from the implementation of these unexpected results if ecologically sound cultivation methods are used. [ABSTRACT FROM AUTHOR]

Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG-modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes. Butirosin is produced by Niallia (formerly Bacillus) circulans and Bacillus vitellinus, with most research focused on the first strain. To date, no whole-genome analysis has been performed on B. vitellinus. In this study, we sequenced the complete genome of B. vitellinus NBRC 13296 and performed a comparative analysis of different butirosin biosyntheric gene clusters (BGCs), including those from N. circulans. The complete genome of B. vitellinus NBRC 13296 comprises a 6,331,192-base circular chromosome with GC content of 52.68%. The annotation revealed the presence of 5605 CDSs, 70 tRNA genes, 30 rRNA genes, and 3 ncRNA genes in NBRC 13296. The highest dDDH and ANI values between NBRC 13296 and the most closely related type strain, Paenibacillus chitinolyticus KCCM 41,400, were 97.8% and 98.66%, respectively. Based on these genome-based comparative analyses, we propose reclassifying B. vitellinus NBRC 13296 as P. chitinolyticus. Genome mining revealed 18 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of B. vitellinus NBRC 13296, indicating the enormous biosynthetic potential of this strain. The predicted structural diversity of the secondary metabolites includes aminoglycosides, PKS, NRPS, PKS–NRPS hybrids, metallophores, phosphonates, terpenes, β-lactones, and RiPP peptides. We then comparatively characterized the butirosin BGCs previously studied in several N. circulans strains. Additionally, the comparative genome analysis revealed complete butirosin BGCs identified from P. chitinolyticus KCCM 41,400, P. chitinolyticus NRRL B-23119, P. chitinolyticus NRRL B-23120, P. chitinolyticus B-14908, P. chitinolyticus YSY-3.1, P. chitinolyticus JMW06, Paenibacillus sp. GbtcB18, Paenibacillus sp. HGH0039, and Paenibacillus sp. MZ04-78.2. Finally, we identified the core region consisting of BtrS, BtrN, BtrM, BtrL, BtrA, BtrB, BtrC, BtrD, BtrD, BtrE, BtrF, BtrG, BtrH, BtrI, BtrI, BtrJ, BtrK, BtrO, BtrP, and BtrV, followed by an upstream region organizing BtrQ, BtrW, BtrX, BtrY, and BtrZ in the same transcriptional direction and sequential genetic arrangement, and a downstream region organizing various proteins based on BtrT, BtrR2, BtrU, and BtrR1. Our study provides insights into the reclassification of B. vitellinus NBRC 13296 to P. chitinolyticus and suggests the need for continued studies on butirosin biosynthesis from an enzymatic perspective. [ABSTRACT FROM AUTHOR]

Bacteria within the Paenibacillus genus are known to secrete a diverse array of enzymes capable of breaking down plant cell wall polysaccharides. We studied the extracellular xylanolytic activity of Paenibacillus xylanivorans and examined the complete range of secreted proteins when grown on carbohydrate-based carbon sources of increasing complexity, including wheat bran, sugar cane straw, beechwood xylan and sucrose, as control. Our data showed that the relative abundances of secreted proteins varied depending on the carbon source used. Extracellular enzymatic extracts from wheat bran (WB) or sugar cane straw (SCR) cultures had the highest xylanolytic activity, coincidently with the largest representation of carbohydrate active enzymes (CAZymes). Scaling-up to a benchtop bioreactor using WB resulted in a significant enhancement in productivity and in the overall volumetric extracellular xylanase activity, that was further concentrated by freeze-drying. The enzymatic extract was efficient in the deconstruction of xylans from different sources as well as sugar cane straw pretreated by alkali extrusion (SCRe), resulting in xylobiose and xylose, as primary products. The overall yield of xylose released from SCRe was improved by supplementing the enzymatic extract with a recombinant GH43 β-xylosidase (EcXyl43) and a GH62 α-l-arabinofuranosidase (CsAbf62A), two activities that were under-represented. Overall, we showed that the extracellular enzymatic extract from P. xylanivorans, supplemented with specific enzymatic activities, is an effective approach for targeting xylan within lignocellulosic biomass. [ABSTRACT FROM AUTHOR]

Copyright of China Brewing is the property of China Brewing Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied. Results We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin. Conclusions This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.

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

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The article investigates the mitigation of copper (Cu) toxicity with copper tolerant plant growth promoting rhizobacteria (PGPR) strains in marigold plant growth. The study discusses the in vitro testing of Cu-tolerant Providentia, Paenibacillus and Lysinibacillus PGPR strains and their effect on Cu accumulation by marigold. It measures plant growth promoting activities including production of siderophores, indole acetic acid, hydrogen cyanide and phosphate solubilization.

Background: Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity of P. polymyxa has been suggested before, the available genomic data is now sufficient for robust comparative genomics analyses. Results: Using 157 genomes, we found significant disparities among strains currently affiliated to P. polymyxa. Multiple taxonomic groups were identified with conserved predicted functions putatively impacting their respective ecology. As strains of this species have been reported to exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic organization to facilitate reliable and durable approval as active ingredients. Conclusions: Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data. [ABSTRACT FROM AUTHOR]

Cellulases are one of the most essential natural factors for cellulose degradation and, thus, have attracted significant interest for various applications. In this study, a cellulase from Paenibacillus elgii TKU051 was produced, purified, and characterized. The ideal fermentation conditions for cellulase productivity were 2% carboxymethyl cellulose (CMC) as the growth substrate, pH = 8, temperature of 31 °C, and 4 days of culturing. Accordingly, a 45 kDa cellulase (PeCel) was successfully purified in a single step using a High Q column with a recovery yield of 35% and purification of 42.2-fold. PeCel has an optimal activity at pH 6 and a temperature of 60 °C. The activity of cellulase was significantly inhibited by Cu2+ and enhanced by Mn2+. The PeCel-catalyzed products of the CMC hydrolysis were analyzed by high-performance liquid chromatography, which revealed chitobiose and chitotriose as the major products. Finally, the clarity of apple juice was enhanced when treated with PeCel. [ABSTRACT FROM AUTHOR]

Recently, plastic wastes are considered a main environmental problem, and many bacterial isolates were tested to biodegrade them. The low-density polyethylene (LDPE) plastic sheets were tested to be degraded by a marine bacterial consortium. The potent marine plastic degrading isolates were biochemically identified as Bacillus licheniformis, Bacillus subtilis, and Paenibacillus xylanilyticus using the BIOLOG identification system. The identification of the most potent plastic-degrading bacterium was confirmed as Bacillus licheniformis FMMA using the 16S rRNA gene sequence. This bacterial consortium was physiologically adjusted as follows: pH 7, temperature 35°C, inoculum size 4ml/ 100ml (1.0X107CFU/ ml), and an incubation period of 30 days. It led to 34.1% plastic loss of weight. The mechanical properties (maximum force and the elongation% at break) of these treated LDPE plastic sheets showed 7.49N and 112.2%, respectively, compared to that of B. licheniformis FMMA, which showed a 25.5% plastic weight loss, with maximum force and elongation% at a breakpoint of 8.9N and 114.2%, respectively. In addition, the plastic biodegradation was also estimated through a scanning electron microscopy and Fourier transform-infrared (FTIR) spectroscopy, were a great reduction in the intensity of the -CH2 peak appeared at 2900cm-1, and the disappearance of the -OH peak at 3500cm-1 was observed. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from Paenibacillus spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the Paenibacillus spp. and the separation of proteins of Streptomyces origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with Paenibacillus spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae. [ABSTRACT FROM AUTHOR]

Background: Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied. Results: We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin. Conclusions: This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics. [ABSTRACT FROM AUTHOR]

Background: The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular medium especially facilitates downstream processing since cell disruption is avoided. Although various heterologous enzymes have been successfully secreted with B. subtilis, the secretion of cytoplasmic enzymes with high molecular weight is challenging. Only a few studies report on the secretion of cytoplasmic enzymes with a molecular weight > 100 kDa. Results: In this study, the cytoplasmic and 120 kDa β-galactosidase of Paenibacillus wynnii (β-gal-Pw) was expressed and secreted with B. subtilis SCK6. Different strategies were focused on to identify the best secretion conditions. Tailormade codon-optimization of the β-gal-Pw gene led to an increase in extracellular β-gal-Pw production. Consequently, the optimized gene was used to test four signal peptides and two promoters in different combinations. Differences in extracellular β-gal-Pw activity between the recombinant B. subtilis strains were observed with the successful secretion being highly dependent on the specific combination of promoter and signal peptide used. Interestingly, signal peptides of both the general secretory- and the twin-arginine translocation pathway mediated secretion. The highest extracellular activity of 55.2 ± 6 µkat/Lculture was reached when secretion was mediated by the PhoD signal peptide and expression was controlled by the PAprE promoter. Production of extracellular β-gal-Pw was further enhanced 1.4-fold in a bioreactor cultivation to 77.5 ± 10 µkat/Lculture with secretion efficiencies of more than 80%. Conclusion: For the first time, the β-gal-Pw was efficiently secreted with B. subtilis SCK6, demonstrating the potential of this strain for secretory production of cytoplasmic, high molecular weight enzymes. [ABSTRACT FROM AUTHOR]

Commercial β-galactosidases exhibit undesirable kinetic properties regarding substrate affinity (Michaelis-Menten constant [ K M ] for lactose) and product inhibition (inhibitor constant [ K i ] for galactose). An in silico screening of gene sequences was done and identified a putative β-galactosidase (Paenibacillus wynnii β-galactosidase, BgaPw) from the psychrophilic bacterium Paenibacillus wynnii. The cultivation of the wild-type P. wynnii strain resulted in very low β-galactosidase activities of a maximum of 150 nkat per liter of medium with o -nitrophenyl-β- d -galactopyranoside (o NPGal) as substrate. The recombinant production of BgaPw in Escherichia coli BL21(DE3) increased the yield ∼9,000-fold. Here, a volumetric activity of 1,350.18 ± 11.82 μkat o NPGal /L culture was achieved in a bioreactor cultivation. The partly purified BgaPw showed a pH optimum at 7.0, a temperature maximum at 40°C, and an excellent stability at 8°C with a half-life of 77 d. Kinetic studies with BgaPw were done in milk or in milk-imitating synthetic buffer (Novo buffer), respectively. Remarkably, the K M value of BgaPw with lactose was as low as 0.63 ± 0.045 m M in milk. It was found that the resulting products of lactose hydrolysis, namely galactose and glucose, did not inhibit the β-galactosidase activity of BgaPw, but instead showed a striking activating effect in both cases (up to 144%). In a comparison study in milk, lactose was completely hydrolyzed by BgaPw in 72 h at 8°C, whereas 2 other known β-galactosidases were less powerful and converted only about 90% of lactose in the same time. Finally, the formation of galactooligosaccharides (GOS) was demonstrated with the new BgaPw, starting with pharma-lactose (400 g/L). A GOS production of about 144 g/L was achieved after 24 h (36.0% yield). [ABSTRACT FROM AUTHOR]

An aerobic, rod-shaped, non-motile, endospore-forming bacterium, strain V-9T, was found in the frozen volcanic ash, Kamchatka peninsula, Russia. Phylogenies based on 16S rRNA gene and genome sequences demonstrated that strain V-9T was affiliated with the family Paenibacillaceae and clustered outside the clade that includes the type species of this genus, Paenibacillus polymyxa, and closely related species. V-9T showed the highest 16S rRNA gene sequences similarity to Paenibacillus chartarius CCUG 55240T (96.7%). The similarity to type strains of other Paenibacillus species were below 94.7%, with 91.8% determined to Paenibacillus polymyxa IAM 13419T. The AAI and POCP values between V-9T and type species of the genera of Paenibacillaceae with available genomes, including Paenibacillus polymyxa, were below the thresholds for defining novel genera. The cell wall of new strain contained a lysine-based peptidoglycan and two teichoic acids, unsubstituted 1,3-poly(glycerol phosphate) and 1,3-poly(glycerol phosphate) substituted at the C(2) of glycerol by glucose. Acid hydrolysates of the cell wall included glucose, galactose and glycerol. Strain V-9T contained menaquinone MK-7 as the sole isoprenoid quinone, anteiso-C15:0, anteiso-C17:0, iso- C15:0 and iso-C16:0a as the dominant fatty acids, and phosphatidylglycerol, diphosphatidylglycerol, acylphosphatidylglycerol, and phosphatidylinositol as the major polar lipids. The DNA G+C content calculated from the whole genome sequence was 55 mol %. Based on the data obtained, a new genus and species, Gordonibacillus kamchatkensis gen. nov., sp. nov., is proposed with the type strain V-9T (=VKM B-2647T = DSM 26726T). [ABSTRACT FROM AUTHOR]

Background: Biosynthesis of metallic nanoparticles using microorganisms are a fabulous and emerging eco-friendly science with well-defined sizes, shapes and controlled monodispersity. Copper nanoparticles, among other metal particles, have sparked increased attention due to their applications in electronics, optics, catalysis, and antimicrobial agents. Results: This investigation explains the biosynthesis and characterization of copper nanoparticles from soil strains, Niallia circulans G9 and Paenibacillus sp. S4c by an eco-friendly method. The maximum reduction of copper ions and maximum synthesis CuNPs was provided by these strains. Biogenic formation of CuNPs have been characterized by UV–visible absorption spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, X-ray analysis and transmission electron microscopy analysis. Using UV-visible spectrum scanning, the synthesised CuNPs' SPR spectra showed maximum absorption peaks at λ304&308 nm. TEM investigation of the produced CuNPs revealed the development of spherical/hexagonal nanoparticles with a size range of 13–100 nm by the G9 strain and spherical nanoparticles with a size range of 5–40 nm by the S4c strain. Functional groups and chemical composition of CuONPs were also confirmed. The antimicrobial activity of the biosynthesized CuNPs were investigated against some human pathogens. CuNPs produced from the G9 strain had the highest activity against Candida albicans ATCC 10,231 and the lowest against Pseudomonas aeruginosa ATCC 9027. CuNPs from the S4c strain demonstrated the highest activity against Escherichia coli ATCC 10,231 and the lowest activity against Klebsiella pneumonia ATCC 13,883. Conclusion: The present work focused on increasing the CuNPs production by two isolates, Niallia circulans G9 and Paenibacillus sp. S4c, which were then characterized alongside. The used analytics and chemical composition techniques validated the existence of CuONPs in the G9 and S4c biosynthesized nano cupper. CuNPs of S4c are smaller and have a more varied shape than those of G9 strain, according to TEM images. In terms of antibacterial activity, the biosynthesized CuNPs from G9 and S4c were found to be more effective against Candida albicans ATCC 10,231 and E. coli ATCC 10,231, respectively. [ABSTRACT FROM AUTHOR]

Bacterial α-1,3-glucanase, classified as glycoside hydrolase (GH) family 87, has been divided into 3 subgroups based on differences in gene sequences in the catalytic domain. The enzymatic properties of subgroups 1 and 3 of several bacteria have been previously investigated and reported; however, the chemical characterization of subgroup 2 enzymes has not been previously conducted. The α-1,3-glucanase gene from Paenibacillus alginolyticus NBRC15375 (PaAgl) belonging to subgroup 2 of GH family 87 was cloned and expressed in Escherichia coli. PgAgl-N1 (subgroup 3) and PgAgl-N2 (subgroup 1) from P. glycanilyticus NBRC16188 were expressed in E. coli , and their enzymatic characteristics were compared. The amino acid sequence of PaAgl demonstrated that the homology was significantly lower in other subgroups when only the catalytic domain was compared. The oligosaccharide products of the mutan-degrading reaction seemed to have different characteristics among subgroups 1, 2, and 3 in GH family 87. [ABSTRACT FROM AUTHOR]

Background & Objectives: American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee. Methods: We investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand. Results: Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae. Conclusions: Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry. [ABSTRACT FROM AUTHOR]

Losses in cereal crops caused by Fusarium species are controlled by using chemical fungicides, which also adversely affect human health and the environment. Therefore, in this study, zinc nanoparticles (ZnNPs) with strong antifungal activity were biosynthesized by the bacterium Paenibacillus polymyxa and then used as a green fungicide to manage root rot disease in wheat. The ZnNPs were 44 nm, spherical, and had a net surface charge of − 28.65 mV and with the active coating, provided significant antioxidant and antifungal activity. The ZnNPs scavenged 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals and at 40 µg/mL, inhibited growth of the pathogenic fungi Fusarium culmorum (FC), F. oxysporum, Candida albicans, and C. gelberta. In an in vivo experiment with FC-infected wheat, ZnNPs in water at 160 µg/mL significantly (p = 0.006) reduced preemergent root rot disease by 86% and significantly prevented postemergent disease (p = 0.001). As a result, incidence and severity of crown and root rot disease decreased by 79% and 89%, respectively. With ZnNPs, root weight remained similar to that in the control, but shoot weight decreased by 33%. Treatment with ZnNPs increased grain yield by 10% in healthy wheat and maintained it in FC-infected plants. Compared with control plants, the 1,000-grain weight increased by 40%. Total chlorophyll, carotenoids, and antioxidant contents were similar between FC-infected wheat and control plants. Thus, on the basis of the results, ZnNPs are recommended as a new green and safe fungicide. [ABSTRACT FROM AUTHOR]

In this work, we assessed the potential of Cel6D, a recently reported exocellulase from Paenibacillus barcinonensis, as a biorefining agent for flax pulp. Pulp fibers were treated with this enzyme, Cel9B (an endocellulase previously shown to possess biorefining action) and the two in combination. Samples of biorefined flax pulp were mechanically refined to obtain handsheets. All three biorefining treatments decreased air permeance in the handsheets. Cel9B increased tensile index and folding endurance, and the Cel6D − Cel9B combination increased tensile index and burst index but also resulted in markedly decreased tear index and folding endurance. On the other hand, Cel6D increased tensile index and burst index; also, more importantly, it increased tear resistance, albeit slightly, relative to the other two treatments. The results of this work can be useful to understand the differential effects of exocellulases and endocellulases as biorefining tools and open up new avenues for exploring their use in other biotechnological applications. [ABSTRACT FROM AUTHOR]

Enumeration of endospores of butyric acid-forming clostridia in cheese milk is an essential part of milk quality monitoring for cheese producers to avoid late blowing, severe spoilage caused by clostridia during ripening. However, due to the lack of an internationally standardized method, different methods are used and it is important to consider how the choice of method affects the results. This is particularly relevant when clostridial spore counts in milk are considered for quality payments. The aim of this study was to evaluate the specificity of the AMP-6000 method for the enumeration of endospores of cheese spoiling clostridia in milk. First, to assess the prevalence of Clostridium diversity and to determine potential non-target species, we identified isolates from positive reactions of the AMP-6000 method used to quantify clostridial endospores in raw milk and teat skin samples by MALDI-TOF MS. Based on these results, a strain library was designed to evaluate method inclusivity and exclusivity using pure cultures of target and non-target strains according to ISO 16140-2:2016. Most target Clostridium tyrobutyricum strains, as well as all tested C. butyricum and C. sporogenes strains were inclusive. However, C. beijerinckii may be underestimated as only some strains gave positive results. All non-target strains of bacilli and lysinibacilli, but not all paenibacilli, were confirmed to be exclusive. This study provides performance data to better understand the results of microbiological enumeration of butyric acid-forming clostridia in milk and serves as a basis for future methodological considerations and improvements. [ABSTRACT FROM AUTHOR]

A new strain of xanthan-degrading bacteria identified as Cohnella sp. has been isolated from a xanthan thickener for food production. The strain was able to utilize xanthan as the only carbon source and to reduce the viscosity of xanthancontaining medium during cultivation. Comparative analysis of the secretomes of Cohnella sp. after growth on different media led to the identification of a xanthanase designated as CspXan9, which was isolated after recombinant production in Escherichia coli. CspXan9 could efficiently degrade the β-1,4-glucan backbone of xanthan after previous removal of pyruvylated mannose residues from the ends of the native xanthan side chains by xanthan lyase treatment (XLTxanthan). Compared with xanthanase from Paenibacillus nanensis, xanthanase CspXan9 had a different module composition at the N- and C-terminal ends. The main putative oligosaccharides released from XLT-xanthan by CspXan9 cleavage were tetrasaccharides and octasaccharides. To explore the functions of the Nand C-terminal regions of the enzyme, truncated variants lacking some of the non-catalytic modules (CspXan9-C, CspXan9-N, CspXan9-C-N) were produced. Enzyme assays with the purified deletion derivatives, which all contained the catalytic glycoside hydrolase family 9 (GH9) module, demonstrated substantially reduced specific activity on XLT-xanthan of CspXan9-C-N compared with fulllength CspXan9. The C-terminal module of CspXan9 was found to represent a novel carbohydrate-binding module of family CBM66 with binding affinity for XLT-xanthan, as was shown by native affinity polyacrylamide gel electrophoresis in the presence of various polysaccharides. The only previously known binding function of a CBM66 member is exo-type binding to the non-reducing fructose ends of the β-fructan polysaccharides inulin and levan. [ABSTRACT FROM AUTHOR]

In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future. [ABSTRACT FROM AUTHOR]

Oleanane-type ginsenosides are a class of compounds with remarkable pharmacological activities. However, the lack of effective preparation methods for specific rare ginsenosides has hindered the exploration of their pharmacological properties. In this study, a novel glycoside hydrolase PlGH3 was cloned from Paenibacillus lactis 154 and heterologous expressed in Escherichia coli. Sequence analysis revealed that PlGH3 consists of 749 amino acids with a molecular weight of 89.5 kDa, exhibiting the characteristic features of the glycoside hydrolase 3 family. The enzymatic characterization results of PlGH3 showed that the optimal reaction pH and temperature was 8 and 50 °C by using p-nitrophenyl-β-d-glucopyranoside as a substrate, respectively. The Km and kcat values towards ginsenoside Ro were 79.59 ± 3.42 µM and 18.52 s−1, respectively. PlGH3 exhibits a highly specific activity on hydrolyzing the 28-O-β-d-glucopyranosyl ester bond of oleanane-type saponins. The mechanism of hydrolysis specificity was then presumably elucidated through molecular docking. Eventually, four kinds of rare oleanane-type ginsenosides (calenduloside E, pseudoginsenoside RP1, zingibroside R1, and tarasaponin VI) were successfully prepared by biotransforming total saponins extracted from Panax japonicus. This study contributes to understanding the mechanism of enzymatic hydrolysis of the GH3 family and provides a practical route for the preparation of rare oleanane-type ginsenosides through biotransformation. Key points: • The glucose at C-28 in oleanane-type saponins can be directionally hydrolyzed. • Mechanisms to interpret PlGH3 substrate specificity by molecular docking. • Case of preparation of low-sugar alternative saponins by directed hydrolysis. [ABSTRACT FROM AUTHOR]

To search for enzymes that improve the efficiency of protoplast production in Tricholoma matsutake, Paenibacillus sp. MU1, which harbors degradation activity for the dried fruit body of T. matsutake, was isolated. The bacterial strain has the potential to degrade the cell wall of T. matsutake, which was isolated from a soil sample using medium including insolubilized fraction of T. matsutake fruit body as a sole nutrient source. The draft genome sequence of the bacterium comprised 36 contigs, totaling 6.6 Mbp, with an average length of 184,698 bp. Whole genome sequence data identified the strain as Paenibacillus sp. MU1. Among its degrading activities, the bacterial α-1,3-glucanase (Mu1Agl) was purified to homogeneity, and its enzymatic properties were characterized. Mu1Agl acts on mutan (D-glucan with α-1,3 and α-1,6 linkages), but other polysaccharides and oligosaccharides are not substrates. Mu1Agl exhibited maximum activity at 40°C at around pH 6.0 in phosphate buffer. The Mu1Agl gene was cloned with reference to mass spectrometry and whole genome analysis information. The deduced amino acid sequence showed high homology with discoidin domain-containing proteins or α-1,3-glucanase of P. glycanilyticus and other Paenibacillus species. These results indicated that Mu1Agl belongs to the minor group (Subgroup 3) of GH family 87. [ABSTRACT FROM AUTHOR]

Aims In this work, we aimed to isolate marine bacteria that produce metabolites with antifungal properties. Methods and results Paenibacillus polymyxa 188 was isolated from a marine sediment sample, and it showed excellent antifungal activity against many fungi pathogenic to plants (Fusarium tricinctum, Pestalotiopsis clavispora, Fusarium oxysporum, F. oxysporum f. sp. Cubense (Foc), Curvularia plantarum , and Talaromyces pinophilus) and to humans (Aspergillus terreus, Penicillium oxalicum , and Microsphaeropsis arundinis). The antifungal compounds produced by P. polymyxa 188 were extracted and analyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The complete genome sequence and biosynthetic gene clusters of P. polymyxa 188 were characterized and compared with those of other strains. A total of 238 carbohydrate-active enzymes (CAZymes) were identified in P. polymyxa 188. Two antibiotic gene clusters, fusaricidin and tridecaptin, exist in P. polymyxa 188, which is different from other strains that typically have multiple antibiotic gene clusters. Conclusions Paenibacilluspolymyxa 188 was identified with numerous biosynthetic gene clusters, and its antifungal ability against pathogenic fungi was verified. [ABSTRACT FROM AUTHOR]

This study assessed the bacteriological quality of raw, treated, and distributed water from Ede-Erinle and Opa reservoirs in Osun State, Nigeria. This was to determine the potability of water from these waterwork stations. Eighteen sampling points were established across the two reservoir networks for this study. Samples were collected bi-monthly for two annual cycles. Serial dilution and pour plate methods were employed for the enumeration of bacterial load. Total heterotrophic bacteria count (THBC) and total coliform bacteria count (TCBC) were enumerated on nutrient and MacConkey agar at 37 °C, respectively. Bacterial isolates were characterized using biochemical identification methods with reference to Bergey’s Manual of Determinative Bacteriology. Bacterial isolates and biofilm formation were further identified molecularly through the PCR method using specific universal primers. Mean values of THBC and TCBC in distributed water from Ede-Erinle (9.61 × 104 ± 1.50 × 104 CFU/mL; 69.56 ± 26.81 CFU/mL) and Opa waterworks (9.58 × 104 ± 2.55 × 104 CFU/mL; 142.94 ± 44.41 CFU/mL) exceeded permissible limits for drinking water. Paenibacillus lautus, Bacillus pseudomycoides, Pseudomonas aeruginosa, and Pseudomonas stutzeri showed biofilm-forming capacity. The study concluded that the presence of coliforms and biofilm-forming bacteria in distributed water implies that the water is unfit for consumption without further treatment. [ABSTRACT FROM AUTHOR]

Simple Summary: American foulbrood is a highly infectious disease that can harm the beekeeping sector if it becomes clinically visible. It is caused by the bacterium Paenibacillus larvae, and its spores are resistant to various disinfectants. It is important to ensure effective final disinfection following eradication measures at apiary in order to prevent the disease from reoccurring. A study was conducted to test ten commercially available disinfectants commonly used in beekeeping, as well as those with proven efficacy in the medicinal and veterinary sectors, on different strains of P. larvae bacterium. Early diagnosis methods and proper control measures can help minimize the disease's clinical signs and its incidence. American foulbrood is an infectious disease of the honeybee brood that causes multiple types of damage to beekeeping. The causative agent of the disease is the bacterium Paenibacillus larvae, which forms resistant infective spores and is viable for decades. After the eradication measures have been implemented, in cases of clinically visible disease, it is necessary to conduct effective final disinfections of equipment and tools. This study aimed to determine the effect of ten commercially available and commonly used disinfectants on certified strains of P. larvae under laboratory conditions, as well as to compare the obtained results among individual genotypes of P. larvae. Selected products were tested by determining the zone of inhibition using an agar diffusion test, a suspension test for viable bacteria, a surface disinfectant test, and a sporicidal effect in the suspension test. Incidin OxyFoam S and Sekusept Aktiv are both effective against all examined genotypes of P. larvae. Despadac and Despadac Secure have a bactericidal effect, but their sporocidal effect is not as satisfactory as that of Genox. Genoll does not exhibit a sporicidal effect, and Ecocide S at 1%, Bee protect H forte, and Bee protect F did not exhibit a satisfactory sporocidal effect. Additionally, EM® PROBIOTIC FOR BEES did not exhibit any bactericidal effect. The effective application of control measures and proper application of final disinfection can reduce the reoccurrence of visible clinical signs of disease, whereas methods of early diagnosis can significantly reduce the incidence of the disease. [ABSTRACT FROM AUTHOR]

It isolated a Gram positive Paenibacillus sp. strain from the soil at an altitude of 3 000 m in the Kalongla Mountains in Mutuo, Tibet. The entire genome of Paenibacillus sp. strain was sequenced by Illumina Hiseq and was annotated with Prokka software (v1. 14. 6). antiSMASH 7. 0 and BAGEL4 were used to predict the secondary metabolites biosynthesis gene cluster in Paenibacillus sp. In order to validate the metabolic pathway, the total strain proteins were extracted by various extraction methods and performed nanoliter liquid chromatography combining with Mass Spectrometry. We could identify a total of 3 383 proteins by using software. Through homologous comparison, there were the N-terminal region of ATP dependent Cysteine protease B1 and ABC transporter in the lasso peptide biosynthesis gene cluster. It was complete by local blast comparison, and Paenibacillus sp. was likely to have the ability to synthesize lasso peptide. Through the above research, we analyed genomic and proteomic information of Paenibacillus sp. [ABSTRACT FROM AUTHOR]

Tropaeolum majus L. is a versatile edible plant that is widely explored due to its medicinal properties and as a key element in intercropping systems. Its growth could be improved by the use of biofertilizers that can enhance nutrient uptake by the plant or provide tolerance to different abiotic and biotic stresses. In a previous study, 101 endophytes isolated from T. majus roots showed more than three plant growth-promoting (PGP) features in vitro, such as phosphate mineralization/solubilization, production of siderophores, antimicrobial substances and indole-related compounds, and presence of the nifH gene. To provide sustainable alternatives for biofertilization, the genomes of two promising endophytes--CAPE95 and CAPE238--were sequenced to uncover metabolic pathways related to biofertilization. Greenhouse experiments were conducted with 216 seeds and 60 seedlings, half co-inoculated with the endophytes (treatment) and half inoculated with 1X PBS (control), and the impact of the co-inoculation on the plant's bacteriome was accessed through 16S rRNA gene metabarcoding. The strains CAPE95 and CAPE238 were taxonomically assigned as Bacillus thuringiensis and Paenibacillus polymyxa, respectively. Metabolic pathways related to the enhancement of nutrient availability (nitrogen fixation, sulfate-sulfur assimilation), biosynthesis of phytohormones (indole-3-acetic acid precursors) and antimicrobial substances (bacilysin, paenibacillin) were found in their genomes. The in vivo experiments showed that treated seeds exhibited faster germination, with a 20.3% higher germination index than the control on the eleventh day of the experiment. Additionally, treated seedlings showed significantly higher plant height and leaf diameters (p < 0.05). The bacterial community of the treated plants was significantly different from that of the control plants (p < 0.001) and showed a higher richness and diversity of species (Chao and Shannon indexes, p < 0.001). A higher relative abundance of potential synergistic PGP bacteria was also shown in the bacteriome of the treated plants, such as Lysinibacillus and Geobacter. For the first time, co-inoculation of B. thuringiensis and P. polymyxa was shown to have great potential for application as a biofertilizer to T. majus plants. The bacterial consortium used here could also be explored in other plant species in the future. [ABSTRACT FROM AUTHOR]

Carbapenems are last-resort antibiotics used to treat multidrug-resistant bacterial infections. Resistance to carbapenems has been designated as an urgent threat and is increasing in healthcare settings. However, little is still known about the distribution and characteristics of carbapenem-resistant bacteria (CRB) outside of healthcare settings. Here, we surveyed the distribution of CRB in ten diverse freshwater and seawater environments in California, U.S., ranging from San Luis Obispo County to San Bernardino County, combining both direct isolation and enrichment approaches to increase the diversity of isolated CRB. From the locations surveyed, we selected 30 CRB for further characterization. These isolates were identified as members of the genera Aeromonas, Enterobacter, Enterococcus, Paenibacillus, Pseudomonas, Sphingobacterium, and Stenotrophomonas. These isolates were resistant to carbapenems, other β-lactams, and often to other antibiotics (tetracycline, gentamicin, or ciprofloxacin). We also found that nine isolates belonging to the genera Aeromonas, Enterobacter (blaIMI-2), and Stenotrophomonas (blaL1) produced carbapenemases. Overall, our findings indicate that sampling different types of aquatic environments and combining different isolation approaches increase the diversity of the environmental CRB obtained. Moreover, our study supports the increasingly recognized role of natural water systems as an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including bacteria carrying carbapenemase genes. [ABSTRACT FROM AUTHOR]

Bacillus and related genera are among the most important contaminants in the pharmaceutical production environment, and the identification of these microorganisms at the species level assists in the investigation of sources of contamination and in preventive and corrective decision making. The aim of this study was to evaluate three methodologies for the characterization of endospore-forming aerobic bacterial strains isolated from a pharmaceutical unit in Rio de Janeiro, Brazil. MALDI-TOF MS was performed using MALDI Biotyper® and VITEK® MS RUO systems, and complete 16S rRNA gene sequencing was performed using the Sanger methodology. The results showed the prevalence of the genera Bacillus (n = 9; 36.0%), Priestia (n = 5; 20.0%), and Paenibacillus (n = 4; 16.0%). Three (20.0%) strains showed <98.7% of DNA sequencing similarity on the EzBioCloud Database, indicating possible new species. In addition, the reclassification of Bacillus pseudoflexus to the genus Priestia as Priestia pseudoflexus sp. nov. is proposed. In conclusion, 16S rRNA and MALDI TOF/MS were not sufficient to identify all strains at the species level, and complementary analyses were necessary. [ABSTRACT FROM AUTHOR]

Background: Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed. Results: In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina (Fr) Schrorter was isolated from the rhizosphere soil of pear trees, and the complete genome sequence of the strain was obtained, annotated, and analyzed to reveal the genetic foundation of its antagonistic ability. The entire genome of this strain contained a circular chromosome of 5,641,488 bp with a GC content of 45.50%. The results of species identification show that the strain belongs to the same species as P. polymyxa Sb3-1 and P. polymyxa CJX518. Sixteen secondary metabolic biosynthetic gene clusters were predicted by antiSMASH, including those of the antifungal peptides fusaricidin B and paenilarvins. In addition, biofilm formation-related genes containing two potential gene clusters for cyclic lactone autoinducer, a gene encoding S-ribosylhomocysteine lyase (LuxS), and three genes encoding exopolysaccharide biosynthesis protein were identified. Conclusions: Antifungal peptides and glucanase biosynthesized by Paenibacillus sp. lzh-N1 may be responsible for its antagonistic effect. Moreover, quorum sensing systems may influence the biocontrol activity of this strain directly or indirectly. [ABSTRACT FROM AUTHOR]

We have previously isolated the Gram-positive chitin-degrading bacterium Paenibacillus sp. str. FPU-7. This bacterium traps chitin disaccharide (GlcNAc)2 on its cell surface using two homologous solute-binding proteins, NagB1 and NagB2. Bacteria use histidine kinase (HK) of the two-component regulatory system as an extracellular environment sensor. In this study, we found that nagS , which encodes a HK, is located next to the nagB1 gene. Biochemical experiments revealed that the NagS sensor domain (NagS30-294) interacts with the NagB1–(GlcNAc)2 complex. However, proof of NagS30-294 interacting with NagB1 without (GlcNAc)2 is currently unavailable. In contrast to NagB1, no complex formation was observed between NagS30-294 and NagB2, even in the presence of (GlcNAc)2. The NagS30-294 crystal structure at 1.8 Å resolution suggested that the canonical tandem-Per-Arnt-Sim fold recognizes the NagB1–(GlcNAc)2 complex. This study provides insight into the recognition of chitin oligosaccharides by bacteria. [ABSTRACT FROM AUTHOR]

Paenibacillus polymyxa is a non‐pathogenic, Gram‐positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next‐generation biofuel. A CRISPR‐Cas9‐based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3‐butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L−1 isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network‐wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose‐6‐phosphate 1‐dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation. [ABSTRACT FROM AUTHOR]

Polymyxin B, produced by Paenibacillus polymyxa, is used as the last line of defense clinically. In this study, exogenous mixture of precursor amino acids increased the level and proportion of polymyxin B1 in the total of polymyxin B analogs of P. polymyxa CJX518-AC (PPAC) from 0.15 g/L and 61.8 % to 0.33 g/L and 79.9 %, respectively. The co-culture of strain PPAC and recombinant Corynebacterium glutamicum-leu01, which produces high levels of threonine, leucine, and isoleucine, increased polymyxin B1 production to 0.64 g/L. When strains PPAC and C. glu-leu01 simultaneously inoculated into an optimized medium with 20 g/L peptone, polymyxin B1 production was increased to 0.97 g/L. Furthermore, the polymyxin B1 production in the co-culture of strains PPAC and C. glu-leu01 increased to 2.21 g/L after optimized inoculation ratios and fermentation medium with 60 g/L peptone. This study provides a new strategy to improve polymyxin B1 production. [ABSTRACT FROM AUTHOR]

Lignocellulose is a core component of plant biomass and the most abundant carbohydrate polymer in nature. It is cheap and renewable and has several potential applications; however, it remains underutilized because of its recalcitrance to degradation. Cellulolytic microbes have been found in the gut of herbivorous insects, such as grasshoppers. This study aimed to isolate lignocellulolytic bacteria from the gut of grasshoppers (Oxya chinensis) and determine their diversity and potential biomass-degrading activity. A total of 27 culturable isolates were obtained from the grasshopper foregut, midgut, and hindgut. The bacteria hydrolyzed cellulose and lignin, as indicated by a cellulolytic index of 0.12-1.23 and ligninolytic index of 0.1-1.47. Five potential cellulolytic bacterial isolates were selected. Based on 16S rRNA sequencing, the isolates were identified as Bacillus wiedmannii (foregut), Bacillus marcorestinctum, Bacillus halotolerans (midgut), Paenibacillus zanthoxyli, and Bacillus hominis (hindgut). The highest specific cellulolytic activity (0.0068 U/mg) was detected in B. wiedmannii (OCF2), which could be exploited as a potential source of cellulases. [ABSTRACT FROM AUTHOR]