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Applied Microbiology and Biotechnology Oct 2023Cyclodextrin glucanotransferase (CGTase) is an extracellular enzyme of the GH13 α-amylase family that catalyzes a unique intramolecular reaction known as cyclization to... (Review)
Review
Cyclodextrin glucanotransferase (CGTase) is an extracellular enzyme of the GH13 α-amylase family that catalyzes a unique intramolecular reaction known as cyclization to transform α-1, 4-glucans and similar starches into cyclodextrins. They also catalyze intermolecular transglycosylation reactions namely coupling, disproportionation, and some hydrolyzing effects on starch. The monomeric structures of the CGTase exhibit five domains (A, B, C, D, and E domains) with different molecular weights and amino acid sequences depending on the source. Among bacteria, Bacillus genus covers approximately 90% of the CGTase producers, while other genera like Klebsiella, Paenibacillus, and Thermoanaerobacter also shown decent contributions in recent studies. CGTase production is highly supported by alkaliphilic bacteria under submerged fermentation rather than solid-state fermentation. The bacterial sources, biochemical properties, production conditions, and structure of CGTases are compiled in this review. Cyclodextrins have the unique property of making inclusion complexes with various compounds, hence widely used in the food, pharmaceutical, cosmetics, laundry, and chemical sectors. This review presents a comprehensive view of CGTase produced by Bacillus spp., and other bacterial genera like Klebsiella, Paenibacillus, and Microbacterium. It also gives insight of the properties and recent biotechnological applications of cyclodextrins. KEY POINTS: • Transglycosylation reactions catalyzed by CGTase and their structural properties. • Comparative data of CGTase production by various genera and Bacillus spp. • Structures, properties, and applications of different cyclodextrins.
Topics: Cyclodextrins; Amino Acid Sequence; Glucans; Glucosyltransferases; Bacillus; Starch
PubMed: 37548666
DOI: 10.1007/s00253-023-12708-9 -
Critical Reviews in Biotechnology Dec 2023Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium has been widely applied in: agriculture, medicine, industry, and... (Review)
Review
Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium has been widely applied in: agriculture, medicine, industry, and environmental remediation. 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 species has long been limited. Genetic manipulation tools and methods continue to improve in , 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, 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 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 as a new microbial chassis for mining bioresources.
PubMed: 38105503
DOI: 10.1080/07388551.2023.2289342 -
Environmental Science and Ecotechnology Jul 2023The potential release capacity of arsenic (As) from sediment was evaluated under a high level of exogenous organic matter (EOM) with both bioreactive and chemically...
The potential release capacity of arsenic (As) from sediment was evaluated under a high level of exogenous organic matter (EOM) with both bioreactive and chemically reactive organic matters (OMs). The OMs were characterized by FI, HIX, BIX, and SUVA fluorescence indices showing the biological activities were kept at a high level during the experimental period. At the genus level, Fe/Mn/As-reducing bacteria (, , , and ) and bacteria (, , , and ) that can participate in metabolic transformation using EOM were identified. The reducing condition occurs which promoted As, Fe, and Mn releases at very high concentrations of OM. However, As release increased during the first 15-20 days, followed by a decline contributed by secondary iron precipitation. The degree of As release may be limited by the reactivity of Fe (hydro)oxides. The EOM infiltration enhances As and Mn releases in aqueous conditions causing the risk of groundwater pollution, which could occur in specific sites such as landfills, petrochemical sites, and managed aquifer recharge projects.
PubMed: 36896144
DOI: 10.1016/j.ese.2023.100243 -
Archives of Microbiology Dec 2023During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38 and TW40. Both strains...
During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38 and TW40. Both strains were catalase positive and oxidase negative. Strains TW38 and TW40 demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38 and TW40 affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17 (98.6%) and Paenibacillus arachidis E3 (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38, TW40, and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38 and TW40 was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38 and TW40 from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38 and TW40 represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38 (= KCTC 43468 = NBRC 116015) and type strain of Paenibacillus humicola is TW40 (= KCTC 43469 = NBRC 116016).
Topics: Phylogeny; Cardiolipins; Forests; Paenibacillus; DNA
PubMed: 38147140
DOI: 10.1007/s00203-023-03763-x -
Nature Communications Sep 2023The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the...
The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by the soil microbiota in rhizosheath formation in barley (a dry crop). We show that barley rhizosheath formation is greater in acid soil than in alkaline soil, and inoculation with microbiota from acid soil enhances rhizosheath formation in alkaline soil. The rhizosheath-promoting activity is associated with the presence of Flavobacteriaceae and Paenibacillaceae bacteria that express genes for biosynthesis of indole-3-acetic acid (IAA, a common auxin), as determined by metagenomics and metatranscriptomics. Two bacterial strains isolated from rhizosheath (Chryseobacterium culicis and Paenibacillus polymyxa) produce IAA and enhance barley rhizosheath formation, while their IAA-defective mutants are unable to promote rhizosheath formation. Co-inoculation with the IAA-producing strains enhances barley grain yield in field experiments through an increase in spike number. Our findings contribute to our understanding of barley rhizosheath formation, and suggest potential strategies for crop improvement.
Topics: Hordeum; Bacteria; Desiccation; Indoleacetic Acids; Soil
PubMed: 37726263
DOI: 10.1038/s41467-023-40916-4 -
International Journal of Biological... Mar 2024Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of... (Review)
Review
Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of many metabolically active substances, including polypeptides, volatile organic compounds, phytohormone, hydrolytic enzymes, exopolysaccharide (EPS), etc. Due to the wide range of compounds that it produces, P. polymyxa has been extensively studied as a plant growth promoting bacterium which provides a direct benefit to plants through the improvement of N fixation from the atmosphere and enhancement of the solubilization of phosphorus and the uptake of iron in the soil, and phytohormones production. Among the metabolites from P. polymyxa, EPS exhibits many activities, for example, antioxidant, immunomodulating, anti-tumor and many others. EPS has various applications in food, agriculture, environmental protection. Particularly, in the field of sustainable agriculture, P. polymyxa EPS can be served as a biofilm to colonize microbes, and also can act as a nutrient sink on the roots of plants in the rhizosphere. Therefore, this paper would provide a comprehensive review of the advancements of diverse aspects of EPS from P. polymyxa, including the production, extraction, structure, biosynthesis, bioactivity and applications, etc. It would provide a direction for future research on P. polymyxa EPS.
Topics: Paenibacillus polymyxa; Paenibacillus; Plant Growth Regulators; Plant Development; Plants
PubMed: 38278396
DOI: 10.1016/j.ijbiomac.2024.129663 -
The Lancet. Microbe Aug 2023Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis,... (Observational Study)
Observational Study
BACKGROUND
Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis, meningitis, and postinfectious hydrocephalus, we aimed to complete three separate studies of Ugandan infants. The first study was on peripartum prevalence of Paenibacillus in mother-newborn pairs. The second study assessed Paenibacillus in blood and cerebrospinal fluid (CSF) from neonates with sepsis. The third study assessed Paenibacillus in CSF from infants with hydrocephalus.
METHODS
In this observational study, we recruited mother-newborn pairs with and without maternal fever (mother-newborn cohort), neonates (aged ≤28 days) with sepsis (sepsis cohort), and infants (aged ≤90 days) with hydrocephalus with and without a history of neonatal sepsis and meningitis (hydrocephalus cohort) from three hospitals in Uganda between Jan 13, 2016 and Oct 2, 2019. We collected maternal blood, vaginal swabs, and placental samples and the cord from the mother-newborn pairs, and blood and CSF from neonates and infants. Bacterial content of infant CSF was characterised by 16S rDNA sequencing. We analysed all samples using quantitative PCR (qPCR) targeting either the Paenibacillus genus or Paenibacillus thiaminolyticus spp. We collected cranial ultrasound and computed tomography images in the subset of participants represented in more than one cohort.
FINDINGS
No Paenibacillus spp were detected in vaginal, maternal blood, placental, or cord blood specimens from the mother-newborn cohort by qPCR. Paenibacillus spp was detected in 6% (37 of 631 neonates) in the sepsis cohort and, of these, 14% (5 of 37 neonates) developed postinfectious hydrocephalus. Paenibacillus was the most enriched bacterial genera in postinfectious hydrocephalus CSF (91 [44%] of 209 patients) from the hydrocephalus cohort, with 16S showing 94% accuracy when validated by qPCR. Imaging showed progression from Paenibacillus spp-related meningitis to postinfectious hydrocephalus over 1-3 months. Patients with postinfectious hydrocephalus with Paenibacillus spp infections were geographically clustered.
INTERPRETATION
Paenibacillus spp causes neonatal sepsis and meningitis in Uganda and is the dominant cause of subsequent postinfectious hydrocephalus. There was no evidence of transplacental transmission, and geographical evidence was consistent with an environmental source of neonatal infection. Further work is needed to identify routes of infection and optimise treatment of neonatal Paenibacillus spp infection to lessen the burden of morbidity and mortality.
FUNDING
National Institutes of Health and Boston Children's Hospital Office of Faculty Development.
Topics: United States; Infant, Newborn; Child; Humans; Infant; Female; Pregnancy; Uganda; Neonatal Sepsis; Placenta; Paenibacillus; Sepsis; Meningitis; Hydrocephalus; Case-Control Studies
PubMed: 37348522
DOI: 10.1016/S2666-5247(23)00106-4 -
Frontiers in Plant Science 2023species are cosmopolitan soil phytopathogens from the division , which produce mycotoxins and cause significant economic losses of crop plants. However, soils... (Review)
Review
species are cosmopolitan soil phytopathogens from the division , which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the , , and species are involved in plant protection from diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for disease management in sustainable agriculture.
PubMed: 38111879
DOI: 10.3389/fpls.2023.1228749 -
Microbial Cell Factories May 2024Biosynthesis of metallic nanoparticles using microorganisms are a fabulous and emerging eco-friendly science with well-defined sizes, shapes and controlled... (Comparative Study)
Comparative Study
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 λ. 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.
Topics: Paenibacillus; Metal Nanoparticles; Copper; Anti-Infective Agents; Microbial Sensitivity Tests; Anti-Bacterial Agents; Ascomycota
PubMed: 38802818
DOI: 10.1186/s12934-024-02422-0 -
International Journal of Systematic and... Nov 2023A milky-white-coloured, aerobic, Gram-stain-positive, rod-shaped and motile bacterial strain (GW78) was isolated from forest soil. GW78 was catalase-positive and...
A milky-white-coloured, aerobic, Gram-stain-positive, rod-shaped and motile bacterial strain (GW78) was isolated from forest soil. GW78 was catalase-positive and oxidase-negative. The strain was able to grow optimally at 37 °C and at pH 7.0 in Reasoner's 2A media. The phylogenetic and 16S rRNA gene sequence analysis of GW78 showed its affiliation with the genus . The 16S rRNA gene sequence of GW78 revealed 98.3 % similarity to its nearest neighbour VKPM B-7519. Its chemotaxonomic properties included MK-7 as the sole menaquinone, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine as major polar lipids, and anteiso-C, C 11 and anteiso-C as predominant fatty acids. Digital DNA-DNA hybridization and average nucleotide identity results with its closest relatives were <74.0 % and <14.0 %, respectively. Overall, 16S rRNA gene sequence comparisons, phylogenetic and genomic evidence, and phenotypic and chemotaxonomic data allow the differentiation of GW78 from other members of the genus . Thus, we propose that strain GW78 represents a novel species of the genus , with the name sp. nov. The type strain is GW78 (=KCTC 43430=NBRC 116023).
Topics: Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Base Composition; DNA, Bacterial; Bacterial Typing Techniques; Soil Microbiology; Paenibacillus; Forests
PubMed: 37982814
DOI: 10.1099/ijsem.0.006171