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International Journal of Systematic and... Apr 2023Two Gram-stain-positive, aerobic, endospore-forming bacterial strains, isolated from the rhizosphere of were studied for their detailed taxonomic allocation. Based on...
Two Gram-stain-positive, aerobic, endospore-forming bacterial strains, isolated from the rhizosphere of were studied for their detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, both strains JJ-7 and JJ-60 were shown to be members of the genus . Strain JJ-7 was most closely related to the type strains of (99.6 %) and (98.7 %), and strain JJ-60 to (99.5 %). The 16S rRNA gene sequence similarities to all other species were ≤98.4 %. Both strains JJ-7 and JJ-60 showed 97.6 % 16S rRNA gene sequence similarity between each other. Genomic comparisons showed that the average nucleotide identity and digital DNA-DNA hybridization values to next related type strain genomes were always <94 and <56 %, respectively. The polar lipid profiles of both strains contain a number of phospholipids including diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, which is in accord with the genus . The major quinone was MK-7 in both strains. Major fatty acids were iso- and anteiso-branched. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strains JJ-7 and JJ-60 from the most closely related species. Thus, each strain represents a novel species of the genus , for which the names sp. nov. and sp. nov. are proposed, with JJ-7 (=CIP 111892=DSM 111785=LMG 32088=CCM 9087) and JJ-60 (=CIP 111894=DSM 111787=LMG 32090=CCM 9086) as the type strains, respectively.
Topics: Fatty Acids; Zea mays; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Phylogeny; Base Composition; DNA, Bacterial; Vitamin K 2; Bacterial Typing Techniques; Paenibacillus
PubMed: 37014794
DOI: 10.1099/ijsem.0.005808 -
Microbial Genomics Feb 2020is a Gram-positive, spore-forming bacterium that is the causative agent of American foulbrood (AFB), the most devastating bacterial disease of the honeybee. is... (Review)
Review
is a Gram-positive, spore-forming bacterium that is the causative agent of American foulbrood (AFB), the most devastating bacterial disease of the honeybee. is antibiotic resistant, complicating treatment efforts. Bacteriophages that target are rapidly emerging as a promising treatment. The first phages were isolated in the 1950s, but as was not antibiotic resistant at the time, interest in them remained scant. Interest in phages has grown rapidly since the first phage genome was sequenced in 2013. Since then, the number of sequenced phage genomes has reached 48 and is set to grow further. All sequenced phages encode a conserved -acetylmuramoyl-l-alanine amidase that is responsible for cleaving the peptidoglycan cell wall of . All phages also encode either an integrase, excisionase or Cro/CI, indicating that they are temperate. In the last few years, several studies have been published on using phages and the phage amidase as treatments for AFB. Studies were conducted on infected larvae and also on hives in the field. The phages have a prophylactic effect, preventing infection, and also a curative effect, helping resolve infection. phages have a narrow range, lysing only , and are unable to lyse even related species. phages thus appear to be safe to use and effective as treatment for AFB, and interest in them in the coming years will continue to grow.
Topics: Animals; Bacteriophages; Bees; Genome, Viral; Paenibacillus larvae
PubMed: 32111267
DOI: 10.1099/mgen.0.000329 -
International Journal of Systematic and... Mar 2022Two Gram-positive, endospore-forming, rod-shaped bacterial strains designated MWE-103 and DLE-14 were isolated from plant roots. The 16S rRNA gene sequence analysis...
Two Gram-positive, endospore-forming, rod-shaped bacterial strains designated MWE-103 and DLE-14 were isolated from plant roots. The 16S rRNA gene sequence analysis indicated that strain MWE-103 was closely related to SY01 with a sequence similarity of 97.82 %, and strain DLE-14 to IZS3-5 with 99.09 % similarity. The orthologous average nucleotide identity and digital DNA-DNA hybridization values using whole genome data indicated that strains MWE-103 and DLE-14 could be readily distinguished from the mostly related species. Both strains grew at mesophilic temperature ranges, and grew best at pH 6 and in the absence of NaCl. The major fatty acid in both strains was anteiso-C, but their relative proportions differed. The predominant quinone of both strains was menaquinone 7, the cell-wall diamino acid was -diaminopimelic acid, and the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, which were consistent with those of related species. Amylase and cellulase activities were positive for both strains. Strain DLE-14 exhibited the potential for lignin degradation. The DNA G+C contents of strain MWE-103 and DLE-14 were 60.9 and 50.8 mol% respectively. The genomes of the two strains revealed potential plant-growth-promoting characteristics such as nitrogen fixation, siderophore production and phosphate solubilization. Based on phylogenetic and phenotypic evidence, strains MWE-103 and DLE-14 should each be recognized as a novel species of , for which the names sp. nov. (type strain: MWE-103=KCTC 43287=JCM 34503) and sp. nov. (type strain: DLE-14=KCTC 43288=JCM 34504) are proposed.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Paenibacillus; Peptidoglycan; Phospholipids; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35234605
DOI: 10.1099/ijsem.0.005270 -
Chembiochem : a European Journal of... Jun 2020Nitrogen is one of the most important nutrients for plant growth. To enhance crop productivity, chemical nitrogen fertilizer is commonly applied in agriculture.... (Review)
Review
Nitrogen is one of the most important nutrients for plant growth. To enhance crop productivity, chemical nitrogen fertilizer is commonly applied in agriculture. Biological nitrogen fixation, the conversion of atmospheric N to NH , is an important source of nitrogen input in agriculture and represents a promising substitute for chemical nitrogen fertilizers. However, nitrogen fixation is only sporadically distributed within bacteria and archaea (diazotrophs). Thus, many biologists hope to reconstitute a nitrogenase biosynthetic pathway in a eukaryotic host, with the final aim of developing N -fixing cereal crops. With the advent of synthetic biology and a deep understanding of the fundamental genetic determinants necessary to sustain nitrogen fixation in bacteria, much progress has been made toward this goal. Transfer of native and refactored nif (nitrogen fixation) genes to non-diazotrophs has been attempted in model bacteria, yeast, and plants. Specifically, nif genes from Klebsiella oxytoca, Azotobacter vinelandii, and Paenibacillus polymyxa have been successfully transferred and expressed in Escherichia coli, Saccharomyces cerevisiae, and even in the tobacco plant. These advances have laid the groundwork to enable cereal crops to "fix" nitrogen themselves to sustain their growth and yield.
Topics: Azotobacter vinelandii; Escherichia coli; Klebsiella oxytoca; Nitrogen Fixation; Paenibacillus polymyxa; Saccharomyces cerevisiae; Nicotiana
PubMed: 32009294
DOI: 10.1002/cbic.201900784 -
Microbiological Research Feb 2021Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N) present in the biosphere into biologically...
Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N) present in the biosphere into biologically available forms of nitrogen. Paenibacillus brasilensis PB24 is a diazotrophic Gram-positive bacterium and is considered ecologically and industrially important because it is able to produce antimicrobial substances and 2,3-butanediol. However, the genetics and regulation of its nitrogen fixing (nif) genes have never been assessed so far. Therefore, the present study aimed to (i) identify the structural and regulatory genes related to BNF in the PB24 genome, (ii) perform comparative genomics analysis of the nif operon among different Paenibacillus species and (iii) study the expression of these genes in the presence and absence of NH. Strain PB24 showed a nif operon composed of nine genes (nifBHDKENXhesAV), with a conserved synteny (with small variations) among the Paenibacillus species evaluated. BNF regulatory genes, glnK and amtB (encoding GlnK signal transduction protein and AmtB transmembrane protein, respectively) and glnR and glnA genes (encoding the transcription factor GlnR and glutamine synthetase) were found in the PB24 genome. Primers were designed for qPCR amplification of the nitrogenase structural (nifH, nifD and nifK) and regulatory (glnA and amtB) BNF genes. The structural gene expression in PB24 was up- and downregulated in the absence and presence of NH, respectively. The gene expression levels indicated a GlnR-mediated repression of genes associated with ammonium import (amtBglnK) and BNF (nif genes). Additionally, the regulatory mechanism of GlnR in P. brasilensis PB24 differed from the other Paenibacillus evaluated, considering the different distribution of binding sites recognized by GlnR.
Topics: Amino Acid Sequence; Bacterial Proteins; Binding Sites; Gene Expression Regulation, Bacterial; Nitrogen Fixation; Paenibacillus
PubMed: 33290933
DOI: 10.1016/j.micres.2020.126647 -
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 -
Biotechnology and Applied Biochemistry Feb 2021The chitinase-producing bacteria Paenibacillus sp. was isolated from soil samples. The chitinase was purified successively by ammonia sulfate fractional precipitation... (Review)
Review
The chitinase-producing bacteria Paenibacillus sp. was isolated from soil samples. The chitinase was purified successively by ammonia sulfate fractional precipitation followed by chromatography on DEAE 52-cellulose column and then on Sephadex G-75 column. The chitinase has a molecular weight of ca. 30 kDa as measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) electrophoresis. Its optimum pH is 4.5, and its optimum temperature is 50 °C with colloidal chitin as a substrate. The enzyme is stable below 45 °C and in pH ranges between 4.5 and 5.5. It is activated by glucosamine, glucose, N-acetylglucosamine, and metal ions including Ca , Fe , Fe , and Ni . It is inhibited by SDS, H O , ascorbic acid, Cu , Mg , Ba , Sn , Cr , and K . With colloidal chitin as substrate, the K and the V of the chitinase are 4.28 mg/mL and 14.29 μg/(Min·mL), respectively, whereas the end products of the enzymatic hydrolysis are 14.33% monomer and 85.67% dimer of N-acetylglucosamine. The viscosity of carboxymethyl chitin decreased rapidly at the initial stages when subjected to chitinase hydrolysis, which indicates that the chitinase acts in an endosplitting pattern.
Topics: Bacterial Proteins; Chitinases; Enzyme Stability; Paenibacillus
PubMed: 31957084
DOI: 10.1002/bab.1889 -
International Journal of Systematic and... Feb 2020Two Gram-positive, rod-shaped, motile, endospore-forming strains, SYSU K30003 and SYSU K30004, were isolated from cave soil sampled in Xingyi County, Guizhou Province,...
Two Gram-positive, rod-shaped, motile, endospore-forming strains, SYSU K30003 and SYSU K30004, were isolated from cave soil sampled in Xingyi County, Guizhou Province, south-west PR China. The 16S rRNA gene sequence results indicated that strains SYSU K30003 and SYSU K30004 had highest sequence similarities to DSM 26310 (93.2 %) and KCTC 33185 (97.8 %), respectively. Optimum growth for both strains occurred at pH 7.0 and 37 °C. Both strains contained -2,6-diaminopimelic acid in their cell-wall peptidoglycan and MK-7 was the only isoprenoid quinone detected. The polar lipid profile of strain SYSU K30004 consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, an unidentified glycolipid, unidentified phospholipids and two unidentified polar lipids. The polar lipid profile of strain SYSU K30003 contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids (>5 %) of strain SYSU K30003 were anteiso-C C, anteiso-C and iso-C, while those of strain SYSU K30004 were anteiso-C, C, anteiso-C, iso-C, iso-C and iso-C. The genome G+C contents of strains SYSU K30003 and SYSU K30004 were 59.0 and 53.6 mol%, respectively. The average nucleotide identity values between strains SYSU K30003 and SYSU K30004 and other closely related members were below the cut-off level (95-96 %) for species identification. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains SYSU K30003 and SYSU K30004 represent two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are SYSU K30003 (=KCTC 33956=CGMCC 1.13505) and SYSU K30004 (=KCTC 33957=CGMCC 1.13872).
Topics: Bacterial Typing Techniques; Base Composition; Caves; Cell Wall; China; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Paenibacillus; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 31746729
DOI: 10.1099/ijsem.0.003870 -
Methods in Molecular Biology (Clifton,... 2020The skin contains three primary layers: epidermis, dermis, and hypodermis. Separation of epidermal components from dermis (dermal-epidermal separation) is an important...
The skin contains three primary layers: epidermis, dermis, and hypodermis. Separation of epidermal components from dermis (dermal-epidermal separation) is an important basic investigation technique for pharmacology, toxicology, and biology. There are different systems of epidermal separation, including typical methods of chemical, enzyme, heat, etc. Each approach has advantages versus disadvantages, and thus the appropriate method should be chosen for a given research question. Here we described the method of enzyme separation.
Topics: Bacterial Proteins; Cell Separation; Dermis; Endopeptidases; Epidermal Cells; Humans; Paenibacillus polymyxa; Skin; Trypsin
PubMed: 31792753
DOI: 10.1007/7651_2019_267 -
Scientific Reports Nov 2022Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial...
Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography-tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC-MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.
Topics: Humans; Proteomics; Chromatography, Liquid; Tandem Mass Spectrometry; Paenibacillus; Anti-Infective Agents; Anti-Bacterial Agents; Genomics
PubMed: 36344671
DOI: 10.1038/s41598-022-23613-y