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Journal of Fish Diseases Jan 2023A new strain of Paenibacillus polymyxa S3 with antagonistic effects on 11 major fish pathogens (especially Aeromonas hydrophila), but had no toxicity to grass carp, was...
A new strain of Paenibacillus polymyxa S3 with antagonistic effects on 11 major fish pathogens (especially Aeromonas hydrophila), but had no toxicity to grass carp, was screened from the sediment of fishponds. In vivo colonization studies showed that strain S3 could be colonized and distributed in the gill and abdomen of the grass carp. Bioassay results showed that the weight growth rate of grass carp in the strain S3 oral group (16.01%) and strain S3 immersion group (16.44%) was significantly higher than those of the control group (8.61%). At the same time, the activities of ACP, AKP, CAT and GSH-Px in the serum of grass carp in oral and immersion groups were significantly higher than those of the control group. In addition, the treatment with strain S3 could significantly upregulate the expression of the antioxidant-related genes and immune-related genes Keap1, Nrf2, C3, LZM, IgM, TLR-4 and MyD-88 in grass carp tissues. The challenge test showed that strain S3 treatment significantly increased the survival rate of grass carp infected with Aeromonas hydrophila. Whole genome sequencing analysis showed that strain S3 had 16 active metabolite gene clusters, indicating that it had abundant gene resources, which provided important support for its development for fish microecological preparations. In summary, a new strain of Paenibacillus polymyxa S3 with antibacterial activity against a variety of fish pathogens was screened in this study and its probiotic function was evaluated, proving its potential value in fisheries.
Topics: Animals; Carps; Disease Resistance; Paenibacillus polymyxa; Kelch-Like ECH-Associated Protein 1; NF-E2-Related Factor 2; Fish Diseases
PubMed: 36097971
DOI: 10.1111/jfd.13714 -
Microbiology Resource Announcements Jun 2022We report the complete genome sequence of Paenibacillus polymyxa DSM 365. The genome consists of a 5,788,318-bp chromosome, with a GC content of 45.48%. Annotation of...
We report the complete genome sequence of Paenibacillus polymyxa DSM 365. The genome consists of a 5,788,318-bp chromosome, with a GC content of 45.48%. Annotation of the genome revealed a total of 5,246 genes (average length, 943 bp). Gene function analysis indicated the ability to fix nitrogen (N) and to produce value-added chemicals.
PubMed: 35575559
DOI: 10.1128/mra.00329-22 -
International Journal of Molecular... Mar 2021Serine is important for nearly all microorganisms in protein and downstream amino acids synthesis, however, the effect of serine on growth and nitrogen fixation was not...
Serine is important for nearly all microorganisms in protein and downstream amino acids synthesis, however, the effect of serine on growth and nitrogen fixation was not completely clear in many bacteria, besides, the regulatory mode of serine remains to be fully established. In this study, we demonstrated that L-serine is essential for growth and nitrogen fixation of WLY78, but high concentrations of L-serine inhibit growth, nitrogenase activity, and expression. Then, we revealed that expression of the whose gene product catalyzes the first reaction in the serine biosynthetic pathway is regulated by the T-box riboswitch regulatory system. The 508 bp mRNA leader region upstream of the coding region contains a 280 bp T-box riboswitch. The secondary structure of the T-box riboswitch with several conserved features: three stem-loop structures, a 14-bp T-box sequence, and an intrinsic transcriptional terminator, is predicted. Mutation and the transcriptional leader- fusions experiments revealed that the specifier codon of serine is AGC (complementary to the anticodon sequence of tRNA). qRT-PCR showed that transcription of is induced by serine starvation, whereas deletion of the specifier codon resulted in nearly no expression of . Deletion of the terminator sequence or mutation of the continuous seven T following the terminator led to constitutive expression of . The data indicated that the T-box riboswitch, a noncoding RNA segment in the leader region, regulates expression of by a transcription antitermination mechanism.
Topics: Amino Acid Sequence; Bacterial Proteins; Base Sequence; Codon; Conserved Sequence; Gene Expression Regulation, Bacterial; Models, Biological; Mutation; Nitrogenase; Nucleic Acid Conformation; Nucleotide Motifs; Paenibacillus polymyxa; RNA, Bacterial; Riboswitch; Serine
PubMed: 33809732
DOI: 10.3390/ijms22063033 -
ACS Synthetic Biology Jan 2022The use of molecular tools based on the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems has rapidly advanced genetic engineering....
The use of molecular tools based on the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems has rapidly advanced genetic engineering. These molecular biological tools have been applied for different genetic engineering purposes in multiple organisms, including the quite rarely explored . However, only limited studies on large cluster deletion and multiplex genome editing have been described for this highly interesting and versatile bacterium. Here, we demonstrate the utilization of a Cas9-based system to realize targeted deletions of four biosynthetic gene clusters in the range of 12-41 kb by the use of a single targeting sgRNA. Furthermore, we also harnessed the system for multiplex editing of genes and large genomic regions. Multiplex deletion was achieved with more than 80% efficiency, while simultaneous integration at two distantly located sites was obtained with 58% efficiency. The findings reported in this study are anticipated to accelerate future research in and related species.
Topics: CRISPR-Cas Systems; Gene Editing; Genetic Engineering; Paenibacillus polymyxa
PubMed: 34914351
DOI: 10.1021/acssynbio.1c00565 -
Journal of Chemical Ecology Dec 2018Social insects are frequently observed in symbiotic association with bacteria that produce antimicrobial natural products as a defense mechanism. There is a lack of...
Social insects are frequently observed in symbiotic association with bacteria that produce antimicrobial natural products as a defense mechanism. There is a lack of studies on the microbiota associated with stingless bees and their antimicrobial compounds. To the best of our knowledge, this study is the first to report the isolation of Paenibacillus polymyxa ALLI-03-01 from the larval food of the stingless bee Melipona scutellaris. The bacterial strain was cultured under different conditions and produced (L)-(-)-3-phenyllactic acid and fusaricidins, which were active against entomopathogenic fungi and Paenibacillus larvae. Our results indicate that such natural products could be related to colony protection, suggesting a defense symbiosis between P. polymyxa ALLI-03-01 and Melipona scutellaris.
Topics: Animals; Anti-Infective Agents; Bees; Depsipeptides; Disk Diffusion Antimicrobial Tests; Fungi; Lactates; Larva; Microbiota; Paenibacillus polymyxa; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 30350228
DOI: 10.1007/s10886-018-1028-z -
Biotechnology Reports (Amsterdam,... Jun 2022We report the phenotypic variation in E681 (E681), a plant growth-promoting rhizobacterium (PGPR) isolated from a winter barley root in Korea. Phenotypic variation...
We report the phenotypic variation in E681 (E681), a plant growth-promoting rhizobacterium (PGPR) isolated from a winter barley root in Korea. Phenotypic variation (F-type) occurred when E681 (B-type) was grown in the media, and F-type was generated from B-type. B- and F-types were characterized by their morphological, Biolog, and GC-MIDI analyses. F-type cells altered the original biological capacity of B-type cells on endospore and flagella formation, changes in pH in culture, and carbon utilization. In growth curve analysis, B-type variants recovered bacterial growth as the variation occurred after the decline phase, but F-type variants did not. To determine this cause, we conducted comparative proteome analysis between B- and F-types using two-dimensional gel electrophoresis (2-DE). Of the identified proteins, 47% were involved in glycolysis and other metabolic pathways associated with carbohydrate metabolism. Therefore, our findings provide new knowledge on the mechanism of phenotypic variation and insights into agricultural biotechnology.
PubMed: 35686012
DOI: 10.1016/j.btre.2022.e00719 -
Genes & Genetic Systems Aug 2020Paenibacillus polymyxa is a well-known Gram-positive biocontrol bacterium. It has been reported that many P. polymyxa strains can inhibit bacteria, fungi and other plant...
Paenibacillus polymyxa is a well-known Gram-positive biocontrol bacterium. It has been reported that many P. polymyxa strains can inhibit bacteria, fungi and other plant pathogens. Paenibacillus polymyxa employs a variety of mechanisms to promote plant growth, so it is necessary to understand the biocontrol ability of bacteria at the genome level. In the present study, thanks to the widespread availability of Paenibacillus genome data and the development of bioinformatics tools, we were able to analyze and mine the genomes of 43 P. polymyxa strains. The strain NCTC4744 was determined not to be P. polymyxa according to digital DNA-DNA hybridization and average nucleotide identity. By analysis of the pan-genome and the core genome, we found that the pan-genome of P. polymyxa was open and that there were 3,192 core genes. In a gene cluster analysis of secondary metabolites, 797 secondary metabolite gene clusters were found, of which 343 are not similar to known clusters and are expected to reveal a large number of new secondary metabolites. We also analyzed the plant growth-promoting genes that were mined and found, surpisingly, that these genes are highly conserved. The results of the present study not only reveal a large number of unknown potential secondary metabolite gene clusters in P. polymyxa, but also suggest that plant growth promotion characteristics are evolutionary adaptations of P. polymyxa to plant-related habitats.
Topics: Biological Control Agents; Data Mining; Genome, Bacterial; Genomics; Metabolome; Metabolomics; Paenibacillus polymyxa; Plants
PubMed: 32611933
DOI: 10.1266/ggs.19-00053 -
Carbohydrate Polymers Feb 2022Paenibacillus polymyxa is an avid producer of exopolysaccharides of industrial interest. However, due to the complexity of the polymer composition, structural...
Paenibacillus polymyxa is an avid producer of exopolysaccharides of industrial interest. However, due to the complexity of the polymer composition, structural elucidation of the polysaccharide remained unfeasible for a long time. By using a CRISPR-Cas9 mediated knock-out strategy, all single glycosyltransferases as well as the Wzy polymerases were individually deleted in the corresponding gene cluster for the first time. Thereby, it was observed that the main polymer fraction was completely suppressed (or deleted) and a pure minor fucose containing polysaccharide could be isolated, which was named paenan II. Applying this combinatorial approach, the monosaccharide composition, sequence and linkage pattern of this novel polymer was determined via HPLC-MS, GC-MS and NMR. Furthermore, we demonstrated that the knock-out of the glycosyltransferases PepQ, PepT, PepU and PepV as well as of the Wzy polymerase PepG led to the absence of paenan II, attributing those enzymes to the assembly of the repeating unit.
Topics: Carbohydrate Conformation; Fucose; Paenibacillus polymyxa; Polysaccharides, Bacterial
PubMed: 34973768
DOI: 10.1016/j.carbpol.2021.118951 -
International Journal of Systematic and... May 2020is one of the genera that has high species diversity and , the type species of the genus, is mainly isolated from plant-associated environments. Among the...
is one of the genera that has high species diversity and , the type species of the genus, is mainly isolated from plant-associated environments. Among the plant-associated species, B.3 (=CECT 5266=DSM 13815=KACC 10925=KCTC 13919) was proposed to be a novel species according to 16S rRNA gene similarity and DNA-DNA relatedness with related species, including . Nevertheless, in the description of the used strain of was not the type strain of this species. In this work we found that the type strains of both species showed 16S rRNA gene similarity of 99.6 %. Therefore, in this study, we sequenced the genome of KACC 10925 and compared it with those of the type strain of ATCC 842 and other phylogenetically related species. Genome relatedness value calculated by DNA-DNA hybridization between type strains of and was 73.5 %, which is higher than the threshold value (70 %). For more objective and repeatable results of genome relatedness, we analysed an average nucleotide identity (ANI) between two strains. Our results showed that ANI value between the type strains of and is 98.5 %, a phylogenetic distance also higher than the threshold values (95~96 %). These values were proposed by Yoon . (2017). In addition, their phylogenetic distance based on 92 bacterial core genes is highly close compared to other species. These mean that and should be reclassified as a single species. Based on the results from genomic level comparison as well as reexamination results of physiological and chemotaxonomic features, we propose reclassification of as a later heterotypic synonym of .
Topics: Bacterial Typing Techniques; DNA, Bacterial; Genes, Bacterial; Genomics; Nucleic Acid Hybridization; Paenibacillus; Paenibacillus polymyxa; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32375953
DOI: 10.1099/ijsem.0.004140 -
Scientific Reports Feb 2017Paenibacillus polymyxa (P. polymyxa) NSY50, isolated from vinegar residue substrate, suppresses the growth of Fusarium oxysporum in the cucumber rhizosphere and protects...
Paenibacillus polymyxa (P. polymyxa) NSY50, isolated from vinegar residue substrate, suppresses the growth of Fusarium oxysporum in the cucumber rhizosphere and protects the host plant from pathogen invasion. The aim of the present study was to evaluate the effects of NSY50 application on cucumber growth, soil properties and composition of the rhizospheric soil microbial community after exposure to Fusarium oxysporum. Bacterial and fungal communities were investigated by Illumina sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) regions (ITS1 and ITS2). The results showed that NSY50 effectively reduced the incidence of Fusarium wilt (56.4%) by altering the soil physico-chemical properties (e.g., pH, C, R, total N and C) and enzyme activities, especially of urease and β-glucosidase, which were significantly increased by 2.25- and 2.64-fold, respectively, relative to the pathogen treatment condition. More specifically, NSY50 application reduced the abundance of Fusarium and promoted potentially beneficial groups, including the Bacillus, Actinobacteria, Streptomyces, Actinospica, Catenulispora and Pseudomonas genera. Thus, our results suggest that NSY50 application can improve soil properties, shift the microbial community by increasing beneficial strains and decreasing pathogen colonization in the cucumber rhizosphere, and reduce the occurrence of cucumber Fusarium wilt, thereby promoting cucumber growth.
Topics: Biodiversity; Cucumis sativus; Fusarium; Paenibacillus polymyxa; Phylogeny; Plant Diseases; Principal Component Analysis; Rhizosphere; Sequence Analysis, RNA; Soil; Soil Microbiology
PubMed: 28198807
DOI: 10.1038/srep41234