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AMB Express Oct 2018Trace elements are essential nutrients for the growth of microorganisms and play an important role in their proliferation. Hence, the purpose of this paper is to explore...
Trace elements are essential nutrients for the growth of microorganisms and play an important role in their proliferation. Hence, the purpose of this paper is to explore the optimal C and N sources for large-scale culture of Paenibacillus polymyxa, and to screen trace elements that can promote their proliferation and improve the activity. First, the concentration of Paenibacillus polymyxa Pp-7250, the number of spores were used as evaluation index. It was found that the four trace elements Cu, Fe, Mn, and Zn could promote the proliferation of Paenibacillus polymyxa at their optimal concentrations. Next, when using wheat starch as carbon source and soybean meal as nitrogen source, it was most suitable for large-scale culture. Finally, field experiments were carried out, and it was discovered that the combination of four trace elements plus the wheat soybean meal group could significantly improve the disease prevention, growth promotion ability of Pp-7250 and its colonization in ginseng. Moreover, the ability of Pp-7250 to transform ginseng roots and leaf saponins were also significantly improved. The group also affected the rhizosphere bacterial community of ginseng and the number showed a significant promotion or inhibition.
PubMed: 30311028
DOI: 10.1186/s13568-018-0694-0 -
RNA Biology Nov 2021Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able...
Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able to cleave their own phosphodiester backbone at a specific site with rates much higher than those of spontaneous RNA degradation. Our study focuses on a bioinformatically predicted pistol ribozyme from the bacterium . We provide a biochemical characterization of this ribozyme, which includes an investigation of the effect of various metal ions on ribozyme cleavage and a kinetic analysis of ribozyme activity under increasing Mg concentrations and pH. Based on the obtained results, we discuss a possible catalytic role of divalent metal ions. Moreover, we investigated the ligation activity of the pistol ribozyme - an aspect that has not been previously analysed for this ribozyme class. We determined that the pistol ribozyme is almost fully cleaved at equilibrium with the ligation rate constant being nearly 30-fold lower than the cleavage rate constant. In summary, we have characterized an additional representative of this recently discovered ribozyme class isolated from . We expect that our biochemical characterization of a pistol representative in a cultivatable, genetically tractable organism will support our future investigation of the biological roles of this ribozyme class in bacteria.
Topics: Biocatalysis; Catalytic Domain; Computational Biology; Kinetics; Models, Molecular; Nucleic Acid Conformation; Paenibacillus polymyxa; RNA, Catalytic
PubMed: 33622172
DOI: 10.1080/15476286.2021.1874706 -
Frontiers in Genetics 2020Many bacteria belonging to are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as...
Comparative and Functional Analyses of Two Sequenced Genomes Provides Insights Into Their Potential Genes Related to Plant Growth-Promoting Features and Biocontrol Mechanisms.
Many bacteria belonging to are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as biological control agents (BCAs). However, the growth promotion and biocontrol mechanisms of have not been thoroughly elucidated thus far. In this investigation, the genome sequences of two strains, ZF129 and ZF197, with broad anti-pathogen activities and potential for growth promotion were comparatively studied. Comparative and functional analyses of the two sequenced genomes showed that the ZF129 genome consists of one 5,703,931 bp circular chromosome and two 79,020 bp and 37,602 bp plasmids, designated pAP1 and pAP2, respectively. The complete genome sequence of ZF197 consists of one 5,507,169 bp circular chromosome and one 32,065 bp plasmid, designated pAP197. Phylogenetic analysis revealed that ZF129 is highly similar to two strains, HY96-2 and SQR-21, while ZF197 is highly similar to strain J. The genes responsible for secondary metabolite synthesis, plant growth-promoting traits, and systemic resistance inducer production were compared between strains ZF129 and ZF197 as well as other strains. The results indicated that the variation of the corresponding genes or gene clusters between strains ZF129 and ZF197 may lead to different antagonistic activities of their volatiles or cell-free supernatants against . This work indicates that plant growth promotion by is largely mediated by phytohormone production, increased nutrient availability and biocontrol mechanisms. This study provides an in-depth understanding of the genome architecture of , revealing great potential for the application of this bacterium in the fields of agriculture and horticulture as a PGPR.
PubMed: 33391337
DOI: 10.3389/fgene.2020.564939 -
Life Science Alliance Oct 2020is an agriculturally important plant growth-promoting rhizobacterium. Many species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions,...
is an agriculturally important plant growth-promoting rhizobacterium. Many species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date, no quorum sensing systems have been described in Here, we show that the type strain ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
Topics: Bacterial Proteins; Genome, Bacterial; Genomics; Paenibacillus; Paenibacillus polymyxa; Plant Development; Quorum Sensing
PubMed: 32764104
DOI: 10.26508/lsa.202000847 -
Frontiers in Microbiology 2020Bacteria belonging to the genus were frequently isolated from legume nodules. The nodule-inhabiting as a resource of biocontrol and plant growth-promoting endophytes...
Bacteria belonging to the genus were frequently isolated from legume nodules. The nodule-inhabiting as a resource of biocontrol and plant growth-promoting endophytes has rarely been explored. This study explored the nodule-inhabiting ' antifungal activities and biocontrol potentials against broad-spectrum important phytopathogenic fungi. We collected strains which were isolated from nodules of , , , , , or and belong to , , , , , , or closely related to , or . These nodule-inhabiting showed diverse antagonistic activities against five phytopathogenic fungi (, , , , and ). Six strains within the complex showed broad-spectrum and potent activities against all the five pathogens, and produced multiple hydrolytic enzymes, siderophores, and lipopeptide fusaricidins. Fusaricidins are likely the key antimicrobials responsible for the broad-spectrum antifungal activities. The nodule-inhabiting strains within the complex were able to epiphytically and endophytically colonize the non-host wheat plants, produce indole acetic acids (IAA), and dissolve calcium phosphate and calcium phytate. strains RP20, RP51, and RP62 could fix N. RP51 and sp. RP31, which showed potent plant colonization and plant growth-promotion competence, effectively control fungal infection . Genome mining revealed that all strains ( = 76) within the complex contain gene encoding indole-3-pyruvate decarboxylase for biosynthesis of IAA, 96% ( = 73) contain the cluster for biosynthesis of fusaricidins, and 43% ( = 33) contain the cluster for nitrogen fixation. Together, our study highlights that endophytic strains within the complex have a high probability to be effective biocontrol agents and biofertilizers and we propose an effective approach to screen strains within the complex.
PubMed: 33537018
DOI: 10.3389/fmicb.2020.618601 -
Applied Microbiology and Biotechnology Dec 2019The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation...
The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation and biocontrol efficacy against Ralstonia solanacearum by Paenibacillus polymyxa HY96-2. luxS mutants were constructed and assayed for biofilm formation of the wild-type (WT) strain and luxS mutants of P. polymyxa HY96-2 in vitro and in vivo. The results showed that luxS positively regulated the biofilm formation of HY96-2. Greenhouse experiments of tomato bacterial wilt found that from the early stage to late stage postinoculation, the biocontrol efficacy of the luxS deletion strain was the lowest with 50.70 ± 1.39% in the late stage. However, the luxS overexpression strain had the highest biocontrol efficacy with 75.66 ± 1.94% in the late stage. The complementation of luxS could restore the biocontrol efficacy of the luxS deletion strain with 69.84 ± 1.09% in the late stage, which was higher than that of the WT strain with 65.94 ± 2.73%. Therefore, we deduced that luxS could promote the biofilm formation of P. polymyxa HY96-2 and further promoted its biocontrol efficacy against R. solanacearum.
Topics: Bacterial Proteins; Biofilms; Biological Control Agents; Carbon-Sulfur Lyases; Gene Expression Regulation, Bacterial; Solanum lycopersicum; Paenibacillus polymyxa; Plant Diseases; Quorum Sensing; Ralstonia solanacearum
PubMed: 31686149
DOI: 10.1007/s00253-019-10162-0 -
BMC Microbiology Oct 2016Paenibacillus polymyxa is a plant-growth promoting rhizobacterium that could be exploited as an environmentally friendlier alternative to chemical fertilizers and...
Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production.
BACKGROUND
Paenibacillus polymyxa is a plant-growth promoting rhizobacterium that could be exploited as an environmentally friendlier alternative to chemical fertilizers and pesticides. Various strains have been isolated that can benefit agriculture through antimicrobial activity, nitrogen fixation, phosphate solubilization, plant hormone production, or lignocellulose degradation. However, no single strain has yet been identified in which all of these advantageous traits have been confirmed.
RESULTS
P. polymyxa CR1 was isolated from degrading corn roots from southern Ontario, Canada. It was shown to possess in vitro antagonistic activities against the common plant pathogens Phytophthora sojae P6497 (oomycete), Rhizoctonia solani 1809 (basidiomycete fungus), Cylindrocarpon destructans 2062 (ascomycete fungus), Pseudomonas syringae DC3000 (bacterium), and Xanthomonas campestris 93-1 (bacterium), as well as Bacillus cereus (bacterium), an agent of food-borne illness. P. polymyxa CR1 enhanced growth of maize, potato, cucumber, Arabidopsis, and tomato plants; utilized atmospheric nitrogen and insoluble phosphorus; produced the phytohormone indole-3-acetic acid (IAA); and degraded and utilized the major components of lignocellulose (lignin, cellulose, and hemicellulose).
CONCLUSIONS
P. polymyxa CR1 has multiple beneficial traits that are relevant to sustainable agriculture and the bio-economy. This strain could be developed for field application in order to control pathogens, promote plant growth, and degrade crop residues after harvest.
Topics: Agriculture; Antibiosis; Arabidopsis; Ascomycota; Bacillus cereus; Biofuels; Biological Control Agents; Biomass; Canada; Cucumis sativus; Fertilizers; Indoleacetic Acids; Lignin; Solanum lycopersicum; Nitrogen Fixation; Paenibacillus polymyxa; Pest Control, Biological; Phosphorus; Phylogeny; Phytophthora; Plant Diseases; Plant Growth Regulators; Plant Roots; Pseudomonas syringae; RNA, Ribosomal, 16S; Rhizoctonia; Soil Microbiology; Solanum tuberosum; Xanthomonas campestris; Zea mays
PubMed: 27756215
DOI: 10.1186/s12866-016-0860-y -
Molecules (Basel, Switzerland) Jan 2019The commonly believed mechanism of colistin against Gram-negative bacteria is to cause cell membrane lysis, whereas the mechanism of colistin against Gram-positive...
The commonly believed mechanism of colistin against Gram-negative bacteria is to cause cell membrane lysis, whereas the mechanism of colistin against Gram-positive bacteria is extremely fragmented. In this study, we found that colistin treatment on WB800, C12 and ATCC842 enhances not only the activities of α-ketoglutaric dehydrogenase and malate dehydrogenase in tricarboxylic acid (TCA) cycle, but also the relative expression levels of their encoding genes. Additionally, the oxaloacetate concentration also increases. Interestingly, the analysis of the relative expression of genes specific for respiratory chain showed that colistin treatment stimulates the respiratory chain in Gram-positive bacteria. Accordingly, the NAD⁺/NADH ratio increases and the oxidative level is then boosted up. As a result, the intensive oxidative damages are induced in Gram-positive bacteria and cells are killed. Notably, both rotenone and oligomycin, respectively, inhibiting NADH dehydrogenase and phosphorylation on respiratory chain can downgrade oxidative stress formation, thus alleviating the colistin-induced killing of Gram-positive cells. Besides, thiourea-based scavenging for reactive oxygen species also rescues the colistin-subjected cells. These data collectively demonstrate that colistin stimulates both TCA cycle and respiratory chain in Gram-positive bacteria, leading to the enhancement of NADH metabolism and resulting in the generation of oxidative damages in Gram-positive cells. Our studies provide a better understanding of antibacterial mechanism of colistin against Gram-positive bacteria, which is important for knowledge on bacterial resistance to colistin happening via the inhibition of respiratory chain and manipulation of its production.
Topics: Anti-Bacterial Agents; Bacillus subtilis; Citric Acid Cycle; Colistin; Electron Transport; NAD; Oxidative Stress; Paenibacillus polymyxa
PubMed: 30678237
DOI: 10.3390/molecules24030387 -
Genomics Jan 2021The legislations on the usage of antibiotics as growth promoters and prophylactic agents have compelled to develop alternative tools to upsurge the animal protection and...
The legislations on the usage of antibiotics as growth promoters and prophylactic agents have compelled to develop alternative tools to upsurge the animal protection and contain antibiotic usage. Probiotics have emerged as an effective antibiotic substitute in animal farming. The present study explores the probiotic perspective of Paenibacillus polymyxa HK4 interlinking the genotypic and phenotypic characteristics. The draft genome of HK4 revealed the presence of ORFs encoding the functions associated with tolerance to gastrointestinal stress and adhesion. The biosynthetic gene clusters encoding non-ribosomally synthesized peptides, polyketides and lanthipeptides such as fusaricidin, tridecaptin, polymyxin, paenilan and paenibacillin were annotated in HK4 genome. The strain harbored the chromosomal gene conferring the resistance to lincosamides. No functional gene encoding virulence or toxins could be identified in the genome of HK4. The genome analysis data was complemented by the in vitro experiments confirming its survival during gastrointestinal transit, antimicrobial potential and antibiotic sensitivity. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The draft-genome sequence of Paenibacillus polymyxa HK4 has been deposited as whole-genome shotgun project at GenBank under the accession number PRJNA603023.
Topics: Anti-Bacterial Agents; Genome, Bacterial; Paenibacillus polymyxa; Polyketides; Polymyxins; Probiotics
PubMed: 33096257
DOI: 10.1016/j.ygeno.2020.10.017 -
Frontiers in Microbiology 2018(formerly known as ) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent....
(formerly known as ) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.
PubMed: 30050512
DOI: 10.3389/fmicb.2018.01520