Complete genome sequence of Paenibacillus polymyxa SC2, a strain of plant growth-promoting Rhizobacterium with broad-spectrum antimicrobial activity

Paenibacillus polymyxa SC2 is an important plant growth-promoting rhizobacterium (PGPR). Here, we report the complete genome sequence of P. polymyxa SC2. Multiple sets of functional genes have been found in the genome. As far as we know, this is the first complete genome sequence of Paenibacillus polymyxa.     

Auxin production and detection of the gene coding for the Auxin Efflux Carrier (AEC) protein in <Emphasis Type="Italic">Paenibacillus polymyxa</Emphasis>

Different species of Paenibacillus are considered to be plant growth-promoting rhizobacteria (PGPR) due to their ability to repress soil borne pathogens, fix atmospheric nitrogen, induce plant resistance to diseases and/or produce plant growth-regulating substances such as auxins. Although it is known that indole-3-acetic acid (IAA) is the primary naturally occurring auxin excreted by Paenibacillus species, its transport mechanisms (auxin efflux carriers) have not yet been characterized. In this study, the auxin production of P. polymyxa and P. graminis, which are prevalent in the rhizospheres of maize and sorghum sown in Brazil, was evaluated. In addition, the gene encoding the Auxin Efflux Carrier (AEC) protein from P. polymyxa DSM36(T) was sequenced and used to determine if various strains of P. polymyxa and P. graminis possessed this gene. Each of the 68 P. polymyxa strains evaluated in this study was able to produce IAA, which was produced at concentrations varying from 1 to 17 microg/ml. However, auxin production was not detected in any of the 13 P. graminis strains tested in this study. Different primers were designed for the PCR amplification of the gene coding for the AEC in P. polymyxa, and the predicted protein of 319 aa was homologous to AEC from Bacillus amyloliquefaciens, B. licheniformis, and B. subtilis. However, no product was observed when these primers were used to amplify the genomic DNA of seven strains of P. graminis, which suggests that this gene is not present in this species. Moreover, none of the P. graminis genomes tested were homologous to the gene coding for AEC, whereas all of the P. polymyxa genomes evaluated were. This is the first study to demonstrate that the AEC protein is present in P. polymyxa genome.     

Draft genome sequence of Paenibacillus peoriae strain KCTC 3763T

Paenibacillus peoriae is a potentially plant-beneficial soil bacterium and is a close relative to Paenibacillus polymyxa, the type species of the genus Paenibacillus. Herein, we present the 5.77-Mb draft genome sequence of the P. peoriae type strain with the aim of providing insight into the genomic basis of plant growth-promoting Paenibacillus species.     

Draft Genome Sequence of Paenibacillus polymyxa OSY-DF, Which Coproduces a Lantibiotic, Paenibacillin, and Polymyxin E1

Paenibacillus polymyxa OSY-DF is a Gram-positive rod-shaped bacterium isolated from a fermented vegetable food. This bacterial strain displays potent antimicrobial activities against Gram-positive and Gram-negative pathogenic bacteria, attributed to the production of the lantibiotic paenibacillin and the colistin peptide polymyxin E1. Here we report the draft genome sequence of Paenibacillus polymyxa OSY-DF.     

Assessment of root-associated paenibacillus polymyxa groups on growth promotion and induced systemic resistance in pepper

Twenty-nine P. polymyxa strains isolated from rhizospheres of various crops were clustered into five genotypic groups on the basis of BOX-PCR analysis. The characteristics of several plant growth-promoting factors among the isolates revealed the distinct attributes in each allocated group. Under gnotobiotic conditions, inoculation of pepper roots with P. polymyxa isolates significantly increased the biomass in 17 of total 29 treated plants with untreated plants. Experiments on induced systemic resistance (ISR) against bacterial spot pathogen Xanthomonas axonopodis pv. vesicatoria in pepper by P. polymyxa strains were conducted and only one isolate (KNUC265) was selected. Further studies into ISR mediation by the KNUC265 strain against the soft-rot pathogen Erwinia carotovora subsp. carotovora in tobacco demonstrated that the tobacco seedlings exposed to either bacterial volatiles or diffusible metabolites exhibited a reduction in disease severity. In conclusion, ISR and plant growth promotion triggered by P. polymyxa isolates were systemically investigated on pepper for the first time. The P. polymyxa KNUC265 strain, which elicited both ISR and plant growth promotion, could be potentially used in improving the yield of pepper and possibly of other crops.     

Cytometric monitoring of growth, sporogenesis and spore cell sorting in Paenibacillus polymyxa (formerly Bacillus polymyxa)

AIMS: Formation of bacterial endospores is a basic process in Gram-positive bacteria and has implications for health, industry and the environment. Flow cytometry offers a practical alternative for the rapid detection, enumeration and characterization of bacterial endospores. METHODS AND RESULTS: Paenibacillus polymyxa was chosen for this study because its spores cause sporangium deformation and have thick walls with a star-shaped section. Sporulating populations were analysed with a particle analyser and a flow cytometer after labelling with propidium iodide and Syto-13. Flow cytometric detection of single spores was confirmed by optical and scanning electron microscopy after cell sorting. Four cell sub-populations were cytometrically detected in P. polymyxa cultures grown in liquid sporulation medium. Two sub-populations consisted of vegetative cells differing in both morphology and viability; the other two sub-populations consisted of spores differing in their viability. CONCLUSIONS: This work has shown that flow cytometry is a simple and fast method (less than 15 minutes for sample preparation and analysis) for the study of the sporulation in P. polymyxa. The use of this technique allowed both detection and quantification of sporulation inside a culture, and distinguished cells that differed in viability despite being morphologically identical under microscopic observation. SIGNIFICANCE AND IMPACT OF THE STUDY: Flow cytometry has been proved to be a valuable tool for the analysis of sporulation in P. polymyxa cultures, with the unique capacity of distinguishing between endospores and vegetative cells, and between live and dead cells, in the same analysis. An important percentage of non-viable endospores has been found in aged cultures using this method.     

Role of Bacillus spp. in antagonism between Pleurotus ostreatus and Trichoderma harzianum in heat-treated wheat-straw substrates

This study aimed to identify bacteria involved in Trichodermaharzianum inhibition while promoting Pleurotus ostreatus defences in order to favour cultivation-substrate selectivity for mushroom production. PCR-DGGE profiles of total DNA from wheat-straw substrate showed weak differences between bacterial communities from substrate inoculated with P. ostreatus with or without T. harzianum. The major cultivable bacteria were isolated from three batches of wheat-straw-based cultivation substrates showing an efficient selectivity. They were screened for their ability to inhibit T.harzianum. By using specific media for bacterial isolation and by sequencing certain 16S-rDNA, we observed that Bacillus spp. were the main inhibitors. Among them, a dominant species was identified as Paenibacillus polymyxa. This species was co-cultivated on agar media with P. ostreatus. The measurement of laccase activities from culture plugs indicated that P. polymyxa induced increases in enzyme activities. Bacillus spp. and specifically P. polymyxa from cultivation substrates are implicated in their selectivity by both inhibiting the growth of T.harzianum and stimulating defences of the mushroom P. ostreatus through the induction of laccases. The management of microbial communities during P.ostreatus cultivation-substrate preparation in order to favour P. polymyxa and other Bacillus spp. growth, can be a way to optimize the development of P. ostreatus for mushroom production or other environmental uses of this fungus.     

Inhibitory Effect of Paenibacillus polymyxa GBR-462 on Phytophthora capsici Causing Phytophthora Blight in Chili Pepper

In the present work 25 strains of Paenibacillus polymyxa isolated from rotted ginseng roots were screened for their antimicrobial activity against Phytophthora capsici in vitro . Based on antimicrobial activity, 15 strains categorized as strongly antimicrobial, among them GBR-462 was found as the most active, and five strains each as weekly antimicrobial and no antimicrobial. Antimicrobial activity was influenced by the initial inoculum density, as strains of P. polymyxa with a strong antimicrobial activity (including P. polymyxa GBR-462) showed the antimicrobial activity against P. capsici and could form biofilm only when they were applied at the higher initial inoculums, 10⁸ cfu/ml. No inhibitory effect was noted on the mycelial growth and zoospore germination of the pathogen when applied at the lower inoculum density of 10⁶ cfu/ml of P. polymyxa GBR-462. However, sporangium formation and zoospore release was significantly inhibited at the lower inoculum density. Also light and electron microscopy revealed the structures of sporangia aberrant with no or few healthy nuclei, indicating sporangium and zoospore formation inhibited at the lower inoculum density. Application of P. polymyxa GBR-462 into potted soil suppressed disease progression as well as disease severity; disease severity was reduced by 30% as compared to untreated pots, suggesting P. polymyxa GBR-462 could be a potential biocontrol agent against Phytopthora capsici .     

Paenibacillus polymyxa antagonizes oomycete plant pathogens Phytophthora palmivora and Pythium aphanidermatum

Aim:  To find sustainable alternatives to the application of synthetic chemicals for oomycete pathogen suppression.
Methods and Results:  Here, we present experiments on an Arabidopsis thaliana model system in which we studied the antagonistic properties of rhizobacterium Paenibacillus polymyxa strains towards the oomycete plant pathogens Phytophthora palmivora and Pythium aphanidermatum . We carried out studies on agar plates, in liquid media and in soil. Our results indicate that P. polymyxa strains significantly reduced P. aphanidermatum and P. palmivora colonization in liquid assays. Most plants that had been treated with P. polymyxa survived the P. aphanidermatum inoculations in soil assays.
Conclusions:  The antagonistic abilities of both systems correlated well with mycoidal substance production and not with the production of antagonistic substances from the biocontrol bacteria.
Significance and Impact of the Study:  Our experiments highlight the need to take biofilm formation and niche exclusion mechanisms into consideration for biocontrol assays performed under natural conditions.     

Functional identification and expression of indole-3-pyruvate decarboxylase from Paenibacillus polymyxa E681

Indole-3-acetic acid (IAA) is produced commonly by plants and many bacteria, however, little is known about the genetic basis involving the key enzymes of IAA biosynthetic pathways from Bacillus spp. IAA intermediates from the Gram-positive spore-forming bacterium Paenibacillus polymyxa E681 were investigated, which showed the existence of only an indole-3-pyruvic acid (IPA) pathway for IAA biosynthesis from the bacterium. Four open reading frames (ORFs) encoding indole-3-pyruvate decarboxylaselike proteins and putative indole-3-pyruvate decarboxylase (IPDC), a key enzyme in the IPA synthetic pathway, were found on the genome sequence database of P. polymyxa and cloned in Escherichia coli DH5alpha. One of the ORFs, PP2_01257, was assigned as probable indole-3-pyruvate decarboxylase. The ORF consisted of 1,743 nucleotides encoding 581 amino acids with a deduced molecular mass of 63,380 Da. Alignment studies of the deduced amino acid sequence of the ORF with known IPDC sequences revealed conservation of several amino acids in PP2_01257, essential for substrate and cofactor binding. Recombinant protein, gene product of the ORF PP2_01257 from P. polymyxa E681, was expressed in E. coli BL21 (DE3) as a glutathione S-transferase (GST)-fusion protein and purified to homogeneity using affinity chromatography. The molecular mass of the purified enzyme showed about 63 kDa, corresponding closely to the expected molecular mass of IPDC. The indole-3-pyruvate decarboxylase activity of the recombinant protein, detected by HPLC, using IPA substrate in the enzyme reaction confirmed the identity and functionality of the enzyme IPDC from the E681 strain.     

A plant growth promoting rhizobacterium, Paenibacillus polymyxa strain GBR-1, suppresses root-knot nematode

Exposure of root-knot nematode, Meloidogyne incognita to various concentrations (5-100%) of culture filtrate of Paenibacillus polymyxa GBR-1 under in vitro conditions significantly reduced egg hatch and caused substantial mortality of its juveniles. The increase in the exposure durations of juveniles to culture filtrate and its concentrations increased the mortality rate. Similarly, higher concentrations increased its inhibitory effect on egg hatch. In higher concentrations (25-100%) egg hatch was inhibited by 84-91% after 2 days of exposures as compared to control in sterile distilled water. Application of various concentrations of culture filtrate extract or bacterial suspension of P. polymyxa GBR-1 into potting soil infested with 2000 J2 of M. incognita, reduced the root galling and nematode populations and increased tomato plant growth and root-mass production compared with untreated control (P< or = 0.05). The beneficial effect of P. polymyxa GBR-1 into potted soil increased exponentially with the increase in dose concentrations. Root gall index was reduced from 4.8 to 1.4 and 1.8 when potting soil was treated with 10% concentrations of culture filtrate extract and bacterial suspension, respectively, compared with untreated control. Application of bacterial suspension of P. polymyxa GBR-1 into potted soil at 3 day pre-inoculation of nematode was the most effective followed by simultaneously and at 2 days post-inoculation; as root galling was reduced by 62.5%, 58.3% and 50.0%, respectively, compared with untreated control.     

Alterations in plant growth and in root hormone levels of lodgepole pines inoculated with rhizobacteria.

The presence of other soil microorganisms might influence the ability of rhizobacterial inoculants to promote plant growth either by reducing contact between the inoculant and the plant root or by interfering with the mechanism(s) involved in rhizobacterially mediated growth promotion. We conducted the following experiments to determine whether reductions in the extent of growth promotion of lodgepole pine mediated by Paenibacillus polymyxa occur in the presence of a forest soil isolate (Pseudomonas fluorescens M20) and whether changes in plant growth promotion mediated by P. polymyxa (i) are related to changes in P. polymyxa density in the rhizosphere or (ii) result from alterations in root hormone levels. The extent of plant growth, P. polymyxa rhizosphere density, and root hormone concentrations were determined for lodgepole pine treated with (i) a single growth-promoting rhizobacterial strain (P. polymyxa L6 or Pw-2) or (ii) a combination of bacteria: strain L6 + strain M20 or strain Pw-2 + strain M20. There was no difference in the growth of pines inoculated with strain L6 and those inoculated with strain L6 + strain M20. However, seedlings inoculated with strain Pw-2 had more lateral roots and greater root mass at 12 weeks after inoculation than plants inoculated with strain Pw-2 + strain M20. The extent of growth promotion mediated by P. polymyxa L6 and Pw-2 in each treatment was not correlated to the average population density of each strain in the rhizosphere. Bacterial species-specific effects were observed in root hormone levels: indole-3-acetic acid concentration was elevated in roots inoculated with P. polymyxa L6 or Pw-2, while dihydrozeatin riboside concentration was elevated in roots inoculated with P. fluorescens M20.     

Disruption of the Paenibacillus polymyxa levansucrase gene impairs its ability to aggregate soil in the wheat rhizosphere

Inoculation of wheat roots with Paenibacillus (formerly Bacillus ) polymyxa CF43 increases the mass of root-adhering soil. We tested the role of levan, a fructosyl polymer produced by strain CF43, in the aggregation of soil adhering to wheat roots. The P. polymyxa gene homologous to the Bacillus subtilis sacB gene encoding levansucrase was cloned and sequenced. The corresponding gene product synthesises high molecular weight levan. A P. polymyxa mutant strain, SB03, whose sacB gene is disrupted, was constructed using heterogramic conjugation. Effects of wheat inoculation with the wild type and the mutant strain were compared using two different cultivated silt loam soils in four independent pot experiments. Roots of wheat plantlets inoculated with CF43 or SB03 were colonized after 7–14 days at the same level, and root and shoot masses were not significantly different from those of the non-inoculated control plants. The ratio of root-adhering soil dry mass to root tissue dry mass was significantly higher for plants inoculated with strain CF43 than for those inoculated with mutant strain SB03: + 30% in Orgeval soil and + 100% in Dieulouard soil. Thus the levan produced by P. polymyxa is implicated in the aggregation of root-adhering soil on wheat.     

Improvement in bioavailability of tricalcium phosphate to Cymbopogon martinii var. motia by rhizobacteria, AMF and Azospirillum inoculation

The interactive effects of phosphate solubilizing bacteria, N2 fixing bacteria and arbuscular mycorrhizal fungi (AMF) were studied in a low phosphate alkaline soil amended with tricalcium insoluble source of inorganic phosphate on the growth of an aromatic grass palmarosa (Cymbopogon martinii). The microbial inocula consisted of the AM fungus Glomus aggregatum, phosphate solubilizing rhizobacteria Bacillus polymyxa and N2 fixing bacteria Azospirillum brasilense. These rhizobacteria behaved as "mycorrhiza helper" and enhanced root colonization by G. aggregatum in presence of tricalcium phosphate at the rate of 200 mg kg(-1) soil (P1 level). Dual inoculation of G. aggregatum and B. polymyxa yielded 21.5 g plant dry weight (biomass), while it was 21.7 g in B. polymyxa and A. brasilense inoculated plants as compared to 14.9 g of control at the same level. Phosphate content was maximum (0.167%) in the combined treatment of G. aggregatum, B. polymyxa and A. brasilense at P1 level, however acid phosphatase activity was recorded to be 4.75 pmol mg(-1) min(-1) in G. aggregatum, B. polymyxa and A. brasilense treatment at P0 level. This study indicates that all microbes inoculated together help in the uptake of tricalcium phosphate which is otherwise not used by the plants and their addition at 200 mg kg(-1) of soil gave higher productivity to palmarosa plants.     

Comparison of the spores of Paenibacillus polymyxa prepared at different temperatures

Paenibacillus polymyxa SQR-21, which is antagonistic against Fusarium oxysporum, is used as a biocontrol agent and, when mixed with organic substances for solid fermentation, produces a bioorganic fertilizer. The spores of P. polymyxa prepared at different temperatures were characterized with respect to the dipicolinic acid content, heat resistance, fatty acid composition and germination. Spores prepared at 37°C showed higher heat resistance than those prepared at 25 and 30°C. However, the germination rate was negatively correlated with the sporulation temperature. The maximum germination rate of the spores prepared at 25°C was 1.3-times higher than the spores prepared at 30°C. The sporulation temperature thus affects the resistance and germination properties of P. polymyxa spores. These results are useful for the production of improved bio-organic fertilizer.     

Use of PCR-targeted mutagenesis to disrupt production of fusaricidin-type antifungal antibiotics in Paenibacillus polymyxa

Paenibacillus polymyxa (formerly Bacillus polymyxa) PKB1 has been identified as a potential agent for biocontrol of blackleg disease of canola, caused by the pathogenic fungus Leptosphaeria maculans. The factors presumed to contribute to disease suppression by strain PKB1 include the production of fusaricidin-type antifungal metabolites that appear around the onset of bacterial sporulation. The fusaricidins are a family of lipopeptide antibiotics consisting of a beta-hydroxy fatty acid linked to a cyclic hexapeptide. Using a reverse genetic approach based on conserved motifs of nonribosomal peptide synthetases, a DNA fragment that appears to encode the first two modules of the putative fusaricidin synthetase (fusA) was isolated from PKB1. To confirm the involvement of fusA in production of fusaricidins, a modified PCR targeting mutagenesis protocol was developed to create a fusA mutation in PKB1. A DNA fragment internal to fusA was replaced by a gene disruption cassette containing two antibiotic resistance genes for independent selection of apramycin resistance in Escherichia coli and chloramphenicol resistance in P. polymyxa. Inclusion of an oriT site in the disruption cassette allowed efficient transfer of the inactivated fusA allele to P. polymyxa by intergeneric conjugation. Targeted disruption of fusA led to the complete loss of antifungal activity against L. maculans, suggesting that fusA plays an essential role in the nonribosomal synthesis of fusaricidins.     

内生多粘类芽孢杆菌S-7对甜菜光合作用及产量和品质的影响

研究了内生多粘类芽孢杆菌（Paenibacillus polymyxa）S-7对甜菜叶片光合参数和产量的影响.结果表明：接种内生多粘类芽孢杆菌S-7能显著促进甜菜光合作用,其中叶片净光合速率(P_n)、气孔限制值(L_s)、气孔导度(G_s)和蒸腾速率(T_r )的平均值分别提高了16.11%、23.82%、41.91%和34.80%;叶片胞间CO₂浓度(C_i)平均值降低了21.09%.生物学产量和含糖率分别提高了25.63%和17.46%,促进了甜菜产量和品质提高.表明内生菌不仅影响甜菜光合参数,而且对甜菜产量和品质的提高具有明显的促进作用.     

Antibiosis plays a role in the context of direct interaction during antagonism of Paenibacillus polymyxa towards Fusarium oxysporum

Interaction of Fusarium oxysporum and Paenibacillus polymyxa starts with polar attachment of bacteria to the fungal hyphae followed by the formation of a large cluster of non-motile cells embedded in an extracellular matrix in which the bacteria develop endospores. Enumeration of fungal viable counts showed that less than one of 36,000 colony-forming units survived in paired cultures for 71 h. Effective antagonism was not observed below pH5 and was specific for the bacterial species. Development of F. oxysporum was inhibited in cell-free filtrates derived from cultures of P. polymyxa, but was much more strongly repressed in the presence of living bacteria. Furthermore, recovery of fungal growth started immediately after addition of antibiotics to paired cultures. Restoration of fungal growth was enhanced in filtrates that were supplemented with MgCl2, which suggests that anti-fungal compounds produced by the bacteria were counteracted by magnesium ions. In paired cultures, fungal counts remained very low, even in the presence of the magnesium salt. This study clearly showed that P. polymyxa antagonizes the plant pathogenic fungus F. oxysporum in liquid medium by means of an interaction process in which the presence of living bacteria is a prerequisite for continuous suppression of fungal growth.     

Cloning and sequencing of the gene encoding thermophilic beta-amylase of Clostridium thermosulfurogenes.

A gene coding for thermophilic beta-amylase of Clostridium thermosulfurogenes was cloned into Bacillus subtilis, and its nucleotide sequence was determined. The nucleotide sequence suggested that the thermophilic beta-amylase is translated from monocistronic mRNA as a secretory precursor with a signal peptide of 32 amino acid residues. The deduced amino acid sequence of the mature beta-amylase contained 519 residues with a molecular weight of 57,167. The amino acid sequence of the C. thermosulfurogenes beta-amylase showed 54, 32, and 32% homology with those of the Bacillus polymyxa, soybean, and barley beta-amylases, respectively. Twelve well-conserved regions were found among the amino acid sequences of the four beta-amylases. To elucidate the mechanism rendering the C. thermosulfurogenes beta-amylase thermophilic, its amino acid sequence was compared with that of the B. polymyxa beta-amylase. The C. thermosulfurogenes beta-amyulase contained more Cys residues and fewer hydrophilic amino acid residues than the B. polymyxa beta-amylase did. Several regions were found in the amino acid sequence of the C. thermosulfurogenes beta-amylase, where the hydrophobicity was remarkably high as compared with that of the corresponding regions of the B. polymyxa beta-amylase.