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Cucumber is an important vegetable crop in China. Fusarium wilt is a soil-borne disease that can significantly reduce cucumber yields. Paenibacillus polymyxa WLY78 can strongly inhibit Fusarium oxysporum f. sp. Cucumerium, which causes Fusarium wilt disease. In this study, we screened the genome of WLY78 and found eight potential antibiotic biosynthesis gene clusters. Mutation analysis showed that among the eight clusters, the fusaricidin synthesis (fus) gene cluster is involved in inhibiting the Fusarium genus, Verticillium albo-atrum, Monilia persoon, Alternaria mali, Botrytis cinereal, and Aspergillus niger. Further mutation analysis revealed that with the exception of fusTE, the seven genes fusG, fusF, fusE, fusD, fusC, fusB, and fusA within the fus cluster were all involved in inhibiting fungi. This is the first time that demonstrated that fusTE was not essential. We first report the inhibitory mode of fusaricidin to inhibit spore germination and disrupt hyphal membranes. A biocontrol assay demonstrated that fusaricidin played a major role in controlling Fusarium wilt disease. Additionally, qRT-PCR demonstrated that fusaricidin could induce systemic resistance via salicylic acid (SA) signal against Fusarium wilt of cucumber. WLY78 is the first reported strain to both produce fusaricidin and fix nitrogen. Therefore, our results demonstrate that WLY78 will have great potential as a biocontrol agent in agriculture.

From 2015 to 2018, we continuously applied the diazotroph Paenibacillus triticisoli BJ-18 as an inoculant to soil cropped winter wheat under field condition. Based on 16S rRNA, nifH, ITS, and shotgun metagenome sequencing, we investigated the influences of diazotroph on the composition and function of the bacterial, diazotrophic, and fungal communities in the rhizosphere and root/shoot endosphere of wheat in 2018. P. triticisoli BJ-18 significantly increased soil total N, available P, organic matter, nitrogenase activity, and wheat yield. The diversities of the rhizospheric bacterial community were higher in the inoculation treatment than the non-inoculation treatment, while the relative abundances of rhizospheric fungal, endospheric bacterial, and diazotrophic communities were lower in the inoculation treatment. Paenibacillus became dominant in the rhizosphere and root, and also the relative abundance of indigenous diazotrophs was increased by inoculation. The microbial inoculation also significantly increased the relative abundances of indigenous plant growth-promoting microbes (Bacillus, Klebsiella, and Podospora) but decreased the relative abundances of indigenous pathogenic fungi (Alternaria). Notably, some nitrogenase gene abundances were significantly enriched by inoculation. These results demonstrated that P. triticisoli BJ-18, acting as a keystone species, can change (optimize) the composition and function of plant microbiome to promote plant growth and productivity.

Paenibacillus polymyxa WLY78 is a nitrogen fixer and it can be potentially applied to biofertilizer in agriculture. In this study, P. polymyxa WLY78 is labelled with gfp gene. The GFP-labelled P. polymyxa WLY78 is used to inoculate wheat, maize and cucumber seedlings grown in the gnotobiotic system and in soil, respectively. Observation by confocal laser scanning microscope reveals that the GFP-labeled bacterial cells are mainly located on the root surface and epidermis of wheat, and only a few cells are present within cortical cells. In maize and cucumber seedlings, bacterial cells were colonized in epidermal and cortical cells, intercellular spaces and vascular system of root, stem and leaf tissue interiors besides on root surfaces. Higher densities of the bacterial cells in roots, stems and leaves indicated that P. polymyxa WLY78 cells could migrate from roots to stems and leaves of maize and cucumber. This study will provide insight into interaction between P. polymyxa WLY78 and host cells.

Bartels–Stewart algorithm is an effective and widely used method with an O ( n 3 ) time complexity for solving a static Sylvester equation. When applied to time-varying Sylvester equation, the computation burden increases intensively with the decrease of sampling period and cannot satisfy continuous realtime calculation requirements. Gradient-based recurrent neural network are able to solve the time-varying Sylvester equation in real time but there always exists an estimation error. In contrast, the recently proposed Zhang neural network has been proven to converge to the solution of the Sylvester equation ideally when time goes to infinity. However, this neural network with the suggested activation functions never converges to the desired value in finite time, which may limit its applications in realtime processing. To tackle this problem, a sign-bi-power activation function is proposed in this paper to accelerate Zhang neural network to finite-time convergence. The global convergence and finite-time convergence property are proven in theory. The upper bound of the convergence time is derived analytically. Simulations are performed to evaluate the performance of the neural network with the proposed activation function. In addition, the proposed strategy is applied to online calculating the pseudo-inverse of a matrix and nonlinear control of an inverted pendulum system. Both theoretical analysis and numerical simulations validate the effectiveness of proposed activation function.

Aims To study nitrogen contribution to cucumber derived from nitrogen fixation of Paenibacillus polymyxa WLY78. Methods The nif gene cluster deletion mutant (Δ nifB-V ) of Paenibacillus polymyxa WLY78 was constructed by a homologous recombination method. The effects of plant-growth promotion were investigated by greenhouse experiments. The nitrogen fixation contribution was estimated by 15 N isotope dilution method (also being called the 15 N natural abundance technique). Results Deletion of nif gene cluster of P. polymyxa WLY78 resulted in complete loss of nitrogenase activity. Greenhouse experiments showed that inoculation with P. polymyxa WLY78 could significantly enhance the lengths and dry weights of cucumber roots and shoots, but inoculation with Δ nifB-V mutant could not. 15 N isotope dilution experiments showed that cucumber plants derive 25.93% nitrogen from nitrogen fixation performed by P. polymyxa WLY78, but the Δ nifB-V mutant nearly could not provide nitrogen for plant growth. Conclusions This present study demonstrated that nitrogen fixation performed by P. polymyxa WLY78 contributes to plant growth.

Two strains HN-1T and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1T and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472T and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1T with P. stellifer DSM 14472T was 90.69, which was below the recommended threshold value (< 95–96% ANI). The dDDH showed 42.1% relatedness between strain HN-1T and P. stellifer DSM 14472T, which was lower than the recommended threshold value (dDDH < 70%). The strain HN-1T contain anteiso-C15:0 as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472T, strain HN-1T or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1T or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1T (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively.

Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N 2 -fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N 2 -fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N 2 -fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis , Fusarium graminearum , Gibberella zeae , Fusarium solani , Colletotrichum gossypii and Alternaria longipes . 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture.

Background Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N 2 -fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the nif ( ni trogen f ixation) operon ( nifBHDKENXhesAnifV ) according to nitrogen availability, which is achieved by binding to the two GlnR-binding sites located in the nif promoter region. However, further study on the GlnR-mediated global regulation in this bacterium is still needed. Results In this study, global identification of the genes directly under GlnR control is determined by using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assays (EMSA). Our results reveal that GlnR directly regulates the transcription of 17 genes/operons, including a nif operon, 14 nitrogen metabolism genes/operons ( glnRA , amtBglnK , glnA1 , glnK1 , glnQHMP , nasA , nasD1 , nasD2EF , gcvH , ansZ , pucR , oppABC , appABCDF and dppABC) and 2 carbon metabolism genes ( ldh3 and maeA1 ). Except for the glnRA and nif operon, the other 15 genes/operons are newly identified targets of GlnR. Furthermore, genome-wide transcription analyses reveal that GlnR not only directly regulates the expression of these 17 genes/operons, but also indirectly controls the expression of some other genes/operons involved in nitrogen fixation and the metabolisms of nitrogen and carbon. Conclusion This study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.

Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.

Phosphate (P) availability often limits biological nitrogen fixation (BNF) by diazotrophic bacteria. In soil, only 0.1% of the total P is available for plant uptake. P solubilizing bacteria can convert insoluble P to plant-available soluble P (ionic P and low molecular-weight organic P). However, limited information is available about the effects of synergistic application of diazotrophic bacteria and P solubilizing bacteria on the nitrogenase activity of rhizosphere and nifH expression of endosphere. In this study, we investigated the effects of co-inoculation with a diazotrophic bacterium ( Paenibacillus beijingensis BJ-18) and a P-solubilizing bacterium ( Paenibacillus sp. B1) on wheat growth, plant and soil total N, plant total P, soil available P, soil nitrogenase activity and the relative expression of nifH in plant tissues. Co-inoculation significantly increased plant biomass (length, fresh and dry weight) and plant N content (root: 27%, shoot: 30%) and P content (root: 63%, shoot: 30%). Co-inoculation also significantly increased soil total N (12%), available P (9%) and nitrogenase activity (69%) compared to P. beijingensis BJ-18 inoculation alone. Quantitative real-time PCR analysis showed co-inoculation doubled expression of nifH genes in shoots and roots. Soil nitrogenase activity and nifH expression within plant tissues correlated with P content of soil and plant tissues, which suggests solubilization of P by Paenibacillus sp. B1 increased N fixation in soils and the endosphere. In conclusion, P solubilizing bacteria generally improved soil available P and plant P uptake, and considerably stimulated BNF in the rhizosphere and endosphere of wheat seedlings.