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1.
BMC Genomics ; 20(1): 283, 2019 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-30975079

RESUMO

BACKGROUND: Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis. RESULTS: A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis. CONCLUSIONS: This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation.


Assuntos
Bacillus/genética , Evolução Molecular , Genômica , Adaptação Fisiológica/genética , Bacillus/metabolismo , Bacillus/fisiologia , Família Multigênica/genética , Filogenia
2.
J Biotechnol ; 295: 19-27, 2019 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-30831123

RESUMO

Paenibacillus polymyxa is a rhizobacterium that has attracted substantial attention due to its ability to produce functional metabolites and promote plant growth. Metabolic and genetic improvements in this species will benefit research and other applications of the bacterium. However, a suitable gene expression system has not been established in this species. In this study, a promoter trap system based on a green fluorescent protein and a chloramphenicol-resistance gene was developed to isolate native promoters of P. polymyxa SC2-M1 to regulate gene expression. Through high-throughput screening, the novel promoter PLH-77 was identified, sequenced, and subsequently characterized. Promoter PLH-77 is a strong, continuous expression system containing the typical -10 and -35 motifs regions. Its effective sequence was evaluated and then cascaded to improve the promotion efficiency. To further verify the existence of PLH-77, a heterogenous xylose isomerase was expressed by PLH-77 in P. polymyxa SC2-M1. In the resulting strain, the amount of xylose consumed was increased by 2.5 g/L during the 78 h fermentation period. Meanwhile, the production levels of lactate and acetate increased. It was confirmed that promoter PLH-77 could effectively mediate gene expression in P. polymyxa SC2-M1 and will further benefit the quantitative monitoring of gene expression in P. polymyxa.


Assuntos
Engenharia Metabólica/métodos , Paenibacillus polymyxa/genética , Paenibacillus polymyxa/metabolismo , Regiões Promotoras Genéticas/genética , Clonagem Molecular , Expressão Gênica/genética , Plasmídeos/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
3.
Artigo em Inglês | MEDLINE | ID: mdl-30834364

RESUMO

Bacillus velezensis DSYZ is a plant growth-promoting rhizobacterium with the capacity to control fungal pathogens. It was isolated from the rhizosphere soil of garlic. Here, we present the complete genome sequence of B. velezensis DSYZ. Several gene clusters that are related to the biosynthesis of antimicrobial compounds were predicted.

4.
Biomed Res Int ; 2018: 2419686, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30255092

RESUMO

Two bacteria, Streptomyces albireticuli MDJK11 and S. alboflavus MDJK44, which are potential plant growth-promoting rhizobacteria against pathogenic fungi were isolated from the rhizosphere soil of peony in Shandong, China. Their biological characteristics and complete genome sequences were reported in this study. The total genome size of MDJK11 was only 8.14 Mb with 6,550 protein-coding genes and a high GC content of 72.8 mol%. The MDJK44 genome comprises a 9.62 Mb chromosome with 72.1 mol% GC content, 7,285 protein-coding genes, and two plasmids. Some gene sequences in these two genomes were analyzed to be heterologously obtained by horizontal transfer. Gene or gene cluster candidates responding to secondary metabolites production, antimicrobial activities, and plant growth-promoting capacities were also analyzed in this paper. The genomic information and biological characteristics will facilitate the understanding and application of S. albireticuli and S. alboflavus species as biocontrol agents in future agriculture.


Assuntos
Microbiologia do Solo , Streptomyces/genética , Sequenciamento Completo do Genoma , China , Paeonia , Desenvolvimento Vegetal , Raízes de Plantas , Rizosfera , Solo , Streptomyces/isolamento & purificação
5.
Biomed Res Int ; 2018: 9473542, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30046614

RESUMO

Bacillus atrophaeus GQJK17 was isolated from the rhizosphere of Lycium barbarum L. in China, which was shown to be a plant growth-promoting rhizobacterium as a new biological agent against pathogenic fungi and gram-positive bacteria. We present its biological characteristics and complete genome sequence, which contains a 4,325,818 bp circular chromosome with 4,181 coding DNA sequences and a G+C content of 43.3%. A genome analysis revealed a total of 8 candidate gene clusters for producing antimicrobial secondary metabolites, including surfactin, bacillaene, fengycin, and bacillibactin. Some other antimicrobial and plant growth-promoting genes were also discovered. Our results provide insights into the genetic and biological basis of B. atrophaeus strains as a biocontrol agent for application in agriculture.


Assuntos
Bacillus/genética , Genoma Bacteriano , Desenvolvimento Vegetal , Rizosfera , Agentes de Controle Biológico , China , Fungos , Lycium
6.
Braz. j. microbiol ; 48(4): 656-670, Oct.-Dec. 2017. tab, graf
Artigo em Inglês | LILACS | ID: biblio-889178

RESUMO

ABSTRACT This study aimed to explore the effects of two siderophore-producing bacterial strains on iron absorption and plant growth of peanut in calcareous soil. Two siderophore-producing bacterial strains, namely, YZ29 and DZ13, isolated from the rhizosphere soil of peanut, were identified as Paenibacillus illinoisensis and Bacillus sp., respectively. In potted experiments, YZ29 and DZ13 enhanced root activity, chlorophyll and active iron content in leaves, total nitrogen, phosphorus and potassium accumulation of plants and increased the quality of peanut kernels and plant biomass over control. In the field trial, the inoculated treatments performed better than the controls, and the pod yields of the three treatments inoculated with YZ29, DZ13, and YZ29 + DZ13 (1:1) increased by 37.05%, 13.80% and 13.57%, respectively, compared with the control. Based on terminal restriction fragment length polymorphism analysis, YZ29 and DZ13 improved the bacterial community richness and species diversity of soil surrounding the peanut roots. Therefore, YZ29 and DZ13 can be used as candidate bacterial strains to relieve chlorosis of peanut and promote peanut growth. The present study is the first to explore the effect of siderophores produced by P. illinoisensis on iron absorption.


Assuntos
Arachis/crescimento & desenvolvimento , Arachis/microbiologia , Bacillus/metabolismo , Ferro/metabolismo , Paenibacillus/metabolismo , Inoculantes Agrícolas/metabolismo , Arachis/química , Arachis/metabolismo , Bacillus/classificação , Bacillus/genética , Bacillus/isolamento & purificação , Transporte Biológico , Paenibacillus/classificação , Paenibacillus/genética , Paenibacillus/isolamento & purificação , Raízes de Plantas/microbiologia , Rizosfera , Sementes/química , Sementes/crescimento & desenvolvimento , Sementes/metabolismo , Sementes/microbiologia , Sideróforos/metabolismo , Microbiologia do Solo , Solo/química
7.
Genome Announc ; 5(35)2017 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-28860261

RESUMO

Bacillus velezensis GQJK49 is a plant growth-promoting rhizobacterium with antifungal activity, which was isolated from Lycium barbarum L. rhizosphere. Here, we report the complete genome sequence of B. velezensis GQJK49. Twelve gene clusters related to its biosynthesis of secondary metabolites, including antifungal and antibacterial antibiotics, were predicted.

8.
Front Microbiol ; 8: 1391, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28785254

RESUMO

Efficient and cost-effective bioethanol production from lignocellulosic materials requires co-fermentation of the main hydrolyzed sugars, including glucose, xylose, and L-arabinose. Saccharomyces cerevisiae is a glucose-fermenting yeast that is traditionally used for ethanol production. Fermentation of L-arabinose is also possible after metabolic engineering. Transport into the cell is the first and rate-limiting step for L-arabinose metabolism. The galactose permease, Gal2p, is a non-specific, endogenous monosaccharide transporter that has been shown to transport L-arabinose. However, Gal2p-mediated transport of L-arabinose occurs at a low efficiency. In this study, homologous modeling and L-arabinose docking were used to predict amino acids in Gal2p that are crucial for L-arabinose transport. Nine amino acid residues in Gal2p were identified and were the focus for site-directed mutagenesis. In the Gal2p transport-deficient chassis cells, the capacity for L-arabinose transport of the different Gal2p mutants was compared by testing growth rates using L-arabinose as the sole carbon source. Almost all the tested mutations affected L-arabinose transport capacity. Among them, F85 is a unique site. The F85S, F85G, F85C, and F85T point mutations significantly increased L-arabinose transport activities, while, the F85E and F85R mutations decreased L-arabinose transport activities compared to the Gal2p-expressing wild-type strain. These results verified F85 as a key residue in L-arabinose transport. The F85S mutation, having the most significant effect, elevated the exponential growth rate by 40%. The F85S mutation also improved xylose transport efficiency and weakened the glucose transport preference. Overall, enhancing the L-arabinose transport capacity further improved the L-arabinose metabolism of engineered S. cerevisiae.

9.
Genome Announc ; 5(22)2017 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-28572331

RESUMO

Bacillus subtilis GQJK2 is a plant growth-promoting rhizobacterium with antifungal activity which was isolated from Lycium barbarum L. rhizosphere. Here, we report the complete genome sequence of B. subtilis GQJK2. Ten gene clusters involved in the biosynthesis of antagonistic compounds were predicted.

10.
Genome Announc ; 5(24)2017 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-28619794

RESUMO

Bacillus velezensis JTYP2 was isolated from the leaves of Echeveria laui in Qingzhou, China, and may control some of the fungal pathogens of the plant. Here, we present the complete genome sequence of B. velezensis JTYP2. Several gene clusters related to its biosynthesis of antimicrobial compounds were predicted.

11.
Genome Announc ; 5(25)2017 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-28642380

RESUMO

Bacillus paralicheniformis MDJK30 was isolated from the rhizosphere of a peony. It could control the pathogen of peony root rot. Here, we report the complete genome sequence of B. paralicheniformis MDJK30. Eleven secondary metabolism gene clusters were predicted.

12.
Braz J Microbiol ; 48(4): 656-670, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28645648

RESUMO

This study aimed to explore the effects of two siderophore-producing bacterial strains on iron absorption and plant growth of peanut in calcareous soil. Two siderophore-producing bacterial strains, namely, YZ29 and DZ13, isolated from the rhizosphere soil of peanut, were identified as Paenibacillus illinoisensis and Bacillus sp., respectively. In potted experiments, YZ29 and DZ13 enhanced root activity, chlorophyll and active iron content in leaves, total nitrogen, phosphorus and potassium accumulation of plants and increased the quality of peanut kernels and plant biomass over control. In the field trial, the inoculated treatments performed better than the controls, and the pod yields of the three treatments inoculated with YZ29, DZ13, and YZ29+DZ13 (1:1) increased by 37.05%, 13.80% and 13.57%, respectively, compared with the control. Based on terminal restriction fragment length polymorphism analysis, YZ29 and DZ13 improved the bacterial community richness and species diversity of soil surrounding the peanut roots. Therefore, YZ29 and DZ13 can be used as candidate bacterial strains to relieve chlorosis of peanut and promote peanut growth. The present study is the first to explore the effect of siderophores produced by P. illinoisensis on iron absorption.


Assuntos
Arachis/crescimento & desenvolvimento , Arachis/microbiologia , Bacillus/metabolismo , Ferro/metabolismo , Paenibacillus/metabolismo , Inoculantes Agrícolas/metabolismo , Arachis/química , Arachis/metabolismo , Bacillus/classificação , Bacillus/genética , Bacillus/isolamento & purificação , Transporte Biológico , Paenibacillus/classificação , Paenibacillus/genética , Paenibacillus/isolamento & purificação , Raízes de Plantas/microbiologia , Rizosfera , Sementes/química , Sementes/crescimento & desenvolvimento , Sementes/metabolismo , Sementes/microbiologia , Sideróforos/metabolismo , Solo/química , Microbiologia do Solo
13.
Biomed Res Int ; 2017: 5318232, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28459063

RESUMO

Efficient and cost-effective fuel ethanol production from lignocellulosic materials requires simultaneous cofermentation of all hydrolyzed sugars, mainly including D-glucose, D-xylose, and L-arabinose. Saccharomyces cerevisiae is a traditional D-glucose fermenting strain and could utilize D-xylose and L-arabinose after introducing the initial metabolic pathways. The efficiency and simultaneous coutilization of the two pentoses and D-glucose for ethanol production in S. cerevisiae still need to be optimized. Previously, we constructed an L-arabinose-utilizing S. cerevisiae BSW3AP. In this study, we further introduced the XI and XR-XDH metabolic pathways of D-xylose into BSW3AP to obtain D-glucose, D-xylose, and L-arabinose cofermenting strain. Benefits of evolutionary engineering: the resulting strain BSW4XA3 displayed a simultaneous coutilization of D-xylose and L-arabinose with similar consumption rates, and the D-glucose metabolic capacity was not decreased. After 120 h of fermentation on mixed D-glucose, D-xylose, and L-arabinose, BSW4XA3 consumed 24% more amounts of pentoses and the ethanol yield of mixed sugars was increased by 30% than that of BSW3AP. The resulting strain BSW4XA3 was a useful chassis for further enhancing the coutilization efficiency of mixed sugars for bioethanol production.


Assuntos
Engenharia Metabólica/métodos , Redes e Vias Metabólicas/genética , Monossacarídeos/metabolismo , Saccharomyces cerevisiae/metabolismo , Biocombustíveis , Etanol , Fermentação , Monossacarídeos/análise , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento
14.
Genome Announc ; 5(6)2017 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-28183774

RESUMO

Paenibacillus polymyxa strain YC0136 is a plant growth-promoting rhizobacterium with antimicrobial activity, which was isolated from tobacco rhizosphere. Here, we report the complete genome sequence of P. polymyxa YC0136. Several genes with antifungal and antibacterial activity were discovered.

15.
Genome Announc ; 5(6)2017 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-28183775

RESUMO

Paenibacillus polymyxa strain YC0573 is a plant growth-promoting rhizobacterium with antimicrobial activity, which was isolated from tobacco rhizosphere. Here, we report the complete genome sequence of P. polymyxa YC0573. Antifungal and antibacterial genes were discovered.

16.
Biomed Res Int ; 2016: 3687619, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27847812

RESUMO

Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. Delftia tsuruhatensis MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced Delftia strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in D. tsuruhatensis MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production.


Assuntos
Delftia/genética , Delftia/metabolismo , Genoma Bacteriano/genética , Peptídeos/metabolismo , Sideróforos/metabolismo , Técnicas de Inativação de Genes , Peptídeos/genética , Filogenia , Sideróforos/genética
17.
Res Microbiol ; 167(6): 472-9, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27208661

RESUMO

Sporulating bacteria such as Bacillus subtilis and Paenibacillus polymyxa exhibit sporulation deficiencies during their lifetime in a laboratory environment. In this study, spontaneous mutants SC2-M1 and SC2-M2, of P. polymyxa SC2 lost the ability to form endospores. A global genetic and transcriptomic analysis of wild-type SC2 and spontaneous mutants was carried out. Genome resequencing analysis revealed 14 variants in the genome of SC2-M1, including three insertions and deletions (indels), 10 single nucleotide variations (SNVs) and one intrachromosomal translocation (ITX). There were nine variants in the genome of SC2-M2, including two indels and seven SNVs. Transcriptomic analysis revealed that 266 and 272 genes showed significant differences in expression in SC2-M1 and SC2-M2, respectively, compared with the wild-type SC2. Besides sporulation-related genes, genes related to exopolysaccharide biosynthesis (eps), antibiotic (fusaricidin) synthesis, motility (flgB) and other functions were also affected in these mutants. In SC2-M2, reversion of spo0A resulted in the complete recovery of sporulation. This is the first global analysis of mutations related to sporulation deficiency in P. polymyxa. Our results demonstrate that a SNV within spo0A caused the sporulation deficiency of SC2-M2 and provide strong evidence that an arginine residue at position 211 is essential for the function of Spo0A.


Assuntos
Mutação de Sentido Incorreto , Paenibacillus polymyxa/citologia , Paenibacillus polymyxa/crescimento & desenvolvimento , Esporos Bacterianos/citologia , Esporos Bacterianos/crescimento & desenvolvimento , Fatores de Transcrição/metabolismo , Substituição de Aminoácidos , Perfilação da Expressão Gênica , Teste de Complementação Genética , Genômica , Paenibacillus polymyxa/genética , Esporos Bacterianos/genética , Fatores de Transcrição/genética
18.
Genome Announc ; 4(1)2016 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-26868409

RESUMO

Bacillus methylotrophicus FKM10 is a strain of plant growth-promoting rhizobacterium with antimicrobial activity, which was isolated from apple rhizosphere. Here, we present the genome sequence of B. methylotrophicus FKM10. Two scaffolds were finally assembled, and several functional genes related to its antimicrobial activity were discovered.

19.
Genome Announc ; 3(4)2015 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-26294619

RESUMO

Brevibacillus brevis DZQ7 is a plant growth-promoting rhizobacterium (PGPR) isolated from tobacco rhizosphere. Here, we report the draft genome sequence of B. brevis DZQ7. Several functional genes related to antimicrobial activity were identified in the genome.

20.
Genome Announc ; 3(4)2015 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-26251486

RESUMO

Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from tobacco rhizosphere. Here, we report the draft genome sequence of D. tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity and environment adaption have been found in the genome. This is the first genome sequence of D. tsuruhatensis related to PGPR.

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