Genome Sequence of Paenibacillus terrae HPL-003, a Xylanase-Producing Bacterium Isolated from Soil Found in Forest Residue

Shin, Sang Heum; Kim, Sewhan; Kim, Jae Young; Song, Ha Young; Cho, Soo-Jin; Kim, Dal Rye; Lee, Kee‐In; Lim, Hee Nam; Park, No‐Joong; Hwang, In Taek; Yang, Kap‐Seok

doi:10.1128/jb.06668-11

Cited by 23 publications

(12 citation statements)

References 10 publications

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“…are shown in Table 4. All these characteristics are within the range of previously sequenced genomes of Bacillus and Paenibacillus [49][50][51]. A total of 5905, 5716 and 5413 predicted genes were identified for PIC28, PIC73 and PIC167, respectively.…”

Section: Whole-genome General Features Of the Newly Identified Bioconsupporting

confidence: 66%

Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae

et al. 2018

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The use of biological control agents (BCAs) is of interest within an integrated management strategy of Verticillium wilt of olive (VWO) caused by the soil-borne fungus Verticillium dahliae Kleb. Previous studies have shown that the root/rhizosphere of healthy olive plants is an important reservoir of microorganisms displaying biocontrol activity against VWO (i.e., Pseudomonas strains PICF7 and PIC141). Moreover, these BCAs are already adapted to the ecological niche where they are deployed. Three novel bacteria (strains PIC28, PIC73 and PIC167) from nursery-produced olive plants were in-depth characterized using a previously implemented approach consisting of in situ isolation, in vitro antagonism tests, in planta bioassays, phenotypic and metabolic characterization, genome analyses and in silico identification of traits involved in plant-bacteria interactions, and multi-locus sequence analyses. All strains displayed in vitro growth inhibition of different olive pathogens and biocontrol effectiveness against Verticillium dahliae, with strain PIC73 being the most effective BCA. Strains PIC73 and PIC167 were identified as Paenibacillus polymyxa (Prazmowski) Ash et al. and Paenibacillus terrae Yoon et al., respectively. Strain PIC28 belongs to the Bacillus genus. Some of these Bacillales members showed in vitro compatibility with previously characterized BCAs (Pseudomonas spp. strains) also originating from the olive rhizosphere, paving the way for the future development of tailored bacterial consortia effective against VWO.

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Section: Whole-genome General Features Of the Newly Identified Bioconsupporting

confidence: 66%

Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae

et al. 2018

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“…However, comparison of the minimal nif cluster of CR1 with available genomic data on the Joint Genome Institute Integrated Microbial Genomics Database [ 62 ] and NCBI Genebank databases did not reveal a potential source of the nif cluster. However, an identical nif cluster (Figure 7 ) was also identified in Paenibacillus terrae HPL-003 [ 63 ], the next closest related Paenibacillacae to the P. polymyxa species (Figure 1 ). Therefore, we speculate that P. polymyxa and P. terrae are likely derived from the same ancestor possessing the nif cluster, which would explain the identical cluster organization and high nucleotide level similarity between the CR1 and HPL-003 nif clusters (94% identity, E-value 0.0).…”

Section: Resultsmentioning

confidence: 99%

Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness

2014

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BackgroundMembers of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported.ResultsHere we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.ConclusionsOur study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-851) contains supplementary material, which is available to authorized users.

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“…For de novo sequencing projects where the bacterium is the first member of its species to be sequenced, the next closest related species may be used for scaffold assembly. For example, alignments of the CR1 draft genome against the complete Paenibacillus terrae strain HPL-003 genome (Shin et al, 2012 ) also resulted in a contig assembly that approximated the alignment against P. polymyxa strain E681 (Figure 3 ).…”

Section: Methods and Resultsmentioning

confidence: 99%

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

Eastman

Yuan

2015

Front. Microbiol.

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Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects.

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Genome Sequence of Paenibacillus terrae HPL-003, a Xylanase-Producing Bacterium Isolated from Soil Found in Forest Residue

Cited by 23 publications

References 10 publications

Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae

Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae

Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

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