Complete genome sequence of plant growth-promoting bacterium Leifsonia xyli SE134, a possible gibberellin and auxin producer

doi:10.1016/j.jbiotec.2016.10.004

Journal of Biotechnology

Volume 239, 10 December 2016, Pages 34-38

https://doi.org/10.1016/j.jbiotec.2016.10.004 Get rights and content

Highlights

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We reported the completed genome sequence of Leifsonia xyli SE134, a strain producing gibberellin (GAs) and auxin (IAA).
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The genome contains a single chromosome that is 3,596,761 bp in length with 70.2% G + C contents.
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The strain SE 134 having genes responsible for central carbohydrate metabolism, including tricarboxylic acid cycle, gluconeogenesis.
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Genes for biosynthesis of indole-3-acetate, putrescine, salicylate and jasmonic acid were detected.
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The genes identified in SE134 can now be studied for specific functions using knockout and knockdown strategies.

Abstract

Leifsonia xyli SE134 is a potential plant growth-promoting bacterium isolated from a soil in Daegu, Republic of Korea, which produces large amounts of gibberellin (GA) and indole acetic acid (IAA). In this study, we sequenced the complete genome of L. xyli SE134 by the Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. The genome of L. xyli SE134 contains a single chromosome that is 3,596,761 bp in length, with 70.2% G + C content. The genome contains 3466 protein-coding genes (CDSs) and 51 rRNA- and 46 tRNA-coding genes. By genomic analysis, we identified genes that are potentially involved in plant growth promotion such as genes participating in indole-3-acetic acid (IAA) biosynthesis, siderophore, and trehalose production. L. xyli SE134 also harbours genes for central carbohydrate metabolism, indicating that it can utilise the root exudates with other organic materials as an energy source. Furthermore, the SE134 genome is equipped with various kinds of genes for adaptation to plant surfaces, e.g. defence against desiccation, nutrient deficiencies, and oxidative stress, and a large proportion of genes related to secretion mechanisms and signalling. The genetic information provided here may help to expand this bacterium’s biotechnological potential and to further improve its plant growth-promoting characteristics.

Section snippets

Nucleotide sequence accession number

The complete genome sequence of L. xyli SE134 was deposited in GenBank under accession number CP014761. The strain was deposited in the Korean Agricultural Culture Collection (KACC) under accession number KACC18812.

Acknowledgments

This study was financially supported by a research fund (311058-05-3-CG000) from the Ministry for Food, Agriculture, Forestry, and Fisheries, Republic of korea.

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Cited by (19)

Corn cob as a carbon source in ecological treatment of farmland runoff: Pollutant removal performance, effluent dissolved organic matter and microbial community structure
2023, Journal of Water Process Engineering
As a cheap, slow-release, environmentally-friendly carbon source, corn cob could promote denitrification performance, and was advantageous to ecological treatment of farmland runoff. The effects of corn cob in the ecological treatment planted with Myriophyllum aquatium were seldom explored. In this study, three treatments (MA: Myriophyllum aquaticum; CC: Corn cob; MACC: Myriophyllum aquaticum and corn cob) were used to decontaminate farmland runoff characterized by nitrate-dominated and low carbon content. Results showed that NO₃⁻-N removal efficiencies increased by 37.08 % in CC and 64.87 % in MACC, TN removal efficiencies of CC and MACC increased by 36.72 % and 70.75 %, respectively, and TP removal efficiencies increased by about 15 % in MACC. Four components were identified in DOM, including fulvic-like (C1), humic-like (C2), tryptophan-like (C3) and a combination of tryptophan- and tyrosine-like substances (C4). C2 showed a correlation with microorganisms, which was consistent with that between TN removal and microorganisms. The proportion of typical genus for denitrification was MACC (19.92 %) > CC (3.35 %) > MA (0.56 %) in the water, and that in the substrate was MACC (38.38 %) > CC (36.48 %) > MA (7.11 %). Cellulose-degrading bacteria Pseudomonas appeared in substrates and the proportion was MACC (7.14 %)>CC (3.84 %)>MA (0.33 %). The coexistence and highest proportion of genus for denitrification and fermentation in MACC promoted carbon source release and nitrate removal. Results provided a natural-based treatment for farmland runoff, an understanding of the relationship among denitrification performance, effluent DOM and microorganisms, and inspiration for achieving more satisfactory nitrogen removal in the ecological treatment with biowaste addition.
Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input
2021, Science of the Total Environment
Citation Excerpt :
We found that PGPB strains IAC/BECa 90, IAC/BECa 135, IAC/BECa 141, and IAC/BECa 152 increased the abundance of bacteria of the genus Leifsonia. Although some species of Leifsonia could act as plant-growth promoter (Kang et al., 2014), this bacteria genus might indicate the presence of Leifsonia xyli which might not be harmful (Kang et al., 2016) but brings the risk of ratoon stunting disease (Monteiro-Vitorello et al., 2004). While we did not detect any symptoms of plant disease in sugarcane during the experiment, successive cycles of inoculation with this strain could raise the risk for sugarcane cultivation.
The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.
Analysis of metabolome and microbiome revealed the resistance mechanisms in sugarcane cultivars with high resistance to pokkah boeng disease
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Effect of Bacteria Inoculation on Colonization of Roots by Tuber melanosporum and Growth of Quercus ilex Seedlings
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Journal of Biotechnology

Highlights

Abstract

Section snippets

Nucleotide sequence accession number

Acknowledgments

References (22)

Molecular basis of plant growth promotion and biocontrol by rhizobacteria

Curr. Opin. Plant Biol.

Rhizobacterial effects on nickel extraction from soil and uptake by Alyssum murale

New Phytol.

Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: effect on radishes (Raphanus sativus L.)

Plant Soil

Physiological roles of trehalose in bacteria and yeasts: a comparative analysis

Arch. Microbiol.

The RAST server: rapid annotations using subsystems technology

BMC Genomics

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Sci. Rep.

Complete genome sequence of Pseudomonas aeruginosa strain yl84, a quorum-sensing strain isolated from compost

Genome Announc.

The complete genome sequence of the plant growth-promoting bacterium pseudomonas sp. UW4

PLoS One

Indole-3-acetic acid in plant-microbe interactions

Anton Leeuw Int. J. G

Bacterial cold-shock proteins

Cell. Mol. Life Sci.

Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia

Appl. Environ. Microb.

Cited by (19)

Corn cob as a carbon source in ecological treatment of farmland runoff: Pollutant removal performance, effluent dissolved organic matter and microbial community structure

Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input

Analysis of metabolome and microbiome revealed the resistance mechanisms in sugarcane cultivars with high resistance to pokkah boeng disease

Genome sequence of Leclercia adecarboxylata QDSM01 with multiple plant growth promoting properties

Effect of Bacteria Inoculation on Colonization of Roots by Tuber melanosporum and Growth of Quercus ilex Seedlings

Whole genome analysis of Enterobacter cloacae Rs-2 and screening of genes related to plant-growth promotion

Short genome communicationsComplete genome sequence of plant growth-promoting bacterium Leifsonia xyli SE134, a possible gibberellin and auxin producer

Highlights

Abstract

Section snippets

Nucleotide sequence accession number

Acknowledgments

Curr. Opin. Plant Biol.

Rhizobacterial effects on nickel extraction from soil and uptake by Alyssum murale

New Phytol.

Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: effect on radishes (Raphanus sativus L.)

Plant Soil

Physiological roles of trehalose in bacteria and yeasts: a comparative analysis

Arch. Microbiol.

The RAST server: rapid annotations using subsystems technology

BMC Genomics

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Sci. Rep.

Complete genome sequence of Pseudomonas aeruginosa strain yl84, a quorum-sensing strain isolated from compost

Genome Announc.

The complete genome sequence of the plant growth-promoting bacterium pseudomonas sp. UW4

PLoS One

Indole-3-acetic acid in plant-microbe interactions

Anton Leeuw Int. J. G

Bacterial cold-shock proteins

Cell. Mol. Life Sci.

Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia

Appl. Environ. Microb.

Short genome communications
Complete genome sequence of plant growth-promoting bacterium Leifsonia xyli SE134, a possible gibberellin and auxin producer