Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains.

Abstract:

:The application of biocontrol biopesticides based on plant growth-promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences' Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140. KEY POINTS: • Whole genome sequence of the active PGPR Bacillus velezensis UCMB5140. • Identification of genetic determinants responsible for PGPR activities. • Role of methyltransferases and epigenetic mechanisms in evolution of bacteria.

authors

Reva ON,Larisa SA,Mwakilili AD,Tibuhwa D,Lyantagaye S,Chan WY,Lutz S,Ahrens CH,Vater J,Borriss R

doi

10.1007/s00253-020-10767-w

subject

Has Abstract

pub_date

2020-09-01 00:00:00

pages

7643-7656

issue

17

eissn

0175-7598

issn

1432-0614

pii

10.1007/s00253-020-10767-w

journal_volume

104

pub_type

杂志文章
  • Internal loop photobiodegradation reactor (ILPBR) for accelerated degradation of sulfamethoxazole (SMX).

    abstract::The internal loop photobiodegradation reactor (ILPBR) was evaluated for the degradation of the pharmaceutical sulfamethoxazole (SMX) using batch experiments following three protocols: photolysis alone (P), biodegradation alone (B), and intimately coupled photolysis and biodegradation (P&B). SMX was removed more rapidl...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-011-3742-0

    authors: Yan N,Xia S,Xu L,Zhu J,Zhang Y,Rittmann BE

    更新日期:2012-04-01 00:00:00

  • Bacterial response to acetate challenge: a comparison of tolerance among species.

    abstract::Although acetate formation and tolerance are important criteria for various aspects of biotechnological process development, available studies on acetate tolerance in different species are disparate. We evaluate the response of eight bacterial strains, including two variants of Escherichia coli, two variants of Staphy...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s002530000339

    authors: Lasko DR,Zamboni N,Sauer U

    更新日期:2000-08-01 00:00:00

  • A novel approach to microbial breeding--low-energy ion implantation.

    abstract::Low-energy ions exist widely in the natural world. People had neglected the interaction between low-energy ions and material; it was even more out of the question to study the relation of low-energy ions and the complicated organism until the biological effects of low-energy ion implantation were discovered in 1989. N...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-007-1312-2

    authors: Gu SB,Li SC,Feng HY,Wu Y,Yu ZL

    更新日期:2008-02-01 00:00:00

  • The occurrence of killer, sensitive, and neutral yeasts in Brazilian Riesling Italico grape must and the effect of neutral strains on killing behaviour.

    abstract::The occurrence of killer toxins amongst yeast in Brazilian Riesling Italico grape must was investigated by using the sensitive strain EMBRAPA-26B as a reference strain at 18 degrees C and 28 degrees C. From a total of 85 previously isolated yeasts, 21 strains showed ability to kill the sensitive strain on unbuffered g...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s002530050791

    authors: da Silva GA

    更新日期:1996-09-01 00:00:00

  • Applications of quorum sensing in biotechnology.

    abstract::Many unicellular microorganisms use small signaling molecules to determine their local concentration. The processes involved in the production and recognition of these signals are collectively known as quorum sensing (QS). This form of cell-cell communication is used by unicellular microorganisms to co-ordinate their ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-010-2521-7

    authors: Choudhary S,Schmidt-Dannert C

    更新日期:2010-05-01 00:00:00

  • Improved production of the insecticidal CryIVD protein in Bacillus thuringiensis using cryIA(c) promoters to express the gene for an associated 20-kDa protein.

    abstract::Previous studies have shown that a 20-kDa protein enhances production of the insecticidal CytA and CryIVA proteins of Bacillus thuringiensis in Escherichia coli as well as CytA production and crystal formation in B. thuringiensis. To determine whether the 20-kDa protein could enhance CryIVD production, an expression v...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/BF00171947

    authors: Wu D,Federici BA

    更新日期:1995-01-01 00:00:00

  • Current state and perspectives of truffle genetics and sustainable biotechnology.

    abstract::Mycorrhizal fungi belonging to the genus Tuber produce, after the establishment of a productive interaction with a plant host, hypogeous fruitbodies of great economic value known as ''truffles''. This review summarizes the state of art on life cycle, genetic, and biotechnological investigations of Tuber spp. The ascoc...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-006-0519-y

    authors: Poma A,Limongi T,Pacioni G

    更新日期:2006-09-01 00:00:00

  • A novel polygalacturonic acid bioflocculant REA-11 produced by Corynebacterium glutamicum: a proposed biosynthetic pathway and experimental confirmation.

    abstract::Corynebacterium glutamicum CCTCC M201005 produces a novel polygalacturonic acid bioflocculant, REA-11, consisting of galacturonic acid as the main structural unit. A biosynthetic pathway of REA-11 in C. glutamicum CCTCC M201005 was proposed. Evidence for the biosynthetic pathway was provided by: (1) analyzing the resp...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-003-1365-9

    authors: Li Y,He N,Guan H,Du G,Chen J

    更新日期:2003-12-01 00:00:00

  • Novel soluble expression technologies derived from unique properties of halophilic proteins.

    abstract::Recombinant production of mammalian cytoplasmic proteins plays a major role in developing pharmaceutical products. Here we describe two expression technologies using unique nature of halophilic bacteria. One of such properties of halophilic bacteria is accumulation of compatible solutes in the cytoplasm. As the compat...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-010-2832-8

    authors: Tokunaga H,Arakawa T,Tokunaga M

    更新日期:2010-12-01 00:00:00

  • Effect of SDS on release of intracellular pneumocandin B0 in extractive batch fermentation of Glarea lozoyensis.

    abstract::Pneumocandin B0 is a hydrophobic secondary metabolite that accumulates in the mycelia of Glarea lozoyensis and inhibits fungal 1,3-β-glucan synthase. Extractive batch fermentation can promote the release of intracellular secondary metabolites into the fermentation broth and is often used in industry. The addition of e...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-019-09920-x

    authors: Yuan K,Huang B,Qin T,Song P,Zhang K,Ji X,Ren L,Zhang S,Huang H

    更新日期:2019-08-01 00:00:00

  • Construction of a flocculent Saccharomyces cerevisiae fermenting lactose.

    abstract::A flocculent Saccharomyces cerevisiae strain with the ability to express both the LAC4 (coding for beta-galactosidase) and LAC12 (coding for lactose permease) genes of Kluyveromyces marxianus was constructed. This recombinant strain is not only able to grow on lactose, but it can also ferment this substrate. To our kn...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s002530051441

    authors: Domingues L,Teixeira JA,Lima N

    更新日期:1999-05-01 00:00:00

  • Oral delivery of Bacillus subtilis spores expressing Clonorchis sinensis paramyosin protects grass carp from cercaria infection.

    abstract::Clonorchis sinensis (C. sinensis), an important fishborne zoonotic parasite threatening public health, is of major socioeconomic importance in epidemic areas. Effective strategies are still urgently expected to prevent against C. sinensis infection. In the present study, paramyosin of C. sinensis (CsPmy) was stably an...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-019-10316-0

    authors: Sun H,Shang M,Tang Z,Jiang H,Dong H,Zhou X,Lin Z,Shi C,Ren P,Zhao L,Shi M,Zhou L,Pan H,Chang O,Li X,Huang Y,Yu X

    更新日期:2020-02-01 00:00:00

  • Simultaneous P-solubilizing and biocontrol activity of microorganisms: potentials and future trends.

    abstract::Phosphate (P)-solubilizing microorganisms as a group form an important part of the microorganisms, which benefit plant growth and development. Growth promotion and increased uptake of phosphate are not the only mechanisms by which these microorganisms exert a positive effect on plants. Microbially mediated solubilizat...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-006-0380-z

    authors: Vassilev N,Vassileva M,Nikolaeva I

    更新日期:2006-06-01 00:00:00

  • A target-specific chimeric toxin composed of epidermal growth factor and Pseudomonas exotoxin A with a deletion in its toxin-binding domain.

    abstract::We have fused the epidermal growth factor (EGF) to the amino terminus of Pseudomonas exotoxin A (PE) to create a cytotoxic agent, designated EGF-PE, which preferentially kills EGF-receptor-bearing cells. In this study, we analyzed the effect of the Ia domain, the binding domain of PE on the cytotoxicity of EGF-PE towa...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/BF00218456

    authors: Liao CW,Hseu TH,Hwang J

    更新日期:1995-07-01 00:00:00

  • Synergistic antidigestion effect of Lactobacillus rhamnosus and bovine colostrums in simulated gastrointestinal tract (in vitro).

    abstract::Probiotics and bovine colostrums had been proven to be beneficial for human health. Lactobacillus rhamnosus ZDY114 and anti-Helicobacter pylori bovine colostrums were used for the preparation of microecological additives, and their synergistic antidigestion effect in the simulated gastrointestinal tract (in vitro) was...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-007-0861-8

    authors: Wei H,Xu Y,Xiong Y,Xu F,Liu G

    更新日期:2007-06-01 00:00:00

  • Asymmetric synthesis of (R)-1,3-butanediol from 4-hydroxy-2-butanone by a newly isolated strain Candida krusei ZJB-09162.

    abstract::Biocatalytic asymmetric preparation of (R)-1,3-butanediol has been attracting much attention in pharmaceuticals industry. A new ideal strain, ZJB-09162, which exhibited high reduction activity and excellent (R)-stereospecificity towards 4-hydroxy-2-butanone, has been successfully isolated from soil samples. Based on m...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-012-3942-2

    authors: Zheng RC,Ge Z,Qiu ZK,Wang YS,Zheng YG

    更新日期:2012-05-01 00:00:00

  • Application of the FLP/FRT recombination system in cyanobacteria for construction of markerless mutants.

    abstract::Due to efficient photosynthetic capability, robust growth, and clear genetic background, cyanobacteria are recently used for production of different biofuel and biochemical molecules by genetic engineering and showed great potentials as the next-generation microbial cell factory. For improving the production of bio-pr...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-013-4837-6

    authors: Tan X,Liang F,Cai K,Lu X

    更新日期:2013-07-01 00:00:00

  • Modeling of exo-inulinase biosynthesis by Kluyveromyces marxianus in fed-batch mode: correlating production kinetics and metabolic heat fluxes.

    abstract::A metabolic heat-based model was used for estimating the growth of Kluyveromyces marxianus, and the modified Luedeking-Piret kinetic model was used for describing the inulinase production kinetics. For the first time, a relationship was developed to relate inulinase production kinetics directly to metabolic heat gener...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-016-7971-0

    authors: Santharam L,Samuthirapandi AB,Easwaran SN,Mahadevan S

    更新日期:2017-03-01 00:00:00

  • Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene.

    abstract::Clean-up of vinyl chloride (VC)-contaminated groundwater could be enhanced by stimulating aerobic VC-oxidizing bacterial populations (e.g., methanotrophs) with amendments such as molecular oxygen. In addition, ethene gas injection could further stimulate a different group of aerobic ethene- and VC-oxidizing bacteria c...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-015-6771-2

    authors: Mattes TE,Jin YO,Livermore J,Pearl M,Liu X

    更新日期:2015-11-01 00:00:00

  • Synthesis of gamma-aminobutyric acid (GABA) by Lactobacillus plantarum DSM19463: functional grape must beverage and dermatological applications.

    abstract::Agriculture surplus were used as substrates to synthesize gamma-aminobutyric acid (GABA) by Lactobacillus plantarum DSM19463 for the manufacture of a functional beverage or as a novel application for dermatological purposes. Dilution of the grape must to 1 or 4% (w/v) of total carbohydrates favored higher cell yield a...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-009-2370-4

    authors: Di Cagno R,Mazzacane F,Rizzello CG,De Angelis M,Giuliani G,Meloni M,De Servi B,Gobbetti M

    更新日期:2010-03-01 00:00:00

  • Description of a cellulose-binding domain and a linker sequence from Aspergillus fungi.

    abstract::A family I cellulose-binding domain (CBD) and a serine- and threonine-rich linker peptide were cloned from the fungi Aspergillus japonicus and Aspergillus aculeatus. A glutathione S-transferase (GST) fusion protein comprising GST and a peptide linker with the CBD fused to its C-terminus, was expressed in Escherichia c...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-002-0937-4

    authors: Quentin M,Ebbelaar M,Derksen J,Mariani C,van Der Valk H

    更新日期:2002-04-01 00:00:00

  • Metabolic engineering of flavonoids in plants and microorganisms.

    abstract::Over 9,000 flavonoid compounds have been found in various plants, comprising one of the largest families of natural products. Flavonoids are an essential factor in plant interactions with the environment, often serving as the first line of defense against UV irradiation and pathogen attacks. Flavonoids are also major ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-011-3449-2

    authors: Wang Y,Chen S,Yu O

    更新日期:2011-08-01 00:00:00

  • Discovery of a thermostable Baeyer-Villiger monooxygenase by genome mining.

    abstract::Baeyer-Villiger monooxygenases represent useful biocatalytic tools, as they can catalyze reactions which are difficult to achieve using chemical means. However, only a limited number of these atypical monooxygenases are available in recombinant form. Using a recently described protein sequence motif, a putative Baeyer...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-004-1749-5

    authors: Fraaije MW,Wu J,Heuts DP,van Hellemond EW,Spelberg JH,Janssen DB

    更新日期:2005-01-01 00:00:00

  • Isolation and characterization of a novel cyanophycin synthetase from a deep-sea sediment metagenomic library.

    abstract::Cyanophycin is non-ribosomally synthesized protein-like copolymer. Synthesis of cyanophycin is catalyzed by cyanophycin synthetase (CphA). In this study, a novel cyanophycin synthetase CphA49 belonging to NOR5 clade of Gammaproteobacteria was identified with primer-based screening from a deep-sea sediment metagenomic ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-013-4872-3

    authors: Du J,Li L,Ding X,Hu H,Lu Y,Zhou S

    更新日期:2013-10-01 00:00:00

  • Development and production of nanobodies specifically against green fluorescence protein.

    abstract::Variable domains of heavy chains of camelid heavy-chain antibodies (VHHs) are known as nanobodies. Nanobodies are approximately 15 kDa in size with high affinity to their antigens. They can be easily manipulated and produced in microorganisms. In this study, an alpaca was immunized with purified green fluorescence pro...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-020-10535-w

    authors: Fang Z,Cao D,Qiu J

    更新日期:2020-06-01 00:00:00

  • Proteomic understanding of intracellular responses of recombinant Chinese hamster ovary cells cultivated in serum-free medium supplemented with hydrolysates.

    abstract::In order to understand the intracellular responses in recombinant CHO (rCHO) cells producing antibody in serum-free medium (SFM) supplemented with optimized hydrolysates mixtures, yielding the highest specific growth rate (μ, SFM#S1) or the highest specific antibody productivity (q(Ab,) SFM#S2), differentially express...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-011-3106-9

    authors: Kim JY,Kim YG,Han YK,Choi HS,Kim YH,Lee GM

    更新日期:2011-03-01 00:00:00

  • Effect of glucose on glycerol bioconversion by Lactobacillus reuteri.

    abstract::The impact of glucose on glycerol metabolism, especially on 3-hydroxypropionaldehyde (3-HPA) accumulation by resting cells of Lactobacillus reuteri has been investigated. Two systems were used in the study: MRS(-) (modified MRS - omitting glucose, acetate and Tween 80) and distilled water (H(2)O). In MRS(-), addition ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-002-1002-z

    authors: Lüthi-Peng Q,Dileme FB,Puhan Z

    更新日期:2002-07-01 00:00:00

  • Production of L-phenylacetylcarbinol by microbial transformation in polyethylene glycol-induced cloud point system.

    abstract::Microbial transformation of benzaldehyde into L: -phenylacetylcarbinol by whole cell Saccharomyces cerevisiae has been carried out in a novel polyethylene glycol (PEG)-induced cloud point system. The system is composed of 80 g PEG 20,000, 75 ml Triton X-100, 20 g peptone, 10 g yeast extract, 25 g glucose, 1 g MgSO(4)....

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-007-1304-2

    authors: Zhang W,Wang Z,Li W,Zhuang B,Qi H

    更新日期:2008-02-01 00:00:00

  • Detecting ligand interactions in real time on living bacterial cells.

    abstract::Time-resolved analysis assays of receptor-ligand interactions are fundamental in basic research and drug discovery. Adequate methods are well developed for the analysis of recombinant proteins such as antibody-antigen interactions. However, assays for time-resolved ligand-binding processes on living cells are still ra...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-018-8919-3

    authors: Encarnação JC,Schulte T,Achour A,Björkelund H,Andersson K

    更新日期:2018-05-01 00:00:00

  • Advances in acrylamide bioproduction catalyzed with Rhodococcus cells harboring nitrile hydratase.

    abstract::Acrylamide is an important bulk chemical used for producing polyacrylamide, which is widely applied in diverse fields, such as enhanced oil recovery and water treatment. Acrylamide production with a superior biocatalyst, free-resting Rhodococcus cells containing nitrile hydratase (NHase), has been proven to be simple ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-019-10284-5

    authors: Jiao S,Li F,Yu H,Shen Z

    更新日期:2020-02-01 00:00:00