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.
journal_name
Appl Microbiol Biotechnoljournal_title
Applied microbiology and biotechnologyauthors
Reva ON,Larisa SA,Mwakilili AD,Tibuhwa D,Lyantagaye S,Chan WY,Lutz S,Ahrens CH,Vater J,Borriss Rdoi
10.1007/s00253-020-10767-wsubject
Has Abstractpub_date
2020-09-01 00:00:00pages
7643-7656issue
17eissn
0175-7598issn
1432-0614pii
10.1007/s00253-020-10767-wjournal_volume
104pub_type
杂志文章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
更新日期:2012-04-01 00:00:00
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
更新日期:2000-08-01 00:00:00
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
更新日期:2008-02-01 00:00:00
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
更新日期:1996-09-01 00:00:00
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
更新日期:2010-05-01 00:00:00
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
更新日期:1995-01-01 00:00:00
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
更新日期:2006-09-01 00:00:00
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
更新日期:2003-12-01 00:00:00
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
更新日期:2010-12-01 00:00:00
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
更新日期:2019-08-01 00:00:00
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
更新日期:1999-05-01 00:00:00
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
更新日期:2020-02-01 00:00:00
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
更新日期:2006-06-01 00:00:00
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
更新日期:1995-07-01 00:00:00
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
更新日期:2007-06-01 00:00:00
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
更新日期:2012-05-01 00:00:00
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
更新日期:2013-07-01 00:00:00
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
更新日期:2017-03-01 00:00:00
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
更新日期:2015-11-01 00:00:00
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
更新日期:2010-03-01 00:00:00
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
更新日期:2002-04-01 00:00:00
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
更新日期:2011-08-01 00:00:00
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
更新日期:2005-01-01 00:00:00
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
更新日期:2013-10-01 00:00:00
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
更新日期:2020-06-01 00:00:00
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
更新日期:2011-03-01 00:00:00
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
更新日期:2002-07-01 00:00:00
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
更新日期:2008-02-01 00:00:00
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
更新日期:2018-05-01 00:00:00
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
更新日期:2020-02-01 00:00:00