-
International Journal of Systematic and... Sep 2020A Gram-stain-negative aerobic bacterium, strain 11K1, was isolated from a rhizosphere soil of broad bean collected from Qujing, Yunnan, PR China and characterized by...
A Gram-stain-negative aerobic bacterium, strain 11K1, was isolated from a rhizosphere soil of broad bean collected from Qujing, Yunnan, PR China and characterized by using polyphasic taxonomy. The bacterial cells of strain 11K1 were rod-shaped, motile by two polar flagella and positive for oxidase and catalase. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain had the highest similarities to DSM 13194 (99.52 %), CFBP 5737 (99.45 %), subsp. s NBRC 3904 (99.31 %), DSM 13647 (99.25 %) and JCM11938 (99.24 %). Multilocus sequence analysis using the 16S rRNA, , and gene sequences demonstrated that strain 11K1 was a member of the subgroup within the lineage, but was distant from all closely related species. The average nucleotide identity and DNA-DNA hybridization values were lower than recommended thresholds of 95 and 70 %, respectively, for species delineation. The major isoprenoid quinone of strain 11K1 was ubiquinone (Q-9) and the major cellular fatty acids were C, summed feature 3 (C ω7/C ω6), summed feature 8 (C ω7/C ω6) and C cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and two unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain 11K1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 11K1 (=GDMCC 1.1743=KACC 21650).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Rhizosphere; Soil Microbiology; Ubiquinone; Vicia faba
PubMed: 32776868
DOI: 10.1099/ijsem.0.004373 -
Archives of Microbiology Apr 2022Genomes of three strains-phenazine producers-Pseudomonas chlororaphis subsp. aurantiaca (B-162 (wild type), mutant strain B-162/255, and its derivative B-162/17) were...
Genomes of three strains-phenazine producers-Pseudomonas chlororaphis subsp. aurantiaca (B-162 (wild type), mutant strain B-162/255, and its derivative B-162/17) were sequenced and compared. Comparison of a wild-type strain and B-162/255 mutant genomes revealed 32 mutations. 19 new mutations were detected in the genome of B-162/17. Further bioinformatics analysis allowed us to predict mutant protein functions and secondary structures of five gene products, mutations which might potentially influence phenazine synthesis and secretion in Pseudomonas bacteria. These genes encode phenylalanine hydroxylase transcriptional activator PhhR, type I secretion system permease/ATPase, transcriptional regulator MvaT, GacA response regulator, and histidine kinase. Amino acid substitutions were found in domains of studied proteins. One deletion in an intergenic region could affect a potential transcription factor binding site that participates in the regulation of gene that encodes ABC transporter.
Topics: Bacterial Proteins; Phenazines; Pseudomonas
PubMed: 35397008
DOI: 10.1007/s00203-021-02648-1 -
Scientific Reports Nov 2023Biocontrol agents are safe and effective methods for controlling plant disease pathogens, such as Fusarium solani, which causes dry wilt, and Pectobacterium spp.,...
Biocontrol agents are safe and effective methods for controlling plant disease pathogens, such as Fusarium solani, which causes dry wilt, and Pectobacterium spp., responsible for potato soft rot disease. Discovering agents that can effectively control both fungal and bacterial pathogens in potatoes has always presented a challenge. Biological controls were investigated using 500 bacterial strains isolated from rhizospheric microbial communities, along with two promising biocontrol strains: Pseudomonas (T17-4 and VUPf5). Bacillus velezensis (Q12 and US1) and Pseudomonas chlororaphis VUPf5 exhibited the highest inhibition of fungal growth and pathogenicity in both laboratory (48%, 48%, 38%) and greenhouse (100%, 85%, 90%) settings. Q12 demonstrated better control against bacterial pathogens in vivo (approximately 50%). Whole-genome sequencing of Q12 and US1 revealed a genome size of approximately 4.1 Mb. Q12 had 4413 gene IDs and 4300 coding sequences, while US1 had 4369 gene IDs and 4255 coding sequences. Q12 exhibited a higher number of genes classified under functional subcategories related to stress response, cell wall, capsule, levansucrase synthesis, and polysaccharide metabolism. Both Q12 and US1 contained eleven secondary metabolite gene clusters as identified by the antiSMASH and RAST servers. Notably, Q12 possessed the antibacterial locillomycin and iturin A gene clusters, which were absent in US1. This genetic information suggests that Q12 may have a more pronounced control over bacterial pathogens compared to US1. Metabolic profiling of the superior strains, as determined by LC/MS/MS, validated our genetic findings. The investigated strains produced compounds such as iturin A, bacillomycin D, surfactin, fengycin, phenazine derivatives, etc. These compounds reduced spore production and caused deformation of the hyphae in F. solani. In contrast, B. velezensis UR1, which lacked the production of surfactin, fengycin, and iturin, did not affect these structures and failed to inhibit the growth of any pathogens. Our findings suggest that locillomycin and iturin A may contribute to the enhanced control of bacterial pectolytic rot by Q12.
Topics: Solanum tuberosum; Tandem Mass Spectrometry; Bacillus; Anti-Bacterial Agents; Bacteria; Plant Diseases
PubMed: 37925555
DOI: 10.1038/s41598-023-46672-1 -
Frontiers in Microbiology 2023Morel mushroom ( spp.) is a rare edible and medicinal fungus distributed worldwide. It is highly desired by the majority of consumers. Bacterial diseases have been...
Morel mushroom ( spp.) is a rare edible and medicinal fungus distributed worldwide. It is highly desired by the majority of consumers. Bacterial diseases have been commonly observed during artificial cultivation of . Bacterial pathogens spread rapidly and cause a wide range of infections, severely affecting the yield and quality of . In this study, two strains of bacterial pathogens, named M-B and M-5, were isolated, cultured, and purified from the tissues of the infected . Koch's postulates were used to determine the pathogenicity of bacteria affecting , and the pathogens were identified through morphological observation, physiological and biochemical analyses, and 16S rRNA gene sequence analysis. Subsequently, the effect of temperature on the growth of pathogenic bacteria, the inhibitory effect of the bacteria on on plates, and the changes in mycelial morphology of mycelium were analyzed when mycelium was double-cultured with pathogenic bacteria on plates. The results revealed that M-B was subsp. and M-5 was . Strain M-B started to multiply at 10-15°C, and strain M-5 started at 15-20°C. On the plates, the pathogenic bacteria also produced significant inhibition of mycelium, and the observation of mycelial morphology under the scanning electron microscopy revealed that the inhibited mycelium underwent obvious drying and crumpling, and the healthy mycelium were more plump. Thus, this study clarified the pathogens, optimal growth environment, and characteristics of bacterial diseases, thereby providing valuable basic data for the disease prevention and control of production.
PubMed: 38029130
DOI: 10.3389/fmicb.2023.1231353 -
Developing a CRISPR-assisted base-editing system for genome engineering of Pseudomonas chlororaphis.Microbial Biotechnology Sep 2022Pseudomonas chlororaphis is a non-pathogenic, plant growth-promoting rhizobacterium that secretes phenazine compounds with broad-spectrum antibiotic activity. Currently...
Pseudomonas chlororaphis is a non-pathogenic, plant growth-promoting rhizobacterium that secretes phenazine compounds with broad-spectrum antibiotic activity. Currently available genome-editing methods for P. chlororaphis are based on homologous recombination (HR)-dependent allelic exchange, which requires both exogenous DNA repair proteins (e.g. λ-Red-like systems) and endogenous functions (e.g. RecA) for HR and/or providing donor DNA templates. In general, these procedures are time-consuming, laborious and inefficient. Here, we established a CRISPR-assisted base-editing (CBE) system based on the fusion of a rat cytidine deaminase (rAPOBEC1), enhanced-specificity Cas9 nickase (eSpCas9pp ) and uracil DNA glycosylase inhibitor (UGI). This CBE system converts C:G into T:A without DNA strands breaks or any donor DNA template. By engineering a premature STOP codon in target spacers, the hmgA and phzO genes of P. chlororaphis were successfully interrupted at high efficiency. The phzO-inactivated strain obtained by base editing exhibited identical phenotypic features as compared with a mutant obtained by HR-based allelic exchange. The use of this CBE system was extended to other P. chlororaphis strains (subspecies LX24 and HT66) and also to P. fluorescens 10586, with an equally high editing efficiency. The wide applicability of this CBE method will accelerate bacterial physiology research and metabolic engineering of non-traditional bacterial hosts.
Topics: Animals; CRISPR-Cas Systems; DNA; Deoxyribonuclease I; Gene Editing; Genome, Bacterial; Pseudomonas chlororaphis; Rats
PubMed: 35575623
DOI: 10.1111/1751-7915.14075 -
Microbial Synthesis of Antibacterial Phenazine-1,6-dicarboxylic Acid and the Role of PhzG in GP72AN.Journal of Agricultural and Food... Feb 2020have been demonstrated to be environmentally friendly biocontrol strains, and most of them can produce phenazine compounds. Phenazine-1,6-dicarboxylic acid (PDC), with...
have been demonstrated to be environmentally friendly biocontrol strains, and most of them can produce phenazine compounds. Phenazine-1,6-dicarboxylic acid (PDC), with a potential antibacterial activity, is generally found in but not in . The present study aimed to explore the feasibility of PDC synthesis and the function of PhzG in . A PDC producer was constructed by replacing in with from . Through gene deletion, common start codon changing, gene silence, and in vitro assay, our result revealed that the yield of PDC in is associated with the relative expression of to and . In addition, it is found that PDC can be spontaneously synthesized without PhzG. This study provides an efficient way for PDC production and promotes a better understanding of PhzG function in PDC biosynthesis. Moreover, this study gives an alternative opportunity for developing new antibacterial biopesticides.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Bacterial Proteins; Gene Deletion; Molecular Sequence Data; Phenazines; Pseudomonas chlororaphis; Sequence Alignment
PubMed: 32013409
DOI: 10.1021/acs.jafc.9b07657 -
Critical Reviews in Biotechnology Dec 2020In recent years, there has been increasing interest in microbial biotechnology for the production of value-added compounds from renewable resources. species have been... (Review)
Review
In recent years, there has been increasing interest in microbial biotechnology for the production of value-added compounds from renewable resources. species have been proposed as a suitable workhorse for high-value secondary metabolite production because of their unique characteristics for fast growth on sustainable carbon sources, a clear inherited background, versatile intrinsic metabolism with diverse enzymatic capacities, and their robustness in an extreme environment. It has also been demonstrated that metabolically engineered strains can produce several industrially valuable aromatic chemicals and natural products such as phenazines, polyhydroxyalkanoates, rhamnolipids, and insecticidal proteins from renewable feedstocks with remarkably high yields suitable for commercial application. In this review, we summarize cell factory construction in for the biosynthesis of native and non-native bioactive compounds in . , . , . , as well as pharmaceutical proteins production by . . Additionally, some novel strategies together with metabolic engineering strategies in order to improve the biosynthetic abilities of as an ideal chassis are discussed. Finally, we proposed emerging opportunities, challenges, and essential strategies to enable the successful development of as versatile microbial cell factories for the bioproduction of diverse bioactive compounds.
Topics: Biological Products; Glycolipids; Industrial Microbiology; Insecticides; Metabolic Engineering; Phenazines; Polyhydroxyalkanoates; Pseudomonas; Secondary Metabolism; Synthetic Biology
PubMed: 32907412
DOI: 10.1080/07388551.2020.1809990 -
Microbiological Research Aug 2020Pseudomonas chlororaphis subsp. aurantiaca strain JD37 is a plant growth-promoting rhizobacterium (PGPR), which has important biotechnological features such as plant...
Genome analysis of plant growth-promoting rhizobacterium Pseudomonas chlororaphis subsp. aurantiaca JD37 and insights from comparasion of genomics with three Pseudomonas strains.
Pseudomonas chlororaphis subsp. aurantiaca strain JD37 is a plant growth-promoting rhizobacterium (PGPR), which has important biotechnological features such as plant growth promotion, rhizosphere colonization and biocontrol activities. In present study, the genome sequence of JD37 was obtained and comparative genomic analysis were performed to explore unique features of the JD37 genome and its relationship with other Pseudomonas PGPR: P. chlororaphis PA23, P. protegens Pf-5 and P. aeruginosa M18. JD37 possessed a single circular chromosome of 6,702,062 bp in length with an average GC content of 62.75 %. No plasmid was detected in JD37. A total of 5003 functional proteins of JD37 were predicted according to the clusters of orthologous groups (COGs) database. The JD37 genome consisted of various genes involved in plant growth promotion, biocontrol activities and defense responses. Genes involved in the rhizosphere colonization and motility were also found in the genome of JD37, suggesting the common plant growth-promoting traits in PGPR. The identified resistance genes (e.g. those related to metal resistance, antibiotics, and osmotic and temperature-shock) and secondary metabolite biosynthesis revealed the pathways for metabolites it produced. Data presented in present study further provided valuable information on its molecular genetics and adaptive capacity in the rhizosphere niche.
Topics: Disease Resistance; Drug Resistance, Microbial; Gene Ontology; Genes, Bacterial; Genome, Bacterial; Genomics; Phylogeny; Plant Development; Pseudomonas; Rhizosphere; Secondary Metabolism
PubMed: 32402945
DOI: 10.1016/j.micres.2020.126483 -
Antibiotics (Basel, Switzerland) Jun 2021Blood-borne therapeutic phages and phage capsids increasingly reach therapeutic targets as they acquire more persistence, i.e., become more resistant to non-targeted...
Blood-borne therapeutic phages and phage capsids increasingly reach therapeutic targets as they acquire more persistence, i.e., become more resistant to non-targeted removal from blood. Pathogenic bacteria are targets during classical phage therapy. Metastatic tumors are potential future targets, during use of drug delivery vehicles (DDVs) that are phage derived. Phage therapy has, to date, only sometimes been successful. One cause of failure is low phage persistence. A three-step strategy for increasing persistence is to increase (1) the speed of lytic phage isolation, (2) the diversity of phages isolated, and (3) the effectiveness and speed of screening phages for high persistence. The importance of high persistence-screening is illustrated by our finding here of persistence dramatically higher for coliphage T3 than for its relative, coliphage T7, in murine blood. Coliphage T4 is more persistent, long-term than T3. phage 201phi2-1 has relatively low persistence. These data are obtained with phages co-inoculated and separately assayed. In addition, highly persistent phage T3 undergoes dispersal to several murine organs and displays tumor tropism in epithelial tissue (xenografted human oral squamous cell carcinoma). Dispersal is an asset for phage therapy, but a liability for phage-based DDVs. We propose increased focus on phage persistence-and dispersal-screening.
PubMed: 34208477
DOI: 10.3390/antibiotics10060723 -
Environmental Microbiology Apr 2021Pseudomonas chlororaphis PCL1606 (PcPCL1606) displays plant-colonizing features and exhibits antagonistic traits against soil-borne phytopathogenic fungi. Biofilm...
Pseudomonas chlororaphis PCL1606 (PcPCL1606) displays plant-colonizing features and exhibits antagonistic traits against soil-borne phytopathogenic fungi. Biofilm formation could be relevant for the PcPCL1606 lifestyle, and in this study the role of some putative extracellular matrix components (EMC; Fap-like fibre, alginate and Psl-like polysaccharides) in the biofilm architecture and biocontrol activity of this bacterium were determined. EMC such as the Fap-like fibre and alginate polysaccharide play secondary roles in biofilm formation in PcPCL1606, because they are not fundamental to its biofilm architecture in flow cell chamber, but synergistically they have shown to favour bacterial competition during biofilm formation. Conversely, studies on Psl-like polysaccharide have revealed that it may contain mannose, and that it is strongly involved in the PcPCL1606 biofilm architecture and niche competition. Furthermore, the Fap-like fibre and Psl-like exopolysaccharide play roles in early surface attachment and contribute to biocontrol activity against the white root rot disease caused by Rosellinia necatrix in avocado plants. These results constitute the first report regarding the study of the extracellular matrix of the PcPCL1606 strain and highlight the importance of a putative Fap-like fibre and Psl-like exopolysaccharide produced by PcPCL1606 in the biofilm formation process and interactions with the host plant root.
Topics: Ascomycota; Biofilms; Extracellular Matrix; Polysaccharides, Bacterial; Pseudomonas aeruginosa; Pseudomonas chlororaphis; Xylariales
PubMed: 33314481
DOI: 10.1111/1462-2920.15355