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International Journal of Systematic and... May 2020A short rod-shaped, Gram-stain-negative strain that can degrade multiple polymers was isolated from forest soil in China and designated as DSWY01. The results of 16S...
A short rod-shaped, Gram-stain-negative strain that can degrade multiple polymers was isolated from forest soil in China and designated as DSWY01. The results of 16S rRNA gene sequence analysis showed that this isolate shared high similarities with NBRC 102411 (99.3 %), NBRC 14162 (99.2%) and NBRC 13583 (99.0%). The results of phylogenetic analysis based on 16S rRNA gene sequence and multilocus sequence analysis (, , , and ) indicated that strain DSWY01 belongs to the genus and is a member of the group in an independent branch. The average nucleotide identity and digital DNA-DNA hybridization between the genome of strain DSWY01 and the genomes of other species (ANIb 77.72-89.65 %; GGDC 15.50-31.10 %) showed that the isolate represents a novel species. The DNA G+C content of strain DSWY01 was 63.67 mol%, and the major cellular fatty acids (>15 %) were a mixture of Cω7/Cω6 and C. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified lipids, and the major quinone was CQ-10. The morphological, physiological and biochemical characteristics of the isolate were then compared with those of reference type strains. The isolate differed considerably from its closest relatives and is representative of a novel species of , for which the name sp. nov. is proposed. The type strain is DSWY01 (=DSM 106702=CCTCC AB 2018053).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Genes, Bacterial; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polymers; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone
PubMed: 32242797
DOI: 10.1099/ijsem.0.004129 -
International Journal of Biological... May 2020Alginate is a family of industrially important linear polymers consisting of β-D-mannuronic acid (M) and its C-5 epimer α-L-guluronic acid (G). The function of...
Alginate is a family of industrially important linear polymers consisting of β-D-mannuronic acid (M) and its C-5 epimer α-L-guluronic acid (G). The function of alginate is closely related to the ratio of M/G. Mannuronan C-5 epimerase, which converts M to G, is a key enzyme involved in the biosynthesis of alginate. A new mannuronan C-5 epimerase isolated from Pseudomonas mendocina. sp. DICP-70 named PmC5A was characterized in this study. From the H NMR analysis of the products, we have found that PmC5A possesses alginate lyase function in addition to mannuronan C-5-epimerase. The optimal pH and temperature of lyase and epimerase were found to be 8.0, 9.0 and 40 °C, 30 °C, respectively. PmC5A also shows lyase activity toward PolyMG and G-blocks.
Topics: Alginates; Bacterial Proteins; Carbohydrate Epimerases; Nuclear Magnetic Resonance, Biomolecular; Polysaccharide-Lyases; Pseudomonas mendocina
PubMed: 32061850
DOI: 10.1016/j.ijbiomac.2020.02.126 -
Bioresource Technology May 2020A strain with efficient biofilm-formation and aerobic denitrification capabilities was isolated and identified as Pseudomonas mendocina IHB602. In pure culture, strain...
A strain with efficient biofilm-formation and aerobic denitrification capabilities was isolated and identified as Pseudomonas mendocina IHB602. In pure culture, strain IHB602 removed almost all NO-N, NO-N, and NH-N (initial concentrations 50 mg/L) within 24 h. The strain produced large amounts of extracellular polymeric substances (maximum 430.33 mg/g cell dry weight) rich in protein but containing almost no humic acid. This, and strong autoaggregation (maximum 47.09%) and hydrophobicity (maximum 85.07%), imparted strain IHB602 with biofilm forming traits. A sequencing batch biofilm reactor bioaugmented with strain IHB602 (SBBR1) had more rapid biofilm-formation than the control without strain IHB602 inoculation (SBBR2). During the stabilization period, the effluent removal ratios for NH-N (95%), NO-N (91%) and TN (88%) in SBBR1 were significantly higher than those in SBBR2 (NH-N: 91%, NO-N: 88%, TN: 82%). Microbial community structure analysis revealed that strain IHB602 successfully proliferated and contributed to nitrogen removal as well as biofilm formation.
Topics: Biofilms; Bioreactors; Denitrification; Nitrogen; Waste Disposal, Fluid; Wastewater
PubMed: 32032938
DOI: 10.1016/j.biortech.2020.122905 -
Current Microbiology Jun 2020Tropical oleaginous seeds are an unexplored source for the discovery of novel lipolytic microorganisms, which could be applied to the bioremediation of agro-industrial...
Tropical oleaginous seeds are an unexplored source for the discovery of novel lipolytic microorganisms, which could be applied to the bioremediation of agro-industrial oily wastes and solve numerous environmental issues. Such wastes hold potential to be revalorized towards a variety of products through microbial bioremediation. In this study, we investigate the microbial diversity and lipase activity from bacterial and fungal isolates obtained from the oil seeds of Elaeis guineensis, Ricinus communis, and Jatropha curcas L. from Costa Rica. A total of 27 strains were confirmed as lipase-producing strains via fluorogenic and colorimetric agar plate assays. The diversity of the isolates comprises 12 fungal ascomycetes from the genera Aspergillus and Fusarium and 15 bacterial isolates classified into four genera: Serratia, Proteus, Pseudomonas, and Bacillus. Microbial isolates from E. guineensis showed the highest diversity of lipolytic microorganisms (6 genera) followed by J. curcas (4 genera) and R. communis (2 genera). Isolates showing the highest activity in agar plates were tested further by submerged fermentation and the specific lipase activity was measured with 4-nitrophenyl laurate as substrate. Accordingly, the highest specific lipase activity was demonstrated by Bacillus pumilus B5 (24.98 U mg), Serratia marcescens B10 (17.65 U mg), Pseudomonas mendocina B16 (8.62 U mg), and Bacillus pumilus B1 (5.72 U mg) in submerged fermentation. These findings indicate the presence of a specialized microbial diversity in tropical oil seeds and highlight their potential to be applied in the bioremediation of agro-industrial oily wastes.
Topics: Agriculture; Arecaceae; Bacteria; Biodegradation, Environmental; Biodiversity; Costa Rica; Fermentation; Fungi; Industrial Waste; Jatropha; Laurates; Lipase; Phylogeny; Ricinus; Seeds
PubMed: 31982967
DOI: 10.1007/s00284-020-01886-8 -
Antonie Van Leeuwenhoek Apr 2020A novel Gram-negative, aerobic, motile and rod-shaped bacterium with the potential to biodegrade polycyclic aromatic hydrocarbons, was isolated from Khazar (Caspian)...
A novel Gram-negative, aerobic, motile and rod-shaped bacterium with the potential to biodegrade polycyclic aromatic hydrocarbons, was isolated from Khazar (Caspian) Sea. Strain TBZ2 grows in the absence of NaCl and tolerates up to 8.5% NaCl. Growth occurred at pH 3.0-10.0 (optimum, pH 6.0-7.0) and 10-45 °C (optimum, 30 °C). The major fatty acids are Cω7C, Cω7C/ C iso 2-OH, C, C C 3-OH, C 3-OH. The major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and the predominant respiratory quinone is ubiquinone Q-9. The 16S rRNA gene sequence analysis showed that strain TBZ2 is a member of the genus Pseudomonas with the highest similarity to P. oleovorans subsp. oleovorans DSM 1045 (98.83%), P. mendocina NBRC 14162 (98.63%), P. oleovorans subsp. lubricantis RS1 (98.61%) and P. alcaliphila JCM 10630 (98.49%) based on EzBioCloud server. Phylogenetic analyses using housekeeping genes (16S rRNA, rpoD, gyrB and rpoB) and genome sequences demonstrated that the strain TBZ2 formed a distinct branch closely related to the type strains of P. mendocina and P. guguanensis. Digital DNA-DNA hybridisation and average nucleotide identity values between strain TBZ2 and its closest relatives, P. mendocina NBRC 14162 (25.3%, 81.5%) and P. guguanensis JCM 18146 (26.8%, 79.0%), rate well below the designed threshold for assigning prokaryotic strains to the same species. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic results, it is recommended that strain TBZ2 is a novel species of the genus Pseudomonas, for which the name Pseudomonas khazarica sp. nov., is proposed. The type strain is TBZ2 (= LMG 29674 = KCTC 52410).
Topics: Adaptation, Physiological; Caspian Sea; Genome, Bacterial; Geologic Sediments; Phylogeny; Polycyclic Aromatic Hydrocarbons; Pseudomonas; Species Specificity; Water
PubMed: 31768782
DOI: 10.1007/s10482-019-01361-w -
International Journal of Biological... Jul 2020In this study, six genes involved in β-oxidation pathway of P. mendocina NK-01 were deleted to construct mutant strains NKU-∆β1 and NKU-∆β5. Compared with the...
In this study, six genes involved in β-oxidation pathway of P. mendocina NK-01 were deleted to construct mutant strains NKU-∆β1 and NKU-∆β5. Compared with the wild strain NKU, the mcl-PHA titers of NKU-∆β5 were respectively increased by 5.58- and 4.85-fold for culturing with sodium octanoate and sodium decanoate. And the mcl-PHA titers of NKU-∆β1 was increased by 10.02-fold for culturing with dodecanoic acid. The contents of dominant monomers 3-hydroxydecanoate (3HD) and 3-hydroxydodecanoate (3HDD) of the mcl-PHA synthesized by NKU-∆β5 were obviously increased to 90.01 and 58.60 mol%, respectively. Further deletion of genes phaG and phaZ, the 3HD and 3HDD contents were further improved to 94.71 and 68.67 mol%, respectively. The highest molecular weight of mcl-PHA obtained in this study was 80.79 × 10 Da, which was higher than the previously reported mcl-PHA. With the increase of dominant monomer contents, the synthesized mcl-PHA showed better thermal properties, mechanical properties and crystallization properties. Interestingly, the cell size of NKU-∆β5 was larger than that of NKU due to the accumulation of more PHA granules. This study indicated that a systematically metabolic engineering approach for P. mendocina NK-01 could significantly improve the mcl-PHA titer, dominant monomer contents and physical properties of mcl-PHA.
Topics: Gene Deletion; Mechanical Phenomena; Metabolic Engineering; Molecular Weight; Polyhydroxyalkanoates; Pseudomonas
PubMed: 31706817
DOI: 10.1016/j.ijbiomac.2019.11.044 -
Food Microbiology Apr 2020Pickle is a type of mildly lactic acid fermented vegetable and is a traditional dish favored in China, Japan, and Korea. Corruption of spoilage bacteria and accumulation...
Pickle is a type of mildly lactic acid fermented vegetable and is a traditional dish favored in China, Japan, and Korea. Corruption of spoilage bacteria and accumulation of nitrite during vegetable fermentation are common problems that affect the pickle industry and consumer health. In this work, cucumber juice was used as a vegetable model to study the dominant mesophilic aerobic bacteria (MAB) producing nitrite during pickle fermentation. Virulent phages infecting the dominant MABs combined with Lactobacillus plantarum M6 were used to control these bacteria. Enterobacter cloacae and Pseudomonas fluorescens are the dominant MABs in the fermentation of cucumber juice containing 4% or 8% NaCl, with isolation percentages reaching 30.6% and 23.1%, respectively. Virulent phages PspYZU5415 and EcpYZU01 were isolated using P. fluorescens J5415 and E. cloacae J01 as the host bacteria, respectively. These two phages show a broad host range and strong lytic activity, and their genomes contain no toxins and antibiotic resistance genes. PspYZU5415 and EcpYZU01 were combined into a cocktail (designated as Phage MIX) that effectively inhibits the growth of E. cloacae and P. fluorescens in cucumber juice with different salt concentrations. PhageMIX combined with L. plantarum M6 decreased the counts of P. mendocina and E. cloacae to undetectable levels at 48 h during the fermentation of cucumber juice artificially contaminated with P. mendocina and E. cloacae. In addition, nitrite content increased to 11.3 mg/L at 20 h and then degraded completely at 36 h. By contrast, P. mendocina and E. cloacae remained in the groups without PhageMIX during fermentation (0-48 h). Nitrite content rapidly increased to 65.7 mg/L at 12 h and then decreased to 21.6 mg/L at 48 h in the control group. This study suggests that PhageMIX combined with lactic acid bacterial strains can be used as an ecological starter for controlling the dominant MABs P. mendocina and E. cloacae and for reducing nitrate production during the early stage of pickle fermentation.
Topics: Aerobiosis; Bacteriophages; Cucumis sativus; Enterobacter cloacae; Fermentation; Fermented Foods; Food Microbiology; Host Specificity; Lactobacillus plantarum; Nitrites; Pseudomonas fluorescens; Vegetables
PubMed: 31703878
DOI: 10.1016/j.fm.2019.103330 -
Ecotoxicology and Environmental Safety Jan 2020Polycyclic aromatic hydrocarbons (PAH) contained in creosote oil are particularly difficult to remove from the soil environment. Their hydrophobic character and low...
Polycyclic aromatic hydrocarbons (PAH) contained in creosote oil are particularly difficult to remove from the soil environment. Their hydrophobic character and low bioavailability to soil microorganisms affects their rate of biodegradation. This study was performed on samples of soil that were (for over forty years) subjected to contamination with creosote oil, and their metagenome and physicochemical properties were characterized. Moreover, the study was undertaken to evaluate the biodegradation of PAHs by autochthonous consortia as well as by selected bacteria strains isolated from long-term contaminated industrial soil. From among the isolated microorganisms, the most effective in biodegrading the contaminants were the strains Pseudomonas mendocina and Brevundimonas olei. They were able to degrade more than 60% of the total content of PAHs during a 28-day test. The biodegradation of these compounds using AT7 dispersant was enhanced only by Serratia marcescens strain. Moreover, the addition of AT7 improved the effectiveness of fluorene and acenaphthene biodegradation by Serratia marcescens 6-fold. Our results indicated that long-term contact with aromatic compounds induced the bacterial strains to use the PAHs as a source of carbon and energy. We observed that supplementation with surfactants does not increase the efficiency of hydrocarbon biodegradation.
Topics: Biodegradation, Environmental; Caulobacteraceae; Creosote; Environmental Monitoring; Industry; Poland; Polycyclic Aromatic Hydrocarbons; Pseudomonas mendocina; Soil; Soil Microbiology; Soil Pollutants
PubMed: 31678701
DOI: 10.1016/j.ecoenv.2019.109843 -
3 Biotech Nov 2019was identified as a novel endophytic isolate of with squalene cyclase activity. The PCR amplification of squalene hopene cyclase () gene from the isolate with the...
was identified as a novel endophytic isolate of with squalene cyclase activity. The PCR amplification of squalene hopene cyclase () gene from the isolate with the primers PA1/PA2 showed a band at 1980 bp specific for the enzyme squalene hopene cyclase. The in silico translation of the squalene hopene cyclase gene showed 96% sequence similarity with squalene hopene cyclase of (WP-060782422). Docking studies of the template and the modeled protein with the ligand squalene showed that the main interacting residues were Asp376 and Asp377. Squalene hopene cyclase template 1 sqc.1A sequence from was used as the template for docking experiments. The gene coding for squalene hopene cyclase from has been cloned in pET-28a vector to produce recombinant vector and was expressed in BL21 (DE3) expression system. Squalene hopene cyclase enzyme was isolated, purified and the molecular weight was confirmed by SDS-PAGE as 75 KDa.
PubMed: 31588405
DOI: 10.1007/s13205-019-1901-7 -
3 Biotech Sep 2019This study aimed to investigate the effects of cytoskeleton protein MreB on bacterial cell morphology and the synthesis of alginate oligosaccharides (AO) and...
This study aimed to investigate the effects of cytoskeleton protein MreB on bacterial cell morphology and the synthesis of alginate oligosaccharides (AO) and polyhydroxyalkanoate (PHA) by NK-01. To overexpress the gene, an expression vector encoding MreB-GFP fusion protein was constructed. The scanning electron microscope (SEM) showed that cells expressing MreB were longer than the wild ones, which agrees with MreB's relationship with the synthesis of peptidoglycan. Cells expressing the MreB-GFP fusion protein emitted green fluorescence under a fluorescence microscope, suggesting that MreB was functionally expressed in strain NK-01. Under a confocal laser scanning microscope, MreB was observed as located around the cell membrane. Furthermore, the recombinant strain could synthesize 0.961 g/L AO, which was 5.86-fold higher than wild-type strain. Through the medium optimization test, we finally selected the addition of 20 g/L glucose as the optimal glycogen addition for AO fermentation based on a high AO yield and high substrate transformation efficiency. The results indicated that overexpression of MreB affected the cell morphology, the activity of AO polymerase, and the efficiency of AO secretion. However, the synthesis of PHA for recombinant strain was slightly reduced. The results suggested that the overexpression of this cytoskeleton protein affected the yield of specific intracellular and extracellular products.
PubMed: 31497462
DOI: 10.1007/s13205-019-1873-7