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Toxics Apr 2023To effectively carry out the bioremediation of a Pb polluted environment, a lead-tolerant strain named D1 was screened from the activated sludge of a factory in Hefei,...
To effectively carry out the bioremediation of a Pb polluted environment, a lead-tolerant strain named D1 was screened from the activated sludge of a factory in Hefei, and its lead removal in a solution with Pb concentration of 200 mg/L could reach 91% under optimal culture conditions. Morphological observation and 16S rRNA gene sequencing were used to identify D1 accurately, and its cultural characteristics and lead removal mechanism were also preliminarily studied. The results showed that the D1 strain was preliminarily identified as the strain. The experiments conducted via orthogonal test showed that the optimal conditions for the growth of strain D1 were pH 7, inoculum volume 6%, 35 °C, and rotational speed 150 r/min. According to the results of scanning electron microscopy and energy spectrum analysis before and after the D1 exposure to lead, it is believed that the lead removal mechanism of D1 is surface adsorption. The Fourier transform infrared spectroscopy (FTIR) results revealed that multiple functional groups on the surface of the bacterial cells are involved in the Pb adsorption process. In conclusion, the D1 strain has excellent application prospects in the bioremediation of lead-contaminated environments.
PubMed: 37235227
DOI: 10.3390/toxics11050412 -
Microorganisms Oct 2022Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource...
Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource depletion, and global waste issues. This has spurred the isolation and characterisation of novel PHA-producing strains through cultivation and non-cultivation approaches, with a particular interest in genes encoding PHA synthesis pathways. Since sea sponges and sediment are marine benthic habitats known to be rich in microbial diversity, sponge tissues ( and ) and sediment samples were collected in this study from Redang and Bidong islands located in the Malaysian Coral Triangle region. PHA synthase () genes were identified from sediment-associated bacterial strains using a cultivation approach and from sponge-associated bacterial metagenomes using a non-cultivation approach. In addition, phylogenetic diversity profiling was performed for the sponge-associated bacterial community using 16S ribosomal ribonucleic acid (16S rRNA) amplicon sequencing to screen for the potential presence of PHA-producer taxa. A total of three genes from the bacterial metagenome of and three genes from sediment isolates ( UMTKB-6, UMTKB-7, UMTKB-8) were identified. Produced PHA polymers were shown to be composed of 5C to C monomers, with previously unreported PHA-producing ability of the strain, as well as a 3-hydroxyvalerate-synthesising ability without precursor addition by the strain.
PubMed: 36296332
DOI: 10.3390/microorganisms10102057 -
Scientific Reports May 2022Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal...
Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the "Microbial Redox Index (MRI)," an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation-reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.
Topics: Gastric Mucosa; Gastritis; Helicobacter Infections; Helicobacter pylori; Humans; Microbiota; Oxidation-Reduction; Peptic Ulcer; RNA, Ribosomal, 16S
PubMed: 35589904
DOI: 10.1038/s41598-022-12431-x -
Environmental Pollution (Barking, Essex... Jul 2022Contamination by tetracycline residues has adverse influences on the environment and is considered a pressing issue. Biodegradation is regarded as a promising way to...
Contamination by tetracycline residues has adverse influences on the environment and is considered a pressing issue. Biodegradation is regarded as a promising way to treat tetracycline residues in the environment. Here, strain Sphingobacterium mizutaii S121, which could degrade 20 mg/L tetracycline completely within 5 days, was isolated from contaminated soil. The characteristics of tetracycline degradation by strain S121 were investigated under various culture conditions. Response surface methodology was used to predict the maximum tetracycline degradation ratio, which can be obtained under the following conditions: 31.36 °C, pH of 7.15, and inoculum volume of 5.5% (v/v). Furthermore, extracellular tetracycline biodegradation products and intracellular metabolic pathways of S121 were detected by ultraperformance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) and UHPLC-quadrupole electrospray (QE)-MS, respectively. The results identified eight possible degradation products, and three putative degradation pathways were proposed. In addition, exposure to tetracycline produced significant influences on metabolic pathways such as pyrimidine, purine, taurine and hypotaurine metabolism and lysine degradation. Consequently, the intracellular metabolic pathway response of S121 in the presence of tetracycline was proposed. These findings are presented for the first time, which will facilitate a comprehensive understanding of the mechanism of tetracycline degradation. Moreover, strain S121 can be a promising bacterium for tetracycline bioremediation.
Topics: Anti-Bacterial Agents; Biodegradation, Environmental; Metabolomics; Sphingobacterium; Tetracycline
PubMed: 35430309
DOI: 10.1016/j.envpol.2022.119299 -
Scientific Reports Dec 2021
PubMed: 34907267
DOI: 10.1038/s41598-021-03738-2 -
Scientific Reports Nov 2021Sulfamethoxazole (SMX) is the most commonly used antibiotic in worldwide for inhibiting aquatic animal diseases. However, the residues of SMX are difficult to eliminate...
Sulfamethoxazole (SMX) is the most commonly used antibiotic in worldwide for inhibiting aquatic animal diseases. However, the residues of SMX are difficult to eliminate and may enter the food chain, leading to considerable threats on human health. The bacterial strain Sphingobacterium mizutaii LLE5 was isolated from activated sludge. This strain could utilize SMX as its sole carbon source and degrade it efficiently. Under optimal degradation conditions (30.8 °C, pH 7.2, and inoculum amount of 3.5 × 10 cfu/mL), S. mizutaii LLE5 could degrade 93.87% of 50 mg/L SMX within 7 days. Four intermediate products from the degradation of SMX were identified and a possible degradation pathway based on these findings was proposed. Furthermore, S. mizutaii LLE5 could also degrade other sulfonamides. This study is the first report on (1) degradation of SMX and other sulfonamides by S. mizutaii, (2) optimization of biodegradation conditions via response surface methodology, and (3) identification of sulfanilamide, 4-aminothiophenol, 5-amino-3-methylisoxazole, and aniline as metabolites in the degradation pathway of SMX in a microorganism. This strain might be useful for the bioremediation of SMX-contaminated environment.
Topics: Anti-Bacterial Agents; Bacteria; Biodegradation, Environmental; Carbon; Environmental Microbiology; High-Throughput Nucleotide Sequencing; Kinetics; Metabolic Networks and Pathways; Phylogeny; RNA, Ribosomal, 16S; Sewage; Sphingobacterium; Sulfamethoxazole; Sulfonamides; Temperature; Water Pollutants, Chemical
PubMed: 34848765
DOI: 10.1038/s41598-021-02404-x -
Journal of Hazardous Materials Jun 2021The fate of doxycycline (DC), a second generation tetracycline antibiotic, in the environment has drawn increasing attention in recent years due to its wide usage....
The fate of doxycycline (DC), a second generation tetracycline antibiotic, in the environment has drawn increasing attention in recent years due to its wide usage. Little is known about the biodegradability of DC in the environment. The objective of this study was to characterize the biotransformation of DC by pure bacterial strains with respect to reaction kinetics under different environmental conditions and biotransformation products. Two bacterial strains, Brevundimonas naejangsanensis DD1 and Sphingobacterium mizutaii DD2, were isolated from chicken litter and characterized for their biotransformation capability of DC. Results show both strains rely on cometabolism to biotransform DC with tryptone as primary growth substrate. DD2 had higher biotransformation kinetics than DD1. The two strains prefer similar pHs (7 and 8) and temperature (30 °C), however, they exhibited opposite responses to increasing background tryptone concentration. While hydrolysis converted DC to its isomer or epimer, the two bacterial strains converted DC to various biotransformation products through a series of demethylation, dehydration, decarbonylation and deamination. Findings from the study can be used to better predict the fate of DC in the environment.
Topics: Biotransformation; Caulobacteraceae; Doxycycline; Sphingobacterium
PubMed: 33486232
DOI: 10.1016/j.jhazmat.2021.125126 -
International Journal of Systematic and... Mar 2020A Gram-stain-negative, rod-shaped, non-motile and non-spore-forming bacterium, designated HAL-9, was isolated from oil-contaminated soil in Daqing oilfield, Heilongjiang...
A Gram-stain-negative, rod-shaped, non-motile and non-spore-forming bacterium, designated HAL-9, was isolated from oil-contaminated soil in Daqing oilfield, Heilongjiang Province, PR China. Strain HAL-9 was able to degrade quizalofop--ethyl and diclofop-methyl. Growth was observed at 10-35 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and salinity of 0 %-5.0 % (w/v; optimum 1.0 %). The results of phylogenetic analysis based on the 16S rRNA gene indicated that strain HAL-9 belongs to the genus and showed the highest sequence similarity (98.3 %) to Y3L14, followed by DSM 11724 (95.1 %) and DSM 22361 (95.1 %). Menaquinone-7 (MK-7) was the only isoprenoid quinone. The predominant cellular fatty acids were summed feature 3 (C 7 and/or C 6), iso-C and iso-C 3-OH. The major polar lipids were phosphatidylethanolamine, three phosphoglycolipids and three unidentified lipids. The draft genome of strain HAL-9 was 5.41 Mb. The G+C content of strain HAL-9 was 40.6 mol%. Furthermore, the average nucleotide identity and DNA-DNA hybridization values between strain HAL-9 and Y3L14 were 86.2 % and 32.8 %, respectively, which were below the standard thresholds for species differentiation. On the basis of phenotypic, genotypic and phylogenetic evidence, strain HAL-9 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HAL-9 (=ACCC 61581=CCTCC AB 2019176=KCTC 72287).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Petroleum Pollution; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium; Vitamin K 2
PubMed: 31967955
DOI: 10.1099/ijsem.0.004000 -
International Journal of Systematic and... Jul 2017A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling...
A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling County, Yunnan Province, south-west China. The new isolate was characterized taxonomically by using a polyphasic approach. The strain grew optimally at 30 °C, at pH 7.0 and with 0-3 % (w/v) NaCl. It was positive for catalase and oxidase but negative for H2S production. Comparative 16S rRNA gene sequence analysis showed that strain YIM X0211T fell within the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii DSM 11724T (97.93 % similarity). The G+C content of the genomic DNA was 41.2 mol%. The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0 2-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, sphingolipid, and several unknown phospholipids or lipids. The DNA-DNA hybridization value between strain YIM X0211T and S. mizutaii DSM 11724T was 42.3±0.4 %, which is below the 70 % limit for species delineation. These chemotaxonomic data supported the affiliation of strain YIM X0211T to the genus Sphingobacterium. Based on the recorded phenotypic and genotypic characteristics, it is determined that the isolate represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium soli sp. nov. is proposed. The type strain is YIM X0211T (=KCTC 42696T=CGMCC 1.15966T).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium; Vitamin K 2
PubMed: 28699577
DOI: 10.1099/ijsem.0.001946 -
International Journal of Systematic and... May 2017The taxonomic position of two isolates belonging to the genus Sphingobacterium was determined. The first isolate, R-53603T, was obtained from purulent discharge from the...
The taxonomic position of two isolates belonging to the genus Sphingobacterium was determined. The first isolate, R-53603T, was obtained from purulent discharge from the toe of a cellulitis patient in Kuwait. Comparative 16S rRNA gene sequence analysis revealed 99.87 % similarity of R-53603T with environmental isolate P031 (=R-53745) originating from activated sludge in Singapore. The two isolates were phylogenetically positioned on the same sub-branch. Highest 16S rRNA gene sequence similarity was found with the type strains of Sphingobacterium mizutaii (98.23 %), Sphingobacterium lactis (97.78 %) and Sphingobacterium daejeonense (97.14 %). DNA-DNA hybridizations revealed <70 % relatedness between the two isolates and the type strains of the close phylogenetic neighbours S. mizutaii(18.0-24.5 %), S. lactis(20.3-25.9 %) and S. daejeonense(13.2-20.0 %). The high relative contribution of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) in the cellular fatty acid profiles of R-53603T and R-53745, the presence of sphingophospholipids, MK-7 as the dominant menaquinone and phosphatidylethanolamine as the major polar lipid in strain R-53603T are typical chemotaxonomic characteristics for members of the genus Sphingobacterium. Phenotypic features most useful for differentiation of the two novel strains from the most closely related species S. mizutaii include growth on MacConkey agar, and utilization of stachyose, guanidine HCl and lithium chloride in Biolog GEN III tests. Strains R-53603T and R-53745 thus represent a novel species, for which the name Sphingobacterium cellulitidis sp. nov. is proposed. The type strain is R-53603T (=LMG 28764T=DSM 102028T).
Topics: Bacterial Typing Techniques; Base Composition; Cellulitis; DNA, Bacterial; Fatty Acids; Humans; Kuwait; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Singapore; Sphingobacterium; Toes; Vitamin K 2
PubMed: 28141505
DOI: 10.1099/ijsem.0.001832