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1.
ACS Omega ; 6(41): 27599, 2021 Oct 19.
Article in English | MEDLINE | ID: mdl-34693182

ABSTRACT

[This retracts the article DOI: 10.1021/acsomega.0c00432.].

2.
Biotechnol Lett ; 43(7): 1395-1402, 2021 Jul.
Article in English | MEDLINE | ID: mdl-33811594

ABSTRACT

OBJECTIVE: Identification and characterization of a novel thermostable amidase (Xam) with wide pH tolerance and broad-spectrum substrate specificity. RESULTS: Xam was identified from non-thermophilic Xinfangfangia sp. DLY26 and its acyl transfer activity was investigated. Recombinant Xam was optimally active at 60 °C and pH 9.0. The enzyme had a half life of 18 h at 55 °C and maintained more than 60 % of its maximum activity in the range of pH 3.0-11.0. Additionally, Xam exhibited broad substrate specificity towards aliphatic, aromatic, and heterocyclic amides. CONCLUSIONS: These unique properties make Xam a promising biocatalyst for production of important hydroxamic acids at elevated temperatures.


Subject(s)
Amidohydrolases/genetics , Amidohydrolases/metabolism , Cloning, Molecular/methods , Rhodobacteraceae/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Enzyme Stability , Hot Temperature , Hydrogen-Ion Concentration , Phylogeny , Rhodobacteraceae/genetics , Substrate Specificity
3.
Protein Expr Purif ; 177: 105751, 2021 01.
Article in English | MEDLINE | ID: mdl-32931916

ABSTRACT

A novel amidase (TAM) was identified and cloned from the genome of Thauera sinica K11. The recombinant protein was purified to homogeneity by one-step affinity chromatography for up to 26.4-fold with a yield of 38.1%. Gel filtration chromatography and SDS-PAGE revealed that the enzyme was a tetramer with a subunit of approximately 37.5 kDa. The amidase exhibited the maximum acyl transfer activity at 45 °C and pH 7.0, and it was highly stable over a wide pH range of 6.0-11.0. Inhibition of enzyme activity was observed in the presence of metal ions, thiol reagents and organic solvents. TAM showed a broad substrate spectrum toward aliphatic, aromatic and heterocyclic amides. For linear aliphatic monoamides, the acyl transfer activity of TAM was decreased with the extension of the carbon chain length, and thus the highest activity of 228.2 U/mg was obtained when formamide was used as substrate. This distinct selectivity of amidase to linear aliphatic monoamides expanded the findings of signature amidases to substrate specificity.


Subject(s)
Amides/metabolism , Amidohydrolases/metabolism , Bacterial Proteins/metabolism , Cloning, Molecular/methods , Protein Subunits/metabolism , Thauera/enzymology , Amidohydrolases/genetics , Amino Acid Sequence , Bacterial Proteins/genetics , Enzyme Assays , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Genome, Bacterial , Hydrogen-Ion Concentration , Kinetics , Phylogeny , Protein Multimerization , Protein Subunits/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Substrate Specificity , Temperature , Thauera/classification , Thauera/genetics
4.
ACS Omega ; 5(29): 17918-17925, 2020 Jul 28.
Article in English | MEDLINE | ID: mdl-32743163

ABSTRACT

In order to assist the refolding of recombinant nitrilase inclusion bodies, a series of thermoresponsive media were prepared by grafting poly(N-isopropylacrylamide-co-butyl-methacrylate) [P(NIPAM-co-BMA)] brushes onto PS microspheres with various particles and pore sizes via an atom transfer radical polymerization (ATRP) method. The effects of particle sizes, pore sizes, and brush grafting amounts of thermoresponsive microspheres on nitrilase refolding were investigated preliminarily. The results showed that the PS-P(NIPAM-co-BMA) microspheres with the medium particle size (74 µm), gigapore size (320 nm), and high grafting amount (35.6 mg/m2) were the most effective candidates. The final nitrilase activity yield could be up to 84.5% with a high initial protein concentration (1 mg/mL) at 30 °C, which was 52.5% higher than that of a simple dilution refolding method at the initial protein concentration (0.1 mg/mL). After the refolding process, the PS-P(NIPAM-co-BMA) microspheres can be easily separated by self-precipitation, and the activity yield of nitrilase still reached 74.5% after being reused for five batches. These results indicated that the thermoresponsive gigaporous medium was an ideal alternative as an artificial chaperone.

5.
Int J Syst Evol Microbiol ; 70(1): 364-372, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31661054

ABSTRACT

A Gram-stain-negative, rod-shaped bacterium, motile by means of a single polar flagellum, designated S-6-2T, was isolated from petroleum polluted river sediment in Huangdao, Shandong Province, PR China. The 16S rRNA gene sequence analysis revealed that S-6-2T represented a member of the genus Pseudomonas, sharing the highest sequence similarities with Pseudomonas parafulva (97.5 %) and Pseudomonas fulva (97.5 %). Phylogenetic analysis based on 16S rRNA gene, concatenated 16S rRNA, gyrB, rpoB and rpoD genes and genome core-genes indicated that S-6-2T was affiliated with the members of the Pseudomonas pertucinogena group. The average nucleotide identity (ANI) and genome-to-genome distance between the whole genome sequences of S-6-2T and closely related species of the genus Pseudomonas within the P. pertucinogena group were less than 77.94 % and 20.5 %, respectively. Differences in phenotypic characteristics were also found between S-6-2T and the closely related species. The major cellular fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ C18  : 1ω6c), C16 : 0, C17 : 0cyclo and C12 : 0. The predominant respiratory quinone was ubiquinone 9. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified lipid (L1), two unidentified phospholipids (PL1 and PL2) and an aminophospholipid (APL). The DNA G+C content of the genome of S-6-2T was 60.1 mol%. On the basis of the evidence from the polyphasic taxonomic study, strain S-6-2T can be classified as representative of a novel species of the genus Pseudomonas, for which the name Pseudomonas phragmitis sp. nov. is proposed. The type strain is S-6-2T (=CGMCC 1.15798T=KCTC 52539T).


Subject(s)
Geologic Sediments/microbiology , Petroleum Pollution , Phylogeny , Pseudomonas/classification , Rivers/microbiology , Water Pollutants, Chemical , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genes, Bacterial , Nucleic Acid Hybridization , Petroleum , Phospholipids/chemistry , Pseudomonas/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Ubiquinone/chemistry
6.
Biotechnol Lett ; 41(4-5): 583-589, 2019 May.
Article in English | MEDLINE | ID: mdl-30888572

ABSTRACT

OBJECTIVE: Identification of a heavy metal ion-stimulated nitrilase with broad-spectrum substrate specificity. RESULTS: A novel nitrilase, PaCNit, was identified from Pannonibacter carbonis Q4.6 and its enzymatic properties were investigated. The maximum activity of PaCNit was observed at 65 °C and pH 7.0. PaCNit showed broad substrate specificity towards aliphatic, aromatic, and heterocyclic nitriles, and was tolerant to different organic solvents. Remarkably, PaCNit activity was highly stimulated by metal ions, particularly by Ag+ and Hg2+. CONCLUSION: PaCNit nitrilase has a broad range of substrate specificity and can be activated by heavy metal ions. This specific characteristic makes it have a great potential for industrial application.


Subject(s)
Aminohydrolases/metabolism , Cloning, Molecular , Gene Expression , Nitriles/metabolism , Rhodobacteraceae/enzymology , Aminohydrolases/chemistry , Aminohydrolases/genetics , Cations/metabolism , Enzyme Activators/metabolism , Hydrogen-Ion Concentration , Metals/metabolism , Rhodobacteraceae/genetics , Substrate Specificity , Temperature
7.
Antonie Van Leeuwenhoek ; 112(8): 1221-1229, 2019 Aug.
Article in English | MEDLINE | ID: mdl-30874924

ABSTRACT

A Gram-stain negative, aerobic, motile, short rod-shaped bacterium, designated as B2.3T, was isolated from coal bed water collected from Jincheng, Shanxi Province, China. The strain was able to grow at 10-40 °C (optimum 28-30 °C), pH 4.0-10.0 (optimum 7.0), and in the presence of 0-5.0% NaCl (optimum 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA and concatenated housekeeping gene recA, atpD and glnA sequences showed strain B2.3T belongs to the genus Mesorhizobium, with Mesorhizobium oceanicum B7T as the closely related type strain. Strain B2.3T exhibited ANI value of 77.5% and GGDC value of 21.5% to M. oceanicum B7T. The major fatty acids were identified as summed feature 8 (C18:1ω7c and/or C18:1ω6c) and 11-methyl C18:1ω7c. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminophospholipid. The predominant ubiquinone was identified as Quinone 10. Phenotypic and biochemical analysis results indicated that strain B2.3T can be distinguished from closely related type strains. On the basis of phenotypic, genotypic and chemotaxonomic characteristics, strain B2.3T is concluded to represent a novel species in the genus Mesorhizobium, for which the name Mesorhizobium carbonis sp. nov. is proposed. The type strain is B2.3T (=CGMCC 1.15730T = KCTC 52461T).


Subject(s)
Mesorhizobium/classification , Mesorhizobium/isolation & purification , Water Microbiology , Bacterial Proteins/genetics , Bacterial Typing Techniques , China , Cluster Analysis , Cytosol/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Mesorhizobium/genetics , Mesorhizobium/physiology , Phospholipids/analysis , Phylogeny , Quinones/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
8.
Int J Syst Evol Microbiol ; 68(6): 2042-2047, 2018 Jun.
Article in English | MEDLINE | ID: mdl-29693544

ABSTRACT

Two bacterial strains were isolated from coal mine water in China. Isolates were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by means of a single polar flagellum, and they did not produce bacteriochlorophyll α. Cells grew in tryptic soy broth with 0-5.5 % (w/v) NaCl, at 4-55 °C and pH 3.5-10.5. Isolates were positive for catalase, oxidase, urease, Voges-Proskauer test, gelatin hydrolysis and H2S production. Analysis of 16S rRNA gene sequences indicated that the closest relatives of strains Q4.6T and Q2.11 were the type strains Labrenzia suaedae DSM 22153T (97.4 %), Pannonibacter phragmitetus DSM 14782T (96.9 and 97.0 %) and Pannonibacter indicus DSM 23407T (96.8 %). The genomic average nucleotide identity (ANI) value for Q4.6T and Q2.11 was 100 %; however, this value was less than 77.7 % for the type strains P. phragmitetus and P. indicus, and less than 74.0 % for the type strain L. suaedae. The cellular fatty acid profile of strains Q4.6T and Q2.11 consisted primarily of C18 : 1ω7c. The principal quinone of the isolates was Q-10. The polar lipid profile consisted of diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine and phosphatidyl choline. On the basis of phylogenetic analysis, genomic ANI analysis, DNA-DNA hybridization results, as well as phenotypic and chemotaxonomic data, strains Q4.6T and Q2.11 are assigned as a novel species within the genus Pannonibacter. The type strain is Pannonibacter carbonis Q4.6T (=CGMCC 1.15703T=KCTC 52466T).


Subject(s)
Coal , Mining , Phylogeny , Rhodobacteraceae/classification , Water Microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Rhodobacteraceae/genetics , Rhodobacteraceae/isolation & purification , Sequence Analysis, DNA , Ubiquinone/analogs & derivatives , Ubiquinone/chemistry
9.
J Basic Microbiol ; 58(3): 255-262, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29380863

ABSTRACT

Catechol 2,3-dioxygenase (C23O) from a new phenolic compound degrader Thauera sp. K11 was purified and characterized. The native form of the enzyme was determined as a homotetramer with a molecular weight of 140 kDa, and its isoelectric point was close to 6.4. One iron per enzyme subunit was detected using atom absorption spectroscopy, and the effective size of C23O in its dilute solution (0.2 g L-1 , pH 8.0) was 14.5 nm. The optimal pH and temperature were 8.4 and 45 °C, respectively. The addition of Mg2+ , Cu2+ , Fe2+ , and Mn2+ could improve the enzyme activity, while Ag+ was found to be a strong inhibitor. C23O was stable in alkali conditions (pH 7.6-11.0) and thermostable below 50 °C. The final purified C23O had a sheet content of 53%, consistent with the theoretical value. This showed that the purified catechol 2,3-dioxygenase folded with a reasonable secondary structure.


Subject(s)
Catechol 2,3-Dioxygenase/isolation & purification , Catechol 2,3-Dioxygenase/metabolism , Thauera/enzymology , Catechol 2,3-Dioxygenase/chemistry , Coenzymes/analysis , Enzyme Stability , Hydrogen-Ion Concentration , Isoelectric Point , Metals/analysis , Molecular Weight , Protein Conformation , Protein Folding , Protein Multimerization , Spectrum Analysis , Temperature
10.
Antonie Van Leeuwenhoek ; 111(3): 353-360, 2018 Mar.
Article in English | MEDLINE | ID: mdl-28993919

ABSTRACT

A Gram-stain positive, non-motile, spherical, red-pigmented and facultatively anaerobic bacterium, designated strain 6.1T, was isolated from a crude oil recovery water sample from the Huabei oil field in China. The novel strain exhibited tolerance of UV irradiation (> 1000 J m-2). Based on 16S rRNA gene sequence comparisons, strain 6.1T shows high similarity to Deinococcus citri DSM 24791T (98.1%) and Deinococcus gobiensis I-0T (97.8%), with less than 93.5% similarity to other closely related taxa. The major cellular fatty acids were identified as summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), followed by iso-C17:1 ω9c and C16:0. The polar lipid profile was found to contain phospholipids, glycolipids, phosphoglycolipids and aminophospholipids. The predominant respiratory quinone was identified as MK-8. The DNA G + C content was determined to be 68.3 mol %. DNA-DNA hybridization between strain 6.1T and D. citri DSM 24791T was 45.6 ± 7.1% and with D. gobiensis I-OT was 36.6 ± 4.7%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, we conclude strain 6.1T represents a novel species of the genus Deinococcus, for which we propose the name Deinococcus petrolearius sp. nov. The type strain is 6.1T (= CGMCC 1.15053T = KCTC 33744T).


Subject(s)
Deinococcus/classification , Petroleum/microbiology , Water Microbiology , Bacterial Typing Techniques , Base Composition , China , Deinococcus/chemistry , Deinococcus/genetics , Deinococcus/isolation & purification , Environmental Microbiology , Metabolomics/methods , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
11.
Antonie Van Leeuwenhoek ; 111(6): 945-954, 2018 Jun.
Article in English | MEDLINE | ID: mdl-29236233

ABSTRACT

A bacterial strain, K11T, capable of degrading phenol derivatives was isolated from activated sludge of a sewage treatment plant in China. This strain, which can degrade more than ten phenol derivatives, was identified as a Gram-stain negative, rod-shaped, asporogenous, facultative anaerobic bacterium with a polar flagellum. The strain was found to grow in tryptic soy broth in the presence of 0-2.5% (w/v) NaCl (optimum 0-1%), at 4-43 °C (optimum 30-35 °C) and pH 4.5-10.5 (optimum 7.5-8). Comparative analysis of nearly full-length 16S rRNA gene sequences showed that this strain belongs to the genus Thauera. The 16S rRNA gene sequence was found to show high similarity (97.5%) to that of Thauera chlorobenzoica 3CB-1T, with lesser similarity to other recognised Thauera strains. The G+C content of the DNA of the strain was determined to be 67.8 mol%. The DNA-DNA hybridization value between K11T and Thauera aromatica DSM6984T was 10.4 ± 4.5%. The genomic OrthoANI values of K11T with the other nine type strains of genus Thauera were less than 81.1%. Chemotaxonomic analysis of strain K11T revealed that Q-8 is the predominant quinone; the polar lipids contain phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and five uncharacterised lipids; the major cellular fatty acid was identified as summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH; 45.9%), followed by C16:0 (20.5%) and C18:1 ω7c (15.8%). Based on the phenotypic and phylogenetic evidence, DNA-DNA hybridisation, OrthoANI, chemotaxonomic analysis and results of the physiological and biochemical tests, a new species named Thauera sinica sp. nov. is proposed with strain K11T (= CGMCC 1.15731T = KACC 19216T) designated as the type strain.


Subject(s)
Thauera/genetics , Bacterial Typing Techniques , Base Composition/genetics , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sewage/microbiology , Thauera/isolation & purification
12.
Antonie Van Leeuwenhoek ; 110(1): 27-32, 2017 Jan.
Article in English | MEDLINE | ID: mdl-27695993

ABSTRACT

A novel bacterium, strain L3T, was isolated from an activated sludge sample retrieved from a municipal wastewater treatment plant in Huangdao, China. On the basis of 16S rRNA gene sequence similarity studies, strain L3T was affiliated to the genus Sinorhodobacter, being most closely related to Sinorhodobacter ferrireducens (98.0 %). The 16S rRNA gene sequence similarity of strain L3T to other related species, Thioclava atlantica DLFJ1-1T (96.5 %), Rhodobacter capsulatus ATCC 11166T (96.3 %), Paenirhodobacter enshiensis DW2-9T (96.3 %) and Rhodobacter viridis JA737T (96.0 %) is less than 96.5 %. Chemotaxonomic characterization further supported classification of the strain to the genus Sinorhodobacter. The major polar lipid profile consists of diphosphatidyglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids are C18:1 ω7c (66.3 %), C16:0 (12.9 %) and C18:0 (8.0 %). The major quinone is Q-10. The G+C content of the genomic DNA of strain L3T is 68.0 mol %. DNA-DNA relatedness value between L3T and the closely related type strain S. ferrireducens SgZ-3T was 35.2 %. Based on these results, a new species Sinorhodobacter huangdaonensis is proposed. The type strain is L3T (= CGMCC 1.12963T = KCTC 42823T).


Subject(s)
Rhodobacteraceae/isolation & purification , Sewage/microbiology , Wastewater/microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhodobacteraceae/classification , Rhodobacteraceae/genetics , Rhodobacteraceae/metabolism , Wastewater/chemistry
13.
Int J Syst Evol Microbiol ; 67(1): 164-169, 2017 Jan.
Article in English | MEDLINE | ID: mdl-27902231

ABSTRACT

Three strains, FXJ8.095T, FXJ8.057 and H201, were isolated from deep-sea hydrothermal plume water collected at the Southwest Indian Ridge at a depth of 2800 m. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates formed a closely related subcluster within the genus Kocuria. The 16S rRNA gene sequence of strain FXJ8.095T shared 99.90 and 99.60 % similarity with those of strains FXJ8.057 and H201, respectively, and 98.81, 98.75, 98.68 and 98.10 % with those of 'Kocuria sediminis' JCM 17929, Kocuria flava HO-9041T, Kocuria turfanensis HO-9042T and Kocuria rosea JCM 11614T, respectively. DNA-DNA hybridization values among the three new isolates were higher than 70 %, while the values between each of the isolates and the closely related type strains were well below 70 %. Random amplified polymorphic DNA fingerprint patterns and a combination of physiological and biochemical properties also distinguished the isolates from the related species. The major cellular fatty acids of the isolates were anteiso-C15 : 0 and iso-C15 : 0, the predominant menaquinones were MK-7(H2) and MK-8(H2), and the main polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C contents of strains FXJ8.095T, FXJ8.057 and H201 were 75.6, 72.8 and 70.4 mol%, respectively. Based on the phylogenetic, phenotypic and chemotaxonomic data, we propose to classify the three strains in a novel species named Kocuria oceani sp. nov., with FXJ8.095T (=CGMCC 4.6946T=DSM 24949T) as the type strain.


Subject(s)
Hydrothermal Vents/microbiology , Micrococcaceae/classification , Phylogeny , Seawater/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Micrococcaceae/genetics , Micrococcaceae/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/chemistry
14.
Article in Chinese | WPRIM (Western Pacific) | ID: wpr-822308

ABSTRACT

Objective @#To investigate the changes of vaspin and TNF-α levels in gingival crevicular fluid (GCF) of type 2 diabetic (T2DM) patients with chronic periodontitis (CP) after non-surgical periodontal treatment.@*Methods@#60 subjects were divided into 4 groups: DM-CP group (patients with both T2DM and CP, n=15); CP group (CP patients without T2DM, n=15); DM group (T2DM patients without CP, n=15), and CTRL group (systemically and periodontally healthy individuals, n=15). The clinical parameters of periodontal tissue and GCF were measured before and 8 weeks after non-surgical periodontal treatment. @*Results@#The levels of vaspin and TNF-α were measured by ELISA. The levels of vaspin and TNF-α in CP group were significantly higher than those in CTRL group (P < 0.05), while the levels of vaspin and TNF-α in CP group were significantly decreased after treatment (P < 0.05). There was a statistically significant positive correlation between the total amount of vaspin and the total amount of TNF-α, the level of HbA1c, gingival index (GI) and probing depth (PD) (P < 0.05). @*Conclusion @#The results shows that vaspin and TNF-α are greatly decreased in periodontitis after non-surgical periodontal treatment. It suggests that vaspin and TNF-α in GCF may serve as inflammatory markers for the diagnosis and prognosis of diabetes and periodontitis.

15.
Front Microbiol ; 7: 1340, 2016.
Article in English | MEDLINE | ID: mdl-27621725

ABSTRACT

The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662-4000 m below water surface. Actinobacterial sequences represented 1.2-9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.

16.
J Biotechnol ; 227: 54-55, 2016 Jun 10.
Article in English | MEDLINE | ID: mdl-27046067

ABSTRACT

Aneurinibacillus sp. XH2 (CGMCC 1.15535) was isolated from Gudao oilfield in China. It is able to use simple carbon resources to accumulate Polyhydroxyalkanoates (PHAs) in a thermophilic fashion. Here, we describe the genomic features of this strain. The total genome size of Aneurinibacillus sp. XH2 is 3,664,835bp and contains 3441 coding sequences and 114 tRNAs. The annotated genome sequence of this strain provides the genetic basis for revealing its role as a themophilic PHAs producing bacterium.


Subject(s)
Genome, Bacterial , Oil and Gas Fields/microbiology , Paenibacillus/genetics , Paenibacillus/isolation & purification , Polyhydroxyalkanoates/biosynthesis , Temperature , Base Sequence , China , Multigene Family , Sequence Analysis, DNA
17.
FEMS Microbiol Lett ; 362(18): fnv146, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26316545

ABSTRACT

This study investigated multidrug resistance in Shewanella xiamenensis isolated from an estuarine water sample in China during 2014. This strain displayed resistance or decreased susceptibility to ampicillin, aztreonam, cefepime, cefotaxime, chloramphenicol, ciprofloxacin, erythromycin, kanamycin and trimethoprim-sulfamethoxazole. The antimicrobial resistance genes aacA3, blaOXA-199, qnrA1 and sul1 were identified by PCR amplification and by sequencing. Pulsed-field gel electrophoresis and DNA hybridization experiments showed that the quinolone resistance gene qnrA1 was chromosomally located. qnrA1 was located in a complex class 1 integron, downstream from an ISCR1, and bracketed by two copies of qacEΔ1-sul1 genes. This integron is similar to In825 with four gene cassettes aacA3, catB11c, dfrA1z and aadA2az. An IS26-mel-mph2-IS26 structure was also detected in the flanking sequences, conferring resistance to macrolides. This is the first identification of the class 1 integron in S. xiamenensis. This is also the first identification of the qnrA1 gene and IS26-mediated macrolide resistance genes in S. xiamenensis. Presence of a variety of resistance genetic determinants in environmental S. xiamenensis suggests the possibility that this species may serve as a potential vehicle of antimicrobial resistance genes in aquatic environments.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Integrons , Quinolones/pharmacology , Shewanella/drug effects , Shewanella/genetics , Water Microbiology , China , Electrophoresis, Gel, Pulsed-Field , Estuaries , Genes, Bacterial , Macrolides/pharmacology , Microbial Sensitivity Tests , Phylogeny , Quinolones/metabolism
18.
Biotechnol Lett ; 37(8): 1671-7, 2015 Aug.
Article in English | MEDLINE | ID: mdl-25851952

ABSTRACT

OBJECTIVE: To enzymatically synthesize aroma acetoin fatty acid esters, useful as flavor and fragrance ingredients in foods. RESULTS: Immobilized Candida antarctica lipase B (CALB), performed significantly better than lipases from Rhizopus niveus and Candida rugosa in carrying out the esterification of acetoin and fatty acids. C4-C12 straight chain fatty acids were suitable acyl donors and CALB had a strong preference for longer straight chains up to ten carbon atoms. Higher temperatures, 40-60 °C, and higher acetoin/fatty acid molar ratios favored the conversion. The maximum yield of acetoin octanoate obtained was (51 ± 1) % after 24 h reaction time in hexane with 0.25 M octanoic acid, 5:1 excess acetoin and an enzyme concentration of 6 g/mol fatty acid at 60 °C. The enzyme activity declined at a steady rate during reuse at 60 °C and after the 10th cycle, 65 % of initial activity was still be retained. CONCLUSION: This is the first report of acetoin fatty acid ester synthesis by biological method and CALB has been shown to be effective for the lipase-catalyzed esterification of acetion and C4-C12 straight chain fatty acids.


Subject(s)
Acetoin/metabolism , Enzymes, Immobilized/metabolism , Fatty Acids/metabolism , Flavoring Agents/metabolism , Fungal Proteins/metabolism , Lipase/metabolism , Temperature
19.
J Basic Microbiol ; 55(9): 1125-33, 2015 Sep.
Article in English | MEDLINE | ID: mdl-25832555

ABSTRACT

Polyhydroxyalkanoates (PHAs) are usually biosynthesized using mesophilic strains, but the fermentation processes often suffer from bacterial contamination. This work reports the screening of thermophilic bacteria capable of producing PHAs under elevated temperatures to reduce the contamination risk. Strain XH2 was isolated from an oilfield and identified as Aneurinibacillus sp. by morphology, physiological-biochemical characterization, and 16S rDNA phylogenetic analysis. This strain can produce PHA granules, which was detected by Nile red staining and transmission electron microscopic imaging. At 55 °C, 111.6 mg l(-1) of PHA was produced in a fermentation medium containing glucose, peptone, and yeast extract. If peptone was removed from the medium, the yield of PHA would be enhanced by 2.4 times. The main monomers of the PHA product were identified to be 3-hydroxybutyrate and 3-hydroxyvalerate with a molar ratio of 17.2:1 by gas chromatography-mass spectroscopy (GC-MS) and nuclear magnetic resonance analyses. Two minor homologues, 3-hydroxyoctanoate, and 3-hydroxy-4-phenylbutanoate, were tentatively identified by GC-MS as well. This is the first report of thermophilic PHA bacterial producer from the Firmicutes phylum.


Subject(s)
Fermentation , Oil and Gas Fields/microbiology , Paenibacillus/metabolism , Polyhydroxyalkanoates/biosynthesis , China , Chromatography, Gas , Mass Spectrometry , Microscopy, Electron , Oil and Gas Fields/chemistry , Paenibacillus/chemistry , Paenibacillus/classification , Paenibacillus/isolation & purification , Phylogeny , Polyhydroxyalkanoates/chemistry
20.
J Microbiol ; 52(5): 407-12, 2014 May.
Article in English | MEDLINE | ID: mdl-24810320

ABSTRACT

In the effluents of a biologically treated wastewater from a heavy oil-refining plant, C5-C8 fatty acids including pentanoic acid, hexanoic acid, heptanoic acid, octanoic acid, and 2-methylbutanoic acid are often detected. As these residual fatty acids can cause further air and water pollution, a new Myroides isolate ZB35 from activated sludge was explored to degrade these C5-C8 fatty acids in this study. It was found that the biodegradation process involved a lag phase that became prolonged with increasing acyl chain length when the fatty acids were individually fed to this strain. However, when fed as a mixture, the ones with longer acyl chains were found to become more quickly assimilated. The branched 2-methylbutanoic acid was always the last one to be depleted among the five fatty acids under both conditions. Metabolite analysis revealed one possible origin of short chain fatty acids in the biologically treated wastewater. Aroma volatiles including 2-methylbutyl isovalerate, isoamyl 2-methylbutanoate, isoamyl isovalerate, and 2-methylbutyl 2-methylbutanoate were subsequently identified from ZB35 extracts, linking the source of the fruity odor to these esters excreted by Myroides species. To our best knowledge, this is the first finding of these aroma esters in bacteria. From a biotechnological viewpoint, this study has revealed the potential of Myroides species as a promising source of aroma esters attractive for food and fragrance industries.


Subject(s)
Fatty Acids/metabolism , Flavobacteriaceae/isolation & purification , Flavobacteriaceae/metabolism , Sewage/microbiology , Volatile Organic Compounds/metabolism , Biotransformation , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Molecular Sequence Data , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Wastewater/chemistry , Wastewater/microbiology , Water Pollutants/metabolism
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