Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol

Bacteria able to mineralize 100 to 200 ppm of pentachlorophenol (PCP) were isolated by selective enrichment from PCP-contaminated soils from three geographic areas of Minnesota. Although differing somewhat in their responses to various biochemical and biophysical tests, all strains were assigned to the genus Flavobacterium. Five representative strains were examined in detail. All strains metabolized PCP as a sole source of carbon and energy; 73 to 83% of all carbon in the form of [U-14C]PCP was returned as 14CO2, with full liberation of chlorine as chloride. A comparison between strains in their ability to metabolize PCP showed some strains to be more efficient than others. Guanine-plus-cytosine contents of DNA ranged from 58.8 to 63.8%, and DNA/DNA hybridization studies with total DNA digests suggested substantial genetic homology between strains. All strains were shown to possess an 80- to 100-kilobase plasmid, and evidence suggested the presence of a larger plasmid (greater than 200 kilobases).     

Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol.

Bacteria able to mineralize 100 to 200 ppm of pentachlorophenol (PCP) were isolated by selective enrichment from PCP-contaminated soils from three geographic areas of Minnesota. Although differing somewhat in their responses to various biochemical and biophysical tests, all strains were assigned to the genus Flavobacterium. Five representative strains were examined in detail. All strains metabolized PCP as a sole source of carbon and energy; 73 to 83% of all carbon in the form of [U-14C]PCP was returned as 14CO2, with full liberation of chlorine as chloride. A comparison between strains in their ability to metabolize PCP showed some strains to be more efficient than others. Guanine-plus-cytosine contents of DNA ranged from 58.8 to 63.8%, and DNA/DNA hybridization studies with total DNA digests suggested substantial genetic homology between strains. All strains were shown to possess an 80- to 100-kilobase plasmid, and evidence suggested the presence of a larger plasmid (greater than 200 kilobases).     

Biodegradation of ethyl t-butyl ether (ETBE), methyl t-butyl ether (MTBE) and t-amyl methyl ether (TAME) by Gordonia terrae

Gordonia terrae strain IFP 2001 was selected from activated sludge for its capacity to grow on ethyl t-butyl ether (ETBE) as sole carbon and energy source. ETBE was stoichiometrically degraded to t-butyl alcohol (TBA) and the activity was inducible. A constitutive strain, G. terrae IFP 2007, derived from strain IFP 2001, was also selected. Methyl t-butyl ether (MTBE) and t-amyl methyl ether (TAME) were not used as carbon and energy sources by the two strains, but cometabolic degradation of MTBE and TAME was demonstrated, to TBA and t-amyl alcohol (TAA) respectively, in the presence of a carbon source such as ethanol. No two-carbon compound was detected during growth on ETBE, but formate was produced during cometabolic degradation of MTBE or TAME. A monooxygenase was involved in the degradation of ethers, because no degradation of ETBE was observed under anaerobic conditions and the presence of a cytochrome P-450 was demonstrated in G. terrae IFP 2001 after induction by cultivation on ETBE.     

Isolation and characterization of bacterial strains that have high ability to degrade 1,4-dioxane as a sole carbon and energy source

Four novel metabolic 1,4-dioxane degrading bacteria possessing high ability to degrade 1,4-dioxane (designated strains D1, D6, D11 and D17) were isolated from soil in the drainage area of a chemical factory. Strains D6, D11 and D17 were allocated to Gram-positive actinomycetes, similar to previously reported metabolic 1,4-dioxane degrading bacteria, whereas strain D1 was allocated to Gram-negative Afipia sp. The isolated strains could utilize a variety of carbon sources, including cyclic ethers, especially those with carbons at position 2 that were modified with methyl- or carbonyl-groups. The cell yields on 1,4-dioxane were relatively low (0.179–0.223 mg-protein (mg-1,4-dioxane)^?1), which was likely due to requiring energy for C–O bond fission. The isolated strains showed 2.6–13 times higher specific 1,4-dioxane degradation rates (0.052–0.263 mg-1,4-dioxane (mg-protein)^?1 h^?1) and 2.3–7.8 fold lower half saturation constants (20.6–69.8 mg L^?1) than the most effective 1,4-dioxane degrading bacterium reported to date, Pseudonocardia dioxanivorans CB1190, suggesting high activity and affinity toward 1,4-dioxane degradation. Strains D1 and D6 possessed inducible 1,4-dioxane degrading enzymes, whereas strains D11 and D17 possessed constitutive ones. 1,4-Dioxane degradation (100 mg L^?1) by Afipia sp. D1 was not affected by the co-existence of up to 3,000 mg L^?1 of ethylene glycol. The effects of initial pH, incubation temperature and NaCl concentration on 1,4-dioxane degradation by the four strains revealed that they could degrade 1,4-dioxane under a relatively wide range of conditions, suggesting that they have a certain adaptability and applicability for industrial wastewater treatment.     

Enzymes and genes involved in the aerobic biodegradation of methyl tert-butyl ether (MTBE)

Fuel oxygenates, mainly methyl tert-butyl ether (MTBE) but also ethyl tert-butyl ether (ETBE), are added to gasoline in replacement of lead tetraethyl to enhance its octane index. Their addition also improves the combustion efficiency and therefore decreases the emission of pollutants (CO and hydrocarbons). On the other hand, MTBE, being highly soluble in water and recalcitrant to biodegradation, is a major pollutant of water in aquifers contaminated by MTBE-supplemented gasoline during accidental release. MTBE was shown to be degraded through cometabolic oxidation or to be used as a carbon and energy source by a few microorganisms. We have summarized the present state of knowledge about the microorganisms involved in MTBE degradation and the MTBE catabolic pathways. The role of the different enzymes is discussed as well as the rare and recent data concerning the genes encoding the enzymes involved in the MTBE pathway. The phylogeny of the microorganisms isolated for their capacity to grow on MTBE is also described.     

Isolation and characterization of Rhodococcus sp. strains TMP2 and T12 that degrade 2,6,10,14-tetramethylpentadecane (pristane) at moderately low temperatures

Branched alkanes including 2,6,10,14-tetramethylpentadecane (pristane) are more resistant to biological degradation than straight-chain alkanes especially under low-temperature conditions, such as 10 degrees C. Two bacterial strains, TMP2 and T12, that are capable of degrading pristane at 10 degrees C were isolated and characterized. Both strains grew optimally at 30 degrees C and were identified as Rhodococcus sp. based on the 16S rRNA gene sequences. Strain T12 degraded comparable amounts of pristane in a range of temperatures from 10 to 30 degrees C and strain TMP2 degraded pristane similarly at 10 and 20 degrees C but did not degrade it at 30 degrees C. These data suggest that the strains have adapted their pristane degradation system to moderately low-temperature conditions.     

Microbial community analyses of three distinct, liquid cultures that degrade methyl tert-butyl ether using anaerobic metabolism

Methyl tert-butyl ether (MTBE) is a prevalent groundwater contaminant. In this study, three distinct MTBE-degrading, anaerobic cultures were derived from MTBE-contaminated aquifer material: cultures NW1, NW2 and NW3. The electron acceptors used are anthraquinone-2,6-disulfonate (AQDS; NW1), sulfate (NW2) and fumarate (NW3), respectively. About 1–2 mM MTBE is consistently degraded within 20–30 days in each culture. The 16S rDNA-based amplified ribosomal DNA restriction analysis (ARDRA) was used to analyze the microbial community in each culture. Results indicate novel microorganisms (i.e. no closely related known genera or species) catalyze anaerobic MTBE biodegradation, and microbial diversity varied with different electron acceptors. Tert-butyl alcohol (TBA) accumulated to nearly stoichiometric levels, and these cultures will be critical to understanding the factors that influence TBA accumulation versus degradation. The cultures presented here are the first stable anaerobic MTBE-degrading cultures that have been characterized with respect to taxonomy.     

Biodegradation of the gasoline oxygenates methyl tert-butyl ether, ethyl tert-butyl ether, and tert-amyl methyl ether by propane-oxidizing bacteria.

Several propane-oxidizing bacteria were tested for their ability to degrade gasoline oxygenates, including methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). Both a laboratory strain and natural isolates were able to degrade each compound after growth on propane. When propane-grown strain ENV425 was incubated with 20 mg of uniformly labeled [14C]MTBE per liter, the strain converted > 60% of the added MTBE to 14CO2 in < 30 h. The initial oxidation of MTBE and ETBE resulted in the production of nearly stoichiometric amounts of tert-butyl alcohol (TBA), while the initial oxidation of TAME resulted in the production of tert-amyl alcohol. The methoxy methyl group of MTBE was oxidized to formaldehyde and ultimately to CO2. TBA was further oxidized to 2-methyl-2-hydroxy-1-propanol and then 2-hydroxy isobutyric acid; however, neither of these degradation products was an effective growth substrate for the propane oxidizers. Analysis of cell extracts of ENV425 and experiments with enzyme inhibitors implicated a soluble P-450 enzyme in the oxidation of both MTBE and TBA. MTBE was oxidized to TBA by camphor-grown Pseudomonas putida CAM, which produces the well-characterized P-450cam, but not by Rhodococcus rhodochrous 116, which produces two P-450 enzymes. Rates of MTBE degradation by propane-oxidizing strains ranged from 3.9 to 9.2 nmol/min/mg of cell protein at 28 degrees C, whereas TBA was oxidized at a rate of only 1.8 to 2.4 nmol/min/mg of cell protein at the same temperature.     

Isolation of Pseudomonas pickettii strains that degrade 2,4,6-trichlorophenol and their dechlorination of chlorophenols.

Three strains of Pseudomonas pickettii that can grow with 2,4,6-trichlorophenol (2,4,6-TCP) as the sole source of carbon and energy were isolated from different mixed cultures of soil bacterial populations that had been acclimatized to 2,4,6-TCP. These strains released 3 mol of chloride ion from 1 mol of 2,4,6-TCP during the complete degradation of the TCP. Of these strains, P. pickettii DTP0602 in high-cell-density suspension cultures dechlorinated various chlorophenols (CPs). Cells that were preincubated with 2,4,6-TCP converted isomers of 4-CP to the corresponding chloro-p-hydroquinones, but those preincubated with 4-CP converted CPs lacking a chlorine atom(s) at the o position to isomers of chlorocatechol. The ability of DTP0602 to dechlorinate 2,4,6-TCP was induced by 2,6-dichlorophenol, 2,3,6- and 2,4,6-TCP, and 2,3,4,6-tetrachlorophenol and was repressed in the presence of succinate or glucose.     

Isolation of Pseudomonas pickettii strains that degrade 2,4,6-trichlorophenol and their dechlorination of chlorophenols.

Three strains of Pseudomonas pickettii that can grow with 2,4,6-trichlorophenol (2,4,6-TCP) as the sole source of carbon and energy were isolated from different mixed cultures of soil bacterial populations that had been acclimatized to 2,4,6-TCP. These strains released 3 mol of chloride ion from 1 mol of 2,4,6-TCP during the complete degradation of the TCP. Of these strains, P. pickettii DTP0602 in high-cell-density suspension cultures dechlorinated various chlorophenols (CPs). Cells that were preincubated with 2,4,6-TCP converted isomers of 4-CP to the corresponding chloro-p-hydroquinones, but those preincubated with 4-CP converted CPs lacking a chlorine atom(s) at the o position to isomers of chlorocatechol. The ability of DTP0602 to dechlorinate 2,4,6-TCP was induced by 2,6-dichlorophenol, 2,3,6- and 2,4,6-TCP, and 2,3,4,6-tetrachlorophenol and was repressed in the presence of succinate or glucose.     

Bioaugmentation and coexistence of two functionally similar bacterial strains in aerobic granules

The survival of the inoculated microbial culture is critical for successful bioaugmentation but impossible to predict precisely. As an alternative strategy, bioaugmentation of a group of microorganisms may improve reliability of bioaugmentation. This study evaluated simultaneous bioaugmentation of two functionally similar bacterial strains in aerobic granules. The two strains, Pandoraea sp. PG-01 and Rhodococcus erythropolis PG-03, showed high phenol degradation and growth rates in phenol medium, but they were characterized as having a poor aggregation activity and weak bioflocculant-producing and biofilm-forming abilities. In the spatially homogeneous batch conditions, strain PG-01 with higher growth rates outcompeted strain PG-03. However, the two strains could stably coexist in the spatially heterogeneous conditions. Then the two strains were mixed and bioaugmented into activated sludge in two sequencing batch reactors, which were operated with the different settling times of 5 and 30 min, respectively. Aerobic granules were developed only in the reactor with a settling time of 5 min. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis showed that the two strains could coexist in aerobic granules but not in activated sludge. These findings suggested that the compact structure of aerobic granules provided spatial isolation for coexistence of competitively superior and inferior strains with similar functions.     

Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential

Background

The number of biotransformations that use nicotinamide recycling systems is exponentially growing. For this reason one of the current challenges in biocatalysis is to develop and optimize more simple and efficient cofactor recycling systems. One promising approach to regenerate NAD⁺ pools is the use of NADH-oxidases that reduce oxygen to hydrogen peroxide while oxidizing NADH to NAD⁺. This class of enzymes may be applied to asymmetric reduction of prochiral substrates in order to obtain enantiopure compounds.

Results

The NADH-oxidase (NOX) presented here is a flavoenzyme which needs exogenous FAD or FMN to reach its maximum velocity. Interestingly, this enzyme is 6-fold hyperactivated by incubation at high temperatures (80°C) under limiting concentrations of flavin cofactor, a change that remains stable even at low temperatures (37°C). The hyperactivated form presented a high specific activity (37.5 U/mg) at low temperatures despite isolation from a thermophile source. Immobilization of NOX onto agarose activated with glyoxyl groups yielded the most stable enzyme preparation (6-fold more stable than the hyperactivated soluble enzyme). The immobilized derivative was able to be reactivated under physiological conditions after inactivation by high solvent concentrations. The inactivation/reactivation cycle could be repeated at least three times, recovering full NOX activity in all cases after the reactivation step. This immobilized catalyst is presented as a recycling partner for a thermophile alcohol dehydrogenase in order to perform the kinetic resolution secondary alcohols.

Conclusion

We have designed, developed and characterized a heterogeneous and robust biocatalyst which has been used as recycling partner in the kinetic resolution of rac-1-phenylethanol. The high stability along with its capability to be reactivated makes this biocatalyst highly re-useable for cofactor recycling in redox biotransformations.     

Biodiversity of microorganisms that degrade bacterial and synthetic polyesters

The biodiversity and occurrence in nature of bioplastic-degrading microorganisms are exemplified by the identification of 695 strains, isolated from different environments, such as soils, composts, natural waters, and sludge, that are able to degrade the bacterial polyester poly(3-hydroxybutyrate)in vitro. These microorganisms belong to at least 57 different taxa, including Gram-negative and Gram-positive bacteria, streptomycetes, and moulds. The literature on the biodiversity of poly(3-hydroxybutyrate)-degrading microorganisms is reviewed. The degrading abilities of 171 streptomycete strains were investigated on four different bacterial poly(3-hydroxyalkanoates), and the synthetic polyesters poly(-caprolactone) and BIONOLLE, and most of these strains degraded at least three different polymers.     

耐盐好氧反硝化菌A-13菌株的分离鉴定及其反硝化特性

[目的]筛选高效好氧脱氮的反硝化细菌,对菌株进行多项鉴定及条件优化,为后续富营养化人工湖水体治理提供理论依据.[方法]利用反硝化培养基分离筛选好氧反硝化细菌,通过形态、生理生化、16S rRNA基因序列分析、周质硝酸还原酶亚基基因( napA)同源性分析进行菌株鉴定;通过反硝化培养基,对菌株生长及反硝化的最适pH、温度、碳源、溶解氧、接种量等进行了考察.[结果]从福州市闽侯县上街镇高岐村某排污口分离出1株耐盐高效好氧反硝化细菌A-13,多项鉴定表明该菌株为Pseudomonas stutzeri,与Pseudomonas stutzeri DSM 50283亲缘关系最近.菌株生长及反硝化的最适pH为6.5,最适温度为33℃,最适碳源为丁二酸钠,最适摇床转速为150 r/min,最适接种量为5％.在此条件下,最大可去除NO3-浓度约为1900 mg/L.该菌能够在高盐培养基( 10％ NaCl)中良好生长.对人工废水的净化效果表明,该菌具有一定的工程应用价值.[结论]分离所得好氧反硝化细菌为Pseudomonas stutzeri,将其命名为P.stutzeri YHA-13.具备高耐盐性的好氧反硝化功能的P.stutzeri未见报道.这对含盐废水/富营养化水体的工程应用有一定的潜在价值.     

Isolation and characterization of two enzymatic activities from chick embryos which degrade double-stranded RNA

Enzymatic activities capable of degrading double-stranded RNA have been solubilized from whole 9-day-old chick embryos and separated by ion exchange chromatography on DEAE-cellulose into two classes, designated nucleases DI and DII. Nuclease DI exhibits an absolute requirement for Mn2+ in the range of 5 to 10 mM. Monovalent cations, including K+, Na+, and NH4+, are inhibitory. The molecular weight of DI is 60,000 to 62,500 as estimated from sedimentation in sucrose density gradients. Following gradient fractionation, nuclease DI possesses the ability to degrade several substrates exhibiting a 250-fold preference for poly(rC) as compared to poly(rC)-poly(rG). The activity responsible for degrading double-stranded RNA functions as an endonuclease generating oligonucleotides with 5'-phosphate termini. Nuclease DII requires both monovalent and divalent cations. Optimal degradation of poly[r(A-U)] is seen at 75 to 100 mM salt and 0.5 to 1.0 mM MgCl2 or MnCl2. The molecular weight estimated from sucrose gradient sedimentation is in the range of 38,000 to 40,000. Nuclease DII acts endonucleolytically producing oligonucleotides terminating in 5'-phosphates. During the isolation and characterization of nucleases DI and DII, a third activity was detected which degrades single-stranded RNA substrates but which, in the presence of either DII or RNase H, significantly enhances the degradation of poly[r(A-U)] or poly(rA)-poly(dT) substrates.     

Separation and characterization of two activities from HeLa cell nuclei that degrade double-stranded RNA

Two enzymatic activities that degrade double-stranded RNA have been partially purified from HeLa cell nuclei using reoviral [3H]RNA as the substrate. The two active fractions, separated by chromatography on phosphocellulose, are designated PC I and PC II. Both fractions degrade a variety of double-stranded RNAs with an absolute requirement for a divalent cation. However, they are distinct by at least five criteria. 1)PC I degrades a variety of single- and double-stranded RNAs, single- and double-stranded DNAs, and DNA.RNA hybrids, in addition to double-stranded reoviral RNA. In contrast, PC II has maximal activity with reoviral RNA, some activity with rRNA, and much less activity with the other substrates. 2) Analyses of reaction products by sucrose gradient centrifugation and chromatography on Sephadex G-100 and DEAE-cellulose indicate that, PC I cleaves reoviral RNA endonucleolytically to a final mixture of mono- and oligonucleotides, whereas the only acid- or alcohol-soluble products of PC II are 5'-XMPs produced exonucleolytically. 3) PC I activity is stimulated 2-fold more by MnCl2 than by MgCl2, whereas PC II activity is stimulated 3-fold more by MgCl2 than by MnCl2. 4) PC I activity is inhibited by NaCl concentrations as low as 10 mM, whereas PC II requires 50 to 80 mM NaCl for optimal activity. 5)Estimated by their sedimentation rates in glycerol gradients, PC I and PC II have apparent molecular weights of 55,000 and 20,000, respectively.     

Isolation and characterization of rhamnolipid-producing bacterial strains from a biodiesel facility

Novel strains of rhamnolipid-producing bacteria were isolated from soils at a biodiesel facility on the basis of their ability to grow on glycerol as a sole carbon source. Strains were identified as Acinetobacter calcoaceticus , Enterobacter asburiae , Enterobacter hormaechei , Pantoea stewartii , and Pseudomonas aeruginosa . The strains of the former five species were found to produce rhamnolipids in quantities the same as, or similar to, coisolated strains of P. aeruginosa . Measurements of surface tension revealed that that emulsifying properties of these strains were similar to levels displayed by rhamnolipids produced by P. aeruginosa . Results of matrix-assisted laser desorption/ionization time-of-flight MS analyses revealed that the predominant compounds made by all strains were C₁₀–C₁₀ mono- and dirhamnolipids. Notably, E. hormaechei and one strain of A. calcoaceticus produced rhamnolipids in amounts similar to the pseudomonads. As all strains examined were from the same taxonomic class of Proteobacteria , further examination of this group may reveal many additional species not previously known to produce rhamnolipids in addition to novel strains of species currently known to produce rhamnolipids.     

Single-walled carbon nanotubes as an effective adsorbent in solid-phase microextraction of low level methyl tert-butyl ether,ethyl tert-butyl ether and methyl tert-amyl ether from human urine

Carbon nanotubes (CNTs) are a kind of new carbon-based nano-materials which have drawn great attention in many application fields. The potential single-walled carbon nanotubes (SWCNTs) as solid-phase microextraction (SPME) adsorbents for the preconcentration of environmental pollutants have been investigated in recent years. The goal of this work was to investigate the feasibility of SWCNTs used as adsorbents for solid-phase microextraction of methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE) and tert-amyl methyl ether (TAME) in human urine. SWCNTs were attached onto a stainless steel wire through organic binder. Potential factors affecting the extraction efficiency were optimized, including extraction time, extraction temperature, desorption time, desorption temperature, and salinity. The developed method showed good performance according to the ICH performance criteria for bioanalytical methods. The calibration curves of the ethers were linear (r² ≥ 0.992) in the range from 10 to 5000 ng L^?1. The limits of detection at a signal-to-noise (S/N) ratio of 3 were 10 ng L^?1 for all the analytes. In addition, compared with the commercial carboxen/polydimethylsiloxane (CAR/PDMS) fiber, the SWCNT fiber showed better thermal stability (over 350 °C) and longer life span (over 150 times). The developed method was applied successfully to determine trace level of the ethers in urine of 10 healthy male volunteers.     

Aerobic biodegradation of methyl tert-butyl ether (MTBE) by pure bacterial cultures isolated from contaminated soil

Summary Methyl tert-Butyl Ether (MTBE) has been used in gasoline as a substitute for lead-based additives, which have been demonstrated to be toxic. MTBE however, is persistent in soil and water, showing high affinity for water and low affinity for soil, and has become an important contaminant. Therefore, the aim of this work was to isolate and identify soil microorganisms capable of degrading MTBE. Two samples were taken from a gasoline-contaminated soil at a service station and 59 different bacterial strains were isolated by enrichment culture with three consecutive selective transfers. Biochemical and morphological characterization of the bacterial isolates classified them into the following groups: Bacillus, Rhodococcus, Micrococcus, Aureobacterium and Proteus. Twelve strains were selected for evaluation of MTBE biodegradation depending on visual growth and biomass production of the isolates in minimal salt broth. Six strains significantly reduced MTBE concentration (22–37%) compared to an abiotic control after 5 days of incubation. Although it has been considered that MTBE is degraded mainly by cometabolism, our results demonstrate that these microorganisms are able to reduce MTBE concentration when MTBE is the sole source of carbon.