Degradation of Chlorinated Dibenzofurans and Dibenzo-p-Dioxins by Sphingomonas sp. Strain RW1

The ability of the dibenzofuran- and dibenzo-p-dioxin-mineralizing bacterium Sphingomonas sp. strain RW1 (R.-M. Wittich, H. Wilkes, V. Sinnwell, W. Francke, and P. Fortnagel, Appl. Environ. Microbiol. 58:1005-1010, 1992) to oxidize chlorinated derivatives of dibenzofuran and dibenzo-p-dioxin was analyzed. Strain RW1 degraded several mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins, but it did not degrade more highly chlorinated congeners. Most mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins investigated in this study were degraded to the corresponding mono- and dichlorinated salicylates and catechols, respectively, together with salicylate and catechol. This indicates an initial dioxygenolytic attack on the substituted as well as on the nonsubstituted aromatic nucleus of most of the target compounds. Strain RW1 could not grow at the expense of monochlorinated dibenzo-p-dioxins and dibenzofurans as carbon sources, with the exception of 4-chlorodibenzofuran, which was stoichiometrically converted to 3-chlorosalicylate.     

Degradation of Bromoxynil Octanoate by Strain Acinetobacter sp. XB2 Isolated from Contaminated Soil

Bromoxynil octanoate (BOO), the most widespread herbicide applied to maize, is potentially toxic to both animals and humans. In this article, a highly effective BOO-degrading bacterial strain, XB2, was isolated from the soil of a herbicide factory. The strain was identified as an Acinetobacter sp. based on its 16S rRNA gene sequence analysis, morphological, physiological, and biochemical properties. This strain could use BOO as its sole carbon source and could degrade 100?mg?l(-1) BOO to non-detectable levels in 72?h (h). The optimal pH and temperature for strain XB2's growth and degradation of BOO in MSM are 7.0 and 30°C, respectively. We propose the following pathway of BOO degradation by strain XB2: the first step is the scission of the ester bond to form bromoxynil, bromoxynil then transformed to 3,5-dibromo-4-hydroxybenzoic acid?due to the hydrolysis of nitriles, and debromination finally results in the formation of 3-bromo-4-hydroxybenzoic acid. Inoculating BOO-treated soil samples with strain XB2 resulted in a higher rate of BOO degradation than in non-inoculated soil, regardless of whether the soil had previously been sterilized.     

Molecular Mechanism of Nicotine Degradation by a Newly Isolated Strain,Ochrobactrum sp. Strain SJY1

A newly isolated strain, SJY1, identified as Ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. Strain SJY1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the VPP pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. A 97-kbp DNA fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain SJY1. Three genes, designated vppB, vppD, and vppE, in the VPP pathway were cloned and heterologously expressed, and the related proteins were characterized. The vppB gene encodes a flavin-containing amine oxidase converting 6-hydroxynicotine to 6-hydroxy-N-methylmyosmine. Although VppB specifically catalyzes the dehydrogenation of 6-hydroxynicotine rather than nicotine, it shares higher amino acid sequence identity with nicotine oxidase (38%) from the pyrrolidine pathway than with its isoenzyme (6-hydroxy-l-nicotine oxidase, 24%) from the pyridine pathway. The vppD gene encodes an NADH-dependent flavin-containing monooxygenase, which catalyzes the hydroxylation of 6-hydroxy-3-succinoylpyridine to 2,5-dihydroxypyridine. VppD shows 62% amino acid sequence identity with the hydroxylase (HspB) from Pseudomonas putida strain S16, whereas the specific activity of VppD is ∼10-fold higher than that of HspB. VppE is responsible for the transformation of 2,5-dihydroxypyridine. Sequence alignment and phylogenetic analysis suggested that the VPP pathway, which evolved independently from nicotinic acid degradation, might have a closer relationship with the pyrrolidine pathway. The proteins and functional pathway identified here provide a sound basis for future studies aimed at a better understanding of molecular principles of nicotine degradation.     

Cometabolic Degradation of Dibenzofuran and Dibenzothiophene by a Newly Isolated Carbazole-Degrading Sphingomonas sp. Strain

A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.     

Aerobic Degradation of N-Methyl-4-Nitroaniline (MNA) by Pseudomonas sp. Strain FK357 Isolated from Soil

N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH₂ substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.     

Chlorobenzene Degradation via Ortho-Cleavage Pathway by Newly Isolated Microbacterium sp. Strain TAS1CB from a Petrochemical-Contaminated Site

Chlorobenzene (CB), a dense nonaqeuous phase liquid (DNAPL), is categorized as a priority pollutant by the US EPA. It enters into ecosystems via solid and liquid waste discharge. Bioremediation is a key technique to remediate such contaminated sites. The present study aimed to isolate a chlorobenzene-degrading bacterium, determine the metabolic pathway for chlorobenzene degradation, and characterize biosurfactant production. Microbacterium sp. strain TAS1CB was isolated from contaminated sites and identified by 16S rRNA gene sequencing. Cells possessing positive chemotaxis for CB indicated their ability to degrade CB. Cells degraded CB via production of chlorobenzene dioxygenase, which converted CB to chlorocatechol. Chlorobenzene dioxygenase production was higher at 7 pH and 30°C. Intermediate metabolite analysis by UV scanning, HPLC, and GC-MS analysis revealed production of chlorocatechol and cis-cis muconate. Thus, Microbacterium was able to degrade CB via an ortho-cleavage pathway. In addition to chlorobenzene dioxygenase production, cells also produced biosurfactant which pseudosolubilized CB and increased degradation rate. Chemical characterization showed it to be a glycolipid-type biosurfactant. A phytotoxity study showed 60% of toxicity decreased after 72 hrs of degradation by isolate.     

Janibacter alkaliphilus sp. nov., isolated from coral Anthogorgia sp

A novel actinobacterium, designated strain SCSIO 10480^T, was isolated from a gorgonian coral sample of Anthogorgia sp. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Janibacter. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between strain SCSIO 10480^T and other type strains of recognized members of the genus Janibacter were 96.0–97.8 %. Growth in the presence of up to 17 % (w/v) NaCl and optimally at pH 9.0–10.0 was a distinctive characteristic of strain SCSIO 10480^T. Other biochemical and physiological properties and the fatty acid profile also differentiated the isolate from other members of Janibacter species. Based on the results obtained in this study, we propose that strain SCSIO 10480^T should be classified within a novel species of the genus Janibacter, for which the name Janibacter alkaliphilus sp. nov. is proposed, with SCSIO 10480^T (=CCTCC AB 2011027^T = DSM 24723^T) as the type strain.     

Degradation of Dimethyl Isophthalate by Viarovorax paradoxus Strain T4 Isolated from Deep-Ocean Sediment of the South China Sea

Viarovorax paradoxusT4 strain was isolated from deep-ocean sediment and demonstrated to be able to degrade dimethyl isophthalate (DMI). When DMI was utilized as the sole source of carbon and energy, it was transformed by hydrolysis initially, forming monomethyl isophthalate (MMI) and isophthalate acid (IA) as degradation intermediates. DMI and MMI were completely transformed to MMI and IA in about 100 h, respectively. Degradation of IA was completed in about 55 h. Analysis of total organic carbon in the culture medium confirmed that more than 80% of the substrate carbon was mineralized. Bacterial esterase induced by a range of substrates could be assessed using p-nitrophenyl acetate as the common substrate using crude enzyme preparation. The decreasing trend of K _m values derived from the Michaelis–Menten equation was dimethyl phthalate (DMP) > monomethyl phthalate (MMP) > dimethyl terephthalate (DMT) > Liver esterase > DMI > MMI > monomethyl terephthalate (MMT), indicating that higher K _m values were obtained by di-esters than mono-ester and the esters induced by terephthalate esters showed the highest activity. This investigation suggests that biochemical pathways for phthalate esters share many common characteristics and the esterases induced by different substrates are highly specific.     

Microbial Degradation of Acetamiprid by Ochrobactrum sp. D-12 Isolated from Contaminated Soil

Neonicotinoid insecticides are one of the most important commercial insecticides used worldwide. The potential toxicity of the residues present in environment to humans has received considerable attention. In this study, a novel Ochrobactrum sp. strain D-12 capable of using acetamiprid as the sole carbon source as well as energy, nitrogen source for growth was isolated and identified from polluted agricultural soil. Strain D-12 was able to completely degrade acetamiprid with initial concentrations of 0–3000 mg·L⁻¹ within 48 h. Haldane inhibition model was used to fit the special degradation rate at different initial concentrations, and the parameters q _max, K _s and K _i were determined to be 0.6394 (6 h)⁻¹, 50.96 mg·L⁻¹ and 1879 mg·L⁻¹, respectively. The strain was found highly effective in degrading acetamiprid over a wide range of temperatures (25–35°C) and pH (6–8). The effects of co-substrates on the degradation efficiency of acetamiprid were investigated. The results indicated that exogenously supplied glucose and ammonium chloride could slightly enhance the biodegradation efficiency, but even more addition of glucose or ammonium chloride delayed the biodegradation. In addition, one metabolic intermediate identified as N-methyl-(6-chloro-3-pyridyl)methylamine formed during the degradation of acetamiprid mediated by strain D-12 was captured by LC-MS, allowing a degradation pathway for acetamiprid to be proposed. This study suggests the bacterium could be a promising candidate for remediation of environments affected by acetamiprid.     

Biodegradation of Benazolin-Ethyl by Strain Methyloversatilis sp. cd-1 Isolated from Activated Sludge

Benazolin-ethyl has been used on a wide range of weeds present in various crops since 1964. Because benazolin-ethyl is a potential hazard to the environment and human health, it is important to remove this herbicide from the environment. However, to the best of our knowledge, no report is available in the literature regarding the microbial degradation of benazolin-ethyl by bacteria. In this study, one strain named cd-1, which is capable of degrading benazolin-ethyl, was isolated from benazolin-ethyl wastewater treatment pool. The isolate was identified as Methyloversatilis sp. according to its morphological, physiological, biochemical properties, and 16S rRNA gene sequences analysis. This strain utilizes benazolin-ethyl as the sole carbon source. and degrades 100?mg?l^?1 benazolin-ethyl to non-detectable level within 48?h. Three metabolites were identified as benazolin, 7-chloro-3-methylbenzo[d]thiazol-2(3H)-one, and 2-chloro-6-(methyleneamino)benzenethiol based on the MS/MS and GC/MS analyses. The first step involved in the degradation of benazolin-ethyl was the cleavage of the ester bond to form benazolin. Benazolin was subsequently subjected to demethylation for decomposition into 7-chloro-3-methylbenzo[d]thiazol-2(3H)-one and methanol. The last step was to form 2-chloro-6-(methyleneamino)benzenethiol.     

Poly(Aspartic Acid) Degradation by a Sphingomonas sp. Isolated from Freshwater

A poly(aspartic acid) degrading bacterium (strain KT-1 [JCM10459]) was isolated from river water and identified as a member of the genus Sphingomonas. The isolate degraded only poly(aspartic acid)s of low molecular masses (<5 kDa), while the cell extract hydrolyzed high-molecular-mass poly(aspartic acid)s of 5 to 150 kDa to yield aspartic acid monomer.     

Aerobic Degradation of 3-Methylindole by Pseudomonas aeruginosa Gs Isolated from Mangrove Sediment

3-Methylindole (3MI), an N-heterocyclic aromatic compound also called skatole, is associated with animal waste and industrial processing. A pure culture of bacterium capable of using 3MI as the sole source of carbon and energy was isolated from mangrove sediment using an enrichment technique and identified as Pseudomonas aeruginosa Gs based on 16S rDNA sequence. Microbial degradation of 3MI was studied in batch culture experiments for several factors, including initial substrate concentrations, pH, and salinity. The optimum pH and salinity was 7.0 and 5‰, respectively. Degradation of 3MI by P. aeruginosa Gs was quantified by reversed-phase high-performance liquid chromatography. Two metabolites of 3MI degradation were detected and proposed to be indoline-3-carboxylic acid and indoline-3-ol based on data obtained from HPLC/MS. Our results suggest that 3MI can be rapidly degraded by indigenous microorganisms found in mangrove sediment.     

Degradation of Fumonisin B1 by a Bacterial Strain Isolated from Soil

A mixed microbial culture degrading fumonisin B l was obtained from soil samples using an enrichment culture procedure. A bacterial isolate from the enrichment culture (strain NCB 1492) degraded fumonisin B1 after incubation for 3 h, as indicated by TLC and HPLC analysis. On the basis of the sequence analysis of 16S rDNA, strain NCB 1492 was related to the Delftia/Comamonas group. Thin-layer chromatographic analysis indicated the presence of metabolites in the NCB 1492 culture filtrates after degradation of fumonisin B1 supplied as sole carbon and nitrogen source in phosphate buffer. Four metabolites were identified by mass spectrometry analysis.     

Degradation of Polycarbonate by a Polyester-Degrading Strain, Amycolatopsis sp. Strain HT-6

Amycolatopsis sp. strain HT-6, a poly(tetramethylene succinate) (PTMS)-degrading actinomycete, was observed to degrade poly(tetramethylene carbonate) (PTMC). In a liquid culture with 150 mg of PTMC film, 59% degradation was achieved, but with a low yield of cell growth. On the other hand, PTMS copolymerized with a small amount of PTMC, forming a copolyester carbonate (PEC) that was completely and rapidly degraded with a high yield of cell growth.     

Degradation of 2-Methylnaphthalene by Pseudomonas sp. Strain NGK1

Pseudomonas sp. strain NGK1, a soil bacterium isolated by naphthalene enrichment from biological waste effluent treatment, capable of utilizing 2-methylnaphthalene as sole source of carbon and energy. To deduce the pathway for biodegradation of 2-methylnaphthalene, metabolites were isolated from the spent medium and identified by thin-layer chromatography and high-performance liquid chromatography. The characterization of purified metabolites, oxygen uptake studies, and enzyme activities revealed that the strain degrades 2-methylnaphthalene through more than one pathway. The growth of the bacterium, utilization of 2-methylnaphthalene, and 4-methylsalicylate accumulation by Pseudomonas sp. strain NGK1 were studied at various incubation periods. Received: 20 March 2001 / Accepted: 25 April 2001     

Janibacter corallicola sp. nov., isolated from coral in Palau

A novel Janibacter species is described on the basis of phenotypic, chemotaxonomic and genotypic data. Two bacterial strains were isolated in Palau, which were both Gram-positive, catalase-positive bacteria with meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. The major menaquinone was MK-8(H(4)). Mycolic acids were not detected. The G+C content of the DNA was 70-71 mol%. Comparative 16S rDNA studies of the two isolated strains revealed that they both belonged to the genus Janibacter. DNA-DNA relatedness data revealed that 04PA2-Co5-61(T) and 02PA-Ca-009 belong to the same species, a new species of the genus Janibacter. From these results, Janibacter corallicola sp. nov. is proposed, with the type strain 04PA2-Co5-61(T) (=MBIC 08265(T), DSM 18906(T)).