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Unrooted phylogenetic tree showing the relationships between strain YT and representative species in the genus Sphingomonas sensu stricto and related genera. The sequence of Escherichia coli 16S rDNA was used as the outgroup. The analysis included a region corresponding to E. coli positions 37 to 1320. The accession numbers for sequences obtained from the EMBL/GenBank databases are as follows: Blastomonas natatoria, AB024288; E. coli, J01859; Novosphingobium capsulatum, D84532; Sphingobium agrestis, Y12803; Sphingobium chlorophenolicum, X87162; Sphingobium yanoikuyae, D16145; Sphingomonas adhaesiva, D84527; Sphingomonas asaccharolytica, Y09639; Sphingomonas cloacea, AB040739; Sphingomonas capsulatum, D84532; Sphingomonas parapaucimobilis, D84525; Sphingomonas paucimobilis, D84528; Sphingomonas pruni, Y09637; Sphingopyxis macrogoltabida, D84530; Sphnigopyxis terrae, D84531. Bar=0.05 nucleotide substitution rate (Knuc) units.
Source publication
A conventional enrichment culture on branched nonylphenol (NP) with diluted nutrient broth as an additional source of organic nutrients yielded a bacterial strain able to degrade branched NP. The isolate (designated YT) was identified as Sphingomonas sp. based on an analysis of its 16S ribosomal RNA genes and cellular lipids. The degradation of NP...
Context in source publication
Context 1
... 125 isolates from our enrichment culture on NB/ 100 medium with 20 ppm of NP, only one was found to de- grade NP. This isolate designated YT was a gram-negative, yellow-pigmented, rod-shaped bacterium. It contained ubiquinone with 10 isoprene units (Q-10). The 16S rRNA sequence of strain YT was determined and then a sequence similarity search in the EMBL/GenBank databases was per- formed. The highest scores were from species in the genus Sphingomonas 35) and related genera (Fig. 2). The closest known relative of the bacterium was Sphingobium yanoikuyae (formerly Sphingomonas yanoikuyae 29) ) (acces- sion no. X85023) with a 16S rRNA similarity value of 98.0%. The 16S rDNA sequence similarity of strain YT with that of the recently described NP-degrading Sphin-gomonas cloacae was 97.8%. Because the genus Sphin- gomonas is characterized by the presence of sphingo- glycolipid 35) , the cellular lipid profile of strain YT was determined. As shown in Fig. 3, TLC of mild alkaline hydrolysates of extractable cellular lipids of strain YT gave a major spot of alkaline-stable glycolipid with an R f value of 0.41 which corresponds to the sphingoglycolipid of the type strain, S. paucimobilis JCM 7515. Although further studies are needed to clarify the taxon, strain YT was assigned to the genus Sphingomonas sensu ...
Citations
... This alcohol is then oxidized to carboxylic acid and finally metabolized by b-oxidation (Vallini et al., 2001a). In the case of an extensively branched alkyl chain, the degradation of NP isomer proceeds through aromatic ring fission (De Vries et al., 2001). The biodegradation rate of NP isomers is also affected by the nature of a-substituent . ...
Nonylphenol (NP) is considered a potential endocrine-disrupting chemical affecting humans and the environment. Due to widespread occurrence in the aquatic environment and neuro-, immuno, reproductive, and estrogenic effects, nonylphenol calls for considerable attention from the scientific community, researchers, government officials, and the public. It can persist in the environment, especially soil, for a long duration because of its high hydrophobic nature. Nonylphenol is incorporated into the water matrices via agricultural run-off, wastewater effluents, agricultural sources, and groundwater leakage from the soil. In this regard, assessment of the source, fate, toxic effect, and removal of nonylphenol seems a high-priority concern. Remediation of nonylphenol is possible through physicochemical and microbial methods. Microbial methods are widely used due to ecofriendly in nature. The microbial strains of the genera, Sphingomonas, Sphingobium, Pseudomonas, Pseudoxanthomonas, Thauera, Novosphingonium, Bacillus, Stenotrophomonas, Clostridium, Arthrobacter, Acidovorax, Maricurvus, Rhizobium, Corynebacterium, Rhodococcus, Burkholderia, Acinetobacter, Aspergillus, Pleurotus, Trametes, Clavariopsis, Candida, Phanerochaete, Bjerkandera, Mucor, Fusarium and Metarhizium have been reported for their potential role in the degradation of NP via its metabolic pathway. This study outlines the recent information on the occurrence, origin, and potential ecological and human-related risks of nonylphenol. The current development in the removal of nonylphenol from the environment using different methods is discussed. Despite the significant importance of nonylphenol and its effects on the environment, the number of studies in this area is limited. This review gives an in-depth understanding of NP occurrence, fate, toxicity, and remediation from the environments.
... TTNP3. Following that study, several BNP-degrading bacteria were isolated, most of which were characterized phylogenetically as members of the Sphingomonas/Sphingobium group: Sphingobium cloacae S-3 T (=JCM 10874 T ) (7), Sphingobium amiense YT T (=DSM 16289 T ) (6,34), Sphingobium xenophagum Bayram (8), and Sphingomonas sp. NP5 (31). ...
Branched nonylphenol (BNP), a degradation product of nonylphenol polyethoxylates, exerts estrogenic effects on various organisms. The genes underlying BNP degradation by Sphingobium amiense DSM 16289T were analyzed by complete genome sequencing and compared with those of the versatile BNP-degrading Sphingobium cloacae JCM 10874T. An opdA homolog (opdADSM16289) encoding BNP degradation activity was identified in DSM 16289T, in contrast with JCM 10874T, possessing both the opdA homolog and nmoA. The degradation profile of different BNP isomers was examined by Escherichia coli transformants harboring opdADSM16289, opdAJCM10874, and nmoAJCM10874 to characterize and compare the expression activities of these genes.
... Taken together, the aforementioned results suggested that the optimum condition for 4-tert-OP degradation by the strain RRKY5 was 30°C, pH 5.0 and an initial 4-tert-OP concentration of 30 mg L À1 . Notably, earlier studies reported that the growth and degradation of long-branched chain APs by bacteria was mainly dependent on the amount of additional organic substrates such as yeast extract in the medium (De Vries et al., 2001). With regard to environmental parameters such as pH and temperature, most of the reported bacterial strains degraded long-chain APs only at neutral pH and temperature above 28°C (Corvini et al., 2006), whereas the degradation of APs under other conditions has not been studied. ...
4-(1, 1, 3, 3-tetramethylbutane)-phenol (4-tert-OP) is one of the most prevalent endocrine disrupting pollutants. Information about bioremediation of 4-tert-OP remains limited, and no study has been reported on the mechanism of 4-tert-OP degradation by yeasts. The yeast Candida rugopelliculosa RRKY5 was proved to be able to utilize 4-methylphenol, bisphenol A, 4-ethylphenol, 4-tert-butylphenol, 4-tert-OP, 4-tert-nonylphenol, isooctane, and phenol under aerobic conditions. The optimum conditions for 4-tert-OP degradation were 30 °C, pH 5.0, and an initial 4-tert-OP concentration of 30 mg L⁻¹; the maximum biodegradation rate constant was 0.107 d⁻¹, equivalent to a minimum half-life of 9.6 d. Scanning electron microscopy revealed formation of arthroconidia when cells were grown in the presence of 4-tert-OP, whereas the cells remained in the budding form without 4-tert-OP. Identification of the 4-tert-OP degradation metabolites using liquid chromatography-hybrid mass spectrometry revealed three different mechanisms via both branched alkyl side chain and aromatic ring cleavage pathways.
... The quaternary α-carbon atom on the branched alkyl chain prevents these compounds from microbial ωand βoxidation and therefore bNP are highly persistent in the environment. Only a few organisms mainly belonging to the genera Sphingomonas, Sphingobium and Pseudomonas are able to use bNP as sole source of carbon and energy (Corvini et al. 2004;deVries et al. 2001;Kolvenbach and Corvini 2012;Tanghe et al. 1999). All these organisms refer to gramnegative bacteria and degrade bNP by ipso-hydroxylation and 1,2-C,O shift. ...
The compound p-tert-amylphenol (p-(1,1-dimethylpropyl)phenol) is a widely used disinfectant belonging to the group of short branched-chain alkylphenols. It is produced in or imported into the USA with more than one million pounds per year and can be found in the environment in surface water, sediments, and soil. We have investigated for the first time the biotransformation of this disinfectant and the accumulation of metabolites by five bacterial strains, three yeast strains, and three filamentous fungi, selected because of their ability to transform either aromatic or branched-chain compounds. Of the 11 microorganisms tested, one yeast strain and three bacteria could not transform the disinfectant despite of a very low concentration applied (0.005 %). None of the other seven organisms was able to degrade the short branched alkyl chain of p-tert-amylphenol. However, two yeast strains, two filamentous fungi, and two bacterial strains attacked the aromatic ring system of the disinfectant via the hydroxylated intermediate 4-(1,1-dimethyl-propyl)-benzene-1,2-diol resulting in two hitherto unknown ring fission products with pyran and furan structures, 4-(1,1-dimethyl-propyl)-6-oxo-6-H-pyran-2-carboxylic acid and 2-[3-(1,1-dimethyl-propyl)-5-oxo-2H-furan-2-yl]acetic acid. While the disinfectant was toxic to the organisms applied, one of the ring cleavage products was not. Thus, a detoxification of the disinfectant was achieved by ring cleavage. Furthermore, one filamentous fungus formed sugar conjugates with p-tert-amylphenol as another mechanism of detoxification of toxic environmental pollutants. With this work, we can also contribute to the allocation of unknown chemical compounds within environmental samples to their parent compounds.
... NP degradation by pure cultures has also been studied to understand its biodegradation mechanisms. An NP-degrading yeast, Candida aquaetextoris (formerly Candida maltosa) LMAR 1 (Corti et al., 1995;Vallini et al., 1997), NP-degrading aquatic fungi with laccases (Junghanns et al., 2005) and several NP-degrading bacterial strains belonging to the sphingomonads (de Vries et al., 2001;Fujii et al., 2000Fujii et al., , 2001Gabriel et al., 2005a;Tanghe et al., 1999;Ushiba et al., 2003) have been isolated and characterized. Intensive studies on the NP degradation pathways of Sphingomonas sp. ...
Sphingomonas sp. NP5 can degrade a wide range of nonylphenol (NP) isomers that have widely contaminated aquatic environments as major endocrine-disrupting chemicals. To understand the biochemical and genetic backgrounds of NP degradation, a gene library of strain NP5 was constructed using a broad-host-range vector pBBR1MCS-2 and introduced into Sphingobium japonicum UT26. Several transformants accumulated reddish brown metabolites on agar plates dispersed with a mixture of NP isomers. Two different DNA fragments (7.6 and 9.3 kb) involved in the phenotype were isolated from the transformants. Sequence analysis revealed that both fragments contained an identical 1593 bp monooxygenase gene (nmoA), the predicted protein sequence of which showed 83 % identity to the octylphenol-4-monooxygenase of Sphingomonas sp. PWE1. The nmoA gene in the 7.6 kb fragment was surrounded by an IS21-type insertion sequence (IS) and IS6100, while another in the 9.3 kb fragment was adjacent to an IS66-type IS, suggesting that they have been acquired through multiple transposition events. A fast-growing recombinant Pseudomonas putida strain harbouring nmoA was constructed and used for degradation of a chemically synthesized NP isomer, 4-(1-ethyl-1-methylhexyl)phenol. This strain converted the isomer into hydroquinone stoichiometrically. 3-Methyl-3-octanol, probably originating from the alkyl side chain, was also detected as the metabolite. These results indicate that these two nmoA genes are involved in the NP degradation ability of strain NP5.
... Stenotrophomonas sp. and Pseudomonas mandelii are isolated from polluted soils ( Soares et al. 2003) and Sphingobium amiense, formerly known as Sphingomonas sp. YT (de Vries et al. 2001;Ushiba et al. 2003), from sediment. Most isolates are able to use NP as a sole carbon and energy source ( Tanghe et al. 1999;Soares et al. 2003;Gabriel et al. 2005a), whereas some strains can only degrade NP cometabolically in the presence of yeast extract as carbon and energy source like S. amiense (de Vries et al. 2001). ...
... YT (de Vries et al. 2001;Ushiba et al. 2003), from sediment. Most isolates are able to use NP as a sole carbon and energy source ( Tanghe et al. 1999;Soares et al. 2003;Gabriel et al. 2005a), whereas some strains can only degrade NP cometabolically in the presence of yeast extract as carbon and energy source like S. amiense (de Vries et al. 2001). ...
Nonylphenol (NP) is an estrogenic pollutant which is widely present in the aquatic environment. Biodegradation of NP can reduce the toxicological risk. In this study, aerobic biodegradation of NP in river sediment was investigated. The sediment used for the microcosm experiments was aged polluted with NP. The biodegradation of NP in the sediment occurred within 8 days with a lag phase of 2 days at 30 degrees C. During the biodegradation, nitro-nonylphenol metabolites were formed, which were further degraded to unknown compounds. The attached nitro-group originated from the ammonium in the medium. Five subsequent transfers were performed from original sediment and yielded a final stable population. In this NP-degrading culture, the microorganisms possibly involved in the biotransformation of NP to nitro-nonylphenol were related to ammonium-oxidizing bacteria. Besides the degradation of NP via nitro-nonylphenol, bacteria related to phenol-degrading species, which degrade phenol via ring cleavage, are abundantly present.
... The presence of NP in soil originates from different non-point sources such as atmospheric deposition, application of sewage sludge and the use of plant protection agents [68] . Only a few pure cultures of aerobic bacteria69707172, one yeast [73] and anaerobic microorganisms [74, 75] have been described to be able to use NP as the sole source of carbon and energy. The sorption to sludges of NP isomers due to their high hydrophobicity (log K ow = 4.48) is the main route of removal of these xenobiotics from wastewaters [62] but it leads to a mere transfer of this type of pollutant to another environmental matrix and not to a destruction or transformation of the substance . ...
The ability of white rot fungi (WRF) and their lignin modifying enzymes (LMEs), i.e. laccase and lignin- and manganese-dependent peroxidase, to treat endocrine disrupting chemicals (EDCs) is extensively reviewed in this paper. These chemicals cause adverse health effects by mimicking endogenous hormones in receiving organisms. The alkylphenolic EDCs nonylphenol, bisphenol A and triclosan, the phthalic acid esters dibutylphthalate, diethylphthalate and di-(2-ethylhexyl)phthalate, the natural estrogens estrone, 17β-estradiol, estriol and 17α-ethynylestradiol and the phytoestrogens genistein and β-sitosterol have been shown to be eliminated by several fungi and LMEs. WRF have manifested a highly efficient removal of EDCs in aqueous media and soil matrices using both LME and non LME-systems. The ligninolytic system of WRF could also be used for the elimination of several EDCs and the associated hormone-mimicking activity. The transformation of EDCs by LMEs and WRF is supported by emerging knowledge on the physiology and biochemistry of these organisms and the biocatalytic properties of their enzymes. Due to field reaction conditions, which drastically differ from laboratory conditions, further efforts will have to be directed towards developing robust and reliable biotechnological processes for the treatment of EDC-contaminated environmental matrices.
... Except for a study reporting the degradation of tNP into 4-nonyl-2-nitrophenol in mixtures of sandy loam soil/ sludge, almost no information exists concerning the degradation pathways of NP in environmental samples (Telscher et al., 2005), while metabolism of NP by axenic cultures of bacteria has been well documented. Several bacterial strains of the genera Sphingomonas, Sphingobium and Pseudomonas are able to degrade branched isomers of NP (Tanghe et al., 1999;de Vries et al., 2001;Fujii et al., 2001;Soares et al., 2003;Ushiba et al., 2003;Gabriel et al., 2005a,b). NP-degradation pathways in Sphingomonads presents similarities, i.e. the corresponding alcohols of the alkyl side-chains of NP (nonanols) are metabolites produced by these bacteria (Fujii et al., 2000;Tanghe et al., 2000;Gabriel et al., 2005a,b). ...
This study shows the important role of humic acids in the degradation of (14)C and (13)C labeled isomer of NP by Sphingomonas sp. strain TTNP3 and the detoxification of the resulting metabolites. Due to the association of NP with humic acids, its solubility in the medium was enhanced and the extent of mineralization of nonylphenol increased from 20% to above 35%. This was accompanied by the formation of significant amounts of NP residues bound to the humic acids, which also occurred via abiotic reactions of the major NP metabolite hydroquinone with the humic acids. Gel permeation chromatography showed a non-homogenous distribution of NP residues with humic acids molecules, with preference towards molecules with high-molecular-weight. Solid state (13)C nuclear magnetic resonance spectroscopy indicated that the nonextractable residues resulted exclusively from the metabolites. The chemical shifts of the labeled carbon indicated the possible covalent binding of hydroquinone to the humic acids via ester and possibly ether bonds, and the incorporation of degradation products of hydroquinone into the humic acids. This study provided evidences for the mediatory role of humic acids in the fate of NP as a sink for bacterial degradation intermediates of this compound.
... NP and OP degradation were initially thought to occur through ring hydroxylation adjacent to the phenolic hydroxyl group (7,35), as was shown for the degradation of 3-and 4-n-alkylphenols, yielding catecholic intermediates with subsequent meta cleavage (19). More recently, Corvini et al. (6) showed that degradation of alkylphenols with branched side chains occurs via oxidation at the quaternary alpha carbon in NP isomers p353NP and p262NP in Sphingomonas sp. ...
... This may have been due to the significantly lower concentration of OP used in those assays than in the wild-type-PWE1 experiments. Others have shown that similar NP metabolites accumulate in culture supernatants and do not undergo further metabolism (6,7,16). It is also possible that some of the HQ produced in E. coli was further transformed to alleviate toxicity or may have polymerized and was therefore not detected using our methods. ...
Octylphenol (OP) is an estrogenic detergent breakdown product. Structurally similar nonylphenols are transformed via type
II ispo substitution, resulting in the production of hydroquinone and removal of the branched side chain. Nothing is known, however,
about the gene(s) encoding this activity. We report here on our efforts to clone the gene(s) encoding OP degradation activity
from Sphingomonas sp. strain PWE1, which we isolated for its ability to grow on OP. A fosmid library of PWE1 DNA yielded a single clone, aew4H12,
which accumulated a brown polymerization product in the presence of OP. Sequence analysis of loss-of-function transposon mutants
of aew4H12 revealed a single open reading frame, opdA, that conferred OP degradation activity. Escherichia coli subclones expressing opdA caused OP disappearance, with the concomitant production of hydroquinone and 2,4,4-trimethyl-1-pentene as well as small amounts
of 2,4,4-trimethyl-2-pentanol. These metabolites are consistent with a type II ipso substitution reaction, the same mechanism described for nonylphenol biodegradation in other sphingomonads. Based on opdA's sequence homology to a unique group of putative flavin monooxygenases and the recovery of hydroxylated OP intermediates
from E. coli expressing opdA, we conclude that this gene encodes the observed type II ipso substitution activity responsible for the initial step in OP biodegradation.
... Beyond a report on metabolites that were possibly hydroxylated at the ring in S. amiense (de Vries et al. 2001), the decisive step in the elucidation of NP metabolism was achieved with Sphingomonas sp. TTNP3 and 4-[1-ethyl-1,3-dimethylpentyl]phenol. ...
... Position and length of alkyl chain As described for cresols and other short-chain AP, the position of substitution of the phenol ring by the nonyl chain seems to be decisive with regard to the degradation of NP by sphingomonads. S. amiense displayed a marked preference for p-NP isomers (de Vries et al. 2001). In the case of Sphingomonas sp. ...
... Particularly interesting is the apparent constitutive expression of this NP-degrading activity in Sphingomonas sp. TTNP3 and S. amiense (de Vries et al. 2001;Corvini et al. 2006a). Resting cells of both strains are able to directly and rapidly degrade NP without having been precultivated with NP. ...
Because the endocrine disrupting effects of nonylphenol (NP) and octylphenol became evident, the degradation of long-chain alkylphenols (AP) by microorganisms was intensively studied. Most NP-degrading bacteria belong to the sphingomonads and closely related genera, while NP metabolism is not restricted to defined fungal taxa. Growth on NP and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. While both bacterial and fungal degradation of short-chain AP, such as cresols, and the bacterial degradation of long-chain branched AP involves aromatic ring hydroxylation, alkyl chain oxidation and the formation of phenolic polymers seem to be preferential elimination pathways of long-chain branched AP in fungi, whereby both intracellular and extracellular oxidative enzymes may be involved. The degradation of NP by sphingomonads does not proceed via the common degradation mechanisms reported for short-chain AP, rather, via an unusual ipso-substitution mechanism. This fact underlies the peculiarity of long-chain AP such as NP isomers, which possess highly branched alkyl groups mostly containing a quaternary alpha-carbon. In addition to physicochemical parameters influencing degradation rates, this structural characteristic confers to branched isomers of NP a biodegradability different to that of the widely used linear isomer of NP. Potential biotechnological applications for the removal of AP from contaminated media and the difficulties of analysis and application inherent to the hydrophobic NP, in particular, are also discussed. The combination of bacteria and fungi, attacking NP at both the phenolic and alkylic moiety, represents a promising perspective.
