Effect of slow desorption on the kinetics of biodegradation of polycyclic aromatic hydrocarbons

The bioavailability to bacteria of 14C-labeled polycyclic aromatic hydrocarbons (PAHs) sorbed onto lake sediments was assessed using a mathematical model and three experimental series. The experiments were performed under similar conditions and included: (1) abiotic desorption of PAHs from sediments by Tenax extraction, (2) mineralization of dissolved PAHs with no sediment present, and (3) mineralization of PAHs sorbed onto sediments. Results obtained from the first two series were used to obtain the parameter values for the model, and the experimental results of the third series were compared to model results. We found that microorganisms were able to promote desorption of the more-labile fractions, but were unable to increase the desorption rate of the slow- and very slow-desorbing fractions. Also, our model predictions indicate that, after very long contact times, and in the concurrence of biodegradation, sorbed PAHs remain not under equilibrium conditions, but rather in a steady state. The net rates of PAH desorption from the three sediment domains considered (fast, slow, and very slow) become similar, and the ratio between the aqueous and the sediment concentration remains constant with time.

Isolation and characterization of phenanthrene-degrading Sphingomonas paucimobilis strain ZX4

Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonas paucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2,3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type metapathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.

16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains

Hexachlorocyclohexane (HCH) is a highly recalcitrant pesticide that persists in soils. Three novel HCH-degrading strains (DS2, DS2-2 and DS3-1) were isolated after enrichment from HCH-contaminated soil from Germany. These strains efficiently degraded the alpha-, gamma- and delta-isomers of HCH, while strain DS3-1 also degraded beta-HCH. Based on 16S rDNA analysis, strain DS3-1 was closely related to Sphingomonas taejonensis, while strains DS2 and DS2-2 were closely related to Sphingomonas flava and seven HCH-degrading strains recently isolated from HCH-contaminated Spanish soil. Hence, geographic origin of the strains was not reflected in their phylogenetic affiliation. Subsequently, lin genes involved in HCH degradation, virtually identical to those from Sphingomonas paucimobilis strains UT26 from Japan and B90A from India, were identified in strains DS3-1, DS2, DS2-2 and five of the strains from Spain. The conserved lin gene sequences and structural organization, as well as the close association with IS6100, suggest a shared lin gene origin and recent horizontal gene transfer among phylogenetically diverged Sphingomonas strains in remote geographic locations. The loss of the ability to degrade gamma-HCH was associated with the deletion of the linA gene, probably due to recombination involving IS6100 elements, of which several copies are located in the lin cluster region.

Biodegradation of bisphenol A by cells and cell lysate from Sphingomonas sp. strain AO1

The capacity and pathway of bisphenol A [BPA; 2,2-bis(4-hydroxyphenyl)propane] degradation in Sphingomonas sp. strain AO1, which was isolated from the soil of a vegetable-growing field in Japan, were investigated. The bacterial strain was able to grow in a basal mineral salt medium containing BPA as the sole carbon source (BSMB medium), and was able to degrade 115 microg ml(-1) BPA in 6 h in L medium. Several BPA metabolites were detected in the culture supernatant by HPLC and then identified by GC-MS and LC-MS-MS. These compounds were confirmed to be the same as those reported for other BPA-degrading bacteria. BPA degradation by cells in the basal mineral salt medium was induced by BPA, and activity was detected only in the intracellular soluble fraction in the presence of coenzymes, such as NADH, NAD+, NADPH or NADP+. The addition of metyrapone, a cytochrome P450 inhibitor, to BSMB medium resulted in a decrease in BPA degradation and cell growth. The BPA-degradation activity of the intracellular soluble fraction was also inhibited by the cytochrome P450 inhibitor. Carbon monoxide difference spectra indicated that cytochrome P450 was present in the cells and that the amount of cytochrome P450 corresponded to the cellular BPA-degradation activity. Our results provide evidence that the cytochrome P450 system is involved in BPA metabolism in Sphingomonas sp. strain AO1.

Microbial community dynamics in bioaugmented sequencing batch reactors for bromoamine acid removal

Sphingomonas xenophaga QYY with the ability to degrade bromoamine acid (BAA) was previously isolated from sludge samples. The enhancement of BAA removal by strain QYY in sequencing batch reactors (SBRs) was investigated in this study. The results showed that augmented SBRs exhibited stronger abilities to degrade BAA than the non-augmented control one. In order to estimate the relationship between community dynamics and function of augmented SBRs, a combined method based on fingerprints (ribosomal intergenic spacer analysis, RISA) and 16S rRNA gene sequencing was used. The results indicated that the microbial community dynamics were substantially changed, and the introduced strain QYY was persistent in the augmented systems. This study suggests that it is feasible and potentially useful to enhance BAA removal using BAA-degrading bacteria, such as S. xenophaga QYY.

Isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source

A bacterial strain able to grow in pure culture with chrysene as sole added carbon and energy source was isolated from PAH-contaminated soil after successive enrichment cultures in a biphasic growth medium. Initially, growth occurred in the form of a biofilm at the interface between the aqueous and non-aqueous liquid phases. However, after a certain time, a transition occurred in the enrichment cultures, with growth occurring in suspension and a concomitant increase in the rate of chrysene degradation. The strain responsible for chrysene degradation in these cultures, named Sphingomonas sp. CHY-1, was identified by 16S rDNA sequencing as a novel sphingomonad, the closest relative in the databases being Sphingomonas xenophaga BN6T (96% sequence identity). Both these strains clustered with members of the genera Sphingobium and Rhizomonas, but could not be categorically assigned to either genus. Sphingomonas sp. CHY-1 was characterized in terms of its growth on chrysene and other PAH, and the kinetics of chrysene degradation and 14C-chrysene mineralization were measured. At an initial chrysene concentration of 0.5 g l(-1) silicone oil, and an organic/aqueous phase ratio of 1:4, chrysene was 50% degraded after 5 days incubation and 97.5% degraded after 35 days. The protein content of cultures reached a maximum value of 11.5 microg ml(-1) aqueous phase, corresponding to 92 mg g(-1) chrysene. 14C-labelled chrysene was 50% mineralized after 6-8 weeks incubation, 10.7% of the radioactivity was incorporated into cell biomass and 8.4% was found in the aqueous culture supernatant. Sphingomonas sp. CHY-1 also grew on naphthalene, phenanthrene and anthracene, and naphthalene was the preferred substrate, with a doubling time of 6.9 h.

[Oligotrophic bacteria and their applications in environmental science]

Oligotrophic bacteria are a group of microbes living in oligotrophic environments. Their diversity and biomass are dominant in biosphere, and thus, play an important role in biogeochemical cycles. Since 1980s, their oligotrophic mechanisms, responses to starvation, and roles in ecosystems have been one of the most advanced subjects in microbial ecological research. Much attention has been paid to the theoretical values and applied perspectives of oligotrophic bacteria. This paper reviewed the concepts, nutritional types, physiological and ecological characteristics, possible oligotrophic mechanisms, and main research methods of oligotrophic bacteria, and their applications in bacteria examination of iatrology and in environmental monitoring for heavy metals. The applied perspectives of oligotrophic bacteria in environmental science were also discussed.

Degradation of a nonylphenol single isomer by Sphingomonas sp. strain TTNP3 leads to a hydroxylation-induced migration product

Sphingomonas sp. strain TTNP3 degrades 4(3',5'-dimethyl-3'-heptyl)-phenol and unidentified metabolites that were described previously. The chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3',5'-dimethyl-3'-heptyl)-1,4-benzenediol. This finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an NIH shift mechanism occurs.

Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a sphingomonas strain that degrades various polycyclic aromatic hydrocarbons

In this study, the enzymes involved in polycyclic aromatic hydrocarbon (PAH) degradation in the chrysene-degrading organism Sphingomonas sp. strain CHY-1 were investigated. [14C]chrysene mineralization experiments showed that PAH-grown bacteria produced high levels of chrysene-catabolic activity. One PAH-induced protein displayed similarity with a ring-hydroxylating dioxygenase beta subunit, and a second PAH-induced protein displayed similarity with an extradiol dioxygenase. The genes encoding these proteins were cloned, and sequence analysis revealed two distinct loci containing clustered catabolic genes with strong similarities to corresponding genes found in Novosphingobium aromaticivorans F199. In the first locus, two genes potentially encoding a terminal dioxygenase component, designated PhnI, were followed by a gene coding for an aryl alcohol dehydrogenase (phnB). The second locus contained five genes encoding an extradiol dioxygenase (phnC), a ferredoxin (phnA3), another oxygenase component (PhnII), and an isomerase (phnD). PhnI was found to be capable of converting several PAHs, including chrysene, to the corresponding dihydrodiols. The activity of PhnI was greatly enhanced upon coexpression of genes encoding a ferredoxin (phnA3) and a reductase (phnA4). Disruption of the phnA1a gene encoding the PhnI alpha subunit resulted in a mutant strain that had lost the ability to grow on PAHs. The recombinant PhnII enzyme overproduced in Escherichia coli functioned as a salicylate 1-hydroxylase. PhnII also used methylsalicylates and anthranilate as substrates. Our results indicated that a single enzyme (PhnI) was responsible for the initial attack of a range of PAHs, including chrysene, in strain CHY-1. Furthermore, the conversion of salicylate to catechol was catalyzed by a three-component oxygenase unrelated to known salicylate hydroxylases.

Dynamics of multiple lin gene expression in Sphingomonas paucimobilis B90A in response to different hexachlorocyclohexane isomers

Sphingomonas paucimobilis B90A is able to degrade the alpha-, beta-, gamma-, and delta-isomers of hexachlorocyclohexane (HCH). It contains the genes linA, linB, linC, linD, linE, and linR, which have been implicated in HCH degradation. In this study, dynamic expression of the lin genes was measured in chemostat-grown S. paucimobilis B90A by RNA dot blot hybridization and real-time reverse transcriptase PCR upon exposure to a pulse of different HCH isomers. Irrespective of the addition of HCH, linA, linB, and linC were all expressed constitutively. In contrast, linD and linE were induced with alpha-HCH (2 mg/liter) and gamma-HCH (7 mg/liter). A sharp increase in mRNA levels for linD and linE was observed from 10 to 45 min after the addition of alpha- or gamma-HCH. Induction of linD and linE was not detectable upon the addition of 0.7 mg of gamma-HCH per liter, although the compound was degraded by the cells. The addition of beta-HCH (5 mg/liter) or delta-HCH (20 mg/liter) did not lead to linE and linD induction, despite the fact that 50% of the compounds were degraded. This suggests that degradation of beta- and delta-HCH proceeds by a different pathway than that of alpha- and gamma-HCH.

Degradation of anthracene and pyrene supplied by microcrystals and non-aqueous-phase liquids

Polycyclic aromatic hydrocarbons (PAHs) are worldwide environmental pollutants. Their bioavailability is limited by a low aqueous solubility, which causes specific adaptations in degrading bacteria. To compare bacterial degrading behavior, a study was conducted on the mineralization, metabolization and formation of biomass from (14)C-anthracene by Sphingomonas sp. BA2 compared with those from (14)C-pyrene by Gordonia-like strain BP9 and Mycobacterium gilvum VF1. Different conditions of PAH supply were used in the medium: crystals <0.5 mm, microcrystals <<0.1 mm formed by sonication, or PAH solubilized in 2,2,4,4,6,8,8-heptamethylnonane (HMN) or silicone oil. Anthracene supply by crystals and silicone oil led to similar maximum mineralization rates 33 ng ml(-1) h(-1) and the same amount of mineralization (24%) after 168 h. Microcrystals increased the rates and amounts only slightly. HMN decreased the values to less than one-third. In comparison with crystals, microcrystals increased overall pyrene mineralization by strain BP9 from 53% to 58%, with maximum mineralization rates of 160 ng ml(-1) h(-1) and 166 ng ml(-1) h(-1). Silicone oil heavily increased the rate to 292 ng ml(-1) h(-1) and the amount mineralized to 71%, whereas HMN inhibited the degradation by one order of magnitude. A similar degradation behavior showing lower mineralization rates and extent was observed with strain VF1. However, inhibition by HMN was less pronounced. Sonication, leading to decreased PAH crystal size, increased the mass transfer and mineralization rates. PAH supply by silicone oil led to a much higher mass transfer, which may be due to emulsification of the oil, whereas such effects were not observed with HMN.

Streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples

Sphingomonas is an organism of major interest for the degradation of organic contaminants in soils and other environments. A medium based on the aminoglycoside antibiotic streptomycin (Sm) was developed, which, together with the yellow pigmentation of Sphingomonas, facilitated the detection, recovery and quantification of culturable Sphingomonas from soils. All 29 previously described bacterial strains belonging to 17 different Sphingomonas species were able to grow on mineral media containing 200 microg ml(-1) streptomycin, showing that the capacity to resist high concentrations of Sm is a common characteristic within Sphingomonas. Incorporation of Sm into the mineral medium led to a significant reduction in the background microbial population and a concomitant 100 times more sensitive detection of Sphingomonas inoculated in non-sterile soil matrices. The Sm-containing medium was used to examine a variety of hydrocarbon-contaminated soils for the presence and biodiversity of Sphingomonas. Incorporation of Sm in the medium led to a significant increase in the number of yellow-pigmented colonies. Comparison of contaminated and non-contaminated soils derived from the same site revealed colonization by culturable yellow-pigmented Sm-resistant bacteria of the polluted location solely. Both yellow and non-yellow-pigmented colonies were purified from plates containing glucose and Sm, and BOX-polymerase chain reaction (PCR) was used to sort out clonally related strains. Representative strains from the major BOX-PCR clusters were identified using FAME and partial 16S rRNA gene sequencing. Forty-eight of 58 Sm-resistant isolates were identified as Sphingomonas sp. Streptomycin-resistant Sphingomonas isolates generated BOX-PCR diversity patterns that were site dependent and represented different species mainly belonging to Sphingomonas subgroups containing species formerly designated as Sphingopyxis and Sphingobium. The ability to degrade phenanthrene was only found in a minority of the Sphingomonas isolates, which all originated from soils containing high phenanthrene concentrations.

[Ion beam implantation in breeding efficient degradation bacteria]

Sphingomonas sp. AN1 was mutagenized and breeded by N+ implantation, mutants capable of degrading anthrancene was obtained. The research review that the degrading rate increased by 29.3% and 36.2% while the mutagenized rate was 80% - 100% and 60% - 80%. In addition, the maximum concentration of enduring anthracene reached 300mg/L and 400mg/L. Their heritance stability were examined for fifteen transfers. Among these strains, two strains,AN815-3 and AN315-5S,showed predominant character of survival ability and degrading activity. Their rate of degrading anthrancene reached 73% and 75% respectively. Effect of positive mutagenesis is evident.

Phosphonium ionic liquids for degradation of phenol in a two-phase partitioning bioreactor

Six ionic liquids (ILs), which are organic salts that are liquid at room temperature, were tested for their biocompatibility with three xenobiotic-degrading bacteria, Pseudomonas putida, Achromobacter xylosoxidans, and Sphingomonas aromaticivorans. Of the 18 pairings, seven were found to demonstrate biocompatibility, with one IL (trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl) amide) being biocompatible with all three organisms. This IL was then used in a two-phase partitioning bioreactor (TPPB), consisting of 1 l aqueous phase loaded with 1,580 mg phenol and 0.25 l IL, inoculated with the phenol degrader P. putida. This initially toxic aqueous level of phenol was substantially reduced by phenol partitioning into the IL phase, allowing the cells to utilize the reduced phenol concentration. The partitioning of phenol from the IL to the aqueous phase was driven by cellular demand and thermodynamic equilibrium. All of the phenol was consumed at a rate comparable to that of previously used organic-aqueous TPPB systems, demonstrating the first successful use of an IL with a cell-based system. A quantitative (31)P NMR spectroscopic assay for estimating the log P values of ILs is under development.

Cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, Sphingopyxis alaskensis

Sphingopyxis (formerly Sphingomonas) alaskensis is a model bacterium for studying adaptation to oligotrophy (nutrient-limitation). It has a unique physiology which is fundamentally different to that of the well studied bacteria such as Escherichia coli. To begin to identify the genes involved in its physiological responses to nutrient-limited growth and starvation, we developed high resolution two-dimensional electrophoresis (2-DE) methods and determined the identity of 12 proteins from a total of 21 spots using mass spectrometric approaches and cross-species matching. The best matches were to Novosphingobium aromaticivorans; a terrestrial, hydrocarbon degrading bacterium which was previously classified in the genus Sphingomonas. The proteins identified are involved in fundamental cellular processes including protein synthesis, protein folding, energy generation and electron transport. We also compared radiolabelled and silver-stained 2-DE gels generated with the same protein samples and found significant differences in the protein profiles. The use of both methods increased the total number of proteins with differential spot intensities which could be identified from a single protein sample. The ability to effectively utilise cross-species matching from radiolabelled and silver-stained gels provides new approaches for determining the genetic basis of microbial oligotrophy.

Comparison of n-eicosane and phenanthrene removal by pure and mixed cultures of two marine bacteria

The biotransformation activities of two hydrocarbonoclastic marine bacteria, Corynebacterium sp. and Sphingomonas sp. 2MPII, on n-eicosane and phenanthrene were investigated. During a 56-day experiment, in pure and mixed cultures, Corynebacterium sp. and Sphingomonas sp. 2MPII removed about 70% of the initial n-eicosane and phenanthrene concentrations (1 and 0.4 g L(-1), respectively). In pure cultures, culturable cell abundances increased over time, from 0.8 to 8.6 x 10(-11) CFU L(-1) (Corynebacterium sp.) and from 2.1 to 16 x 10(-11) CFU L(-1) (Sphingomonas sp. 2MPII ) but remained barely constant in mixed cultures. We defined a biotransformation index based on the number of culturable cells rather than the culture protein content, with the biotransformation cell yield (BCY) expressed in grams hydrocarbon CFU(-1) per day to better characterize hydrocarbon removal in pure and mixed cultures. The BCY was markedly higher in mixed than in pure cultures, increasing by a factor of 2-10.7 and 2.3-4.7 for n-eicosane and phenanthrene removal, respectively.

Green fluorescent protein as a marker for monitoring a pentachlorophenol degrader Sphingomonas chlorophenolica ATCC39723

Sphingomonas chlorophenolica ATCC39723 was successfully labeled with the gfp (green fluorescent protein) gene inserted into the pcpB gene by homologous recombination. As the gfp recombinant was easily distinguished from other indigenous organisms, the population of gfp recombinant was monitored after being released into the soil microcosms. Their population density dropped from 10(8) to 10(6) (cfu/ml) in the non-sterilized soil microcosms during the first 6 days. Moreover, the gfp recombinant was not detected even at lower dilution rates after a certain time period. The recombinant, however, survived for at least 28 days in the sterilized soil microcosms. Although the gfp recombinant did not degrade pentachlorophenol (PCP), this experiment showed the possibility of using gfp as a monitoring reporter system for S. chlorophenolica ATCC39723 and potentially other species of Sphingomonas.

Requirement of a relatively high threshold level of Mg(2+) for cell growth of a rhizoplane bacterium, Sphingomonas yanoikuyae EC-S001

Mg(2+) is one of the essential elements for bacterial cell growth. The presence of the magnesium cation (Mg(2+)) in various concentrations often affects cell growth restoration in plant-associating bacteria. This study attempted to determine whether Mg(2+) levels in Sphingomonas yanoikuyae EC-S001 affected cell growth restoration in the host plant and what the threshold level is. S. yanoikuyae EC-S001, isolated from the rhizoplane of spinach seedlings grown from surface-sterilized seeds under aseptic conditions, displayed uniform dispersion and attachment throughout the rhizoplane and phylloplane of the host seedlings. S. yanoikuyae EC-S001 did not grow in potato-dextrose broth medium but grew well in an aqueous extract of spinach leaves. Chemical investigation of the growth factor in the spinach leaf extract led to identification of the active principle as the magnesium cation. A concentration of ca. 0.10 mM Mg(2+) or more allowed S. yanoikuyae EC-S001 to grow in potato-dextrose broth medium. Some saprophytic and/or diazotrophic bacteria used in our experiment were found to have diverse threshold levels for their Mg(2+) requirements. For example, Burkholderia cepacia EC-K014, originally isolated from the rhizoplane of a Melastoma sp., could grow even in Mg(2+)-free Hoagland's no. 2 medium with saccharose and glutamine (HSG medium) and requires a trace level of Mg(2+) for its growth. In contrast, S. yanoikuyae EC-S001, together with Bacillus subtilis IFO12113, showed the most drastic restoring responses to subsequent addition of 0.98 mM Mg(2+) to Mg(2+)-free HSG medium. Our studies concluded that Mg(2+) is more than just the essential trace element needed for cell growth restoration in S. yanoikuyae EC-S001 and that certain nonculturable bacteria may require a higher concentration of Mg(2+) or another specific essential element for their growth.

Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6

Sphingomonas paucimobilis SYK-6 is able to grow on various lignin-derived biaryls as the sole source of carbon and energy. These compounds are degraded to vanillate and syringate by the unique and specific enzymes in this strain. Vanillate and syringate are converted to protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively, by the tetrahydrofolate-dependent O-demethylases. Previous studies have suggested that these compounds are further degraded via the PCA 4,5-cleavage pathway. However, our subsequent analysis of the ligB insertion mutant, which encodes the beta subunit of PCA 4,5-dioxygenase, suggested that at least one alternative route is involved in 3MGA degradation. In the present study, we isolated the desZ gene, which confers 3MGA degradation activity on Escherichia coli. The deduced amino acid sequence of desZ showed ca. 20 to 43% identity with the type II extradiol dioxygenases. Gas chromatography-mass spectrometry analysis suggested that DesZ catalyzes the 3,4-cleavage of 3MGA. Disruption of both desZ and ligB in SYK-6 resulted in loss of the dioxygen-dependent 3MGA transformation activity, but the resulting mutant retained the ability to grow on syringate. We found that the cell extract of the desZ ligB double mutant was able to convert 3MGA to gallate when tetrahydrofolate was added to the reaction mixture, and the cell extract of this mutant degraded gallate to the same degree as the wild type did. All these results suggest that syringate is degraded through multiple 3MGA degradation pathways in which ligAB, desZ, 3MGA O-demethylase, and gallate dioxygenase are participants.

Degradation of aromatic hydrocarbons by Sphingomonas paucimobilis strain EPA505

To determine the substrate range capability of Sphingomonas paucimobilis strain EPA505, a number of aromatic compounds were tested as potential growth substrates. Strain EPA505 grew on phenanthrene, naphthalene, fluoranthene, toluene, benzoic acid, 2,3- and 3,4-dihydroxybenzoic acids, 1-chloro-2,4-dinitrobenzene, anthracene, 2-hydroxy-3-naphthoic acid and 1-hydroxy- 2-naphthoic acid, salicylic acid, and catechol. Strain EPA505 was unable to grow on coumarine 3-carboxylic acid, naphthalene dicarboxylic acid, acenaphthene, chrysene, pyrene, benzo[b]fluoranthene, and fluorene. Catabolic products were not detected or identified when the bacterium was incubated with coumarine 3-carboxylic acid, naphthalene dicarboxylic acid, acenaphthene, chrysene, or benzo[b]fluoranthene. Dihydroxypyrene, the ortho ring fission product of pyrene, and 10-hydroxy-1- phenanthroic acid were detected when the bacterium was incubated with pyrene. The open rings of benzo[b]fluoranthene, hydroxyacephenanthroic acid, hydroxyacephenanthrene, and phenanthrene anhydride, catabolites of benzo[b]fluoranthene degradation, were detected with Tn5 mutants of EPA505. With strain EPA505, both 9-fluorenone and an open ring fission product accumulated during incubation with fluorene. Other catabolites beyond the open ring of fluorene were detected, specifically dihydroxyfluorene, hydroxy-9-fluorenone, dihydroxy-9-fluorenone, hydroxyindane, and a putative glutathione-conjugated benzylanhydride. Benzylanhydride appeared to be a final end product of fluorene degradation by strain EPA505.

Are some putative glycogen accumulating organisms (GAO) in anaerobic : aerobic activated sludge systems members of the α-Proteobacteria?

Activated sludge plants designed to remove phosphorus microbiologically often perform unreliably. One suggestion is that the polyphosphate-accumulating organisms (PAO) are out-competed for substrates by another group of bacteria, the glycogen-accumulating organisms (GAO) in the anaerobic zones of these processes. This study used fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) to analyse the communities from laboratory-scale anaerobic : aerobic sequencing batch reactors. Members of the genus Sphingomonas in the α-Proteobacteria were present in large numbers in communities with poor phosphorus removal capacity where the biomass had a high glycogen content. Their ability to store poly-β-hydroxyalkanoates anaerobically, but not aerobically, and not accumulate polyphosphate aerobically is consistent with these organisms behaving as GAO there. No evidence was found to support an important role for the γ-Proteobacteria as possible GAO in these communities, although these bacterial populations have been considered in other studies to act as possible competitors for the PAO.

A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate

Sphingomonas paucimobilis SYK-6 degrades syringate to 3-O-methylgallate (3MGA), which is finally converted to pyruvate and oxaloacetate via multiple pathways in which protocatechuate 4,5-dioxygenase, 3MGA dioxygenase, and gallate dioxygenase are involved. Here we isolated the syringate O-demethylase gene (desA), which complemented the growth deficiency on syringate of a Tn5 mutant of the SYK-6 derivative strain. The desA gene is located 929 bp downstream of ferA, encoding feruloyl-coenzyme A synthetase, and consists of a 1,386-bp open reading frame encoding a polypeptide with a molecular mass of 50,721 Da. The deduced amino acid sequence of desA showed 26% identity in a 325-amino-acid overlap with that of gcvT of Escherichia coli, which encodes the tetrahydrofolate (H(4)folate)-dependent aminomethyltransferase involved in glycine cleavage. The cell extract of E. coli carrying desA converted syringate to 3MGA only when H(4)folate was added to the reaction mixture. DesA catalyzes the transfer of the methyl moiety of syringate to H(4)folate, forming 5-methyl-H(4)folate. Vanillate and 3MGA were also used as substrates for DesA; however, the relative activities toward them were 3 and 0.4% of that toward syringate, respectively. Disruption of desA in SYK-6 resulted in a growth defect on syringate but did not affect growth on vanillate, indicating that desA is essential to syringate degradation. In a previous study the ligH gene, which complements the growth deficiency on vanillate and syringate of a chemical-induced mutant of SYK-6, DC-49, was isolated (S. Nishikawa, T. Sonoki, T. Kasahara, T. Obi, S. Kubota, S. Kawai, N. Morohoshi, and Y. Katayama, Appl. Environ. Microbiol. 64:836-842, 1998). Disruption of ligH resulted in the same phenotype as DC-49; its cell extract, however, was found to be able to convert vanillate and syringate in the presence of H(4)folate. The possible role of ligH is discussed.

Microbial degradation of high and low molecular weight polyaromatic hydrocarbons in a two-phase partitioning bioreactor by two strains of Sphingomonas sp

A mixture of six polyaromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene, pyrene, chyrysene and benzo[a]pyrene), varying in size from 2 to 5 rings, was dissolved in dodecane, and used as the delivery phase of a partitioning bioreactor. Two species of Sphingomonas were then used individually, and as a consortium, to determine which of the PAHs were degraded. Only low molecular weight PAHs (naphthalene, phenanthrene and fluoranthene) were degraded by the individual strains, but the consortium degraded all substrates either to completion or near completion.

Degradation of the Radioactive and Non-labelled Branched 4(3',5'-dimethyl 3'-heptyl)-phenol Nonylphenol Isomer by Sphingomonas TTNP3

The degradation of the 4(3',5'-dimethyl-3'-heptyl)-phenol (p353NP) nonylphenol isomer in cultures of Sphingomonas TTNP3 supplemented with the technical mixture of nonylphenol was first assessed. Then the radioactive and non-labelled form of these diastereomers were both synthesised. The radioactive isomers were synthesised using [ring-U-14C]-labelled phenol and 3,5-dimethyl-3-heptanol by Friedel and Crafts alkylation. The time-course of degradation was performed with and without 14C-p353NP; balancing of radioactivity was calculated from different soluble fractions (organic, aqueous), bacterial biomass, and 14CO2 evolved as mineralization product. The noticeable portion of 14C bound to biomass showed that at least the aromatic ring of 14C-p353NP was degraded and served as energy source and probably as carbon source for bacterial growth. In addition, the appearance of 3,5-dimethyl-3-heptanol, the nonanol corresponding with the side-chain of p353NP, was demonstrated in the bacterial media, and its concentration determined during the course of fermentation. Besides the parent 14C-p353NP, no other radioactive compounds, i.e. metabolites of 14C-p353NP were detected in the media.

Organization of genes required for gellan polysaccharide biosynthesis in Sphingomonas elodea ATCC 31461

Sphingomonas elodea ATCC 31461 produces gellan, a capsular polysaccharide that is useful as a gelling agent for food and microbiological media. Complementation of nonmucoid S. elodea mutants with a gene library resulted in identification of genes essential for gellan biosynthesis. A cluster of 18 genes spanning 21 kb was isolated. These 18 genes are homologous to genes for synthesis of sphingan polysaccharide S-88 from Sphingomonas sp. ATCC 31554, with predicted amino acid identities varying from 61% to 98%. Both polysaccharides have the same tetrasaccharide repeat unit, comprised of [-->4)-alpha- l-rhamnose-(1-->3)-beta- d-glucose-(1-->4)-beta- d-glucuronic acid-(1-->4)-beta- d-glucose-(1-->]. Polysaccharide S-88, however, has mannose or rhamnose in the fourth position and has a rhamnosyl side chain, while gellan has no sugar side chain but is modified by glyceryl and acetyl substituents. Genes for synthesis of the precursor dTDP- l-rhamnose were highly conserved. The least conserved genes in this cluster encode putative glycosyl transferases III and IV and a gene of unknown function, gelF. Three genes ( gelI, gelM, and gelN) affected the amount and rheology of gellan produced. Four additional genes present in the S-88 sphingan biosynthetic gene cluster did not have homologs in the gene cluster for gellan biosynthesis. Three of these gene homologs, gelR, gelS, and gelG, were found in an operon unlinked to the main gellan biosynthetic gene cluster. In a third region, a gene possibly involved in positive regulation of gellan biosynthesis was identified.

Bioavailability of a nonylphenol isomer in dependence on the association to dissolved humic substances

Humic substances are important environmental components since they represent a very large part of organic compounds on earth. According to many reports, dissolved humic substances are a determinant parameter for the bioavailability of xenobiotic compounds. For the present bioavailability studies, two kinds of dissolved humic substances, a commercially available humic acid and fulvic acids isolated from peat were used. As the relevant xenobiotic, a defined branched nonylphenol isomer, 4(3',5'-dimethyl-3'-heptyl)-phenol (p353NP) was synthesised according to Friedel-Crafts alkylation. Equilibrium dialysis studies were implemented in order to investigate the association between 14C-labelled p353NP and dissolved humic substances. The biodegradability in the presence of dissolved humic substances was examined in experiments with the nonylphenol degrading bacterium strain Sphingomonas TTNP3 and with p353NP as sole carbon source. The results showed that p353NP-humic acid associates were formed in high amounts, whereas no adducts with fulvic acids occurred. In the degradation studies with Sphingomonas TTNP3, no effects of dissolved humic substances on the bioavailability of p353NP could be observed. It was assumed that the association between nonylphenol and humic acids occurs rapidly and is reversible. Thus, the formation of "labile" complexes did not influence biodegradation rates, which were quite low.

Biodegradation kinetics of volatile hydrophobic organic compounds in cultures with variable fractional volumes

An extension of the models developed by Guha and Jaffé (Biotechnol Bioeng [1996] 50:693-699) to describe the phenanthrene biodegradation kinetics for the cultures with variable fractional volumes is presented. Batch experiments were conducted with a culture capable of degrading the phenanthrene using a single culture vessel from which samples were withdrawn over time to monitor the disappearance of phenanthrene. For accurate measurement of phenanthrene concentrations, a sampling procedure designed for quantifying the sorption of phenanthrene onto glassware was also introduced. The Monod parameters were estimated by nonlinear regression analyses of simultaneous solutions to the substrate utilization/volatilization and Monod equations for growth of the cell mass. The results demonstrate that the models were able to be extended to phenanthrene-degrading cultures with variable fractional volumes. When the ratio between sampling volume and volume of the culture medium was relatively small, the parameters obtained were similar to those which would be obtained using constant fractional volumes of culture medium. It was also found that the model's fit to the phenanthrene disappearance data in this study were better than those obtained by Guha and Jaffé, implying that the sorption process of phenanthrene during the sampling period could significantly affect the measurement of phenanthrene concentrations. Failing to account for these losses led to less accurate measurements of substrate concentrations, which in turn resulted in a poor estimation of the parameters. The findings of this study reduce considerably the experimental work necessary in the estimation of Monod kinetic parameters for the purpose of modeling.

Bioavailability of pentachlorophenol to acclimatised bacteria under batch and flow-through conditions

Biodegradation of organic contaminants in multi-phase systems, such as soils and aquifers, is often limited by the extent and the rate of contaminant sorption onto the solid matrix. However, information about biodegradation in complex matrices is largely limited to studies of closed systems under batch conditions in which potential bioavailability is characterised by the aqueous-phase concentration of a contaminant. There is little knowledge regarding the influence of flow-through conditions on the availability of contaminants to microbes (contaminant bioavailability). Thus, the aim of this study was to assess and compare contaminant bioavailability, in the presence of a sorptive medium, under both batch and flow-through conditions. Accordingly, experiments were designed in which pentachlorophenol (PCP) was introduced into a mixture of inoculated silica sand and a PCP-retaining resin, under either batch or flow-through (columns) conditions. The results indicated that an increase in the amount of resin (0.1-0.2 g) clearly lowered PCP availability to microbes after 170 h under batch conditions (30 and 45% respectively); whereas, the initial decrease in bioavailability observed under flow-through conditions (45 and 70% respectively) was reversed and no longer observable after 170 h. This increase in PCP availability was linked to an improvement in the contaminant biodegradation capacity from 0.03 to 0.13 mg x l(-1) x h(-1) over 200 h.

Characteristics of bacterial strains inhabiting the wood of coniferous trees

The presented studies embraced samples of wood chips from coniferous trees which contained layers of duramen, alburnum and bark. Microbiological analysis involved qualitative and quantitative determination of bacterial flora inhabiting the studied wood material. The wood chips were found to contain primarily species belonging to the genera Bacillus and Pseudomonas. The presence of the potentially pathogenic species Bacillus cereus 1, Sphingomonas paucimobilis, Aeromonas salmonicida and Chryseomonas luteola was also demonstrated.

Biodegradation of methyl tertiary butyl ether (MTBE) by a bacterial enrichment consortia and its monoculture isolates

Methyl tertiary butyl ether (MTBE), an important gasoline additive, is a recalcitrant compound posing serious environmental health problems. In this study, MTBE-degrading bacteria were enriched from five environmental samples. Enrichments from Stewart Lake sediments and an MTBE contaminated soil displayed the highest rate of MTBE removal; 29.6 and 27.8% respectively, in 28 days. A total of 12 bacterial monocultures isolated from enrichment cultures were screened for MTBE degradation in liquid cultures. In a nutrient-limited medium containing MTBE as the sole source of carbon and energy, the highest rate of MTBE elimination was achieved with IsoSL1, which degraded 30.6 and 50.2% in 14 and 28 days, respectively. In a nutrient-rich medium containing ethanol and yeast extract, the bacterium (Iso2A) substantially removed MTBE (20.3 and 28.1% removal in 14 and 28 days, respectively). Based upon analysis of the 16s rRNA gene sequence and data base comparison, IsoSL1 and Iso2A were identified as a Streptomyces sp. and Sphingomonas sp., respectively. The Streptomyces sp. is a new genera of bacteria degrading MTBE and could be useful for MTBE bioremediation.

Potential of a new biotreatment: Sphingomonas cloacae S-3T degrades nonylphenol in industrial wastewater

Sphingomonas cloacae S-3(T), a nonylphenol (NP)-degrading bacterium, was evaluated for its utility in the remediation of NP-contaminated wastewater. In flask-scale experiments, S-3(T) cells immobilized on porous polypropylene carriers (beads) efficiently degraded NP to concentrations routinely measured in aquatic environments [a few parts per billion (ppb), or micrograms per liter). Therefore, we constructed and evaluated a laboratory-scale wastewater treatment system with a 3-l carrier-filled column. The system worked properly and consistently removed several hundred ppb of NP to ecologically safe concentrations of less than 10 ppb in industrial wastewater without the addition of nutrients. The effect of wastewater pH on the system performance was also evaluated; and wastewater samples with pH values of 6 or 8 were treated efficiently without pH adjustment. These results suggest that a biotreatment system using NP-degrading bacteria can efficiently remediate industrial wastewater and contribute to the preservation of aquatic environments.

A novel Antarctic microbial endolithic community within gypsum crusts

A novel endolithic microbial habitat is described from a climatically extreme site at Two Step Cliffs, Alexander Island, Antarctic Peninsula (71 degrees 54'S, 68 degrees 13'W). Small endolithic colonies (<3 mm in diameter) are found within the translucent gypsum crust that forms on the surface of sandstone boulders. Gypsum crusts are found on ice-free rocks throughout the Antarctic and therefore offer potential colonization sites at more inhospitable locations, including sites at higher latitudes. Cyanobacterial, bacterial and fungal components were cultured from the crust material and have been identified as Chloroglea sp., Sphingomonas sp. and Verticillium sp. respectively. A non-cultured, black-pigmented fungus was also found. Cyanobacterial primary productivity is low: at depths of 1.2 and 2.5 mm within the crust, estimates of possible cell divisions per year were < 38 and four respectively. This microniche is proposed to provide protection from desiccation, rapid temperature variation and UV radiation flux while allowing penetration of photosynthetically active radiation (PAR) for utilization by phototrophs. The endolithic communities are less extensive than those of the Dry Valleys, continental Antarctica, probably owing to only recent deglaciation (<7000 year ago).

Simultaneous and rapid monitoring of biomass and biopolymer production by Sphingomonas paucimobilis using Fourier transform-near infrared spectroscopy

The application of Fourier Transform near infrared spectroscopy (FT-NIRS) to near real-time monitoring of polysaccharide and biomass concentration was investigated using a gellan-producing strain of Sphingomonas paucimobilis grown in a stirred tank reactor. Successful models for both biomass and gellan were constructed despite the physichochemical complexity of the viscous process fluid. Modelling of biomass proved more challenging than for gellan, partly because of the low range of biomass concentration but a model with a good correlation coefficient (0.94) was formulated based on second derivative spectra. The gellan model was highly satisfactory, with an excellent correlation coefficient (0.98), again based on second derivative spectra. No sample pre-treatment was required and all spectral scanning was carried out on whole broth. Additionally, both models should be robust in practice since both were formulated using low numbers of factors. Thus, the near real time simultaneous monitoring of gellan and biomass in this highly complex matrix using FT-NIRS potentially opens the way to greatly improved process control strategies.

Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway

Five genes involved in the two initial steps of the tetralin biodegradation pathway of Sphingomonas macrogolitabida strain TFA have been characterized. ThnA1A2 and ThnA3A4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. ThnA1, ThnA2, and ThnA3 were essential for tetralin ring-hydroxylating dioxygenase activity. ThnB was identified as a dehydrogenase required for tetralin biodegradation.

Saccharin as a sole source of carbon and energy for Sphingomonas xenophaga SKN

A bacterium, strain SKN, that was able to utilize saccharin as the sole source of carbon and energy for aerobic growth, was enriched and isolated from communal sewage. The isolate was identified as a strain of Sphingomonas xenophaga. Saccharin was quantitatively converted to cell material, sulfate, ammonium and, presumably, CO(2). The specific rate of saccharin-dependent oxygen uptake during growth reached a maximum before the culture entered the stationary phase and then fell to undetectable levels. Saccharin was degraded only in the presence of molecular oxygen. Catechol was detected as an intermediate during degradation of saccharin in whole cells and catechol 1,2-dioxygenase was expressed inducibly during growth with saccharin. There was an apparent requirement of 2 mol O(2)/mol saccharin to remove the substituents on the ring and to cleave the ring. We presume that S. xenophaga SKN synthesizes a multi-component saccharin dioxygenase that simultaneously cleaves off both vicinal substituents from the aromatic ring to yield catechol and the undefined precursor of CO(2) as well as sulfate and ammonium ions.

In-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative Sphingomonas spp. and soil pH

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field.

Isolation and taxonomic and catabolic characterization of a 3,6-dimethylphenanthrene-utilizing strain of Sphingomonas sp

A bacterial strain capable of utilizing 3,6-dimethylphenanthrene (3,6-DMP) as its sole source of carbon and energy was isolated from a creosote-contaminated soil. The isolate was identified as a strain of Sphingomonas sp. and was designated strain JS1. Utilization of 3,6-DMP was demonstrated by an increase in bacterial biomass concomitant with a decrease in 3,6-DMP in a liquid mineral medium with this compound as its sole source of carbon and energy. Strain JS1 showed a high specificity in the use of the most abundant alkylderivatives of crude oils, such as alkylnaphthalenes and other alkylphenanthrenes, as the sole source of carbon and energy. It can also use several polycyclic aromatic hydrocarbons of three and four rings and their alkylated derivatives as growth substrates or transform them. The identification of several intermediate metabolites points to extensive metabolic activity, including the following: (i) aromatic ring oxidation and cleavage, (ii) methyl group oxidations, and (iii) methylenic oxidations. The metabolic actions of Sphingomonas sp. JS1 on the aromatic fraction extracted from a creosote-contaminated soil are also examined.

Degradation of polyvinyl alcohol by Sphingomonas sp. SA3 and its symbiote

A total of 800 samples was taken from Taegu province, Korea, where many textile factories provide a source of polyvinyl alcohol (PVA) waste. These samples were screened for PVA-degrading bacteria. A new strain, SA3, was discovered which formed yellow colonies and used PVA as the sole carbon and energy source. Strain SA3 was identified as a Sphingomonas sp., based on the partial nucleotide sequence analysis of 16S ribosomal RNA, the presence of 2-hydroxymyristic acid (14:O 2-OH) and sphingolipids with d-17:0, d-18:0, d-19:1, and d-20:1 as the main dihydrosphingosines. This genus has not previously been reported as a PVA-degrading bacterium. Sphingomonas sp. SA3 needs a symbiote strain, SA2, for PVA degradation as a growth factor producer. In mixed cultures of these strains, the optimum temperature for PVA biodegradation ranged from 30 degrees C to 35 degrees C. The optimum pH was 8.0 and the most effective nitrogen source was NH(4)(+).

Cadmium biosorption by Sphingomonas paucimobilis biomass

Among microorganisms isolated in Bangkok, the gram-negative bacterium Sphingomonas paucimobilis exhibited the greatest cadmium tolerance. It was able to survive in the medium containing cadmium as high as 200 mg/l. However, concentrations of cadmium at 25-200 mg/l inhibited its growth. The biosorption properties for cadmium of this bacterial biomass and the effects of environmental factors (i.e., biosorbent type, initial pH and biosorbent concentration) on the cadmium biosorption were explored. The results showed that the cadmium removal capacity of living cells was markedly higher than that of nonliving cells. Cadmium biosorption by S. paucimobilis biomass was also affected by the initial pH and biosorbent concentration.

Isolation and characterization of Sphingomonas sp. GTIN11 capable of carbazole metabolism in petroleum

A bacterial culture was isolated from a manufactured gas plant (MGP) soil based on its ability to metabolize the nitrogen-containing heterocycle carbazole. The culture was identified as a Sphingomonas sp. and was given the designation GTIN11. A cloned 4.2kb DNA fragment was confirmed to contain genes responsible for carbazole degradation. DNA sequence analysis revealed that the fragment contained five open reading frames (ORFs) with the deduced amino acid sequence showing homology to; carbazole terminal dioxygenase (ORF1), 2,3-dihydroxybiphenyl dioxygenase subunits (ORF2 and ORF3), meta-cleavage compound hydrolases (ORF4), and ferrodoxin component of bacterial multicomponent dioxygenases (ORF5). The percent similarity was 61% of these proteins or less to known proteins. The specific activity of Sphingomonas sp. GTIN11 for the degradation of carbazole at 37 degrees C was determined to be 8.0 micromol carbazole degraded/min/g dry cell. This strain is unique in expressing the carbazole degradation trait constitutively. Resting cells of Sphingomonas sp. GTIN11 removed 95% of carbazole and 50% of C1-carbazoles from petroleum in a 16-h treatment time.

Degradation of phenanthrene, methylphenanthrenes and dibenzothiophene by a Sphingomonas strain 2mpII

Strain Sphingomonassp. (2MPII), isolated from marine sediment, was able to utilize phenanthrene (P) or 2-methylphenanthrene (2MP) as the sole carbon source. However, 9-methylphenanthrene (9MP) and dibenzothiophene (DBT) were weakly degraded. The degradation rates of 9MP and DBT increased in the presence of 2MP, whilst the degradation rate of 2MP increased in the presence of 9MP. However, the presence of DBT inhibited the degradation of 2MP. DBT sulfone, a DBT metabolite, was not assimilated by the bacteria and its presence also decreased the degradation rate of 2MP.

Isolation and characterization of dibenzofuran-degrading bacteria

Two bacterial strains capable of utilizing dibenzofuran (DF) as a sole carbon source were isolated from soil samples of reclaimed land. The strains designated HL1 and HL7 were identified as Klebsiella sp. and Sphingomonas sp., respectively, on the basis of biochemical characteristics and the sequences of the 16S ribosomal DNA. Sphingomonas sp. strain HL7 degraded non-, mono- and also dichlorinated DF and dibenzo-p-dioxin (DD). Klebsiella sp. strain HL1 was able to degrade non- and monochlorinated DFs and DDs, but not dichlorinated ones. The metabolites formed from DF by strains HL1 and HL7 were similar to those by dioxin-degrading bacteria Sphingomonas sp. strain RW1 except for salicylic acid and catechol. Strain HL7 had a gene homologous to that encoding the dioxin dioxygenase alpha-subunit (dxnA1) gene of Sphingomonas sp. strain RW1. However, Southern hybridization analysis showed that the size of an EcoRV-digested genomic fragment involving the dioxin dioxygenase gene of strain HL7 was smaller than that of strain RW1, and that strain HL1 did not have the homologous gene. Strains HL1 and HL7 provided useful information regarding the dioxygenase genes.

Detection of mega plasmid from polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. strain KS14

Polycyclic aromatic hydrocarbon (PAH) degrading Sphingomonas sp. strain KS14 was isolated from soil. Strain KS14 was able to utilize phenanthrene and naphthalene as sole source of carbon and energy, and mineralize phenanthrene to carbon dioxide. Strain KS14 cometabolically degraded pyrene using phenanthrene as secondary growth substrate. A large degradative plasmid (>500 kb) was detected from the strain KS14. This study suggests that this mega plasmid could be responsible for the degradation of PAH by strain KS14.

Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface

Several strains of Sphingomonas isolated from deep Atlantic coastal plain aquifers at the US Department of Energy Savannah River Site (SRS) near Aiken, SC were shown to degrade a variety of aromatic hydrocarbons in a liquid culture medium. Sphingomonas aromaticivorans strain B0695 was the most versatile of the five strains examined. This strain was able to degrade acenaphthene, anthracene, phenanthrene, 2,3-benzofluorene, 2-methylnaphthalene, 2,3-dimethylnaphthalene, and fluoranthene in the presence of 400 mg l(-1) Tween 80. Studies involving microcosms composed of aquifer sediments showed that S. aromaticivorans B0695 could degrade phenanthrene effectively in sterile sediment and could enhance the rate at which this compound was degraded in nonsterile sediment. These findings indicate that it may be feasible to carry out (or, at least, to enhance) in situ bioremediation of phenanthrene-contaminated soils and subsurface environments with S. aromaticivorans B0695. In contrast, strain B0695 was unable to degrade fluoranthene in microcosms containing aquifer sediments, even though it readily degraded this polynuclear aromatic hydrocarbon (PAH) in a defined liquid growth medium.

Specific growth rate plays a critical role in hydrogen peroxide resistance of the marine oligotrophic ultramicrobacterium sphingomonas alaskensis strain RB2256

The marine oligotrophic ultramicrobacterium Sphingomonas alaskensis RB2256 has a physiology that is distinctly different from that of typical copiotrophic marine bacteria, such as Vibrio angustum S14. This includes a high level of inherent stress resistance and the absence of starvation-induced stress resistance to hydrogen peroxide. In addition to periods of starvation in the ocean, slow, nutrient-limited growth is likely to be encountered by oligotrophic bacteria for substantial periods of time. In this study we examined the effects of growth rate on the resistance of S. alaskensis RB2256 to hydrogen peroxide under carbon or nitrogen limitation conditions in nutrient-limited chemostats. Glucose-limited cultures of S. alaskensis RB2256 at a specific growth rate of 0.02 to 0.13 h(-1) exhibited 10,000-fold-greater viability following 60 min of exposure to 25 mM hydrogen peroxide than cells growing at a rate of 0.14 h(-1) or higher. Growth rate control of stress resistance was found to be specific to carbon and energy limitation in this organism. In contrast, V. angustum S14 did not exhibit growth rate-dependent stress resistance. The dramatic switch in stress resistance that was observed under carbon and energy limitation conditions has not been described previously in bacteria and thus may be a characteristic of the oligotrophic ultramicrobacterium. Catalase activity varied marginally and did not correlate with the growth rate, indicating that hydrogen peroxide breakdown was not the primary mechanism of resistance. More than 1,000 spots were resolved on silver-stained protein gels for cultures growing at rates of 0.026, 0.076, and 0.18 h(-1). Twelve protein spots had intensities that varied by more than twofold between growth rates and hence are likely to be important for growth rate-dependent stress resistance. These studies demonstrated the crucial role that nutrient limitation plays in the physiology of S. alaskensis RB2256, especially under oxidative stress conditions.

A simple and easy method for the monitoring of environmental pollutants using oligotrophic bacteria

Sphingomonas paucimobilis KPS01, an oligotrophic bacterium isolated from soil, may be a useful tool for monitoring heavy metals. Previous methods relying on counting of viable cells require a relatively long time and some skill; we have developed a method based on optical density (O.D.) measurements which is significantly faster and does not require skilled personnel. The results of the O.D. and viable count methods were consistent; both methods detected heavy metals at concentrations ranging from 10-3 to 10-5 mmol l-1 and identified heavy metal contamination in 13 of 18 river water samples. Our results demonstrate that biological detection using this O.D. method and S. paucimobilis KPS01 may be useful for routine environmental monitoring of heavy metals, particularly in water sources.

The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6

Sphingomonas paucimobilis SYK-6 is able to grow on various dimeric lignin compounds, which are converted to vanillate and syringate by the actions of unique lignin degradation enzymes in this strain. Vanillate and syringate are degraded by the O-demethylase and converted into protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively. PCA is further degraded via the PCA 4,5-cleavage pathway, while the results suggested that 3MGA is degraded through another pathway in which PCA 4,5-dioxygenase is not involved. In a 10.5-kb EcoRI fragment carrying the genes for PCA 4,5-dioxygenase (ligAB), 2-pyrone-4,6-dicarboxylate hydrolase (ligI), and a portion of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (ligC), we found the ligJ gene encoding 4-oxalomesaconate (OMA) hydratase, which catalyzes the conversion of OMA into 4-carboxy-4-hydroxy-2-oxoadipate. The ligJ gene is transcribed in the same direction as ligABC genes and consists of an 1,023-bp open reading frame encoding a polypeptide with a molecular mass of 38,008 Da, which is located 73-bp upstream from ligA. The ligJ gene product (LigJ), expressed in Escherichia coli, was purified to near homogeneity and was estimated to be a homodimer (69.5 kDa) by gel filtration chromatography. The isoelectric point was determined to be 4.9, and the optimal temperature is 30 degrees C. The K(m) for OMA and the V(max) were determined to be 138 microM and 440 U/mg, respectively. LigJ activity was inhibited by the addition of thiol reagents, suggesting that some cysteine residue is part of the catalytic site. The ligJ gene disruption in SYK-6 caused the growth defect on and the accumulation of common metabolites from both vanillate and syringate, indicating that the ligJ gene is essential to the degradation of these two compounds. These results indicated that syringate is converted into OMA via 3MGA, and it enters the PCA 4,5-cleavage pathway.

Microbial degradation of phenanthrene by addition of a sophorolipid mixture

The influence of sophorolipids on microbial degradation of poorly soluble phenanthrene in liquid and soil suspension culture was evaluated in the work presented. Experiments were carried out in two parts. In the first part, important basic physico-chemical characteristics of the biosurfactant and the pollutant used were determined. The critical micelle concentration (CMC) and the solubilization ratio of the biosurfactant were found to be in a good range compared with synthetic surfactants. Also, a reduction to 71% of the detectable amount of phenanthrene was measured within 4 d in soil suspension without any biotic influence. In the second part, culture experiments were done with Sphingomonas yanoikuyae, the bacterium used throughout the work presented here with the aim to assess the toxicity of the sophorolipids on these bacteria and the effect of the surfactant on biodegradation. In exponential growth tests, no toxicity up to 1 g l(-1) sophorolipids could be detected, whereas in an agar plate test, slight growth hindrance was measured at a lower concentration of 250 mg l(-1). The above mentioned data were important for planning further experiments. In the following cultivations with liquid and soil suspension media, enhancements of the biodegradation with surfactant addition were measurable. Fluorescence measurements showed that this effect was not due to an increasing biomass, but to an augmentation of bioavailability of the phenanthrene through increasing the apparent dissolved pollutant. Surfactant addition had the consequence of decreasing the residual detectable pollutant concentration (after 36 h 0.5 compared with 2.3 mg l(-1) soil suspension) and increasing the maximal degradation rate (127 instead of 80 mg l(-1) soil suspension x 10 h). Therefore, the two main problems of biological soil remediation techniques, longer process time and residual pollutants, may be solved by the use of surfactants.

Identification of novel metabolites in the degradation of phenanthrene by Sphingomonas sp. strain P2

Sphingomonas sp. strain P2, which is capable of utilizing phenanthrene as a sole carbon and energy source, was isolated from petroleum-contaminated soil in Thailand. Gas chromatography-mass spectrometry and (1)H and (13)C nuclear magnetic resonance analyses revealed two novel metabolites from the phenanthrene degradation pathway. One was identified as 5,6-benzocoumarin, which was derived by dioxygenation at the 1- and 2-positions of phenanthrene, and the other was determined to be 1,5-dihydroxy-2-naphthoic acid. Other metabolites from phenanthrene degradation were identified as 7, 8-benzocoumarin, 1-hydroxy-2-naphthoic acid and coumarin. From these results, it is suggested that strain P2 can degrade phenanthrene via dioxygenation at both 1,2- and 3,4-positions followed by meta-cleavage.

Horizontal transfer of an exopolymer complex from one bacterial species to another

Alasan, the exocellular polymeric emulsifier produced by Acinetobacter radioresistens KA53 was shown to bind to the surface of Sphingomonas paucimobilis EPA505 and Acinetobacter calcoaceticus RAG-1. The presence of alasan on the surface of S. paucimobilis EPA505 and A. calcoaceticus RAG-1 caused a decrease in their cell-surface hydrophobicities. Binding was proportional to the concentration of recipient cells and input alasan. At the highest concentration of A. calcoaceticus RAG-1 (4 x 10(9) ml(-1)) and alasan (20 microg ml(-1)) tested, 75% of the alasan was cell bound. Alasan binding was measured by the loss of emulsifying activity and alasan protein and polysaccharide from the aqueous phase after incubation of alasan with the recipient cells. In addition, alasan was visualized on the surface of the recipient cells by staining with anti-alasan antibodies and rhodamine-labelled secondary antibodies. Moreover, when the alasan-producing A. radioresistens KA53 was grown together with A. calcoaceticus RAG-1, alasan was released from the producing strain and became bound to the recipient RAG-1 cells, as demonstrated by fluorescence microscopy. This horizontal transfer of exopolymers from one bacterial species to another has significant implications in natural microbial communities, coaggregation and biofilms.