Diversity of PAH-degrading bacteria in an airlift-suspension reactor system for waste-water cleaning

Different samples from a reactor system for the cleaning of an emulsified waste oil containing approximately 1% of different polycyclic aromatic hydrocarbons (PAH) were studied for the diversity of phenanthrene, anthracene, and acenaphthene-metabolizing bacteria. From more than 28 different taxa found in the airlift-suspension reactor, nine were able to mineralize at least one of the PAH, belonging to the genera Bacillus, Mycobacterium, Nocardia, Sphingomonas, Alcaligenes, Pseudomonas, and the Flavobacterium/Cytophaga group. In the sludge from the thickener of the reactor system, a reduced number of metabolically active groups could be detected. The impact of different precultivation substrates on the degradation capability was investigated with five PAH-degrading bacterial strains. Four isolates were influenced by the precultivation substrates, however, one isolate (Alcaligenes-like) as well as the mixture of the five strains showed no changes in their degradation capability. The results indicated a strong impact of the precultivation methods on the composition of bacterial communities and the activity and the degradation characteristics of bacteria with respect to different PAH.     

Cell surface properties of five polycyclic aromatic compound-degrading yeast strains

To investigate the effects of physiological properties on polycyclic aromatic compound (PAH) degradation, the surface tension and emulsification activities, and cell surface hydrophobicity of five PAH-degrading yeast isolates were compared to Saccharomyces cerevisiae from cultures grown with glucose, hexadecane, or naphthalene as carbon sources. The cell surface hydrophobicity values for the five yeast strains were significantly higher than for S. cerevisiae for all culture conditions, although these were highest with hexadecane and naphthalene. Strains with higher hydrophobicity showed higher rates of naphthalene and phenanthrene degradation, indicating that increased cell hydrophobicity might be an important strategy in PAH degradation for the five strains. Emulsification activities increased for all five yeast strains with naphthalene culturing, although no relationship existed between emulsification activity and PAH degradation rate. Surface tensions were not markedly reduced with naphthalene culturing.     

Polycyclic Aromatic Hydrocarbon Degradation by a New Marine Bacterium, Neptunomonas naphthovorans gen. nov., sp. nov.

Two strains of bacteria were isolated from creosote-contaminated Puget Sound sediment based on their ability to utilize naphthalene as a sole carbon and energy source. When incubated with a polycyclic aromatic hydrocarbon (PAH) compound in artificial seawater, each strain also degraded 2-methylnaphthalene and 1-methylnaphthalene; in addition, one strain, NAG-2N-113, degraded 2,6-dimethylnaphthalene and phenanthrene. Acenaphthene was not degraded when it was used as a sole carbon source but was degraded by both strains when it was incubated with a mixture of seven other PAHs. Degenerate primers and the PCR were used to isolate a portion of a naphthalene dioxygenase iron-sulfur protein (ISP) gene from each of the strains. A phylogenetic analysis of PAH dioxygenase ISP deduced amino acid sequences showed that the genes isolated in this study were distantly related to the genes encoding naphthalene dioxygenases of Pseudomonas and Burkholderia strains. Despite the differences in PAH degradation phenotype between the new strains, the dioxygenase ISP deduced amino acid fragments of these organisms were 97.6% identical. 16S ribosomal DNA-based phylogenetic analysis placed these bacteria in the gamma-3 subgroup of the Proteobacteria, most closely related to members of the genus Oceanospirillum. However, morphologic, physiologic, and genotypic differences between the new strains and the oceanospirilla justify the creation of a novel genus and species, Neptunomonas naphthovorans. The type strain of N. naphthovorans is strain NAG-2N-126.     

Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization

Twenty different strains of Pseudomonas, Mycobacterium, Gordona, Sphingomonas, Rhodococcus and Xanthomonas which degrade polycyclic aromatic hydrocarbons (PAH) were characterized in respect to genes encoding degradation enzymes for PAH. Genomic DNA from these strains was hybridized with a fragment of ndoB, coding for the large iron sulfur protein (ISP alpha) of the naphthalene dioxygenase from Pseudomonas putida PaW736 (NCIB 9816). A group of seven naphthalene-degrading Pseudomonas strains showed strong hybridization with the ndoB probe, and five Gordona, Mycobacterium, Rhodococcus and Pseudomonas strains able to degrade higher molecular weight PAH showed weaker hybridization signals. Using a polymerase chain reaction (PCR) approach, seven naphthalene-degrading Pseudomonas strains showed a PCR fragment of the expected size with ndoB-specific primers and additionally ten strains of Gordona, Mycobacterium, Pseudomonas, Sphingomonas and Xanthomonas able to degrade higher molecular weight PAH were detected with degenerate primer-pools specific for the ISP alpha [2Fe-2S]-Rieske center of diverse aromatic hydrocarbon dioxygenases. This suggests a molecular relationship between genes coding for PAH catabolism in various PAH-degrading bacterial taxa, which could be used to evaluate the PAH-degradation potential of mixed populations.     

Degradation of polycyclic aromatic hydrocarbons by pure strains and by defined strain associations: inhibition phenomena and cometabolism

Six bacterial strains capable of using, as sole carbon and energy source, at least one of the following polycyclic aromatic hydrocarbons (PAH), naphthalene, fluorene, phenanthrene, anthracene, fluoranthene and pyrene, were isolated. The interactions between these PAH during their biodegradation were studied in experiments involving PAH pairs, one PAH at least being used as a carbon source. All individual strains were found capable of cometabolic degradation of PAH in a range varying among strains. Inhibition phenomena, sometimes drastic, were often observed but synergistic interactions were also detected. Naphthalene was toxic to all strains not isolated on this compound. Strain associations were found efficient in relieving inhibition phenomena, including the toxic effect of naphthalene. Accumulation of water-soluble metabolites was consistently observed during PAH degradation.     

Evaluation of a creosote-based medium for the growth and preparation of a PAH-degrading bacterial community for bioaugmentation

Creosote was evaluated as an inexpensive carbon source for growing inocula of a polycyclic aromatic hydrocarbon (PAH)-degrading bacterial community (community five). Creosote was a poor growth substrate when provided as sole carbon source in a basal salts solution (BSM). Alternatively, peptone, yeast extract or glucose in BSM supported high growth rates, but community five could not subsequently degrade pyrene. A combination of creosote and yeast extract in BSM (CYEM) supported growth and maintained the pyrene-degrading capacity of community five. Optimum pyrene-degrading activity occurred when the inocula were grown in creosote and yeast extract concentrations of 2 ml L⁻¹ and 1 g L⁻¹ respectively: concentrations outside these values resulted in either low biomass yields or loss of PAH-degrading activity. CYEM-grown community five inocula degraded 250 mg L⁻¹ of pyrene in BSM at a rate comparable to cultures inoculated with community five grown in BSM-pyrene. However, the CYEM-grown community showed a 40% lower rate of PAH degradation in a synthetic PAH mixture compared with pyrene-grown cells and there was an increase in the lag period before the onset of PAH degradation. This appears to reflect a weaker induction of PAH catabolism by CYEM compared to BSM-pyrene. Journal of Industrial Microbiology & Biotechnology (2000) 24, 277–284. Received 24 August 1999/ Accepted in revised form 20 January 2000     

Limited Roles for Salicylate and Phthalate in Bacterial PAH Bioremediation

We have isolated and identified 12 previously unreported strains of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria. Three of these isolates belong to the genus Burkholderia, with the remainder comprised of two Pseudomonas species, and seven strains from the genus Sphingomonas. These isolates were examined for their ability to utilize a variety of three- to five-ring PAHs as sole sources of carbon and energy. All were also checked for the ability to grow on salicylic acid and phthalic acid, two compounds that are key intermediates in almost all published PAH degradative pathways. Only 3 of the 12 strains were able to grow on both of these monoaromatic acids, while three others (all Sphingomonas) could not grow on either. The implications of these findings on the universal applicability of known PAH catabolic pathways, and on possible induction of PAH degradation by pathway intermediates, are discussed.     

Efficient bioconversion of compactin to pravastatin by the quinoline-degrading microorganism Pseudonocardia carboxydivorans isolated from petroleum-contaminated soil

Pravastatin is one of the first available statins on the market. The purpose of this study was to isolate and identify the quinoline-degrading microorganism from petroleum-contaminated soil that could bioconvert compactin to pravastatin. There were 10,011 microorganism colonies isolated; five strains showed a higher capability for quinoline biodegradation. These five strains were evaluated for their pravastatin bioconversion ability; Pseudonocardia sp. had the highest efficiency for conversion of compactin to pravastatin. The strain was further identified as Pseudonocardia carboxydivorans PAH4. The bioconversion rates were studied under difference incubation conditions. Pre-incubation in medium containing 0.005% compactin sodium, resulted in the compactin utilization rate of almost 100% in a 1mg/ml compactin-containing medium. The rate of conversion of pravastatin was up to 68% after 6 days of incubation. In conclusion, the results of this study suggest that P. carboxydivorans PAH4 could be considered a candidate for the production of pravastatin on an industrial scale.     

Enrichment for enhanced competitive plant root tip colonizers selects for a new class of biocontrol bacteria

Our group studies tomato foot and root rot, a plant disease caused by the fungus Forl (Fusarium oxysporum f.sp. radicis-lycopersici ). Several bacteria have been described to be able to control the disease, using different mechanisms. Here we describe a method that enables us to select, after application of a crude rhizobacterial mixture on a sterile seedling, those strains that reach the root tip faster than our best tomato root colonizer tested so far, the Pseudomonas fluorescens biocontrol strain WCS365. Of the five tested new isolates, four appeared to be able to reduce the number of diseased plants. Analysis of one of these strains, P. fluorescens PCL1751, suggests that it controls the disease through the mechanism 'competition for nutrients and niches', a mechanism novel for biocontrol bacteria. Moreover, this is the first report describing a method to enrich for biocontrol strains from a crude mixture of rhizobacteria. Another advantage of the method is that four out of five strains do not produce antifungal metabolites, which is preferential for registration as a commercial product.     

Biodegradation of a mixture of PAHs by non-ligninolytic fungal strains isolated from crude oil-contaminated soil

Nine native non-ligninolytic fungal strains were isolated from Maya crude oil-contaminated soil and selected based on their ability to grow and use crude oil and several polycyclic aromatic hydrocarbons (PAHs) as carbon source, for their application to PAH removal in soil. The fungi were identified by PCR amplification of intergenic transcribed sequences regions and microbiological techniques, and results showed them to be part of the genera Fusarium, Neurospora, Aspergillus, Scedosporium, Penicillium, Neosartorya and Talaromyces. A primary selection of fungi was made in minimal medium plates, considering the tolerance to different concentrations of PAHs for each strain. The radial extension rate exhibited significant differences (p < 0.05) from 200 to 1,000 mg of PAHs mixture l^?1. A secondary selection of Aspergillus terreus, Talaromyces spectabilis, and Fusarium sp. was achieved based on their tolerance to 2,000 mg of a mixture of Phenanathrene and Pyrene kg^?1 of soil in a solid-state microcosm system for 2 weeks. The percentage of PAH removal obtained by the three strains was approximately 21 % of the mixture.     

Characterization of bacterial strains able to grow on high molecular mass residues from crude oil processing

Oil residues containing high molecular mass hydrocarbons, rich in polyaromatic compounds, are frequent end-products of crude oil processing and are poorly biodegradable. Their disposal poses an environmental problem. Through batch-enrichments from contaminated soils we have isolated and characterized seven bacterial strains that can use a residue from crude oil processing as a source of carbon and energy. The residue was a complex mixture of high molecular mass compounds, including saturated, aromatic and polycyclic aromatic hydrocarbons (PAHs). Analysis of the metabolic profiles of the strains isolated showed that they could all metabolize long-chain-length alkanes efficiently, but not PAHs. Strains degrading naphthalene, a simple PAH, did exist in the soil inocula used, but could be isolated only when enrichments were performed using pure naphthalene as the sole carbon source. All strains tested emulsified the oil residue and their ability to produce surfactants was studied.     

Biodegradation of polycyclic aromatic hydrocarbons by new isolates of white rot fungi.

Eight rapid Poly R-478 dye-decolorizing isolates from The Netherlands were screened in this study for the biodegradation of polycyclic aromatic hydrocarbons (PAH) supplied at 10 mg liter(-1). Several well-known ligninolytic culture collection strains, Phanerochaete chrysosporium BKM-F-1767, Trametes versicolor Paprican 52, and Bjerkandera adusta CBS 595.78 were tested in parallel. All of the strains significantly removed anthracene, and nine of the strains significantly removed benzo(a)pyrene beyond the limited losses observed in sterile liquid and HgCl2-poisoned fungus controls. One of the new isolates, Bjerkandera sp. strain Bos 55, was the best degrader of both anthracene and benzo(a)pyrene, removing 99.2 and 83.1% of these compounds after 28 days, respectively. Half of the strains, exemplified by strains of the genera Bjerkandera and Phanerochaete, converted anthracene to anthraquinone, which was found to be a dead-end metabolite, in high yields. The extracellular fluids of selected strains were shown to be implicated in this conversion. In contrast, four Trametes strains removed anthracene without significant accumulation of the quinone. The ability of Trametes strains to degrade anthraquinone was confirmed in this study. None of the strains accumulated PAH quinones during benzo(a)pyrene degradation. Biodegradation of PAH by the various strains was highly correlated to the rate by which they decolorized Poly R-478 dye, demonstrating that ligninolytic indicators are useful in screening for promising PAH-degrading white rot fungal strains.     

Biodegradation of polycyclic aromatic hydrocarbons by new isolates of white rot fungi.

Eight rapid Poly R-478 dye-decolorizing isolates from The Netherlands were screened in this study for the biodegradation of polycyclic aromatic hydrocarbons (PAH) supplied at 10 mg liter(-1). Several well-known ligninolytic culture collection strains, Phanerochaete chrysosporium BKM-F-1767, Trametes versicolor Paprican 52, and Bjerkandera adusta CBS 595.78 were tested in parallel. All of the strains significantly removed anthracene, and nine of the strains significantly removed benzo(a)pyrene beyond the limited losses observed in sterile liquid and HgCl2-poisoned fungus controls. One of the new isolates, Bjerkandera sp. strain Bos 55, was the best degrader of both anthracene and benzo(a)pyrene, removing 99.2 and 83.1% of these compounds after 28 days, respectively. Half of the strains, exemplified by strains of the genera Bjerkandera and Phanerochaete, converted anthracene to anthraquinone, which was found to be a dead-end metabolite, in high yields. The extracellular fluids of selected strains were shown to be implicated in this conversion. In contrast, four Trametes strains removed anthracene without significant accumulation of the quinone. The ability of Trametes strains to degrade anthraquinone was confirmed in this study. None of the strains accumulated PAH quinones during benzo(a)pyrene degradation. Biodegradation of PAH by the various strains was highly correlated to the rate by which they decolorized Poly R-478 dye, demonstrating that ligninolytic indicators are useful in screening for promising PAH-degrading white rot fungal strains.     

Role of aromatic transmembrane residues of the organic anion transporter,rOAT3, in substrate recognition

Organic anion transporters (OATs, SLC21) are important in the excretion of endogenous and exogenous compounds in the kidney. The rat organic anion transporter, rOAT3, mediates the transport of organic anions such as p-aminohippurate (PAH) and estrone sulfate as well as the basic compound, cimetidine. In the present study, we examined the role of conserved transmembrane aromatic amino acid residues of rOAT3 in substrate recognition and transport. Alanine scanning followed by amino acid replacements was used to construct mutants of rOAT3. The uptake of model compounds was studied in Xenopus laevis oocytes expressing the mutant transporters. We observed that four mutants in transmembrane domain 7 (TMD 7), W334A, F335A, Y341A, and Y342Q, and one mutant in transmembrane domain 8 (TMD 8), F362S, exhibited a less than 2-fold enhanced uptake of PAH and cimetidine in comparison to wild-type rOAT3, which exhibited a 16-fold enhanced uptake of PAH and an 8-fold enhanced uptake of cimetidine. Estrone sulfate uptake in oocytes expressing any one of these five mutants remained at least 8-fold enhanced. The data suggest that the five residues, W334, F335, Y341, Y342, and F362, contribute differently to the transport of the small hydrophilic organic substrates PAH and cimetidine in comparison to the large hydrophobic organic substrate estrone sulfate. The effects of side chains of these five residues on transporter functions were also evaluated by constructing conservative mutations. We observed that the residues contribute to PAH and cimetidine transport in different ways: the -OH group of Y342, the indole ring of W334, and the aromatic rings of F335, Y341, and F362 are important for PAH and cimetidine transport by rOAT3. These data suggest that there is an aromatic pocket composed mainly of residues in TMD 7 in the translocation pathway of rOAT3, which is important for the transport of PAH and cimetidine. Aromatic residues in this pocket may interact directly with substrates of rOAT3 through hydrogen bonds and pi-pi interactions.     

Degradation of phenanthrene,fluorene and fluoranthene by pure bacterial cultures

Summary Bacterial mixed cultures able to degrade the polycyclic aromatic hydrocarbons (PAH) phenanthrene, fluorene and fluoranthene, were obtained from soil using conventional enrichment techniques. From these mixed cultures three pure strains were isolated:Pseudomonas paucimobilis degrading phenanthrene;P. vesicularis degrading fluorene andAlcaligenes denitrificans degrading fluoranthene. The maximum rates of PAH degradation ranged from 1.0 mg phenanthrene/ml per day to 0.3 mg fluoranthene/ml per day at doubling times of 12 h to 35 h for growth on PAH as sole carbon source. The protein yield during PAH degradation was about 0.25 mg/mg C for all strains. Maximum PAH oxidation rates and optimum specific bacterial growth were obtained near pH 7.0 and 30°C. After growth entered the stationary phase, no dead end-products of PAH degradation could be detected in the culture fluid.     

Degradation of fluoranthene, pyrene, benz[a]anthracene and dibenz[a,h]anthracene by Burkholderia cepacia

Microbiological analysis of soils from a polycyclic aromatic hydrocarbon (PAH)-contaminated site resulted in the enrichment of five microbial communities capable of utilizing pyrene as a sole carbon and energy source. Communities 4 and 5 rapidly degraded a number of different PAH compounds. Three pure cultures were isolated from community 5 using a spray plate method with pyrene as the sole carbon source. The cultures were identified as strains of Burkholderia ( Pseudomonas ) cepacia on the basis of biochemical and growth tests. The pure cultures (VUN 10 001, VUN 10 002 and VUN 10 003) were capable of degrading fluorene, phenanthrene and pyrene (100 mg l⁻¹) to undetectable levels within 7–10 d in standard serum bottle cultures. Pyrene degradation was observed at concentrations up to 1000 mg l⁻¹. The three isolates were also able to degrade other PAHs including fluoranthene, benz[ a ]anthracene and dibenz[ a , h ]anthracene as sole carbon and energy sources. Stimulation of dibenz[ a , h ]anthracene and benzo[ a ]pyrene degradation was achieved by the addition of small quantities of phenanthrene to cultures containing these compounds. Substrate utilization tests revealed that these micro-organisms could also grow on n -alkanes, chlorinated- and nitro-aromatic compounds.     

Characterization of aerobic polycyclic aromatic hydrocarbon-degrading bacteria from Bizerte lagoon sediments, Tunisia

Aims: To characterize polycyclic aromatic hydrocarbon (PAH)‐degrading bacteria from sediments of the Bizerte lagoon, and to determine their ability to resist other pollutants such as antibiotics and heavy metals. Methods and Results: More than 100 strains were isolated for their ability to use fluoranthene as the sole carbon and energy source. Most of them showed antibiotic and heavy metal resistance; 20 representative strains were selected for further analysis. 16S rRNA coding sequences analysis showed that the majority of the selected bacteria (75%) were affiliated to the Gammaproteobacteria. The selected strains also utilized high molecular weight PAHs containing up to four benzene rings and showed different profiles of PAH substrate usage suggesting different PAH degradation pathways. These results are consistent with the fact that nah‐like genes and idoA‐like genes, involved in PAH degradation, were detected in 6 and 1 strains respectively. Conclusions: The Bizerte lagoon, polluted by many human activities, leads to the co‐selection of strains able to cope with multiple contaminants. Significance and Impact of the Study: Polluted areas are often characterized by the concomitant presence of organic pollutants, heavy metals and antibiotics. This study is one of the first showing bacterial strains adapted to multiple contaminants, a promising potential for the development of bioremediation processes.     

Non-selective precultivation of bacteria able to degrade different polycyclic aromatic hydrocarbons (PAH)

The influence of the precultivation with different carbon sources on the ability of three different bacterial strains (Sphingomonas sp. strain BA2, Gordona sp. strain BP9, Mycobacterium sp. strain VF1) to grow on phenanthrene. anthracene, pyrene or fluoranthene as the sole source of carbon and energy were studied. The strains were found to maintain their ability to grow on two of the four PAH after 30 serial transfers in liquid nutrient broth medium without selective pressure. The ability to grow on these PAH as the sole carbon and energy source was also maintained after curing experiments with acridine orange. The high stability of the PAH-degradation phenotype suggests that the tested strains carry at least parts of the PAH-degradation pathway genes on the chromosome. The PAH-degradation versatility of the strains was also influenced by the carbon source being used for precultivation. Possible reasons for the particularly good impact of the precultivation on hexadecane on the PAH degradation are discussed in this paper.     

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

A microbial consortium (AM) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (PAH) mixture of three- and four-ringed PAHs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (DGGE), and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and seven by both DGGE and clone libraries were obtained. The comparison of three variable regions (V3-V5) of the 16S rRNA gene between the sequences obtained yielded 19 different microbial components. Proteobacteria were the dominant group, representing 83% of the total, while the Cytophaga-Flexibacter-Bacteroides group (CFB) was 11% and the Ascomycota fungi 6%. Beta-proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences were achieved by the cultivation method that showed members of the alpha-, beta-, and gamma-Proteobacteria; CFB bacterial group; and Ascomycota fungi. Only six of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1), which were similar to Sphingomonas sp. and Fusarium sp., respectively, achieved the greatest PAH depletion. The results indicate that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium.     

Multiple origins for phenylketonuria in Europe

Phenylketonuria (PKU), a disorder of amino acid metabolism prevalent among Caucasians and other ethnic groups, is caused primarily by a deficiency of the hepatic enzyme phenylalanine hydroxylase (PAH). PKU is a highly heterogeneous disorder, with more than 60 molecular lesions identified in the PAH gene. The haplotype associations, relative frequencies, and distributions of five prevalent PAH mutations (R158Q, R261Q, IVS10nt546, R408W, and IVS12n1) were established in a comprehensive European sample population and subsequently were examined to determine the potential roles of several genetic mechanisms in explaining the present distribution of the major PKU alleles. Each of these five mutations was strongly associated with only one of the more than 70 chromosomal haplotypes defined by eight RFLPs in or near the PAH gene. These findings suggest that each of these mutations arose through a single founding event that occurred within time periods ranging from several hundred to several thousand years ago. From the significant differences observed in the relative frequencies and distributions of these five alleles throughout Europe, four of these putative founding events could be localized to specific ethnic subgroups. Together, these data suggest that there were multiple, geographically and ethnically distinct origins for PKU within the European population.