Hydrocarbon utilization by nodule bacteria and plant growth-promoting rhizobacteria

Standard and locally isolated nodule bacteria and plant growth-promoting rhizobacteria (PGPR) were grown on crude oil and individual pure hydrocarbons as sole sources of carbon and energy. The nodule bacteria included two standard Rhizobium leguminosarum strains, two standard Bradyrhizobium japonicum strains, and one unknown nodule bacterial strain that was locally isolated from Vicia faba nodules. The PGPR included one standard Serratia liquefaciens strain and two locally isolated strains of Pseudomonas aeruginosa and Flavobacterium sp. The pure hydrocarbons tested included n-alkanes with chain lengths from C9 to C40 and the aromatic hydrocarbons benzene, biphenyle, naphthalene, phenanthrene, and toluene. Quantitative gas liquid chromatographic analyses confirmed that pure cultures of representative nodule bacteria and PGPR could attenuate n-octadecane and phenanthrene in the surrounding nutrient medium. Further, intact nodules of V. faba containing bacteria immobilized on and within those nodules reduced hydrocarbon levels in a medium in which those nodules were shaken. It was concluded that legume crops are suitable phytoremediation tools for oily soil, since they enrich such soils not only with fixed nitrogen, but also with hydrocarbon-utilizing microorganisms. Further, legume nodules may have biotechnological value as materials for cleaning oily liquid wastes.     

微生物降解多环芳烃(PAHs)的研究进展

从多环芳烃(PAHs)的降解菌株的筛选、降解机制以及PAHs污染的生物修复等方面介绍了微生物降解PAHs的最新研究进展。     

Bacterial cis-dihydrodiol dehydrogenases: comparison of physicochemical and immunological protperties.

Cells of Pseudomonas putida NP, Pseudomonas species (NCIB 9816), and a Nocardia species, after growth on naphthalene as sole source of carbon and energy, contain a nicotinamide adenine dinucleotide (NAD+)-dependent enzyme that oxidizes cis-dihydrodiols of mono- and polycyclic aromatic compounds. Similarly, cells of a strain of P. putida biotype A, when grown either on toluene or benzene vapors, were found to contain a dehydrogenase that oxidized dihydrodiols of aromatic hydrocarbons with cis stereochemistry and required NAD+ as an electron acceptor. In all these cases, no enzymatic activity was detected when trans-naphthalene dihydrodiol was used as a substrate. Purified cis-naphthalene dihydrodiol dehydrogenase was injected into rabbits to obtain antibodies. Physiocochemical and immunological properties of cis-dihydrodiol:NAD+ oxidoreductases from four different organisms were examined. Kinetic analysis showed that, in all the cases, enzymes exhibited higher affinity for cis-dihydrodiols than for NAD+ and had pH optima between 8.8 and 9.0. except in the case of the enzyme from Nocarida sp., which showed maximum activity at pH 8.4. Molecular-weight determination of the dehydrogenases from the four different organisms by gel filtration on a Sephadex G-200 column gave values ranging from 92,000 for the enzyme from Nocardia sp. to 160,000 for that from P. putida biotype A. All the dehydrogenases, except the one from Nocardia sp., exhibited immunological cross-reaction with the antibodies prepared against the enzyme purified from P. putida NP.     

PAH utilization by Pseudomonas rhodesiae KK1 isolated from a former manufactured-gas plant site

Pseudomonas rhodesiae KK1 was isolated from a former manufactured-gas plant site, due to its ability to grow rapidly in a mixture of polycyclic aromatic hydrocarbons (PAHs). Radiorespirometric analysis revealed that strain KK1 was found to be able to mineralize anthracene, naphthalene and phenanthrene. Notably, phenanthrene-grown cells were able to mineralize anthracene much more rapidly than naphthalene-grown cells. Comparative analysis of amino acid sequences from 17 randomly selected dioxygenases capable of hydroxylating unactivated aromatic nuclei indicated that the enzymes for catabolism of PAHs, such as naphthalene and phenanthrene, might exist redundantly in strain KK1. Northern hybridization for cells grown on naphthalene or phenanthrene, using the putative naphthalene or phenanthrene dioxygenase gene fragment as a probe, suggested that the enzyme for naphthalene catabolism might share some homology in deduced amino acid sequences with phenanthrene dioxygenases. Also, it was found that three lipids (17:0 cyclo, 18:1 omega7c, 19:0 cyclo) increased in response to both naphthalene and phenanthrene, while the shift of other lipids varied from substrate to substrate.     

Involvement of a rhamnolipid-producing strain of Pseudomonas aeruginosa in the degradation of polycyclic aromatic hydrocarbons by a bacterial community

A rhamnolipid-producing strain of Pseudomonas aeruginosa GL1 was isolated from a bacterial community growing on a mixture of polycyclic aromatic hydrocarbons (PAH) as sole carbon source. Strain GL1 did not grow on PAH but grew on known degradation metabolites of phenanthrene ( o -phthalic acid) and of naphthalene (salicylic acid). In co-culture with a phenanthrene-degrading strain, Ps. aeruginosa GL1 accelerated the degradation of phenanthrene. Strain GL1 was resistant to toxic amphiphilic compounds such as cationic and anionic detergents. Rhamnolipid production took place in a late stage growth in cultures of strain GL1 on glycerol or n -hexadecane. It coincided with a substantial decrease in cell hydrophobicity and with morphological changes of the outer membrane as observed by transmission electronic microscopy. The rhamnolipids produced inhibited the growth of bacteria such as Rhodococcus erythropolis , Bacillus cereus and Ps. fluorescens . The overall results suggested an outer membrane origin for the rhamnolipids. They also indicate that the utilization of PAH metabolites by strain GL1 is important for the stability of the PAH-degrading community.     

The potential of established turf cover for cleaning oily desert soil using rhizosphere technology

The rhizosphere of two turf cover sorts; Bermuda grass and American grass contained high numbers, 8.1 to 16.8 x 10(6) g(-1) of cultivable oil-utilizing and diazotrophic bacteria belonging predominantly to the genera Agrobacterium, Arthrobacter, Pseudomonas, Gordonia, and Rhodococcus. Those bacteria also grew on a nitrogen-free medium and demonstrated the ability to reduce acetylene to ethylene. These isolates grew on a wide range of n-alkanes (C9 to C40) and aromatic hydrocarbons, as sole sources of carbon. Quantitative determinations revealed that predominant bacteria consumed crude oil and representative aliphatic (n-octadecane) and aromatic (phenanthrene) hydrocarbons efficiently. The fact that those organisms had the combined activities of hydrocarbon-utilization and nitrogen-fixation makes them suitable tools for bioremediating oily desert areas that are normally poor in nitrogenous compounds. Phytoremediation experiments showed that spreading turf cover on oily desert soil inhibited oil volatilization and enhanced oil loss in soil by about 15%. Oil loss was also enhanced in turf free soil samples fertilized with NH4NO3. In conclusion, covering this oil-polluted soil with turf cover minimized atmospheric pollution, increased the numbers of the oil-utilizing/nitrogen-fixing bacteria by about 20 to 46% thus, encouraging oil attenuation.     

Plasmid-mediated mineralization of naphthalene, phenanthrene, and anthracene.

The well-characterized plasmid-encoded naphthalene degradation pathway in Pseudomonas putida PpG7(NAH7) was used to investigate the role of the NAH plasmid-encoded pathway in mineralizing phenanthrene and anthracene. Three Pseudomonas strains, designated 5R, DFC49, and DFC50, were recovered from a polynuclear aromatic hydrocarbon-degrading inoculum developed from a manufactured gas plant soil slurry reactor. Plasmids pKA1, pKA2, and pKA3, approximately 100 kb in size, were isolated from these strains and characterized. These plasmids have homologous regions of upper and lower NAH7 plasmid catabolic genes. By conjugation experiments, these plasmids, including NAH7, have been shown to encode the genotype for mineralization of [9-14C]phenanthrene and [U-14C]anthracene, as well as [1-14C]naphthalene. One strain, Pseudomonas fluorescens 5RL, which has the complete lower pathway inactivated by transposon insertion in nahG, accumulated a metabolite from phenanthrene and anthracene degradation. This is the first direct evidence to indicate that the NAH plasmid-encoded catabolic genes are involved in degradation of polynuclear aromatic hydrocarbons other than naphthalene.     

Anaerobic degradation of non-substituted aromatic hydrocarbons

Aromatic hydrocarbons are among the most prevalent organic pollutants in the environment. Their removal from contaminated systems is of great concern because of the high toxicity effect on living organisms including humans. Aerobic degradation of aromatic hydrocarbons has been intensively studied and is well understood. However, many aromatics end up in habitats devoid of molecular oxygen. Nevertheless, anaerobic degradation using alternative electron acceptors is much less investigated. Here, we review the recent literature and very early progress in the elucidation of anaerobic degradation of non-substituted monocyclic (i.e. benzene) and polycyclic aromatic hydrocarbons (PAH such as naphthalene and phenanthrene). A focus will be on benzene and naphthalene as model compounds. This review concerns the microbes involved, the biochemistry of the initial activation and subsequent enzyme reactions involved in the pathway.     

Isolation and characterization of four polycyclic aromatic hydrocarbon degrading bacteria from soil near an oil refinery

Four bacterial strains (I-IV) capable of optimum growth on 0·1% naphthalene, anthracene or a mixture of naphthalene and phenanthrene were isolated from soil near an oil refinery. Two isolates (I and II) were identified as belonging to the genus Micrococcus , while strains III and IV were identified as Pseudomonas and Atcaligenes respectively. All the isolates were found to bear high molecular weight plasmid DNA (isolate I and IV 89%, II 67·5% and III 92·1% of Λ DNA), which is presumed to aid in the metabolism of polycyclic aromatic hydrocarbons. The strains also showed appreciable growth at high concentrations of NaCl (up to 7·5%).     

Biodegradation of phenanthrene by<Emphasis Type="Italic"> Pseudomonas</Emphasis> sp. strain PP2: novel metabolic pathway,role of biosurfactant and cell surface hydrophobicity in hydrocarbon assimilation

Pseudomonas sp. strain PP2 isolated in our laboratory efficiently metabolizes phenanthrene at 0.3% concentration as the sole source of carbon and energy. The metabolic pathways for the degradation of phenanthrene, benzoate and p-hydroxybenzoate were elucidated by identifying metabolites, biotransformation studies, oxygen uptake by whole cells on probable metabolic intermediates, and monitoring enzyme activities in cell-free extracts. The results obtained suggest that phenanthrene degradation is initiated by double hydroxylation resulting in the formation of 3,4-dihydroxyphenanthrene. The diol was finally oxidized to 2-hydroxymuconic semialdehyde. Detection of 1-hydroxy-2-naphthoic acid, alpha-naphthol, 1,2-dihydroxy naphthalene, and salicylate in the spent medium by thin layer chromatography; the presence of 1,2-dihydroxynaphthalene dioxygenase, salicylaldehyde dehydrogenase and catechol-2,3-dioxygenase activity in the extract; O(2) uptake by cells on alpha-naphthol, 1,2-dihydroxynaphthalene, salicylaldehyde, salicylate and catechol; and no O(2) uptake on o-phthalate and 3,4-dihydroxybenzoate supports the novel route of metabolism of phenanthrene via 1-hydroxy-2-naphthoic acid --> [alpha-naphthol] --> 1,2-dihydroxy naphthalene --> salicylate --> catechol. The strain degrades benzoate via catechol and cis,cis-muconic acid, and p-hydroxybenzoate via 3,4-dihydroxybenzoate and 3-carboxy- cis,cis-muconic acid. Interestingly, the culture failed to grow on naphthalene. When grown on either hydrocarbon or dextrose, the culture showed good extracellular biosurfactant production. Growth-dependent changes in the cell surface hydrophobicity, and emulsification activity experiments suggest that: (1) production of biosurfactant was constitutive and growth-associated, (2) production was higher when cells were grown on phenanthrene as compared to dextrose and benzoate, (3) hydrocarbon-grown cells were more hydrophobic and showed higher affinity towards both aromatic and aliphatic hydrocarbons compared to dextrose-grown cells, and (4) mid-log-phase cells were significantly (2-fold) more hydrophobic than stationary phase cells. Based on these results, we hypothesize that growth-associated extracellular biosurfactant production and modulation of cell surface hydrophobicity plays an important role in hydrocarbon assimilation/uptake in Pseudomonas sp. strain PP2.     

Production of Proteinase on Noncarbohydrate Carbon Sources by Pseudomonas aeruginosa

Proteinase production by Pseudomonas aeruginosa was studied in medium containing noncarbohydrate materials, especially various hydrocarbons, as the sole carbon source. On heavy oil, kerosene, n-paraffinic hydrocarbon of C₁₂, C₁₄, or C₁₆, and propylene glycol, the bacteria grew well and high protinase production was observed. However, production on paraffinic hydrocarbon differed remarkably with strains of varied origins. The elastase-positive strain, IFO 3455, showed abundant growth and high proteinase production on medium containing a paraffin of C₁₂, C₁₄, or C₁₆, whereas the elastase-negative strain, IFO 3080, showed little growth on the same medium. Neither elastase-positive nor elastase-negative strains, however, utilized n-paraffins of C₅ to C₁₀, or various aromatic hydrocarbons such as benzene, naphthalene, phenanthrene, and anthracene. The proteinases produced on the noncarbohydrate medium were identical with those produced in glucose medium.     

Isolation of phenanthrene-degrading bacteria and characterization of phenanthrene metabolites

Three aerobic bacterial consortia GY2, GS3 and GM2 were enriched from polycyclic aromatic hydrocarbon-contaminated soils with water-silicone oil biphasic systems. An aerobic bacterial strain utilizing phenanthrene as the sole carbon and energy source was isolated from bacterial consortium GY2 and identified as Sphingomonas sp. strain GY2B. Within 48 h and at 30°C the strain metabolized 99.1% of phenanthrene (100 mg/l) added to batch culture in mineral salts medium and the cell number increased by about 40-fold. Three metabolites 1-hydroxy-2-naphthoic acid, 1-naphthol and salicylic acid, were identified by gas chromatographic mass spectrometry and UV–visible spectroscopy analysis. A degradation pathway was proposed based on the identified metabolites. In addition to phenanthrene, strain GY2B could use other aromatic compounds such as naphthalene, 2-naphthol, salicylic acid, catechol, phenol, benzene and toluene as a sole source of carbon and energy.     

Substrate interactions during aerobic biodegradation of benzene

This study dealt with the interactions with benzene degradation of the following aromatic compounds in a mixed substrate: toluene, o-xylene, naphthalene, 1,4-dimethylnaphthalene, phenanthrene, and pyrrole. The experiment was performed as a factorial experiment with simple batch cultures. The effect of two different types of inocula was tested. One type of inoculum was grown on a mixture of aromatic hydrocarbons; the other was grown on a mixture of aromatic hydrocarbons and nitrogen-, sulfur-, and oxygen-containing aromatic compounds (NSO compounds), similar to some of the compounds identified in creosote waste. The culture grown on the aromatic hydrocarbons and NSO compounds was much less efficient in degrading benzene than the culture grown on only aromatic hydrocarbons. The experiments indicated that toluene- and o-xylene-degrading bacteria are also able to degrade benzene, whereas naphthalene-, 1,,4-dimethylnaphthalene-, and phenanthrene-degrading bacteria have no or very little benzene-degrading ability. Surprisingly, the stimulating effect of toluene and o-xylene was true only if the two compounds were present alone. In combination an antagonistic effect was observed, i.e., the combined effect was smaller than the sum from each of the compounds. The reason for this behavior has not been identified. Pyrrole strongly inhibited benzene degradation even at concentrations of about 100 to 200 micrograms/liter. Future studies will investigate the generality of these findings.     

Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field.

Microbiological analyses of sediments chronically exposed to petrogenic hydrocarbons resulted in the isolation of a gram-positive, rod-shaped bacterium which mineralized naphthalene (59.5% of the original amount), phenanthrene (50.9%), fluoranthene (89.7%), pyrene (63.0%), 1-nitropyrene (12.3%), 3-methylcholanthrene (1.6%), and 6-nitrochrysene (2.0%) to carbon dioxide when grown for 2 weeks in pure culture with organic nutrients. The bacterium tolerated salt concentrations up to 4% and grew well at 24 to 30 degrees C. The use of this bacterium may be an attractive alternative to existing physicochemical methods for the remediation of polycyclic aromatic hydrocarbons in the environment.     

Transposon and spontaneous deletion mutants of plasmid-borne genes encoding polycyclic aromatic hydrocarbon degradation by a strain of Pseudomonas fluorescens

Pseudomonas fluorescens strain LP6a, isolated from petroleum condensate-contaminated soil, utilizes the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, anthracene and 2-methylnaphthalene as sole carbon and energy sources. The isolate also co-metabolically transforms a suite of PAHs and heterocycles including fluorene, biphenyl, acenaphthene, 1-methylnaphthalene, indole, benzothiophene, dibenzothiophene and dibenzofuran, producing a variety of oxidized metabolites. A 63 kb plasmid (pLP6a) carries genes encoding enzymes necessary for the PAH-degrading phenotype of P. fluorescens LP6a. This plasmid hybridizes to the classical naphthalene degradative plasmids NAH7 and pWW60, but has different restriction endonuclease patterns. In contrast, plasmid pLP6a failed to hybridize to plasmids isolated from several phenanthrene-utilizing strains which cannot utilize naphthalene. Plasmid pLP6a exhibits reproducible spontaneous deletions of a 38 kb region containing the degradative genes. Two gene clusters corresponding to the archetypal naphthalene degradation upper and lower pathway operons, separated by a cryptic region of 18 kb, were defined by transposon mutagenesis. Gas chromatographic-mass spectrometric analysis of metabolites accumulated by selected transposon mutants indicates that the degradative enzymes encoded by genes on pLP6a have a broad substrate specificity permitting the oxidation of a suite of polycyclic aromatic and heterocyclic substrates.     

Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field

Microbiological analyses of sediments chronically exposed to petrogenic hydrocarbons resulted in the isolation of a gram-positive, rod-shaped bacterium which mineralized naphthalene (59.5% of the original amount), phenanthrene (50.9%), fluoranthene (89.7%), pyrene (63.0%), 1-nitropyrene (12.3%), 3-methylcholanthrene (1.6%), and 6-nitrochrysene (2.0%) to carbon dioxide when grown for 2 weeks in pure culture with organic nutrients. The bacterium tolerated salt concentrations up to 4% and grew well at 24 to 30 degrees C. The use of this bacterium may be an attractive alternative to existing physicochemical methods for the remediation of polycyclic aromatic hydrocarbons in the environment.     

Substrate interactions during aerobic biodegradation of benzene.

This study dealt with the interactions with benzene degradation of the following aromatic compounds in a mixed substrate: toluene, o-xylene, naphthalene, 1,4-dimethylnaphthalene, phenanthrene, and pyrrole. The experiment was performed as a factorial experiment with simple batch cultures. The effect of two different types of inocula was tested. One type of inoculum was grown on a mixture of aromatic hydrocarbons; the other was grown on a mixture of aromatic hydrocarbons and nitrogen-, sulfur-, and oxygen-containing aromatic compounds (NSO compounds), similar to some of the compounds identified in creosote waste. The culture grown on the aromatic hydrocarbons and NSO compounds was much less efficient in degrading benzene than the culture grown on only aromatic hydrocarbons. The experiments indicated that toluene- and o-xylene-degrading bacteria are also able to degrade benzene, whereas naphthalene-, 1,,4-dimethylnaphthalene-, and phenanthrene-degrading bacteria have no or very little benzene-degrading ability. Surprisingly, the stimulating effect of toluene and o-xylene was true only if the two compounds were present alone. In combination an antagonistic effect was observed, i.e., the combined effect was smaller than the sum from each of the compounds. The reason for this behavior has not been identified. Pyrrole strongly inhibited benzene degradation even at concentrations of about 100 to 200 micrograms/liter. Future studies will investigate the generality of these findings.     

Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments

The diversity of indigenous bacteria in sediments from several sites in the Elizabeth River (Virginia) able to degrade multiple polycyclic aromatic hydrocarbons (PAHs) was investigated by the use of classical selective enrichment and molecular analyses. Enrichment cultures containing naphthalene, phenanthrene, fluoranthene, or pyrene as a sole carbon and energy source were monitored by denaturing gradient gel electrophoresis (DGGE) to detect changes in the bacterial-community profile during enrichment and to determine whether the representative strains present were successfully cultured. The DGGE profiles of the final enrichments grown solely on naphthalene and pyrene showed no clear relationship with the site from which the inoculum was obtained. The enrichments grown solely on pyrene for two sample sites had >80% similarity, which suggests that common pyrene-degrading strains may be present in these sediments. The final enrichments grown on fluoranthene and phenanthrene remained diverse by site, suggesting that these strains may be influenced by environmental conditions. One hundred and one isolates were obtained, comprising representatives of the actinomycetes and alpha-, beta-, and gammaproteobacteria, including seven novel isolates with 16S rRNA gene sequences less than 98% similar to known strains. The ability to degrade multiple PAHs was demonstrated by mineralization of 14C-labeled substrate and growth in pure culture. This supports our hypothesis that a high diversity of bacterial strains with the ability to degrade multiple PAHs can be confirmed by the combined use of classical selective enrichment and molecular analyses. This large collection of diverse PAH-degrading strains provides a valuable resource for studies on mechanisms of PAH degradation and bioremediation.     

Indigenous PAH-degrading bacteria from oil-polluted sediments in Caleta Cordova,Patagonia Argentina

Indigenous bacteria with the capability to degrade polycyclic aromatic hydrocarbons (PAH) were isolated from polluted sediment samples recovered from Caleta Cordova by using selective enrichment cultures supplemented with phenanthrene. Bacterial communities were evaluated by denaturing gradient gel electrophoresis (DGGE) in order to detect changes along enrichment culture and relationships with the representative strains subsequently isolated. Members of these communities included marine bacteria such as Lutibacter, Polaribacter, Arcobacter and Olleya, whose degradation pathway of PAH has not been studied yet. However, isolated bacteria obtained from this enrichment comprised the genus Pseudomonas, Marinobacter, Salinibacterium and Brevibacterium. The ability of isolates to grow and degrade naphthalene, phenanthrene and pyrene was demonstrated by detection of the residual substrate by HPLC. Archetypical naphthalene and catechol dioxygenase genes were found in two isolates belonging to genus Pseudomonas (Pseudomonas monteilii P26 and Pseudomonas xanthomarina N12), suggesting biodegradation potential in these sediments. The successful bacterial isolation with the ability to degrade PAH in pure culture suggest the possibility to study and further consider strategies like growth stimulation in situ, in order to increase the intrinsic bioremediation opportunities in the polluted Caleta Cordova harbor.     

Biodegradation of mixtures of substituted benzenes by Pseudomonas sp. strain JS150.

Pseudomonas sp. strain JS150 was isolated as a nonencapsulated variant of Pseudomonas sp. strain JS1 that contains the genes for the degradative pathways of a wide range of substituted aromatic compounds. Pseudomonas sp. strain JS150 grew on phenol, ethylbenzene, toluene, benzene, naphthalene, benzoate, p-hydroxybenzoate, salicylate, chlorobenzene, and several 1,4-dihalogenated benzenes. We designed experiments to determine the conditions required for induction of the individual pathways and to determine whether multiple substrates could be biodegraded simultaneously. Oxygen consumption studies with whole cells and enzyme assays with cell extracts showed that the enzymes of the meta, ortho, and modified ortho cleavage pathways can be induced in strain JS150. Strain JS150 contains a nonspecific toluene dioxygenase with a substrate range similar to that found in strains of Pseudomonas putida. The presence of the dioxygenase along with multiple pathways for metabolism of substituted catechols allows facile extension of the growth range by spontaneous mutation and degradation of mixtures of substituted benzenes and phenols. Chlorobenzene-grown cells of strain JS150 degraded mixtures of chlorobenzene, benzene, toluene, naphthalene, trichloroethylene, and 1,2- and 1,4-dichlorobenzenes in continuous culture. Under similar conditions, phenol-grown cells degraded a mixture of phenol, 2-chloro-, 3-chloro, and 2,5-dichlorophenol and 2-methyl- and 3-methylphenol. These results indicate that induction of appropriate biodegradative pathways in strain JS150 permits the biodegradation of complex mixtures of aromatic compounds.