Identification of distinct communities of sulfate-reducing bacteria in oil fields by reverse sample genome probing

Thirty-five different standards of sulfate-reducing bacteria, identified by reverse sample genome probing and defined as bacteria with genomes showing little or no cross-hybridization, were in part characterized by Southern blotting, using 16S rRNA and hydrogenase gene probes. Samples from 56 sites in seven different western Canadian oil field locations were collected and enriched for sulfate-reducing bacteria by using different liquid media containing one of the following carbon sources: lactate, ethanol, benzoate, decanoate, propionate, or acetate. DNA was isolated from the enrichments and probed by reverse sample genome probing using master filters containing denatured chromosomal DNAs from the 35 sulfate-reducing bacterial standards. Statistical analysis of the microbial compositions at 44 of the 56 sites indicated the presence of two distinct communities of sulfate-reducing bacteria. The discriminating factor between the two communities was the salt concentration of the production waters, which were either fresh water or saline. Of 34 standards detected, 10 were unique to the fresh water and 18 were unique to the saline oil field environment, while only 6 organisms were cultured from both communities.

Surface changes in mild steel coupons from the action of corrosion-causing bacteria

Changes which occur on the surface of mild steel coupons submerged in cultures of an Fe(III)-reducing bacterium, isolated from corroded pipe systems carrying crude oil, were studied microscopically to investigate the interaction between the corrosion-causing bacterium and the corroding mild steel coupon. Under micro-aerobic conditions and in the absence of the bacteria, a dense, crystalline, amorphous coat formed on the surface of the steel coupons. In the presence of bacteria the surface coat was extensively removed, exposing the bare metal to the environment. After about 2 weeks of exposure, the removal of the surface coating was followed by colonization of the metal surface by the bacteria. Colonization was mediated by fibrous, exopolysaccharidic material formed by the bacteria. Extension of studies to other bacteria isolated from crude oil and corroded pipes reveals that the formation of exopolysaccharide fibers and possession of adherent properties are common characteristics of bacteria from crude oil systems.

Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples

A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a "standard") to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples.

Distribution of Hydrogenase Genes in Desulfovibrio spp. and Their Use in Identification of Species from the Oil Field Environment

The distribution of genes for [Fe], [NiFe], and [NiFeSe] hydrogenases was determined for 22 Desulfovibrio species. The genes for [NiFe] hydrogenase were present in all species, whereas those for the [Fe] and [NiFeSe] hydrogenases had a more limited distribution. Sulfate-reducing bacteria from 16S rRNA groups other than the genus Desulfovibrio (R. Devereux, M. Delaney, F. Widdel, and D. A. Stahl, J. Bacteriol. 171:6689-6695, 1989) did not react with the [NiFe] hydrogenase gene probe, which could be used to identify different Desulfovibrio species in oil field samples following growth on lactate-sulfate medium.

Comparison of oil composition changes due to biodegradation and physical weathering in different oils

The well-characterized Alberta Sweet Mixed Blend oil and several other oils which are commonly transported in Canada were physically weathered and then incubated with a defined microbial inoculum. The purpose was to produce quantitative data on oil components and component groups which are more susceptible or resistant to biodegradation, and to determine how oils rank in relation to each other in terms of biodegradation potential. The biodegraded oils were characterized by quantitative determination of changes in important hydrocarbon groups including the total petroleum hydrocarbons, total saturates and aromatics, and also by quantitation of more than 100 individual target aliphatic, aromatic and biomarker components. The study reveals a pattern of distinct oil composition changes due to biodegradation, which is significantly different from the pattern due to physical or short-term weathering. It is important to be able to distinguish between these two forms of loss, so that loss due to weathering is not interpreted as loss due to biodegradation in the laboratory or in the field. Based on these findings, the oil composition changes due to biodegradation can be readily differentiated from those due to physical weathering. To rank the tested oils with respect to biodegradability, losses in total petroleum hydrocarbons and aromatics were used to calculate biodegradation potential indices, employing equations proposed by Environment Canada and the US National Oceanic and Atmospheric Administration. The different methods produced very similar biodegradation trends, confirming that patterns of oil biodegradability do exist.

Environmental gasoline-utilizing isolates and clinical isolates of Pseudomonas aeruginosa are taxonomically indistinguishable by chemotaxonomic and molecular techniques

A total of 42 Pseudomonas aeruginosa strains was isolated previously from clinical sources (27 strains) and from a gasoline-contaminated aquifer (15 strains). Selected strains were subjected to taxonomic tests involving chemical and molecular biological techniques, including membrane fatty acid analysis, phage-sensitivity, growth temperature range, presence of plasmids, and PCR-amplification and sequencing of a species-specific 16S-23S rDNA internal transcribed spacer region. The clinical and environmental isolates formed a coherent taxonomic group with few distinguishing characteristics. Of the phenotypes observed, a consistent difference was the ability of the aquifer strains to utilize gasoline supplied in the gas phase as sole carbon source and, conversely, the inability of the clinical strains to do so. Fourteen of the 15 environmental strains possessed similar-sized cryptic plasmids. The clinical isolates either lacked detectable plasmids or contained plasmids of a different size. The observation that the clinical and environmental isolates of P. aeruginosa were taxonomically indistinguishable is discussed in terms of its relevance to environmental-regulatory guidelines because P. aeruginosa, a known opportunistic pathogen, is a prime candidate for use in bioremediation processes involving deliberate release of this organism to 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 specificity permitting the oxidation of a suite of polycyclic aromatic and heterocyclic substrates.

Characterization of the diversity of sulfate-reducing bacteria in soil and mining waste water environments by nucleic acid hybridization techniques

Nucleic acid hybridization techniques were used to characterize the sulfate-reducing bacterial communities at seven waste water and two soil sites in Canada. Genomic DNA was obtained from liquid enrichment cultures of samples taken from these nine sites. The liquid enrichment protocol favored growth of the sulfate-reducing bacterial component of the communities at these sites. The genomic DNA preparations were analyzed with (i) a specific gene probe aimed at a single genus (Desulfovibrio), (ii) a general 16S rRNA gene probe aimed at all genera of sulfate-reducing bacteria and other bacteria, and (iii) whole genome probes aimed at specific bacteria. This three-pronged approach provided information on the sulfate-reducing bacterial community structures for the nine sites. These were compared with each other and with the sulfate-reducing bacterial communities of western Canadian oil field production waters, studied previously. It was found that there is considerable diversity in the sulfate-reducing bacterial community at each site. Most sulfate-reducing bacteria isolated from distinct sites are genomically different and differ also from sulfate-reducing bacteria found in oil field production waters.

Lignin Peroxidase Oxidation of Aromatic Compounds in Systems Containing Organic Solvents

Lignin peroxidase from Phanerochaete chrysosporium was used to study the oxidation of aromatic compounds, including polycyclic aromatic hydrocarbons and heterocyclic compounds, that are models of moieties of asphaltene molecules. The oxidations were done in systems containing water-miscible organic solvents, including methanol, isopropanol, N, N -dimethylformamide, acetonitrile, and tetrahydrofuran. Of the 20 aromatic compounds tested, 9 were oxidized by lignin peroxidase in the presence of hydrogen peroxide. These included anthracene, 1-, 2-, and 9-methylanthracenes, acenaphthene, fluoranthene, pyrene, carbazole, and dibenzothiophene. Of the compounds studied, lignin peroxidase was able to oxidize those with ionization potentials of <8 eV (measured by electron impact). The reaction products contain hydroxyl and keto groups. In one case, carbon-carbon bond cleavage, yielding anthraquinone from 9-methylanthracene, was detected. Kinetic constants and stability characteristics of lignin peroxidase were determined by using pyrene as the substrate in systems containing different amounts of organic solvent. Benzyl alkylation of lignin peroxidase improved its activity in a system containing water-miscible organic solvent but did not increase its resistance to inactivation at high solvent concentrations.

Quantitative Reverse Sample Genome Probing of Microbial Communities and Its Application to Oil Field Production Waters

This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters.

Effect of water-miscible organic solvents on the catalytic activity of cytochrome c

The effect of five water-miscible organic solvents (tetrahydrofuran, N,N-dimethylformamide, acetonitrile, 2-propanol, and methanol) on the oxidation of pinacyanol chloride (Quinaldine Blue) by horse heart cytochrome c was determined. Hydrogen peroxide was used as the oxidant, and a change in catalytic property of the dissolved protein was observed after a certain threshold concentration of the organic solvent had been reached. The maximum specific activity was correlated with the Dimroth-Reichardt parameter for the solvents, which is directly related to the free energy of the solvation process. The kinetic constants for the oxidation of pinacyanol chloride were determined in systems containing different proportions of tetrahydrofuran. The best catalytic efficiency (kcat/KM,app) was obtained in a system containing 50% tetrahydrofuran in phosphate buffer. In a mixture containing 90% tetrahydrofuran, cytochrome c showed 18% of its maximum activity. The inactivation of cytochrome c was mainly due to the presence of hydrogen peroxide, and a direct correlation was found between the inactivation constant and the concentration of hydrogen peroxide in the system. The chemical modifications and immobilization of cytochrome c were able to change its biocatalytic activity and stability in the organic solvent system. The kinetic constants and the inactivation of three other type c cytochromes, from Saccharomyces cerevisiae, Pseudomonas aeruginosa, and Desulfovibrio vulgaris Hildenborough in a system containing 90% tetrahydrofuran were compared with those of cytochrome c from horse heart. Cytochrome c551 from P. aeruginosa showed the best stability against hydrogen peroxide and a higher catalytic efficiency than that of horse heart cytochrome c.

Production of Streptomyces clavuligerus isopenicillin N synthase in Escherichia coli using two-cistron expression systems

Streptomyces clavuligerus isopenicillin N synthase (IPNS) gene expression was achieved in Escherichia coli by the construction of two-cistron expression systems formed in the high copy number plasmid vector pUC119. These two-cistron constructions were composed of the IPNS gene and its flanking sequences which encoded an upstream open reading frame (ORF), the IPNS ribosome binding site and a putative transcription terminator. No E. coli- like Streptomyces promoter motif was present upstream of the IPNS gene therefore transcriptional regulation of the two-cistron system was provided by the lac promoter of pUC119. Enzymatically active IPNS was detected in E. coli cells harboring the recombinant plasmids thereby providing evidence for the activity of the IPNS ORF and for the feasibility of production of S. clavuligerus IPNS in E. coli. These results indicate that simple two-cistron constructions involving foreign gene flanking sequences may be used to express foreign proteins in E. coli.

Purification and partial characterization of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase from Streptomyces clavuligerus

delta-(L-alpha-Aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) was purified from Streptomyces clavuligerus by a combination of salt precipitation, ultrafiltration, and anion-exchange chromatography. The final purified material gave two protein bands with molecular weights of 283,000 and 32,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Electrophoresis in nondenaturing gels gave a single protein band with an estimated molecular weight of 560,000. These results suggest that ACVS is a multimer composed of nonidentical subunits.

Expression of dibenzothiophene-degradative genes in two Pseudomonas species

The genes encoding dibenzothiophene (DBT) degradation in Pseudomonas alcaligenes strain DBT2 were cloned into plasmid pC1 by other workers. This plasmid was conjugally transferred into a spontaneous variant of Pseudomonas sp. HL7b (designated HL7bR) incapable of oxidizing DBT (Dbt- phenotype). Acquisition of plasmid pC1 simultaneously restored oxidation of DBT and naphthalene to the transconjugant, although the primary DBT metabolite produced by transconjugant HL7bR(pC1) corresponded to that produced by wild-type strain DBT2 rather than that from wild-type strain HL7b. Inducers of the naphthalene pathway (naphthalene, salicylic acid, and 2-aminobenzoate) stimulated DBT oxidation in transconjugant HL7bR(pC1) when present at 0.1 mM concentrations but had no effect on wild-type strain HL7b. Higher concentrations (5 mM) of salicylic acid and naphthalene were inhibitory to DBT oxidation in all strains. DNA-DNA hybridization was not observed between plasmid pC1 and genomic DNA from strains HL7b or HL7bR, nor between authentic naphthalene-degradative genes (plasmid NAH2) and either plasmid pC1 or strain HL7b, despite the observation that the degradative genes encoded on plasmid pC1 functionally resembled broad-specificity naphthalene-degradative genes. Transconjugant HL7bR(pC1) is a mosaic of the parental types regarding DBT metabolite production, regulation, and use of carbon sources.

Oxygen derepresses deacetoxycephalosporin C synthase and increases the conversion of penicillin N to cephamycin C in Streptomyces clavuligerus

When dissolved oxygen (DO) was maintained at saturation level during batch fermentations of Streptomyces clavuligerus (NRRL 3585), the accumulation of the intermediate penicillin N was lowered while formation of the end product cephamycin C was increased relative to fermentations without DO control. The specific activity of the penicillin ring-expansion enzyme deacetoxycephalosporin C synthase (DAOCS) was increased 2.3-fold under oxygen saturated conditions, whereas the penicillin ring-cyclizing enzyme isopenicillin N synthase (IPNS) showed only a 1.3-fold increase. Thus oxygen derepression of DAOCS appears to be an important regulatory mechanism in the conversion of penicillin N to cephamycin C in S. clavuligerus. IPNS, an early acting enzyme in cephamycin C biosynthesis, and DAOCS, which acts late in the pathway, both disappeared from cell extracts at 60 h, just prior to cessation of cephamycin production.

Mineralization of [14C]hexadecane and [14C]phenanthrene in crude oil: specificity among bacterial isolates

Bacteria isolated from freshwater, marine, and estuarine samples were tested for the ability to produce 14CO2 from n-[1-14C]hexadecane or [9-14C]phenanthrene added to Prudhoe Bay crude oil. Of 138 isolates tested, 54 (39%) mineralized the model aliphatic compound hexadecane and 6 (4%) mineralized the model aromatic compound phenanthrene. None mineralized both compounds. There was no apparent correlation between degradative ability and genus or source. Additional hydrocarbon-degrading bacteria from diverse sources were tested and found to mineralize either hexadecane or phenanthrene. Of 61 hexadecane- and 21 phenanthrene-mineralizing bacteria tested, none mineralized both model compounds. Selected isolates and commercially available cultures were tested for mineralization of specific 14C-labelled mono-, di-, and tri-cyclic aromatics. An apparent hierarchy of degradation was observed: strains mineralizing the mono- and di-cyclic aromatics toluene and naphthalene did not mineralize biphenyl or the tricyclic aromatics anthracene and phenanthrene, whereas those strains that mineralized the tricyclic aromatics also mineralized the smaller substrates. Similarly, not all n-alkane-mineralizing isolates tested mineralized the isoprenoid pristane. A combined culture consisting of one aliphatic- and one aromatic-degrading isolate was tested for mineralization of the model compounds and for degradation of other crude oil components by gas chromatography. No synergism or antagonism was observed compared with degradation by the individual isolates.

Isopenicillin N synthase and desacetoxycephalosporin C synthase activities during defined medium fermentations of Streptomyces clavuligerus: effect of oxygen and iron supplements

When the level of dissolved oxygen was increased to saturation in defined media fermentations of Streptomyces clavuligerus, the total duration of activity of the penicillin ring cyclization enzyme, isopenicillin N synthase (IPNS), was extended by at least 20 h; however, no increase in the stability of the ring expansion enzyme, desacetoxycephalosporin C synthase (DAOCS), was observed. Consequently, the conversion of the excreted intermediate penicillin N to cephamycin C was 15-20% less efficient at this high oxygen concentration. The increased dissolved oxygen level also led to the complete loss of IPNS and DAOCS activities for 4 h during the period of fastest growth, and the rate of specific cephamycin C production fell to zero. A several hundred fold increase in the level of iron in the defined media resulted in a sixfold improvement in the rate of specific cephamycin C production after 60 h fermentation. This increased rate appeared to be due to an elevation in the in vivo activities of a number of the cephamycin biosynthetic enzymes, particularly those catalysing later pathway steps.

Effect of Emulsan on Biodegradation of Crude Oil by Pure and Mixed Bacterial Cultures

Crude oil was treated with purified emulsan, the heteropolysaccharide bioemulsifier produced by Acinetobacter calcoaceticus RAG-1. A mixed bacterial population as well as nine different pure cultures isolated from various sources was tested for biodegradation of emulsan-treated and untreated crude oil. Biodegradation was measured both quantitatively and qualitatively. Recovery of 14 CO 2 from mineralized 14 C-labeled substrates yielded quantitative data on degradation of specific compounds, and capillary gas chromatography of residual unlabeled oil yielded qualitative data on a broad spectrum of crude oil components. Biodegradation of linear alkanes and other saturated hydrocarbons, both by pure cultures and by the mixed population, was reduced some 50 to 90% after emulsan pretreatment. In addition, degradation of aromatic compounds by the mixed population was reduced some 90% in emulsan-treated oil. In sharp contrast, aromatic biodegradation by pure cultures was either unaffected or slightly stimulated by emulsification of the oil.

Purification and initial characterization of deacetoxycephalosporin C synthase from Streptomyces clavuligerus

Deacetoxycephalosporin C synthase, the penicillin N ring expansion enzyme from Streptomyces clavuligerus, was purified to near homogeneity, as judged by sodium dodecyl sulphate - polyacrylamide gel electrophoresis. The synthase was monofunctional and could be completely separated from deacetoxycephalosporin C hydroxylase activity early in the purification sequence. Synthase specific activity was increased 97-fold over crude cell-free extracts, and the purified enzyme appeared to be a monomer with a molecular weight of 36,000 and a Km for the penicillin N substrate of 50 microM. Deacetoxycephalosporin C synthase activity required alpha-ketoglutarate, Fe2+, and oxygen and was specifically stimulated by ascorbate and dithiothreitol. The enzyme was sensitive to thiol-specific inhibitors, the most effective of which was N-ethylmaleimide.

Degradation of polycyclic aromatic hydrocarbons and aromatic heterocycles by a Pseudomonas species

Enrichment cultures were established with the aromatic fraction of a crude oil and screened for aromatic-degrading pseudomonads, using a sprayed plate technique. One isolate identified as Pseudomonas sp. HL7b was chosen for further study because it oxidized several polycyclic aromatic hydrocarbons and aromatic heterocycles without an apparent lag. Using capillary gas chromatography, spectrophotometry, and radiorespirometry, it was found to be capable of mineralizing and (or) oxidizing a wide range of polycyclic aromatic hydrocarbons, S-, N-, and O-heterocyclic analogues, and alkyl polycyclic aromatic hydrocarbons, but not aliphatic hydrocarbons. The isolate displayed two colonial morphologies which correlated with variation in degradative phenotype and hydrophobicity as measured by polystyrene adherence. Four cryptic plasmids were observed in both colonial types. Pseudomonas sp. HL7b degraded dibenzothiophene co-metabolically by a recognized pathway, but this degradation was constitutive, rather than inducible as reported for other bacteria.

Microbial degradation of n-alkyl tetrahydrothiophenes found in petroleum

Although n-alkyl-substituted tetrahydrothiophenes are found in nonbiodegraded petroleums, they are not found in petroleums which have undergone biodegradation in their reservoirs. These observations suggested that this group of compounds with alkyl chain lengths from approximately C10 to at least C30 is biodegradable. Two of these sulfides, 2-n-dodecyltetrahydrothiophene (DTHT) and 2-n-undecyltetrahydrothiophene, were synthesized, and their biodegradabilities were tested by using five gram-positive, n-alkane-degrading bacterial isolates. The alkyl side chains of these compounds were oxidized, and the major intermediates found in 2-n-undecyltetrahydrothiophene- and DTHT-metabolizing cultures were 2-tetrahydrothiophenecarboxylic acid (THTC) and 2-tetrahydrothiopheneacetic acid (THTA), respectively. Four n-alkane-degrading fungi were also shown to degrade DTHT, yielding both THTA and THTC. Quantitation of tetrahydrothiophene ring-containing products in 28-day-old bacterial and fungal cultures suggested that THTC and THTA were metabolized further to unidentified products. In addition, two of the bacterial isolates were shown to degrade a mixture of n-alkyl tetrahydrothiophenes isolated from Bellshill Lake crude oil.

Cloning and nucleotide sequence determination of the isopenicillin N synthetase gene from Streptomyces clavuligerus

The isopenicillin N synthetase (IPNS) gene from Streptomyces clavuligerus was isolated from an Escherichia coli plasmid library of S. clavuligerus genomic DNA fragments using a 44-mer mixed oligodeoxynucleotide probe. The nucleotide sequence of a 3-kb region of the cloned fragment from the plasmid, pBL1, was determined and analysis of the sequence showed an open reading frame that could encode a protein of 329 amino acids with an Mr of 36,917. When the S. clavuligerus DNA from pBL1 was introduced into an IPNS-deficient mutant of S. clavuligerus on the Streptomyces vector pIJ941, the recombinant plasmid was able to complement the mutation and restore IPNS activity. The protein coding region of the S. clavuligerus IPNS gene shows about 63% and 62% similarity to the Cephalosporium acremonium and Penicillium chrysogenum IPNS nucleotide sequences, respectively, and the predicted amino acid sequence of the encoded protein showed about 56% similarity to both fungal sequences.

Purification of isopenicillin N synthetase from Streptomyces clavuligerus

Isopenicillin N synthetase was purified from Streptomyces clavuligerus by sequential salt precipitation, ion-exchange and gel-filtration chromatography using both conventional open column and high-performance liquid chromatographic techniques. Material from the final purification step had a specific activity of 204.1 X 10(-3) units/mg of protein which represented a 130-fold purification over the cell-free extract. The purified isopenicillin N synthetase was determined to have a molecular weight of 33,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and to have a Km of 0.32 mM with respect to its substrate delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine. The enzyme showed a sensitivity to thiol-specific inhibitors with N-ethylmaleimide giving the strongest inhibitory effect.

Microbial release of 226Ra2+ from (Ba,Ra)SO4 sludges from uranium mine wastes

226Ra2+ is removed from uranium mine effluents by coprecipitation with BaSO4. (Ba,Ra)SO4 sludge samples from two Canadian mine sites were found to contain active heterotrophic populations of aerobic, anaerobic, denitrifying, and sulfate-reducing bacteria. Under laboratory conditions, sulfate reduction occurred in batch cultures when carbon sources such as acetate, glucose, glycollate, lactate, or pyruvate were added to samples of (Ba,Ra)SO4 sludge. No external sources of nitrogen or phosphate were required for this activity. Further studies with lactate supplementation showed that once the soluble SO4(2-) in the overlying water was depleted, Ba2+ and 226Ra2+ were dissolved from the (Ba,Ra)SO4 sludge, with the concurrent production of S2-. Levels of dissolved 226Ra2+ reached approximately 400 Bq/liter after 10 weeks of incubation. Results suggest that the ultimate disposal of these sludges must maintain conditions to minimize the activity of the indigenous sulfate-reducing bacteria to ensure that unacceptably high levels of 226Ra2+ are not released to the environment.

Synthesis of benzylpenicillin by cell-free extracts from Streptomyces clavuligerus

Cell-free enzyme concentrates from Streptomyces clavuligerus were found to convert phenylacetyl-L-cysteinyl-D-valine (PCV) directly into benzylpenicillin when incubated under reaction conditions which support the activity of isopenicillin N synthetase. The formation of benzylpenicillin was detected both by biological assay and by high performance liquid chromatography. Supplementation of PCV-containing reaction mixtures with cofactors required for ring expansion activity did not result in the production of cephalosporins. Incubation of phenoxyacetyl-L-cysteinyl-D-valine (PoCV) under the same reaction conditions did not result in the formation of penicillin V or any cephalosporin product.

Fungal Metabolism of n -Alkylbenzenes

Isolates of Paecilomyces, Verticillium, Beauveria , and Penicillium species were tested for ability to metabolize a variety of n -alkylbenzenes. Minimum side chain lengths were required for metabolism of these substrates. These were C 4 for the Paecilomyces sp., C 8 for the Verticillium sp., and C 9 for the other two isolates. Growth on dodecylbenzene yielded benzoic and phenylacetic acids as transient intermediates, and these acids supported growth of the isolates.

Enzymatic approach to syntheses of unnatural beta-lactams

Four enzymes associated with the transformation of the peptide delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) into the beta-lactam antibiotic desacetylcephalosporin C have been isolated from the prokaryotic organism Streptomyces clavuligerus and immobilized. Appropriate choice of the cofactors allows continuous and quantitative conversion of the peptide into either penicillins or cephalosporins at room temperature. The overall process includes four oxidations, two ring closures, and one epimerization. In contrast, cell-free transformations with the eukaryotic organism Cephalosporium acremonium do not proceed beyond the oxidation level of penicillin. The amino acids of the natural peptide ACV can be altered by chemical means; several of the resulting peptides are converted into novel antibiotics by the enzymes of Streptomyces clavuligerus.

Enzymatic synthesis of the penicillin and cephalosporin nuclei from an acyclic peptide containing carboxymethylcysteine

The tripeptide delta-(L- carboxymethylcysteinyl )-L-cysteinyl-D-valine (L-CMC-CV) is converted sequentially into the CMC analog of isopenicillin N, the CMC analog of penicillin N, and the CMC analog of desacetoxycephalosporin C by, respectively, isopenicillin N synthetase, isopenicillin N epimerase, and desacetoxycephalosporin C synthetase, all isolated from the beta-lactam producing prokaryote Streptomyces clavuligerus.

Microbial Degradation of Alkyl Carbazoles in Norman Wells Crude Oil

Norman Wells crude oil was fractionated by sequential alumina and silicic acid column chromatography methods. The resulting nitrogen-rich fraction was analyzed by gas chromatography-mass spectrometry and showed 26 alkyl (C 1 to C 5 ) carbazoles to be the predominant compounds. An oil-degrading mixed bacterial culture was enriched on carbazole to enhance its ability to degrade nitrogen heterocycles. This culture was used to inoculate a series of flasks of mineral medium and Norman Wells crude oil. Residual oil was recovered from these cultures after incubation at 25°C for various times. The nitrogen-rich fraction was analyzed by capillary gas chromatography, using a nitrogen-specific detector. Most of the C 1 -, C 2 -, and C 3 - carbazoles and one of the C 4 -isomers were degraded within 8 days. No further degradation occurred when incubation was extended to 28 days. The general order of susceptibility of the isomers to biodegradation was C 1 > C 2 > C 3 > C 4 . The carbazole-enriched culture was still able to degrade n -alkanes, isoprenoids, aromatic hydrocarbons, and sulfur heterocycles in the crude soil.

Partial purification and characterization of isopenicillin N epimerase activity from Streptomyces clavuligerus

Epimerase activity, which converts isopenicillin N to penicillin N, has been partially purified from cell-free extracts of Streptomyces clavuligerus. No stimulating cofactors of this activity were found, and neither EDTA nor anaerobic incubation caused significant inhibition of activity. Although pyridoxal phosphate did not stimulate epimerase activity, the presence of this cofactor was necessary for the stabilization of enzymic activity during the purification process. Epimerase activity was purified 35.5-fold by a combination of salt precipitation, gel filtration, and ion exchange chromatography. Gel filtration indicated that the epimerase has a molecular weight of 60 000 and sodium dodecyl sulphate-polyacrylamide gel electrophoresis of the 35.5-fold purified epimerase showed a major protein band running near that location. Pyridoxal phosphate antagonists did not uniformly inhibit epimerase activity, but the inhibitory effect of hydroxylamine could be partially reversed by pyridoxal phosphate.

Analysis of penicillin N ring expansion activity from Streptomyces clavuligerus by ion-pair high-pressure liquid chromatography

An ion-pair, reversed-phase, high-pressure liquid chromatographic method for the analysis of penicillin N ring expansion activity has been developed which allows simultaneous measurement of both substrate and product. The high-pressure liquid chromatography conditions were as follows: stationary phase, C18; flow rate, 2 ml/min; detection, 220 nm. The stationary phase was preconditioned with 4.5 mM tetrabutylammonium bromide in 0.05 M KH2PO4 (pH 4.0)-methanol (85:15, vol/vol) and then equilibrated with 0.06 mM tetrabutylammonium bromide in 0.05 M KH2PO4 (pH 4.0)-methanol (95:5, vol/vol) for analysis of reaction mixtures. These conditions separated authentic samples of penicillin N and desacetoxycephalosporin C and allowed cell-free studies of the ring expansion of penicillin N to desacetoxycephalosporin C by a partially purified enzyme from Streptomyces clavuligerus to be followed conveniently.

Cephalosporin formation by cell-free extracts from Streptomyces clavuligerus

Cell-free extracts of Streptomyces clavuligerus convert delta-L-(alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) into an antibiotic product which is 30 approximately 50% penicillinase-insensitive. Thin-layer chromatography resolves this antibiotic product into one major penicillinase-sensitive component and one major and one minor penicillinase-resistant component. The major and minor penicillinase-resistant antibiotics co-chromatograph with deacetoxycephalosporin C and deacetylcephalosporin C, respectively. Ring expansion of a penicillin intermediate, as evidenced by the production of penicillinase-resistant antibiotic, shows an absolute requirement for alpha-ketoglutarate, while ATP, K+ and Mg2+ have lesser effects. Ring expansion activity is not sedimented by high speed centrifugation and is unaffected by membrane-disrupting treatments. Penicillin N and ACV (presumably via penicillin N) are the only substrates so far accepted by the ring expanding enzyme. New syntheses of penicillin N and isopenicillin N are described.

High performance liquid chromatographic assay of cyclization activity in cell-free systems from Streptomyces clavuligerus

A thirteen-fold excess of dithiothreitol maintains delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) in its monomeric form under the conditions normally encountered in an ACV cyclization assay system, using Streptomyces clavuligerus. A reversed phase high performance liquid chromatographic (HPLC) system which separates ACV monomer from isopenicillin N, penicillin N and from other cyclization assay components has been developed as follows; mobile phase: 5% methanol-95% KH2PO4 (0.05 M adjusted to pH 4.0 with concentrated H3PO4; stationary phase: muBondapak-C18; flow rate: 2 ml/minute for 5 minutes, 3 ml/minute for the remainder; detection: 220 nm). Under these conditions, authentic samples of isopenicillin N and penicillin N elute with a retention time of 5.25 minutes, which coincides with a peak of newly-formed material observed in cyclization reaction mixtures. The combined concentration of isopenicillin N and penicillin N[(iso)penicillin N] in cyclization reaction mixtures corresponds closely to the concomitant decrease in the ACV monomer. Cyclization reaction mixtures, in which crude cell-free extract from S. clavuligerus NRRL 3585 is the enzyme source, contain (iso)penicillin N at a concentration of 43.3 micrograms/ml after a 1-hour incubation period. Cyclization reaction mixtures, in which salt-precipitated cell-free extract from S. clavuligerus is the enzyme source, contain 39.0 micrograms/ml (iso)penicillin N.

Effects of medium composition on cell pigmentation, cytochrome content, and ferric iron reduction in a Pseudomonas sp. isolated from crude oil

Cells of a pseudomonad associated with pipeline corrosion grown on a complex medium were orange in color and vigorously reduced ferric iron. The intensity of orange color of cells grown on a synthetic medium and their ability to reduce ferric iron was directly related to the iron content of the medium. Absorption spectrophotometric data show a direct relationship between color of cells, cytochrome content, and ability to reduce ferric iron. Carbon monoxide markedly, but not completely, inhibits the reduction of ferric iron. The data presented indicate that ferric iron can serve as a terminal electron acceptor for cytochrome-associated respiratory processes of this corrosive pseudomonad.

Cyclization of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine to penicillins by cell-free extracts of Streptomyces clavuligerus

Cell-free extracts prepared by sonication of Streptomyces clavuligerus cyclized delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) into a penicillin-type antibiotic. The antibacterial spectrum of this antibiotic suggested it was a mixture of isopenicillin N and penicillin N indicating that both cyclization and racemase activities were present. Cyclization activity was optimal in extracts prepared from 48 hours cultures. Extracts incubated at 20 degrees C produced antibiotic for 2 hours before activity ceased. Cyclization activity showed an absolute requirement for dithiothreitol (DTT) and O2 and was stimulated by ascorbic acid and FeSO4. No requirement for ATP was observed.

Effect of nitrate on reduction of ferric iron by a bacterium isolated from crude oil

A Pseudomonas sp. isolated from crude oil reduced ferric ions (Fe(III)) to ferrous ions (Fe(II)). In the presence of nitrate (NO3-) after prolonged incubation, the amount of Fe(II) was lower than in its absence. However, during short incubation periods, the presence of NO3- significantly increased (99.5% confidence limit) the amount of Fe(II) produced. The decrease in Fe(II) on prolonged incubation was associated with increased production and accumulation of nitrite (NO2-). Under low NO3- levels, where the production of NO2- was limited, a decrease in NO2- concentration was accompanied by an increase in Fe(II) production to levels comparable with those obtained in the absence of NO3-. Preinduction of cells for nitrate reductase, which favoured rapid NO2- production, resulted in a more rapid decrease in Fe(II) production than in cells that were not preinduced. It is proposed that the inhibitory effect of NO3- on microbial reduction of Fe(III) is due to a secondary reaction, which involves the chemical oxidation of Fe(II) by NO2-.

Microbial degradation of aromatics and saturates in Prudhoe Bay crude oil as determined by glass capillary gas chromatography

Water samples obtained from three different marine environments (including a commercial harbor, a pristine area, and an oil tanker dock area) from the coast of Washington State were challenged with Prudhoe Bay crude oil under shake-flask conditions at 8 degrees C. Replicate cultures were grown with and without nitrogen (NO3-, NH4+) and phosphate supplementation. After varying incubation periods, the residual oil was extracted and separated on silica gel columns into saturate aromatic fractions and these were analyzed by glass capillary gas chromatography to detect the degradation of various compounds. After 27 days of incubation, both the aromatic and saturate fractions were extensively degraded by the microorganisms from these environments when supplemented with nitrogen and phosphorus. Without nutrient supplementation, the aromatics were more readily attacked than the saturates by the populations from the pristine environment and from the commercial harbor area. Under these limited nutrient conditions, samples from near oil tanker docks showed moderate degradation of both the saturate and aromatic fractions. Time course studies, using nutrient-supplemented marine samples, showed that the simple aromatics (e.g., naphthalene and 2-methylnaphthalene) were more readily degraded than the n-alkanes. However, once the breakdown of these saturates commenced, these were quickly removed from the oil. The aromatic degradation continued to progress from lower molecular weight, less complex molecules to larger, more complex molecules in the approximate series C2 naphthalenes; phenanthrene and dibenzothiophene; C3 naphthalenes and methylphenathrenes; C2 phenanthrenes.

Biosynthesis of chloramphenicol in Streptomyces species 3022a: the nature of the arylamine synthetase system

The arylamine synthetase which catalyses the conversion of chorismic acid to p-aminophenylalanine in Streptomyces species 3022a was separated from aminotransferase by DEAE-cellulose chromatography. Recovered activity was further fragmented into three separate components by passage through a Sephadex G-100 column. Only one component produced p-aminophenylalanine but in combination the three stimulated each other activity. Although the products of the other two components were unstable, an infrared spectrum of one of them was obtained and confirmed the presence of an aromatic amine, but other functional groups could not be ascertained. This product was not recognized as a substrate by the arylamine synthetase complex and it was suggested that it may be a degradation product of an intermediate of p-aminophenylalanine biosynthesis or an unknown intermediate of later biosynthetic steps of the chloramphenicol pathway. It is further suggested that acrylamine compounds produced by this organism are the result of interaction of a core protein with other macromolecules and small molecular weight effect or molecules.

Crude oil utilization by fungi

Sixty fungal isolates, 34 obtained by a static enrichment technique from soils of northern Canadian oil-producing areas and 26 from culture collections, were screened for their ability to grow on n-tetradecane, toluene, naphthalene, and seven crude oils of varying composition. Forty cultures, including 28 soil isolates, were capable of growth on one or more crude oils. The genera most frequently isolated from soils were those producing abundant small condida, e.g. Penicillium and Verticillium spp. Oil-degrading strains of Beauveria bassiana, Mortieriella sp., Phoma sp., Scolecobasidium obovatum, and Tolypocladium inflatum were also isolated. Qualitative and quantitative differences were noted among the capacities of different crude oils to sustain the growth of individual fungal isolates. Data are presented which show that ability to grow on a pure n-alkane is not a good indicator of ability to grow on crude oil. Degradation of Rainbow Lake crude oil by individual isolates was demonstrated by gravimetric and gas-chromatographic techniques. The problems involved in determining the response and the potential of fungi to degrade oil spilled in the environment are discussed.

Characterization of the bacterial flora associated with root systems of Pinus contorta var. latifolia

Root systems of young and mature lodgepole pine (Pinus contorta Dougl. var. latifolia Englem.) were removed from forest stands and the associated aerobic bacterial flora isolated. Characterization of rhizoplane and control soil isolates from these tree root systems demonstrated differences from that reported for agricultural crops. Ammonifying, proteolytic, and amylolytic organisms were proportionately reduced within the rhizoplane. The rhizoplane organisms grew more slowly than the control soil isolates, although they responded in greater numbers to the addition of an amino acid supplement to the growth media. The rhizoplane organisms also showed an increased ability to solubilize phosphate. The chitinolytic organisms were suppressed within the rhizoplane of the mature tree but were stimulated by the young trees. With this exception, the rhizoplane microflora of older and younger trees were similar.

Characterization and regulation of anthranilate synthetase from a chloramphenicol-producing streptomycete

In Streptomyces sp. 3022a, anthranilate synthetase is composed of two non-identical subunits. The major subunit (molecular weight, 72,000) converts chorismic acid to anthranilic acid, using ammonia as the source of the amino group. The smaller subunit (molecular weight 28,000 to 29,000) confers on the enzyme the ability to use glutamine instead of ammonia as a substrate. In this study, reactivity with glutamine reached its maximum at pH 7.2 to 7.6, whereas that with ammonia increased linearly through pH 9.0 without reaching a maximum. Activity was increased and stabilized by adding glutamine and magnesium chloride to the buffer system. Both activities of the enzyme were inhibited by anthranilic acid and by tryptophan. Synthesis was repressed by histidine, anthranilic acid, tryptophan, and p-aminobenzoic acid. When activity was repressed by anthranilic acid and by tryptophan, there was a concomitant increase in the activity of arylamine synthetase, an enzyme involved in chloramphenicol production. Stimulating arylamine synthetase, however, did not increase antibiotic synthesis.

In situ degradation of oil in a soil of the boreal region of the Northwest Territories

Replicate field plots comprising a control; control plus oil; control plus oil and fertilizer (urea phosphate, 27:27:0); control plus oil and bacteria; and control plus oil, fertilizer, and bacteria were established at Norman Wells, N.W.T., Canada. Plots were monitored over a 3-year period for changes in microbial numbers and the chemical composition of recovered oil. Where fertilizer was applied, there was a rapid increase in bacterial numbers, but no increase in fungal propagules. This was followed by a rapid disappearance of n-alkanes, isoprenoids, and a continuous loss in weight of saturate compounds in recovered oil. Changes in the content of asphaltenes, aromatics, and nitrogen-, sulphur-, and oxygen-containing fractions also are discussed. The seeding of oil-soaked plots with oil-degrading bacteria did not have any effect on the composition of recovered oil. Fertilized plots showed a more rapid rate of vegetation with cotton grass and Labrador tea being the dominant species in revegetation.

Bouyant density, conversion formulae, and the mole percent guanosine + cytosine content of Desulfovibrio sp

A reevaluation of the original buoyant density conversion formula used to calculate the molar percentage guanosine + cytosine (% G + C) contents of the accepted species of genus Desulfovibrio has been undertaken. It would appear that the formula used gives values 4-5% lower than those obtained using formulae more generally cited in modern literature. Recalculations of % G + C content values for Lesulfovibrio DNA are presented using the formulae of three different workers, and are compared with those values originally used in the classification of genus Desulfovibrio.

Microbial utilization of raw and hydrogenated shale oils

The biodegradability of raw and hydrogenated shale oils prepared by a retort process were studied under psychrophilic and mesophilic conditions. Changes in bacterial numbers and the chemical composition of the oils were monitored using a plate count and chromatographic techniques respectively. Raw shale oil was found to be relatively resistant to microbial attack whereas hydrogenated shale oil was readily utilized for microbial growth. Populations enriched on raw shale oil had a reduced ability to use hydrogenated shale oil under similar conditions. Gram-negative rods predominated in all enrichment populations. It is recommended that to facilitate clean up of shale oil spills, raw shale oil be reduced at the extraction site before transport.

Quantitative assessment of the bacterial rhizosphere flora of Pinus contorta var. latifolia

The bacterial flora associated with root systems of young and mature lodgepole pine was investigated by sampling forest-grown trees. Counts were performed and expressed on a surface-area basis to give a more realistic comparison of organism density or activity within the control soil, rhizosphere soil, and rhizoplane. On this basis, densities increased by an order of 10(4)- to 10(6)-fold from control soil to rhizoplane, with the degree of stimulation being inversely related to root radius.

Changes in pattern of respiration and glucose utilisation in Candida utilis during the cell cycle: some variations with growth rate

The release of 14CO2 from 14C-labelled glucose(G-1(-14)C, G-3,4(-14)C, G-6(-14)C) was followed in phased cultures of Candida utilis grown in a glucose- mineral salts medium under altered conditions of carbon:nitrogen limitation at doubling times of 2,4 and 6, h. Changes in oxygen uptake and CO2 evolution were observed and respirometric studies showed that the relative contributions of the Embden-Meyerhof-Parnas and hexose monophosphate pathways varied over the cell cycle and changed with growth rate. The results are discussed in relation to the growth metabolism of the cells.

Utilization of triaryl phosphates by a mixed bacterial population

A mixed bacterial population that has been isolated by enrichment culture is capable of growth on Fyrquel 220, a commercial triaryl phosphate lubricant, as sole carbon source. The mixture was dominated by a yellow, Gram-negative rod which made up greater than 60% of the mixture. However, all attempts to grow this organism in pure culture on triaryl phosphate were unsuccessful. The mixed population was also capable of growth on tri-o-cresyl phosphate, trixylenyl phosphate, and triphenyl phosphate as sole carbon sources. Viable cell numbers increased 20- to 30-fold, reaching a maximum after 72-96 h growth. Only a small portion of the triaryl phosphate was used for growth; the major part was emulsified and remained in the culture medium. No evidence of extracellular enzymes capable of triaryl phosphate degradation could be found in concentrates of the culture supernatant after growth, though traces of what may have been triaryl phosphate breakdown products were observed. Cell-free extracts of the mixed culture catalyzed the release of inorganic phosphate when incubated with Fyrquel 220, tri-o-cresyl phosphate, trixylenyl phosphate, or triphenyl phosphate, indicating the presence of a phosphotriesterase or of a phosphodiesterase of wide specificity.