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

1999 ◽  
Vol 65 (1) ◽  
pp. 251-259 ◽  
Author(s):  
Brian P. Hedlund ◽  
Allison D. Geiselbrecht ◽  
Timothy J. Bair ◽  
James T. Staley
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Puget Sound ◽  
Amino Acid Sequences ◽  
Genotypic Differences ◽  
Degenerate Primers ◽  
Genes Encoding ◽  
Polycyclic Aromatic

ABSTRACT 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 andBurkholderia 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 ofN. naphthovorans is strain NAG-2N-126.

scholarly journals Isolation of Marine Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Cycloclasticus Strains from the Gulf of Mexico and Comparison of Their PAH Degradation Ability with That of Puget Sound Cycloclasticus Strains

1998 ◽  
Vol 64 (12) ◽  
pp. 4703-4710 ◽  
Author(s):  
Allison D. Geiselbrecht ◽  
Brian P. Hedlund ◽  
Mary A. Tichi ◽  
J. T. Staley
Keyword(s):  
Polycyclic Aromatic Hydrocarbon ◽  
Gulf Of Mexico ◽  
Aromatic Hydrocarbon ◽  
Dna Sequences ◽  
Puget Sound ◽  
Amino Acid Sequences ◽  
Most Probable Number ◽  
Probable Number ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic

ABSTRACT Phenanthrene- and naphthalene-degrading bacteria were isolated from four offshore and nearshore locations in the Gulf of Mexico by using a modified most-probable-number technique. The concentrations of these bacteria ranged from 102 to 106cells per ml of wet surficial sediment in mildly contaminated and noncontaminated sediments. A total of 23 strains of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria were obtained. Based on partial 16S ribosomal DNA sequences and phenotypic characteristics, these 23 strains are members of the genus Cycloclasticus. Three representatives were chosen for a complete phylogenetic analysis, which confirmed the close relationship of these isolates to type strain Cycloclasticus pugetii PS-1, which was isolated from Puget Sound. PAH substrate utilization tests which included high-molecular-weight PAHs revealed that these isolates had similar, broad substrate ranges which included naphthalene, substituted naphthalenes, phenanthrene, biphenyl, anthracene, acenaphthene, and fluorene. Degradation of pyrene and fluoranthene occurred only when the strains were incubated with phenanthrene. Two distinct partial PAH dioxygenase iron sulfur protein (ISP) gene sequences were PCR amplified from Puget Sound and Gulf of Mexico Cycloclasticus strains. Phylogenetic analyses of these sequences revealed that one ISP type is related to the bph type of ISP sequences, while the other ISP type is related to the nah type of ISP sequences. The predicted ISP amino acid sequences for the Gulf of Mexico and Puget Sound strains are identical, which supports the hypothesis that these geographically separated isolates are closely related phylogentically.Cycloclasticus species appear to be numerically important and widespread PAH-degrading bacteria in both Puget Sound and the Gulf of Mexico.

Polycyclic aromatic hydrocarbon degrading gene islands in five pyrene-degrading Mycobacterium isolates from different geographic locations

2012 ◽  
Vol 58 (1) ◽  
pp. 102-111 ◽  
Author(s):  
Chun Zhang ◽  
Anne J. Anderson
Keyword(s):  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Gc Content ◽  
The United States ◽  
Pcr Analysis ◽  
Transcript Accumulation ◽  
Circular Plasmid ◽  
Genes Encoding ◽  
Polycyclic Aromatic ◽  
Induced Proteins

Mycobacterium sp. strain KMS utilizes pyrene, a high-molecular weight polycyclic aromatic hydrocarbon (PAH), as a sole carbon source. Bioinformatic analysis of the genome of isolate KMS predicted 25 genes with the potential to encode 17 pyrene-induced proteins identified by proteomics; these genes were clustered on both the chromosome and a circular plasmid. RT-PCR analysis of total RNA isolated from KMS cells grown with or without pyrene showed that the presence of pyrene increased the transcript accumulation of 20 of the predicted chromosome- and plasmid-located genes encoding pyrene-induced proteins. The transcribed genes from both the chromosome and a circular plasmid were within larger regions containing genes required for PAH degradation constituting PAH-degrading gene islands. Genes encoding integrases and transposases were found within and outside the PAH-degrading gene islands. The lower GC content of the genes within the gene island (61%–64%) compared with the average genome content (68%) suggested that these mycobacteria initially acquired these genes by horizontal gene transfer. Synteny was detected for the PAH-degrading islands in the genomes of two additional Mycobacterium isolates from the same PAH-polluted site and of two other pyrene-degrading Mycobacterium from different sites in the United States of America. Consequently, the gene islands have been conserved from a common ancestral strain.

scholarly journals Multiple Nonidentical Reductive-Dehalogenase-Homologous Genes Are Common in Dehalococcoides

2004 ◽  
Vol 70 (9) ◽  
pp. 5290-5297 ◽  
Author(s):  
Tina Hölscher ◽  
Rosa Krajmalnik-Brown ◽  
Kirsti M. Ritalahti ◽  
Friedrich von Wintzingerode ◽  
Helmut Görisch ◽  
...  
Keyword(s):  
Amino Acid ◽  
Restriction Analysis ◽  
Sequence Similarity ◽  
Comparative Sequence Analysis ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Degenerate Primers ◽  
Reductive Dehalogenase ◽  
Genes Encoding ◽  
Reductive Dehalogenase Genes

ABSTRACT Degenerate primers were used to amplify large fragments of reductive-dehalogenase-homologous (RDH) genes from genomic DNA of two Dehalococcoides populations, the chlorobenzene- and dioxin-dechlorinating strain CBDB1 and the trichloroethene-dechlorinating strain FL2. The amplicons (1,350 to 1,495 bp) corresponded to nearly complete open reading frames of known reductive dehalogenase genes and short fragments (approximately 90 bp) of genes encoding putative membrane-anchoring proteins. Cloning and restriction analysis revealed the presence of at least 14 different RDH genes in each strain. All amplified RDH genes showed sequence similarity with known reductive dehalogenase genes over the whole length of the sequence and shared all characteristics described for reductive dehalogenases. Deduced amino acid sequences of seven RDH genes from strain CBDB1 were 98.5 to 100% identical to seven different RDH genes from strain FL2, suggesting that both strains have an overlapping substrate range. All RDH genes identified in strains CBDB1 and FL2 were related to the RDH genes present in the genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain BAV1; however, sequence identity did not exceed 94.4 and 93.1%, respectively. The presence of RDH genes in strains CBDB1, FL2, and BAV1 that have no orthologs in strain 195 suggests that these strains possess dechlorination activities not present in strain 195. Comparative sequence analysis identified consensus sequences for cobalamin binding in deduced amino acid sequences of seven RDH genes. In conclusion, this study demonstrates that the presence of multiple nonidentical RDH genes is characteristic of Dehalococcoides strains.

1,1’-Biaceanthrylene and 2,2'-Biaceanthrylene: Models for Linking Larger Polycyclic Aromatic Hydrocarbons via Five-Membered Rings

2019 ◽  
Author(s):  
Yachu Du ◽  
Kyle Plunkett
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Electronic Properties ◽  
Aromatic Hydrocarbons ◽  
Model Systems ◽  
Redox Potentials ◽  
Dimer Model ◽  
Optical And Electronic Properties ◽  
Polycyclic Aromatic

We show that polycyclic aromatic hydrocarbon (PAH) chromophores that are linked between two five-membered rings can access planarized structures with reduced optical gaps and redox potentials. Two aceanthrylene chromophores were connected into dimer model systems with the chromophores either projected outward (2,2’-biaceanthrylene) or inward (1,1’-biaceanthrylene) and the optical and electronic properties were compared. Only the planar 2,2’-biaceanthrylene system showed significant reductions of the optical gaps (1 eV) and redox potentials in relation to the aceanthrylene monomer.<br>

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