scholarly journals Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons

2010 ◽  
Vol 60 (3) ◽  
pp. 504-509 ◽  
Author(s):  
Arturo Rodríguez-Blanco ◽  
Gilles Vetion ◽  
Marie-Line Escande ◽  
Daniel Delille ◽  
Jean-François Ghiglione
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Mass ◽  
Aromatic Hydrocarbons ◽  
Direct Sequencing ◽  
High Molecular Mass ◽  
Intertidal Sediment ◽  
Rrna Gene ◽  
Polycyclic Aromatic

A Gram-negative, rod-shaped, halotolerant bacterium, designated strain CEE_131T, which degraded high-molecular-mass polycyclic aromatic hydrocarbons of four and five rings, was isolated from intertidal sediment of Corcubion Ria in Cee, A Coruña, Spain. Direct sequencing showed ambiguities and suggested heterogeneity. Cloned 16S rRNA gene sequence PCR products yielded five different sequences varying at five positions. Strain CEE_131T showed rather distant relationships to its phylogenetically closest neighbours, including the genera Rheinheimera and Serratia, exhibiting 91 % sequence similarity with Rheinheimera perlucida BA131T and Serratia proteamaculans subsp. quinovora DSM 4597T. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 41.7 mol%. On the basis of these distinct phenotypic and genotypic characteristics, strain CEE_131T is considered to represent a novel species in a new genus in the class Gammaproteobacteria, for which the name Gallaecimonas pentaromativorans gen. nov., sp. nov. is proposed. The type strain is CEE_131T (=DSM 21945T=CECT 7479T).

scholarly journals Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

2004 ◽  
Vol 70 (4) ◽  
pp. 1944-1955 ◽  
Author(s):  
Natalie M. E. J. Leys ◽  
Annemie Ryngaert ◽  
Leen Bastiaens ◽  
Willy Verstraete ◽  
Eva M. Top ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Soil Dna ◽  
Detection Techniques ◽  
Polycyclic Aromatic

ABSTRACT Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil−1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

Determination of High Molecular Mass Polycyclic Aromatic Hydrocarbons in a Typical Italian Smoked Cheese by HPLC-FL

2003 ◽  
Vol 51 (17) ◽  
pp. 5111-5115 ◽  
Author(s):  
Giampiero Pagliuca ◽  
Teresa Gazzotti ◽  
Elisa Zironi ◽  
Gian Paolo Serrazanetti ◽  
Domenico Mollica ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Molecular Mass ◽  
Aromatic Hydrocarbons ◽  
High Molecular Mass ◽  
Polycyclic Aromatic

scholarly journals How to add a five-membered ring to polycyclic aromatic hydrocarbons (PAHs) – molecular mass growth of the 2-naphthyl radical (C10H7) to benzindenes (C13H10) as a case study

2019 ◽  
Vol 21 (30) ◽  
pp. 16737-16750 ◽  
Author(s):  
Long Zhao ◽  
Matthew Prendergast ◽  
Ralf I. Kaiser ◽  
Bo Xu ◽  
Utuq Ablikim ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Molecular Mass ◽  
Aromatic Hydrocarbons ◽  
Membered Ring ◽  
Growth Processes ◽  
Mass Growth ◽  
Aryl Radicals ◽  
Polycyclic Aromatic

The reaction of aryl radicals with allene/methylacetylene leads to five-membered ring addition in PAH growth processes.

scholarly journals Influences of Infaunal Burrows on the Community Structure and Activity of Ammonia-Oxidizing Bacteria in Intertidal Sediments

2006 ◽  
Vol 73 (4) ◽  
pp. 1341-1348 ◽  
Author(s):  
Hisashi Satoh ◽  
Yoshiyuki Nakamura ◽  
Satoshi Okabe
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Copy ◽  
Sediment Surface ◽  
Intertidal Sediment ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Intertidal Sediments ◽  
Burrow Wall ◽  
Microelectrode Measurements

ABSTRACT Influences of infaunal burrows constructed by the polychaete (Tylorrhynchus heterochaetus) on O2 concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O2 transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by Nitrosomonas sp. strain Nm143-like sequences, and most of the clones in Nitrospira-like NOB clone libraries of the sediment surface and the burrow walls were related to the Nitrospira marina lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and Nitrospira-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH4 + consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH4 + and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O2 transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH4 + consumption capacity. Consequently, the infaunal burrow became an important site for NH4 + consumption in the intertidal sediment.

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