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.

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).

Effect of nanomaterials on remediation of polycyclic aromatic hydrocarbons-contaminated soils: A review

2021 ◽  
Vol 284 ◽  
pp. 112023
Author(s):  
Mahmoud Mazarji ◽  
Tatiana Minkina ◽  
Svetlana Sushkova ◽  
Saglara Mandzhieva ◽  
Gholamreza Nabi Bidhendi ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Polycyclic Aromatic

Bioaugmentation strategy to enhance polycyclic aromatic hydrocarbons anaerobic biodegradation in contaminated soils

Chemosphere ◽  
2021 ◽  
Vol 275 ◽  
pp. 130091
Author(s):  
Alberto Ferraro ◽  
Giulia Massini ◽  
Valentina Mazzurco Miritana ◽  
Antonio Panico ◽  
Ludovico Pontoni ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Anaerobic Biodegradation ◽  
Polycyclic Aromatic

scholarly journals Molecular Diversity Assessment of Plant Growth Promoting Rhizobacteria Using Denaturing Gradient Gel Electrophoresis (DGGE) of 16s rRNA Gene

2017 ◽  
Vol 5 (1) ◽  
pp. 72-80
Author(s):  
Umesh Prasad Shrivastava
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Uttar Pradesh ◽  
Plant Growth Promoting Rhizobacteria ◽  
Melting Behavior ◽  
Rrna Gene ◽  
Dgge Profile ◽  
Diversity Assessment

The rhizobacteria were isolated from rhizosphere of rice plant of different fields of 4 districts of Nepal and 5 districts of Bihar and Uttar Pradesh, adjoining states of India with Nepal. The DGGE analysis was performed for diversity analysis. For the construction of dendrogram, 16S rRNA gene was amplified by two different sets of primers. The DGGE ladder consisting of PCR amplified products of nine pure bacterial cultures were obtained. The first DGGE ladder was prepared by 400 bp fragment of 16S rDNA with GC clamp and the second DGGE ladder was prepared with 200 bp fragment of 16S rDNA with GC clamp. The perpendicular DGGE of these amplicons based on their melting behavior clearly demonstrated separation of different isolates. The 16S rDNA fragment amplified with primer set of V2-V3 regions with GC clamp showed separation between 40-60% of denaturant. The DGGE profile based on primer set F352T and 519r for various bacteria present in soil samples of 5 districts of India and 4 districts of Nepal revealed that the number of bands which might be specific for diazotrophic isolates varied from 2 to 11. The dendrogram constructed based on DGGE profile of various samples of 5 districts of India and 4 districts of Nepal showed that all the samples could be clustered in nine groups with 58-96% similarity to each other. Among all these 37 samples, only Var-4 and Var-5 showed 100% similarity, no other samples from any site showed 100% similarity. Int. J. Appl. Sci. Biotechnol. Vol 5(1): 72-80

scholarly journals Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease

2015 ◽  
Vol 81 (21) ◽  
pp. 7582-7592 ◽  
Author(s):  
Mireia Lopez-Siles ◽  
Margarita Martinez-Medina ◽  
Carles Abellà ◽  
David Busquets ◽  
Miriam Sabat-Mir ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bowel Disease ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gastrointestinal Disease ◽  
Rrna Gene ◽  
Content Type ◽  
Faecalibacterium Prausnitzii ◽  
Inflammatory Bowel

ABSTRACTFaecalibacterium prausnitziidepletion in intestinal diseases has been extensively reported, but little is known about intraspecies variability. This work aims to determine if subjects with gastrointestinal disease host mucosa-associatedF. prausnitziipopulations different from those hosted by healthy individuals. A new species-specific PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method targeting the 16S rRNA gene was developed to fingerprintF. prausnitziipopulations in biopsy specimens from 31 healthy control (H) subjects and 36 Crohn's disease (CD), 23 ulcerative colitis (UC), 6 irritable bowel syndrome (IBS), and 22 colorectal cancer (CRC) patients. The richness ofF. prausnitziisubtypes was lower in inflammatory bowel disease (IBD) patients than in H subjects. The most prevalent operational taxonomic units (OTUs) consisted of four phylotypes (OTUs with a 99% 16S rRNA gene sequence similarity [OTU99]), which were shared by all groups of patients. Their distribution and the presence of some disease-specificF. prausnitziiphylotypes allowed us to differentiate the populations in IBD and CRC patients from that in H subjects. At the level of a minimum similarity of 97% (OTU97), two phylogroups accounted for 98% of the sequences. Phylogroup I was found in 87% of H subjects but in under 50% of IBD patients (P= 0.003). In contrast, phylogroup II was detected in >75% of IBD patients and in only 52% of H subjects (P= 0.005). This study reveals that even though the main members of theF. prausnitziipopulation are present in both H subjects and individuals with gut diseases, richness is reduced in the latter and an altered phylotype distribution exists between diseases. This approach may serve as a basis for addressing the suitability ofF. prausnitziiphylotypes to be quantified as a putative biomarker of disease and depicting the importance of the loss of these subtypes in disease pathogenesis.

scholarly journals Application of Programmed Temperature Vaporization Large Volume Injection Gas Chromatography (PTV-LVI-GC) to the Analysis of Polycyclic Aromatic Hydrocarbons (PAHs) in Soils

2017 ◽  
Vol 57 (2) ◽  
Author(s):  
Miguel Ángel Delgadillo-Marín ◽  
Araceli Peña-Álvarez ◽  
Mario Villalobos Villalobos
Keyword(s):  
Gas Chromatography ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Large Volume ◽  
Contaminated Soils ◽  
Large Volume Injection ◽  
Method Performance ◽  
Flame Ionization ◽  
Polycyclic Aromatic ◽  
Programmed Temperature Vaporization

A sensitive, selective and robust method was developed to quantify low levels of polycyclic aromatic hydrocarbons (PAHs) in soils by means of Programmed Temperature Vaporization - Large Volume Injection (PTV-LVI) coupled to gas chromatography with flame ionization detection. Optimal vent pressure and flux at the PTV inlet of the GC system were determined by comparison of peak areas obtained from injection of a standard PAHs mixture at different conditions. Assessment of method performance was carried out with home-made standards prepared by spiking three non-PAH contaminated soils that contained 1.8%, 4.6% and 25% natural organic matter (NOM), with mixtures of six different PAHs at low concentration levels. Detection limits between 9 and 12 ng g<sup>-1</sup> and variation coefficients below 11% were determined from analysis of spiked samples of the soil with lowest NOM content. PAHs recoveries typically ranged from 61% to 96% for the three studied soils.

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