scholarly journals Spatial Distribution of Bacterial Communities and Phenanthrene Degradation in the Rhizosphere of Lolium perenne L

2004 ◽  
Vol 70 (6) ◽  
pp. 3552-3557 ◽  
Author(s):  
S. C. Corgi� ◽  
T. Beguiristain ◽  
C. Leyval
Keyword(s):  
Bacterial Community ◽  
Root Exudates ◽  
Bacterial Communities ◽  
Pcr Amplification ◽  
Phenanthrene Degradation ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic ◽  
Gradient Gel Electrophoresis ◽  
Direct Dna Extraction ◽  
Phenanthrene Biodegradation

ABSTRACT Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.

scholarly journals Quantification of phnAc andnahAc in Contaminated New Zealand Soils by Competitive PCR

2000 ◽  
Vol 66 (5) ◽  
pp. 1814-1817 ◽  
Author(s):  
Andrew D. Laurie ◽  
Gareth Lloyd-Jones
Keyword(s):  
Competitive Pcr ◽  
Phenanthrene Degradation ◽  
Iron Sulfur ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic ◽  
Sulfur Protein ◽  
Iron Sulfur Protein ◽  
Microbial Potential ◽  
Α Subunits ◽  
Different Soils

ABSTRACT Unculturable polycyclic aromatic hydrocarbon (PAH)-degrading bacteria are a significant reservoir of the microbial potential to catabolize low-molecular-weight PAHs. The population of these bacteria is larger than the population of nah-like bacteria that are the dominant organisms in culture-based studies. We used the recently described phn genes of Burkholderia sp. strain RP007, which feature only rarely in culture-based studies, as an alternative genotype for naphthalene and phenanthrene degradation and compared this genotype with the genotypically distinct but ubiquitousnah-like class in different soils. Competitive PCR quantification of phnAc and nahAc, which encode the iron sulfur protein large (α) subunits of PAH dioxygenases innah-like and phn catabolic operons, revealed that the phn genotype can have a greater ecological significance than the nah-like genotype.

Changes in the structure and diversity of bacterial communities during the process of adaptation to organic wastewater

2010 ◽  
Vol 56 (4) ◽  
pp. 352-355 ◽  
Author(s):  
Junmin Li ◽  
Zexin Jin ◽  
Binbin Yu
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Similarity Index ◽  
Pcr Amplification ◽  
Genotypic Diversity ◽  
Diversity Indices ◽  
Inhibitory Effect ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gradient Gel Electrophoresis

To explore changes in the structure and diversity of activated sludge-derived microbial communities during adaptation to gradual increases in the concentration of wastewater, RAPD–PCR and the combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis (DGGE) analysis were used. In bacterial communities exposed to 0%, 5%, 10%, 20%, or 40% wastewater, there were 27, 25, 18, 17 and 16 bands, respectively, based on DGGE data, while there were 69, 83, 97, 86, and 88 bands, respectively, based on RAPD data. The community similarity index among bacterial communities during the process of adaptation to different concentrations of wastewater was different based on DGGE and RAPD data. Based on DGGE and RAPD profiles, the Shannon–Weiner and Simpson’s diversity indices decreased sharply upon exposure to 10% wastewater, indicating that 10% wastewater might be a critical point at which the growth of bacteria could be significantly inhibited and the genotypic diversity could change. This indicated that changes in structure and diversity might have an inhibitory effect on the toxicity of organic matter and that selection and adaptation could play important roles in the changes.

Effects of Long-Term Elevated CO2 on Rhizosphere and Bulk Soil Bacterial Community Structure in Pinus sylvestriformis Seedlings Fields

2011 ◽  
Vol 343-344 ◽  
pp. 351-356
Author(s):  
Xia Jia ◽  
Chun Juan Zhou
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pinus Sylvestriformis ◽  
Soil Bacterial Community Structure ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain

The effect of long-term elevated CO2(as open top chambers) on rhizosphere and bulk bacterial community structure in Pinus sylvestriformis seedlings field was investigated in July, August, and September. The bacterial communities were processed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA fragments amplified by PCR (Polymerase Chain Reaction) from DNA extracted directly from soil. DGGE profiles from rhizosphere samples showed large changes in rhizosphere bacterial community under elevated CO2compared to ambient except for that in September. For bulk samples, bacterial community structure changed when exposed to elevated CO2in three months. With the exception of bulk samples in August, a similitude of bacterial communities structures existed between different elevated CO2concentrations by analyzing UPGMA dendrogram based on Jaccard’s coefficient.

Characteristics of phenanthrene-degrading bacteria isolated from soils contaminated with polycyclic aromatic hydrocarbons

1998 ◽  
Vol 44 (8) ◽  
pp. 743-752 ◽  
Author(s):  
Michael D Aitken ◽  
William T Stringfellow ◽  
Robert D Nagel ◽  
Chikoma Kazunga ◽  
Shu-Hwa Chen
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Acid Methyl Ester ◽  
Aqueous Solubility ◽  
Bacterial Strains ◽  
Phenanthrene Degradation ◽  
Acid Methyl ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic

Ten bacterial strains were isolated from seven contaminated soils by enrichment with phenanthrene as the sole carbon source. These isolates and another phenanthrene-degrading strain were examined for various characteristics related to phenanthrene degradation and their ability to metabolize 12 other polycyclic aromatic hydrocarbons (PAH), ranging in size from two to five rings, after growth in the presence of phenanthrene. Fatty acid methyl ester analysis indicated that at least five genera (Agrobacterium, Bacillus, Burkholderia, Pseudomonas, and Sphingomonas) and at least three species of Pseudomonas were represented in this collection. All of the strains oxidized phenanthrene according to Michaelis-Menten kinetics, with half-saturation coefficients well below the aqueous solubility of phenanthrene in all cases. All but one of the strains oxidized 1-hydroxy-2-naphthoate following growth on phenanthrene, and all oxidized at least one downstream intermediate from either or both of the known phenanthrene degradation pathways. All of the isolates could metabolize (oxidize, mineralize, or remove from solution) a broad range of PAH, although the exact range and extent of metabolism for a given substrate were unique to the particular isolate. Benz[a]anthracene, chrysene, and benzo[a]pyrene were each mineralized by eight of the strains, while pyrene was not mineralized by any. Pyrene was, however, removed from solution by all of the isolates, and the presence of at least one significant metabolite from pyrene was observed by radiochromatography for the five strains in which such metabolites were sought. Our results support earlier indications that the mineralization of pyrene by bacteria may require unique metabolic capabilities that do not appear to overlap with the determinants for mineralization of phenanthrene or other high molecular weight PAH.Key words: kinetics, polycyclic aromatic hydrocarbons, phenanthrene, mineralization, benzo[a]pyrene.

scholarly journals Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill

2009 ◽  
Vol 75 (11) ◽  
pp. 3407-3418 ◽  
Author(s):  
Jorge Alonso-Gutiérrez ◽  
Antonio Figueras ◽  
Joan Albaigés ◽  
Núria Jiménez ◽  
Marc Viñas ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Oil Spill ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Mycolic Acids ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Northwestern Spain

ABSTRACT The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.

scholarly journals Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis

2002 ◽  
Vol 68 (10) ◽  
pp. 5142-5150 ◽  
Author(s):  
Hiroyuki Sekiguchi ◽  
Masataka Watanabe ◽  
Tadaatsu Nakahara ◽  
Baohua Xu ◽  
Hiroo Uchiyama
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Clone Library ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Changjiang River ◽  
The Changjiang River ◽  
Clone Library Analysis ◽  
Gradient Gel Electrophoresis

ABSTRACT Bacterial community structure along the Changjiang River (which is more than 2,500 km long) was studied by using denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal bacterial primer sets. DGGE profiles and principal-component analysis (PCA) demonstrated that the bacterial community gradually changed from upstream to downstream in both 1998 and 1999. Bacterial diversity, as determined by the Shannon index (H′), gradually decreased from upstream to downstream. The PCA plots revealed that the differences in the bacterial communities among riverine stations were not appreciable compared with the differences in two adjacent lakes, Lake Dongting and Lake Poyang. The relative stability of the bacterial communities at the riverine stations was probably due to the buffering action of the large amount of water flowing down the river. Clone library analysis of 16S rDNA revealed that the dominant bacterial groups changed from β-proteobacteria and the Cytophaga-Flexibacter-Bacteroides group upstream to high-G+C-content gram-positive bacteria downstream and also that the bacterial community structure differed among the stations in the river and the lakes. The results obtained in this study should provide a reference for future changes caused by construction of the Three Gorges Dam.

scholarly journals Enrichment, Isolation, and Phylogenetic Identification of Polycyclic Aromatic Hydrocarbon-Degrading Bacteria from Elizabeth River Sediments†

2007 ◽  
Vol 74 (4) ◽  
pp. 1176-1182 ◽  
Author(s):  
Edward J. Hilyard ◽  
Joanne M. Jones-Meehan ◽  
Barry J. Spargo ◽  
Russell T. Hill
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
River Sediments ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Molecular Analyses ◽  
Selective Enrichment ◽  
Elizabeth River ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic ◽  
Gradient Gel Electrophoresis

ABSTRACT 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.

scholarly journals Products from the Incomplete Metabolism of Pyrene by Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

2000 ◽  
Vol 66 (5) ◽  
pp. 1917-1922 ◽  
Author(s):  
Chikoma Kazunga ◽  
Michael D. Aitken
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Pseudomonas Stutzeri ◽  
Minor Effect ◽  
Bacterial Strains ◽  
Phenanthrene Degradation ◽  
Degrading Bacteria ◽  
Subsequent Degradation ◽  
Polycyclic Aromatic ◽  
A Minor

ABSTRACT Pyrene is a regulated pollutant at sites contaminated with polycyclic aromatic hydrocarbons (PAH). It is mineralized by some bacteria but is also transformed to nonmineral products by a variety of other PAH-degrading bacteria. We examined the formation of such products by four bacterial strains and identified and further characterized the most apparently significant of these metabolites.Pseudomonas stutzeri strain P16 and Bacillus cereus strain P21 transformed pyrene primarily tocis-4,5-dihydro-4,5-dihydroxypyrene (PYRdHD), the first intermediate in the known pathway for aerobic bacterial mineralization of pyrene. Sphingomonas yanoikuyae strain R1 transformed pyrene to PYRdHD and pyrene-4,5-dione (PYRQ). Both strain R1 and Pseudomonas saccharophila strain P15 transform PYRdHD to PYRQ nearly stoichiometrically, suggesting that PYRQ is formed by oxidation of PYRdHD to 4,5-dihydroxypyrene and subsequent autoxidation of this metabolite. A pyrene-mineralizing organism,Mycobacterium strain PYR-1, also transforms PYRdHD to PYRQ at high initial concentrations of PYRdHD. However, strain PYR-1 is able to use both PYRdHD and PYRQ as growth substrates. PYRdHD strongly inhibited phenanthrene degradation by strains P15 and R1 but had only a minor effect on strains P16 and P21. At their aqueous saturation concentrations, both PYRdHD and PYRQ severely inhibited benzo[a]pyrene mineralization by strains P15 and R1. Collectively, these findings suggest that products derived from pyrene transformation have the potential to accumulate in PAH-contaminated systems and that such products can significantly influence the removal of other PAH. However, these products may be susceptible to subsequent degradation by organisms able to metabolize pyrene more extensively if such organisms are present in the system.

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