nahR, encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA b bThe GenBank accession number for the sequences of the tnpA-like gene, nahG and nahR of P. putida NCIB 9816-4 is AF491307. The GenBank accession numbers for the sequences of the nahR–nahG intergenic region and the nahR homologue genes of strains Cg1, Cg2, Cg5, Cg7, Cg9, Cg11, Hg8 and N1 are AF491308–AF491315, respectively. The GenBank accession numbers for the sequences of nahR from sediment-extracted DNA are AF491316–AF491324.

ABSTRACT We developed procedures for isolating and characterizing in situ-transcribed mRNA from groundwater microorganisms catabolizing naphthalene at a coal tar waste-contaminated site. Groundwater was pumped through 0.22-μm-pore-size filters, which were then frozen in dry ice-ethanol. RNA was extracted from the frozen filters by boiling sodium dodecyl sulfate lysis and acidic phenol-chloroform extraction. Transcript characterization was performed with a series of PCR primers designed to amplify nahAc homologs. Several primer pairs were found to amplify nahAc homologs representing the entire diversity of the naphthalene-degrading genes. The environmental RNA extract was reverse transcribed, and the resultant mixture of cDNAs was amplified by PCR. A digoxigenin-labeled probe mixture was produced by PCR amplification of groundwater cDNA. This probe mixture hybridized under stringent conditions with the corresponding PCR products from naphthalene-degrading bacteria carrying a variety of nahAchomologs, indicating that diverse dioxygenase transcripts had been retrieved from groundwater. Diluted and undiluted cDNA preparations were independently amplified, and 28 of the resulting PCR products were cloned and sequenced. Sequence comparisons revealed two major groups related to the dioxygenase genes ndoB anddntAc, previously cloned from Pseudomonas putida NCIB 9816-4 and Burkholderia sp. strain DNT, respectively. A distinctive subgroup of sequences was found only in experiments performed with the undiluted cDNA preparation. To our knowledge, these results are the first to directly document in situ transcription of genes encoding naphthalene catabolism at a contaminated site by indigenous microorganisms. The retrieved sequences represent greater diversity than has been detected at the study site by culture-based approaches.

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Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation

Environmental Science and Pollution Research ◽

10.1007/s11356-021-18300-w ◽

2022 ◽

Author(s):

Sinchan Banerjee ◽

Anna Bedics ◽

Péter Harkai ◽

Balázs Kriszt ◽

Nagaraju Alpula ◽

...

Keyword(s):

Microbial Community ◽

Primary Objective ◽

Community Diversity ◽

Contaminated Site ◽

Whole Genome Analysis ◽

Contaminated Aquifer ◽

Degrading Bacteria ◽

Research Outcome ◽

Xylene Isomers ◽

Set Up

AbstractTo develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.

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Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site

Applied and Environmental Microbiology ◽

10.1128/aem.72.4.2331-2342.2006 ◽

2006 ◽

Vol 72 (4) ◽

pp. 2331-2342 ◽

Cited By ~ 167

Author(s):

Mary Beth Leigh ◽

Petra Prouzová ◽

Martina Macková ◽

Tomáš Macek ◽

David P. Nagle ◽

...

Keyword(s):

Plant Species ◽

Polychlorinated Biphenyl ◽

Root Zone ◽

Pinus Nigra ◽

Contaminated Site ◽

Rrna Gene ◽

Mature Trees ◽

Salix Caprea ◽

Root Zones ◽

Degrading Bacteria

ABSTRACT The abundance, identities, and degradation abilities of indigenous polychlorinated biphenyl (PCB)-degrading bacteria associated with five species of mature trees growing naturally in a contaminated site were investigated to identify plants that enhance the microbial PCB degradation potential in soil. Culturable PCB degraders were associated with every plant species examined in both the rhizosphere and root zone, which was defined as the bulk soil in which the plant was rooted. Significantly higher numbers of PCB degraders (2.7- to 56.7-fold-higher means) were detected in the root zones of Austrian pine (Pinus nigra) and goat willow (Salix caprea) than in the root zones of other plants or non-root-containing soil in certain seasons and at certain soil depths. The majority of culturable PCB degraders throughout the site and the majority of culturable PCB degraders associated with plants were identified as members of the genus Rhodococcus by 16S rRNA gene sequence analysis. Other taxa of PCB-degrading bacteria included members of the genera Luteibacter and Williamsia, which have not previously been shown to include PCB degraders. PCB degradation assays revealed that some isolates from the site have broad congener specificities; these isolates included one Rhodococcus strain that exhibited degradation abilities similar to those of Burkholderia xenovorans LB400. Isolates with broad congener specificity were widespread at the site, including in the biostimulated root zone of willow. The apparent association of certain plant species with increased abundance of indigenous PCB degraders, including organisms with outstanding degradation abilities, throughout the root zone supports the notion that biostimulation through rhizoremediation is a promising strategy for enhancing PCB degradation in situ.

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Isolation and identification of phenol-degrading bacteria in the industrial wastewater from the coal tar mine of Zarand in Iran

10.5004/dwt.2019.23705 ◽

2019 ◽

Vol 147 ◽

pp. 125-134

Author(s):

Mehdi Hassanshahian ◽

Moslem Abarian ◽

Kiana Bahramzadeh ◽

Maria Genovese

Keyword(s):

Industrial Wastewater ◽

Coal Tar ◽

Isolation And Identification ◽

Degrading Bacteria

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Isolation and Characterization of Petroleum Hydrocarbon Degrading Bacteria from the Bohai Sea, China

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.955-959.728 ◽

2014 ◽

Vol 955-959 ◽

pp. 728-731

Author(s):

Ping Guo ◽

Jian Guo Lin ◽

Bin Xia Cao ◽

Na Ta

Keyword(s):

Petroleum Hydrocarbon ◽

Bohai Sea ◽

Diesel Oil ◽

Contaminated Site ◽

Oil Degradation ◽

Isolation And Characterization ◽

Degrading Bacteria ◽

Luxuriant Growth ◽

Diesel Oil Degradation

Fourteen petroleum hydrocarbon degrading bacteria strains were isolated from oil-contaminated site. Isolated strains were able use diesel oil as sole carbon and energy source. Bacterial strain HD1 was selected due to the luxuriant growth on oil agar. The oil degradation rate of strain HD1 was analyzed using UV-spectrometry-based methods. The result showed that the rate of diesel oil degradation of 75% was observed after 14days of cultivation.

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Phenylobacterium Korensee Best Indigenous Petroleum Hydrocarbon Degrading Bacteria Isolated from Contaminated Soil of Bahror, Alwar Region, India

International Journal of Contemporary Research and Review ◽

10.15520/ijcrr.v10i08.729 ◽

2019 ◽

Vol 10 (08) ◽

pp. 20203-20211 ◽

Cited By ~ 2

Author(s):

Mohan Lal Kuri ◽

Vidhya Kumari ◽

Shikha Roy

Keyword(s):

Contaminated Soil ◽

Engine Oil ◽

Contaminated Site ◽

Spectroscopy Analysis ◽

Global Issue ◽

Degrading Bacteria ◽

Term Basis ◽

Agar Media ◽

Gas Chromatography Mass Spectroscopy

Contamination of soil, water and air due to hydrocarbons are a global issue and bioremediation provides probably the best way to remediate the contaminants. The current study shows the biodegradation of crude oil, diesel and used engine oil by a newly isolated Phenylobacterium korensee from contaminated soil of Bahror, Alwar, Rajasthan. Hydrocarbon degrading strain was screened on BHA (Bushnell Haas Agar) media supplemented with 2T engine oil as sole carbon source. The strain was found to be degrading at 1%, 4% and 10% of used 2T engine oil respectively after 14 days. Degradation was confirmed both gravimetrically and by Gas Chromatography Mass Spectroscopy analysis. The degradation was found very well at long term basis. The optimization of growth also studied at temperature and pH basis also. The significance of the study is that the percentage degradation of the complex petroleum supplements used in the study was found to be far higher than some of the previously reported values and this bacterial strain was firstly found from this contaminated site.

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