Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

scientific article published on 21 August 2009

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1128/AEM.01091-09
P932PMC publication ID2765153
P698PubMed publication ID19700556
P5875ResearchGate publication ID26760903

P2093author name stringEugene L Madsen
Jane M Yagi
P2860cites worknag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolismQ28345381
Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradationQ28768504
Abundance of dioxygenase genes similar to Ralstonia sp. strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sedimentsQ28775687
Global physiological analysis of carbon- and energy-limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilizationQ30232996
Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of PatagoniaQ30398078
Novel forms of ring-hydroxylating dioxygenases are widespread in pristine and contaminated soilsQ30654957
How stable is stable? Function versus community composition.Q30746278
Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sedimentQ30890373
Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbonsQ30919533
Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sedimentQ31022763
Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrateQ31104835
Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer watersQ32144489
Stability in a denitrifying fluidized bed reactorQ33252119
Annually reoccurring bacterial communities are predictable from ocean conditionsQ33255661
Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compoundsQ33293603
Comparative quantitative prevalence of Mycobacteria and functionally abundant nidA, nahAc, and nagAc dioxygenase genes in coal tar contaminated sediments.Q33297790
Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levelsQ33331708
Diversity of ring-hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels.Q33355630
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyreQ33407692
Revising the nitrogen cycle in the Peruvian oxygen minimum zoneQ33414079
Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us.Q33497533
Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial communityQ33506252
In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater.Q33984027
Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kineticsQ34010030
Responses of Gram-negative bacteria to certain environmental stressors.Q34205000
Principles of microbial PAH-degradation in soil.Q34343120
Polycyclic aromatic hydrocarbons: environmental pollution and bioremediationQ34635340
Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environmentsQ34993063
Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic BacteriaQ35120441
Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39.Q35188244
Kinetics of the simultaneous utilization of sugar mixtures by Escherichia coli in continuous culture.Q35190198
Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarraysQ35663092
Bacterial transcriptional regulators for degradation pathways of aromatic compoundsQ35880920
Diversity of ndo genes in mangrove sediments exposed to different sources of polycyclic aromatic hydrocarbon pollutionQ36313713
Quantification of functional genes from procaryotes in soil by PCR.Q36663745
Bioremediation and monitoring of aromatic-polluted habitatsQ36836675
Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization.Q37032962
Microbial biodegradation of polyaromatic hydrocarbonsQ37228802
Quantification of phnAc and nahAc in contaminated new zealand soils by competitive PCR.Q39536073
Genetics of naphthalene catabolism in pseudomonadsQ39645190
Maintenance and induction of naphthalene degradation activity in Pseudomonas putida and an Alcaligenes sp. under different culture conditionsQ39798780
Specific and quantitative assessment of naphthalene and salicylate bioavailability by using a bioluminescent catabolic reporter bacterium.Q39893925
Characterization of multiple-substrate utilization by anthracene-degrading Mycobacterium frederiksbergense LB501T.Q39913688
Adaptation of natural microbial communities to degradation of xenobiotic compounds: effects of concentration, exposure time, inoculum, and chemical structure.Q40072435
Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and presentQ40591468
In situ expression of nifD in Geobacteraceae in subsurface sedimentsQ40622759
Concentrations and fluxes of organic carbon substrates in the aquatic environmentQ40800359
Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways.Q42637200
Utilization of mixtures of polycyclic aromatic hydrocarbons by bacteria isolated from contaminated sedimentQ43285594
Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar waste by subsurface microbial communitiesQ43354103
Insights into the genetic diversity of initial dioxygenases from PAH-degrading bacteriaQ43645983
Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization with tyramide signal amplificationQ43953986
Benzene degradation by Ralstonia pickettii PKO1 in the presence of the alternative substrate succinateQ46224662
Functional gene abundances (nahAc, alkB, xylE) in the assessment of the efficacy of bioremediationQ46508607
The abundance of nahAc genes correlates with the 14C-naphthalene mineralization potential in petroleum hydrocarbon-contaminated oxic soil layersQ46836866
Simultaneous biodegradation of creosote-polycyclic aromatic hydrocarbons by a pyrene-degrading MycobacteriumQ46855045
Molecular diagnostics of polycyclic aromatic hydrocarbon biodegradation in manufactured gas plant soilsQ47276988
Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites.Q50931646
Mineralization of PAHs in coal-tar impacted aquifer sediments and associated microbial community structure investigated with FISH.Q50959788
The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes.Q51586952
Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDalpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples.Q54542941
A targeted real-time PCR assay for studying naphthalene degradation in the environment.Q54578546
Variations in the abundance and identity of class II aromatic ring-hydroxylating dioxygenase genes in groundwater at an aromatic hydrocarbon-contaminated siteQ57135989
In situ biodegradation: microbiological patterns in a contaminated aquiferQ70148267
Rapid construction of deleted DNA fragments for use as internal standards in competitive PCRQ72398431
P433issue20
P407language of work or nameEnglishQ1860
P921main subjectaquiferQ208791
biodegradationQ696715
P304page(s)6478-6487
P577publication date2009-08-21
P1433published inApplied and Environmental MicrobiologyQ4781593
P1476titleDiversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer
P478volume75

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cites work (P2860)
Q30394877Abundance, dynamics, and biogeographic distribution of seven polycyclic aromatic hydrocarbon dioxygenase gene variants in coastal sediments of Patagonia.
Q36212422Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community
Q90557443Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater
Q35080675Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples
Q57260047DNA- and RNA-Based Stable Isotope Probing of Hydrocarbon Degraders
Q51533388Pyrosequencing analysis of the bacterial community in drinking water wells.
Q41877719Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders.
Q33585023Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes by using a novel PCR detection system
Q36080812Spatial Patterns of bphA Gene Diversity Reveal Local Adaptation of Microbial Communities to PCB and PAH Contaminants
Q33847778Subsurface cycling of nitrogen and anaerobic aromatic hydrocarbon biodegradation revealed by nucleic Acid and metabolic biomarkers
Q38488726Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges

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