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  • 1
    Electronic Resource
    Electronic Resource
    Detection and Isolation of Methanotrophic Bacteria Possessing Soluble Methane Monooxygenase (sMMO) Genes Using the Polymerase Chain Reaction (PCR) (1997)
    Springer
    Microbial ecology 33 (1997), S. 21 -31 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Methanotrophic bacteria possessing sMMO activity have gained notoriety in recent years due to their ability to oxidize a wide variety of halogenated aliphatic compounds, including trichloroethylene (TCE), and are being used as the basis for developing new bioremediation processes. PCR primers were designed from DNA sequences of the alpha and beta subunits of the hydroxylase component of the sMMO from Methylococcus capsulatus (Bath). The mmoY1-mmoY2 primer set was derived from the beta subunit and was specific for the mmoY gene from M. capsulatus, but failed to produce the expected 395-nucleotide (nt) fragment from Methylosinus sporium (ATCC 35069) or from Methylosinus trichosporium (ATCC 36070), even at low stringency. A second primer set, primers mmoX1-mmoX2, was derived from the alpha subunit and produced the expected 369-nt fragment from all three methanotrophic cultures tested at the highest stringency used (72°C). Soil and groundwater samples were tested for the presence of sMMO-containing bacteria using these two primer sets. One diesel-contaminated soil sample and one TCE-contaminated groundwater sample gave positive results after amplification of total extracted DNA using the mmoX1-mmoX2 primers. Culture enrichment in small chemostats inoculated with the same positive samples led to the isolation of 13 cultures possessing sMMO activity and containing DNA amplifiable by the mmoX1-mmoX2 primers. Our results indicated that attempts to directly cultivate sMMO-positive bacteria may give false negative results with some environmental samples. We recommend that primers and/or gene probes based on the sMMO be used in parallel with the naphthalene oxidation test for any environmental assessment of the methanotrophic population. RAPD-PCR analysis revealed that half of these isolates appeared to be different from each other and from M. capsulatus, M. sporium, or M. trichosporium.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002489900004
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  • 2
    Electronic Resource
    Electronic Resource
    Catabolic Gene Probe Analysis of an Aquifer Microbial Community Degrading Creosote-Related Polycyclic Aromatic and Heterocyclic Compounds (1997)
    Springer
    Microbial ecology 34 (1997), S. 81-89 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The biodegradation of a mixture of several creosote-related compounds, p-cresol, phenanthrene, fluorene, and carbazole was examined in columns containing aquifer sands. The aquifer material, itself, had an effect on the migration of the test compounds, with p-cresol being retarded the least, followed by carbazole, then fluorene, and finally phenanthrene. The biodegradation of all the compounds was greatly enhanced by the inclusion of p-cresol (10 ppm) in the substrate mixture. Associated with this enhanced degradation was a 100-fold increase in the total culturable bacterial population, and increases in the xylE- and ndoB-positive bacterial populations of more than three orders of magnitude. The products of these two genes are involved in the degradation of monocyclic and polycyclic aromatic compounds, respectively. In columns that did not receive p-cresol, there was no significant change in either the total culturable bacterial population density or the xylE-positive bacterial population, but there were significant increases of one to two orders of magnitude in the ndoB-positive bacterial populations. The results suggest that the ndoB gene probe can detect bacteria capable of utilizing phenanthrene, carbazole, and possibly fluorene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002489900037
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  • 3
    Electronic Resource
    Electronic Resource
    Cloning and expression of the polychlorinated biphenyl-degradation gene cluster from Arthrobacter M5 and comparison to analogous genes from Gram-negative bacteria
    Amsterdam : Elsevier
    Gene 125 (1993), S. 35-40 
    Details
    ISSN: 0378-1119
    Keywords: Biodegradation ; Pseudomonas ; bphC gene ; chlorobiphenyl ; nucleotide sequencing
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0378-1119(93)90742-L
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  • 4
    Electronic Resource
    Electronic Resource
    Analysis of carrageenan from Hypnea musciformis by using κ- and ι-carrageenanases and ^1^3C-n.m.r. spectroscopy
    Amsterdam : Elsevier
    Carbohydrate Research 129 (1984), S. 189-196 
    Details
    ISSN: 0008-6215
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0008-6215(84)85311-2
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  • 5
    Electronic Resource
    Electronic Resource
    Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 33 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The cold-adapted bacterial communities in petroleum hydrocarbon-contaminated and non-impacted soils from two northern Canadian environments, Kuujjuaq, Que., and Alert, Nunavut, were analyzed using a polyphasic approach. Denaturing gradient gel electrophoresis (DGGE) separation of 16S rDNA PCR fragments from soil total community DNA revealed a high level of bacterial diversity, as estimated by the total number of bands visualized. Dendrogram analysis clustered the sample sites on the basis of geographical location. Comparison of the overall microbial molecular diversity suggested that in the Kuujjuaq sites, contamination negatively impacted diversity whereas in the Alert samples, diversity was maintained or increased as compared to uncontaminated controls. Extraction and sequencing analysis of selected 16S rDNA bands demonstrated a range of similarity of 86–100% to reference organisms, with 63.6% of the bands representing high G+C Gram-positive organisms in the order Actinomycetales and 36.4% in the class Proteobacteria. Community level physiological profiles generated using Biolog GN plates were analyzed by cluster analysis. Based on substrate oxidation rates, the samples clustered into groups similar to those of the DGGE dendrograms, i.e. separation based upon geographic origin. The coinciding results reached using culture-independent and -dependent analyses reinforces the conclusion that geographical origin of the samples, rather than petroleum contamination level, was more important in determining species diversity within these cold-adapted bacterial communities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00746.x
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  • 6
    Electronic Resource
    Electronic Resource
    Reduction in denitrification activity in field soils exposed to long term contamination by 2,4,6-trinitrotoluene (TNT) (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 32 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Terrestrial sites contaminated with 2,4,6-trinitrotoluene (TNT) are a widespread and persistent problem and often contain non-vegetated areas with TNT concentrations well in excess of 1000 mg kg−1. In this study, we examined the effect of TNT on denitrification activity in field soils, and compared the sensitivity of denitrifying enzymes to TNT. DNA probes assessed the prevalence of nirS, nirK and nosZ (encoding cd1 or copper nitrite reductase and nitrous oxide reductase, respectively), denitrifying genotypes in the culturable and total microbial community. The nitrate (NaR), nitrite (NiR) and nitrous oxide (N2OR) reductase activities in field soil and in isolates were assessed by gas chromatography. The relative occurrence of the nirK, nirS or nosZ genotypes increased in the cultured community and in total uncultured community DNA as nitroaromatic concentrations increased. However, denitrifying activity decreased in response to increasing TNT concentrations, with an IC50 for NaR+NiR+nitric oxide reductase (NOR) of 400 mg TNT kg−1 soil and for N2OR of 26 mg TNT kg−1 soil. The denitrifying activity of four soil isolates also decreased in response to TNT, with N2OR activity being three times more sensitive to TNT than NaR+NiR+NOR activity. Interestingly, there were 118 times more nirK isolates than nirS isolates in uncontaminated soil but only 1.5 times more in soil containing 17 400 mg kg−1 TNT. The results from this study indicated that TNT reduced denitrification activity in field soils, and N2OR was much more sensitive to TNT than NaR+NiR+NOR.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00699.x
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  • 7
    Electronic Resource
    Electronic Resource
    Effect of experimental contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine on soil bacterial communities (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 43 (2003), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The effect of contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on an indigenous soil bacterial community was examined in two uncontaminated loam soil columns possessing native grasses. One column was spiked twice with RDX crystals for a total RDX load of 1000 mg (kg soil)−1. The reduced metabolite of RDX degradation, hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine, was observed in the column leachate, suggesting anaerobic degradation of RDX. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA from both contaminated and uncontaminated columns produced identical banding patterns which were stable over the course of the experimental period. The bacterial diversity remained high in the contaminated column, as determined by restriction fragment length polymorphism and rarefaction analyses of random 16S rDNA clones. These combined results suggested that long-term exposure to 1000 mg RDX (kg soil)−1 did not produce an observable effect on bacterial diversity or the numerically dominant members of the indigenous soil bacterial community.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2003.tb01065.x
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  • 8
    Electronic Resource
    Electronic Resource
    Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 41 (2002), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The prevalence of four alkane monooxygenase genotypes (Pseudomonas putida GPo1, Pp alkB; Rhodococcus sp. strain Q15, Rh alkB1 and Rh alkB2; and Acinetobacter sp. strain ADP-1, Ac alkM) in hydrocarbon-contaminated and pristine soils from the Arctic and Antarctica were determined by both culture-independent (PCR hybridization analyses) and culture-dependent (colony hybridization analyses) molecular methods, using oligonucleotide primers and DNA probes specific for each of the alk genotypes. PCR hybridization of total soil community DNA detected the rhodococcal alkB genotypes in most of the contaminated (Rh alkB1, 18/20 soils; Rh alkB2, 13/20) and many pristine soils (Rh alkB1, 9/10 soils; Rh alkB2, 7/10), while Pp alkB was generally detected in the contaminated soils (15/20) but less often in pristine soils (5/10). Ac alkM was rarely detected in the soils (1/30). The colony hybridization technique was used to determine the prevalence of each of the alk genes and determine their relative abundance in culturable cold-adapted (5°C) and mesophilic populations (37°C) from eight of the polar soils. The cold-adapted populations, in general, possessed relatively higher percentages of the Rh alkB genotypes (Rh alkB1, 1.9% (0.55); Rh alkB2, 2.47% (0.89)), followed by the Pp alkB (1.13% (0.50)), and then the Ac alkM (0.53% (0.36)). The Rh alkB1 genotype was clearly more prevalent in culturable cold-adapted bacteria (1.9% (0.55)) than in culturable mesophiles (0.41 (0.55)), suggesting that cold-adapted bacteria are the predominant organisms possessing this genotype. Overall, these results indicated that (i) Acinetobacter spp. are not predominant members of polar alkane degradative microbial communities, (ii) Pseudomonas spp. may become enriched in polar soils following contamination events, and (iii) Rhodococcus spp. may be the predominant alkane-degradative bacteria in both pristine and contaminated polar soils.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00975.x
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  • 9
    Electronic Resource
    Electronic Resource
    The influence of moisture on microbial transport, survival and 2,4-D biodegradation with a genetically marked Burkholderia cepacia in unsaturated soil columns (1997)
    Springer
    Biodegradation 8 (1997), S. 87-96 
    Details
    ISSN: 1572-9729
    Keywords: genetically engineered microbes ; survival ; transport ; degradation ; moisture
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The influence of moisture on the survival, movement anddegradation activity of a 2,4-D degrading bacterium,Burkholderia cepacia strain BRI6001L, geneticallyengineered to contain bioluminescent and lactoseutilization genes, was studied in unsaturated soil columns.The distance traveled by BRI6001L was dependent on theclay content of the soil, higher clay contents beingresponsible for higher filtration coefficients. Long termsurvival, in excess of one year, was attributed to strainBRI6001L's ability to survive dry conditions. Changes inthe 2,4-D biodegradation rate showed a better correlationwith the BRI6001L population density than with the totalviable bacterial population. At moisture levels betweenfield capacity and 40% moisture (− 33 kPa to −100 kPa)2,4-D degradation was attributed mainly to BRI6001L. Atmoisture levels between 6 and 15%, 2,4-D disappearancewas attributed to the indigenous microbial population,with no degradation occurring at moisture levels below6%. Returning the moisture to above 40% led to anincrease of 4 orders of magnitude in the BRI6001Lpopulation density and to a 10-fold increase in the 2,4-Ddegradation rate. The ability to monitor a specificmicrobial population using reporter genes hasdemonstrated the importance of controlling moisturelevels for maximizing biodegradation rates in unsaturatedsoil environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008236401342
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