Molecular Techniques of Xenobiotic-Degrading Bacteria and Their Catabolic Genes in Bioremediation

2016 ◽  
pp. 1-30
Author(s):  
K. Inoue ◽  
J. Widada ◽  
T. Omori ◽  
H. Nojiri
Keyword(s):  
Molecular Techniques ◽  
Catabolic Genes ◽  
Degrading Bacteria

scholarly journals CRUDE OIL BIOREMEDIATION BY INDIGENOUS BACTERIA ISOLATED FROM OILY SLUDGE

2016 ◽  
Vol 78 (11-2) ◽  
Author(s):  
Nur Hafizah Azizan ◽  
Kasing Ak Apun ◽  
Lesley Maurice Bilung ◽  
Micky Vincent ◽  
Hairul Azman Roslan ◽  
...  
Keyword(s):  
Crude Oil ◽  
Enrichment Culture ◽  
Molecular Techniques ◽  
Oily Sludge ◽  
Minimal Salt Medium ◽  
Alkane Degradation ◽  
Growth Study ◽  
The Third ◽  
Cell Counts ◽  
Degrading Bacteria

Enrichment culture technique leads to the discovery of six presumptive TPH-degrading bacteria. Identification and characterization tests using morphological, biochemical and molecular techniques have successfully isolated Pseudomonas aeruginosa (UMAS1PF), Serratia marcescens (UMAS2SF) and Klebsiella spp. (UMAS3KF). All strains were able to use crude oil as sole carbon and energy source for their growth since they were able to survive in Minimal Salt medium supplemented with 1% (v/v) crude oil. Growth study showed that they produced the highest cell counts on the third or fourth day by 108 – 1011 CFU/ml. Six artificial consortium inoculums have been produced from the growth study. Gas chromatography analysis showed that all isolates had the ability to degrade aliphatic hydrocarbon with 100% degradation of nC19 – C24. Among the isolates, UMAS2SF was the best and fastest n-alkane degrader with degradation percentage between 55 – 90% of n-C14 – C18 in 14 days. This was followed by UMAS1PF and UMAS3KF with 11 – 82% and 1.3% degradation, respectively. Enhancement study showed that plot with inoculum and NPK addition successfully enhanced n-alkane degradation. Plot A2:B3+NPK degraded n-alkane the fastest followed by plot treated by C+NPK, A1:B2, B+NPK and A2:B3. Result showed that UMAS1PF was the best PAHs degrader as most of the high molecular weight PAHs was degraded. In the enhancement study, the plot amended with A2:B3 showed the highest PAHs degradation, followed by plots A1:B2, A3:B1:C2 and A1:C3 that was assigned as the third, fourth and fifth best in mineralizing PAHs, respectively.

Impact of nanoparticles on transcriptional regulation of catabolic genes of petroleum hydrocarbon-degrading bacteria in contaminated soil microcosms

2018 ◽  
Vol 59 (2) ◽  
pp. 166-180
Author(s):  
Wael S. El-Sayed ◽  
Yasser Elbahloul ◽  
Mohamed E. Saad ◽  
Ahmed M. Hanafy ◽  
Abdelrahman H. Hegazi ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Contaminated Soil ◽  
Petroleum Hydrocarbon ◽  
Soil Microcosms ◽  
Catabolic Genes ◽  
Degrading Bacteria

scholarly journals Cross-Regulation of Biphenyl- and Salicylate-Catabolic Genes by Two Regulatory Systems in Pseudomonas pseudoalcaligenes KF707

2006 ◽  
Vol 188 (13) ◽  
pp. 4690-4697 ◽  
Author(s):  
Hidehiko Fujihara ◽  
Hideyuki Yoshida ◽  
Tetsuya Matsunaga ◽  
Masatoshi Goto ◽  
Kensuke Furukawa
Keyword(s):  
Gene Cluster ◽  
Coenzyme A ◽  
Regulatory Gene ◽  
Pseudomonas Pseudoalcaligenes ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Regulatory Systems ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
Regulatory Model

ABSTRACT Pseudomonas pseudoalcaligenes KF707 grows on biphenyl and salicylate as sole sources of carbon. The biphenyl-catabolic (bph) genes are organized as bphR1A1A2(orf3)A3A4BCX0X1X2X3D, encoding the enzymes for conversion of biphenyl to acetyl coenzyme A. In this study, the salicylate-catabolic (sal) gene cluster encoding the enzymes for conversion of salicylate to acetyl coenzyme A were identified 6.6-kb downstream of the bph gene cluster along with a second regulatory gene, bphR2. Both the bph and sal genes were cross-regulated positively and/or negatively by the two regulatory proteins, BphR1 and BphR2, in the presence or absence of the effectors. The BphR2 binding sequence exhibits homology with the NahR binding sequences in various naphthalene-degrading bacteria. Based on previous studies and the present study we propose a new regulatory model for biphenyl and salicylate catabolism in strain KF707.

scholarly journals Construction of Chimeric Catechol 2,3-Dioxygenase Exhibiting Improved Activity against the Suicide Inhibitor 4-Methylcatechol

2004 ◽  
Vol 70 (3) ◽  
pp. 1804-1810 ◽  
Author(s):  
Akiko Okuta ◽  
Kouhei Ohnishi ◽  
Shigeaki Harayama
Keyword(s):  
Ascorbic Acid ◽  
Pseudomonas Putida ◽  
Gene Sequence ◽  
Mixed Cultures ◽  
Enzyme Inactivation ◽  
Host Cells ◽  
Ring Cleavage ◽  
Gene Sequences ◽  
Catabolic Genes ◽  
Degrading Bacteria

ABSTRACT Catechol 2,3-dioxygenase (C23O; EC 1.3.11.2), exemplified by XylE and NahH, catalyzes the ring cleavage of catechol and some substituted catechols. C23O is inactivated at an appreciable rate during the ring cleavage of 4-methylcatechol due to the oxidation of the Fe(II) cofactor to Fe(III). In this study, a C23O exhibiting improved activity against 4-methylcatechol was isolated. To isolate this C23O, diverse C23O gene sequences were PCR amplified from DNA which had been isolated from mixed cultures of phenol-degrading bacteria and subcloned in the middle of a known C23O gene sequence (xylE or nahH) to construct a library of chimeric C23O genes. These chimeric C23O genes were then introduced into Pseudomonas putida possessing some of the toluene catabolic genes (xylXYZLGFJQKJI). When a C23O gene (e.g., xylE) is introduced into this strain, the transformants cannot generally grow on p-toluate because 4-methylcatechol, a metabolite of p-toluate, is a substrate as well as a suicide inhibitor of C23O. However, a transformant of this strain capable of growing on p-toluate was isolated, and a chimeric C23O (named NY8) in this transformant was characterized. The rate of enzyme inactivation by 4-methylcatechol was lower in NY8 than in XylE. Furthermore, the rate of the reactivation of inactive C23O in a solution containing Fe(II) and ascorbic acid was higher in NY8 than in XylE. These properties of NY8 might allow the efficient metabolism of 4-methylcatechol and thus allow host cells to grow on p-toluate.

Design of PCR Primers for the mcrA Genes Detection of Methanogen Communities

2011 ◽  
Vol 135-136 ◽  
pp. 408-413 ◽  
Author(s):  
Nguyen Ngoc Tuan ◽  
Shir Ly Huang
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Biogas Production ◽  
Pcr Primers ◽  
Molecular Techniques ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Mcra Gene ◽  
Catabolic Genes ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

Methanogens play an important role to carbon cycling, catalyzing the production of methane and carbon dioxide, both potent green house gases, during organic matter degradation in anaerobic environments. Therefore, it is necessary to better understand microorganisms that produce natural gas. Indeed, methanogens are difficult to perform through culture based methods. In addition, the culture independent methods using the 16S rRNA gene also revealed some disadvantages. For these reasons, the culture independent molecular techniques using the specific catabolic genes such as methyl coenzyme M reductase (MCR) were studied. In this study, a primer set which can amplify specific fragments from a wide variety of mcrA gene was designed based on the homologous regions of 100 mcrA genes listed in the GenBank. PCR with the mcrA primers amplified DNA fragments of the expected size from all the six samples which obtained from biogas production reactors. In addition, denaturing gradient gel electrophoresis PCR analysis using our designed primers also revealed the diversity of mcrA gene in each sample. These results revealed that our primers were successfully to detect the mcrA genes and it is also helpful to know the diversity of mcrA genes in methanogen communities.

scholarly journals The Atrazine Catabolism Genes atzABC Are Widespread and Highly Conserved

1998 ◽  
Vol 180 (7) ◽  
pp. 1951-1954 ◽  
Author(s):  
Mervyn L. de Souza ◽  
Jennifer Seffernick ◽  
Betsy Martinez ◽  
Michael J. Sadowsky ◽  
Lawrence P. Wackett
Keyword(s):  
Cyanuric Acid ◽  
Pairwise Comparisons ◽  
Sequence Identity ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
Herbicide Atrazine ◽  
Bacterial Genes ◽  
Globally Distributed ◽  
Average Sequence Identity ◽  
Sequence Identities

ABSTRACT Pseudomonas strain ADP metabolizes the herbicide atrazine via three enzymatic steps, encoded by the genesatzABC, to yield cyanuric acid, a nitrogen source for many bacteria. Here, we show that five geographically distinct atrazine-degrading bacteria contain genes homologous toatzA, -B, and -C. The sequence identities of the atz genes from different atrazine-degrading bacteria were greater than 99% in all pairwise comparisons. This differs from bacterial genes involved in the catabolism of other chlorinated compounds, for which the average sequence identity in pairwise comparisons of the known members of a class ranged from 25 to 56%. Our results indicate that globally distributed atrazine-catabolic genes are highly conserved in diverse genera of bacteria.

scholarly journals DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil

2020 ◽  
Author(s):  
Harry Lerner ◽  
Başak Öztürk ◽  
Anja B. Dohrmann ◽  
Joice Thomas ◽  
Kathleen Marchal ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Sequence Similarity ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
Agricultural Field ◽  
Bacterial Populations ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
History Of

AbstractThe frequent exposure of agricultural soils to pesticides often leads to microbial adaptation, including the development of dedicated microbial populations that utilize the pesticide compound as a carbon and energy source. Soil from an agricultural field in Halen (Belgium) with a history of linuron exposure has been studied for its linuron-degrading bacterial populations at two time points over the past decade and Variovorax was appointed as a key linuron degrader. Like most studies on pesticide degradation, these studies relied on isolates that were retrieved through bias-prone enrichment procedures and therefore might not represent the in situ active pesticide-degrading populations. In this study, we revisited the Halen field and applied, in addition to enrichment-based isolation, DNA stable isotope probing (DNA-SIP), to identify the in situ linuron degrading bacteria. DNA-SIP unambiguously linked Variovorax and its linuron catabolic genes to linuron dissipation, likely through synergistic cooperation between two species. Additionally, two linuron mineralizing Variovorax isolates were obtained with high 16S rRNA gene sequence similarity to strains isolated from the same field a decade earlier. The results confirm Variovorax as the in situ degrader of linuron in the studied agricultural field and corroborate the genus as key in the maintenance of a robust genetic memory regarding linuron degradation functionality in the examined field.

scholarly journals ISOLATION AND CHARACTERIZATION OF PHENANTHRENE DEGRADATING BACTERIA FROM DAIRY WASTE SAMPLES

2020 ◽  
Vol 8 (12) ◽  
pp. 372-380
Author(s):  
Gunti Vijay Kumar ◽  
◽  
Pandu Brahmaji Rao ◽  
Keyword(s):  
Agar Medium ◽  
Micrococcus Luteus ◽  
Pcr Amplification ◽  
Molecular Techniques ◽  
Biochemical Tests ◽  
Hazardous Chemical ◽  
Isolation And Characterization ◽  
Dairy Waste ◽  
Degrading Bacteria

Phenanthrene is the commonly used hazardous chemical in various industries and the detoxification is a big problem till today. In this study, phenanthrene degrading bacteria were isolated from dairy waste samples, characterized by molecular techniques. A total of 10 samples were collected respectively from different spots of dairy industry. Minimum salt agar medium with phenanthrene composition was used to isolate the pure culture of resistant bacterium. Morphological, biochemical tests were done to identify the phenanthrene degrading bacteria. The colonies of the isolates were circular to irregular in dairy samples. Phenanthrene tolerant bacteria were isolated after the dairy waste soil samples was serially diluted and transferred onto M9 minimal agar medium amended with 10mg/l of phenanthrene. A concentration of 10 mg/l was chosen based on the prevailing concentration. Four Phenanthrene tolerant bacteria from dairy waste (HW2, HW1, HW3, HW5) were isolated. From the biochemical and 16srRNA PCR amplification, the bacterium identified was Micrococcus leuteus. The resistance to Phenanthrene by the isolate was tested with various concentrations of Phenanthrene from 0 to 10mM. The Micrococcus luteus showed a MTC value of 28Cfu/ml at 8mM and Bacillus cereus showed least.

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