scholarly journals Anaerobic Biodegradation of n-Hexadecane by a Nitrate-Reducing Consortium

2008 ◽  
Vol 75 (5) ◽  
pp. 1339-1344 ◽  
Author(s):  
Amy V. Callaghan ◽  
Meghan Tierney ◽  
Craig D. Phelps ◽  
L. Y. Young
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Mass Spectrometry Analysis ◽  
Chain Elongation ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Pentadecanoic Acid ◽  
Spectrometry Analysis ◽  
Tridecanoic Acid ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis

ABSTRACT Nitrate-reducing enrichments, amended with n-hexadecane, were established with petroleum-contaminated sediment from Onondaga Lake. Cultures were serially diluted to yield a sediment-free consortium. Clone libraries and denaturing gradient gel electrophoresis analysis of 16S rRNA gene community PCR products indicated the presence of uncultured alpha- and betaproteobacteria similar to those detected in contaminated, denitrifying environments. Cultures were incubated with H34-hexadecane, fully deuterated hexadecane (d 34-hexadecane), or H34-hexadecane and NaH13CO3. Gas chromatography-mass spectrometry analysis of silylated metabolites resulted in the identification of [H29]pentadecanoic acid, [H25]tridecanoic acid, [1-13C]pentadecanoic acid, [3-13C]heptadecanoic acid, [3-13C]10-methylheptadecanoic acid, and d 27-pentadecanoic, d 25-, and d 2 4-tridecanoic acids. The identification of these metabolites suggests a carbon addition at the C-3 position of hexadecane, with subsequent β-oxidation and transformation reactions (chain elongation and C-10 methylation) that predominantly produce fatty acids with odd numbers of carbons. Mineralization of [1-14C]hexadecane was demonstrated based on the recovery of 14CO2 in active cultures.

scholarly journals Toxicity and Molecular Identification of Green ToadfishLagocephalus lunarisCollected from Kyushu Coast, Japan

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Yuji Nagashima ◽  
Takuya Matsumoto ◽  
Keisuke Kadoyama ◽  
Shoichiro Ishizaki ◽  
Makoto Terayama
Keyword(s):  
Food Poisoning ◽  
Mass Spectrometry Analysis ◽  
Nucleotide Sequence Analysis ◽  
Rrna Gene ◽  
Liquid Chromatography Mass Spectrometry ◽  
Spectrometry Analysis ◽  
Pcr Products ◽  
Western Japan ◽  
Mouse Unit ◽  
The 16S Rrna Gene

Green toadfishLagocephalus lunarisinhabits tropical and subtropical seas and contains high tetrodotoxin (TTX) levels in the muscle as well as liver and gonad. In 2008 to 2009, food poisoning due to ingestingL. lunaisoccurred in Western Japan. Five specimens of green toadfish caught in Kyushu coast, Japan, were analyzed for toxicity, toxins, and species identification. All five specimens were toxic by bioassay. Comparing the maximum toxicity in tissues, ovary contained the most toxin (1810 mouse unit [MU]/g), followed by liver (341 MU/g), muscle (135 MU/g), skin (79 MU/g), and intestine (72 MU/g). Liquid chromatography/mass spectrometry analysis revealed that TTX was the major toxin. Nucleotide sequence analysis of the 16S rRNA gene fragment of muscle mitochondrial DNA indicated that partial sequences of PCR products of four specimens were identical with that ofL. lunaris. The sequence of one specimen was indistinguishable from that of the brown-backed toadfishLagocephalus wheeleri, a nontoxic species.

scholarly journals Molecular Profiling of the Clostridium leptum Subgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis and Clone Library Analysis

2006 ◽  
Vol 72 (8) ◽  
pp. 5232-5238 ◽  
Author(s):  
Jian Shen ◽  
Baorang Zhang ◽  
Guifang Wei ◽  
Xiaoyan Pang ◽  
Hua Wei ◽  
...  
Keyword(s):  
Clone Library ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Clone Library Analysis ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Universal Bacterial Primer ◽  
Group Specific Primer

ABSTRACT A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of the Clostridium leptum subgroup in human feces. PCR products (length, 239 bp) were amplified using C. leptum cluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bp C. leptum cluster-specific amplicons, and the remaining 14 clones did not produce these amplicons but still phylogenetically belong to the subgroup. Sixty-four percent of the clones were related to Faecalibacterium prausnitzii (similarity, 97 to 99%), 6% were related to Subdoligranulum variabile (similarity, ∼99%), 2% were related to butyrate-producing bacterium A2-207 (similarity, 99%), and 28% were not identified at the species level. The identities of most bands in the DGGE profiles for the same adult were determined by comigration analysis with the 86 clones that harbored the 239-bp group-specific fragments. Our results suggest that DGGE combined with clone library analysis is an effective technique for monitoring and analyzing the composition of this important population in the human gut flora.

scholarly journals Diversity of 4-Chloro-2-nitrophenol-Degrading Bacteria in a Waste Water Sample

2016 ◽  
Vol 2016 ◽  
pp. 1-5 ◽  
Author(s):  
Pankaj Kumar Arora ◽  
Alok Srivastava ◽  
Vijay Pal Singh
Keyword(s):  
Waste Water ◽  
Water Sample ◽  
Mass Spectrometry Analysis ◽  
Contaminated Site ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Spectrometry Analysis ◽  
Waste Water Sample ◽  
Degrading Bacteria

Eighteen bacterial strains, isolated from a waste water sample collected from a chemically contaminated site, Patancheru (17°32′N 78°16′E/17.53°N 78.27°E), India, were able to decolorize 4-chloro-2-nitrophenol (4C2NP) in the presence of an additional carbon source. These eighteen 4C2NP-decolorizing strains have been identified as members of four different genera, includingBacillus,Paenibacillus,Pseudomonas, andLeuconostocbased on the 16S rRNA gene sequencing and phylogenetic analysis. Most of the bacteria (10) belonged to the genusBacillusand contributed 56% of the total 4C2NP-degrading bacteria, whereas the members of generaPaenibacillusandPseudomonasrepresented 22% and 17%, respectively, of total 4C2NP-degrading isolates. There was only one species ofLeuconostoccapable of degrading 4C2NP. This is the first report of the diversity of 4C2NP-decolorizing bacteria in a waste water sample. Furthermore, one bacterium,Bacillus aryabhattaistrain PC-7, was able to decolorize 4C2NP up to a concentration of 2.0 mM. Gas chromatography-mass spectrometry analysis identified 5-chloro-2-methylbenzoxazole as the final product of 4C2NP decolorization in strain PC-7.

scholarly journals Biodegradation of an Alicyclic Hydrocarbon by a Sulfate-Reducing Enrichment from a Gas Condensate-Contaminated Aquifer

2003 ◽  
Vol 69 (1) ◽  
pp. 434-443 ◽  
Author(s):  
Luis A. Rios-Hernandez ◽  
Lisa M. Gieg ◽  
Joseph M. Suflita
Keyword(s):  
Mass Spectrometry ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Analysis ◽  
Gas Condensate ◽  
Microbial Community Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Contaminated Aquifer ◽  
Sulfate Reducing ◽  
Gradient Gel Electrophoresis

ABSTRACT We used ethylcyclopentane (ECP) as a model alicyclic hydrocarbon and investigated its metabolism by a sulfate-reducing bacterial enrichment obtained from a gas condensate-contaminated aquifer. The enrichment coupled the consumption of ECP with the stoichiometrically expected amount of sulfate reduced. During ECP biodegradation, we observed the transient accumulation of metabolite peaks by gas chromatography-mass spectrometry, three of which had identical mass spectrometry profiles. Mass-spectral similarities to analogous authentic standards allowed us to identify these metabolites as ethylcyclopentylsuccinic acids, ethylcyclopentylpropionic acid, ethylcyclopentylcarboxylic acid, and ethylsuccinic acid. Based on these findings, we propose a pathway for the degradation of this alicyclic hydrocarbon. Furthermore, a putative metabolite similar to ethylcyclopentylsuccinic acid was also found in samples of contaminated groundwater from the aquifer. However, no such finding was evident for samples collected from wells located upgradient of the gas condensate spill. Microbial community analysis of the ECP-degrading enrichment by denaturing gradient gel electrophoresis revealed the presence of at least three different organisms using universal eubacterial primers targeting 550 bp of the 16S rRNA gene. Based on sequence analysis, these organisms are phylogenetically related to the genera Syntrophobacter and Desulfotomaculum as well as a member of the Cytophaga-Flexibacter-Bacteroides group. The evidence suggests that alicyclic hydrocarbons such as ECP can be anaerobically activated by the addition to the double bond of fumarate to form alkylsuccinate derivatives under sulfate-reducing conditions and that the reaction occurs in the laboratory and in hydrocarbon-impacted environments.

scholarly journals Molecular Method To Assess the Diversity of Burkholderia Species in Environmental Samples

2002 ◽  
Vol 68 (4) ◽  
pp. 1595-1603 ◽  
Author(s):  
Joana Falcão Salles ◽  
Francisco Adriano De Souza ◽  
Jan Dirk van Elsas
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Direct Method ◽  
Soil Samples ◽  
Rrna Gene ◽  
Migration Behavior ◽  
Soil Dna ◽  
Soil Microbial ◽  
Specificity And Sensitivity ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis

ABSTRACT In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the Burkholderia diversity in soil samples. Primers specific for the genus Burkholderia were developed based on the 16S rRNA gene sequence and were evaluated in PCRs performed with genomic DNAs from Burkholderia and non-Burkholderia species as the templates. The primer system used exhibited good specificity and sensitivity for the majority of established species of the genus Burkholderia. DGGE analyses of the PCR products obtained showed that there were sufficient differences in migration behavior to distinguish the majority of the 14 Burkholderia species tested. Sequence analysis of amplicons generated with soil DNA exclusively revealed sequences affiliated with sequences of Burkholderia species, demonstrating that the PCR-DGGE method is suitable for studying the diversity of this genus in natural settings. A PCR-DGGE analysis of the Burkholderia communities in two grassland plots revealed differences in diversity mainly between bulk and rhizosphere soil samples; the communities in the latter samples produced more complex patterns.

scholarly journals Evaluations of Different Hypervariable Regions of Archaeal 16S rRNA Genes in Profiling of Methanogens by Archaea-Specific PCR and Denaturing Gradient Gel Electrophoresis

2007 ◽  
Vol 74 (3) ◽  
pp. 889-893 ◽  
Author(s):  
Zhongtang Yu ◽  
Rubén García-González ◽  
Floyd L. Schanbacher ◽  
Mark Morrison
Keyword(s):  
16S Rrna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
V Region

ABSTRACT Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.

Isolation, development and identification of salt-tolerant bacterial consortium from crude-oil-contaminated soil for degradation of di-azo dye Reactive Blue 220

2015 ◽  
Vol 72 (2) ◽  
pp. 311-321 ◽  
Author(s):  
Vipul R. Patel ◽  
Nikhil Bhatt
Keyword(s):  
Oxygen Demand ◽  
Bacterial Consortium ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Cod Reduction ◽  
Spectrometry Analysis ◽  
Wide Range

The objective of this study was development and characterization of a halophilic bacterial consortium for rapid decolorization and degradation of a wide range of dyes and their mixtures. The 16S rRNA gene analysis of developed halophilic consortium VN.1 showed that the bacterial consortium contained six bacterial strains, which were identified as Pseudomonas fluorescens HM480360, Enterobacter aerogenes HM480361, Shewanella sp. HM589853, Arthrobacter nicotianae HM480363, Bacillus beijingensis HM480362 and Pseudomonas aeruginosa JQ659549. Halophilic consortium VN.1 was able to decolorize up to 2,500 mg/L RB220 with >85% chemical oxygen demand (COD) reduction under static condition at 30 °C and pH 8.0 in the presence of 7% NaCl. VN.1 also exhibited more than 85% COD reduction with >25 mg/(L h) rate of decolorization in the case of different reactive dye mixtures. We propose the symmetric cleavage of RB220 using Fourier transform infrared, high-performance liquid chromatography (HPLC), nuclear magnetic resonance and gas chromatography-mass spectrometry analysis, and confirmed the formation of sodium-4-aminobenzenesulfonate, sodium-6-aminonepthalenesulfonate, and sodiumbenzene/nepthalenesulfonate. Toxicity studies confirm that the biodegraded products of RB220 effluent stimulate the growth of plants as well as the bacterial community responsible for soil fertility.

MICROBIAL COMMUNITY DURING BIOREMEDIATION EXPERIMENTAL ON OIL SPILL IN COASTAL OF PARI ISLAND

2011 ◽  
Vol 3 (1) ◽  
Author(s):  
Lies Indah Sutiknowati
Keyword(s):  
Oil Spill ◽  
Deoxyribonucleic Acid ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gas Chromatography Mass Spectrometry ◽  
Oil Degradation ◽  
Sequence Determination ◽  
Blast Search ◽  
Degrading Bacteria ◽  
Gradient Gel Electrophoresis

There is an information how to identify hydrocarbon degrading bacteria for bioremediation of marine oil spill. We have Bioremediation treatment for degradation of oil spill on Pari island and need two kind of experiment there are tanks experiment (sampling 0 to 90 days) and semi enclosed system (sampling 0 to 150 days). Biostimulation with nutrients (N and P) was done to analyze biodegradation of hydrocarbon compounds. Experiment design using fertilizer Super IB and Linstar will stimulate bacteria can degrade oil, n-alkane, and alkane as poly aromatic hydrocarbon. The bacteria communities were monitored and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE) and Clone Library; oil chemistry was analyzed by Gas Chromatography Mass Spectrometry (GCMS). DNA (deoxyribonucleic acid) was extracted from colonies of bacteria and sequence determination of the 16S rDNA was amplified by primers U515f and U1492r. Strains had been sequence and had similarity about 90-99% to their closest taxa by homology Blast search and few of them suspected as new species. The results showed that fertilizers gave a significant effect on alkane, PAH and oil degradation in tanks experiment but not in the field test. Dominant of the specific bacteria on this experiment were Alcanivorax, Marinobacter and Prosthecochloris. Keywords: Bioremediation, Biostimulation, DGGE, PAH, Pari Island

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