scholarly journals Genetic diversity of bacterial strains isolated from soils, contaminated with polycyclic aromatic hydrocarbons, by 16S rRNA gene sequencing and amplified fragment length polymorphism fingerprinting

2006 ◽  
Vol 161 (2) ◽  
pp. 150-157 ◽  
Author(s):  
G. La Rosa ◽  
E. De Carolis ◽  
M. Sali ◽  
M. Papacchini ◽  
C. Riccardi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Fragment Length Polymorphism ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Polycyclic Aromatic ◽  
Rrna Gene Sequencing

scholarly journals Xylanolytic Psychotrophs From Andosolic Sedge Fens and Moss Heaths in Iceland

Fine Focus ◽  
2018 ◽  
Vol 4 (2) ◽  
pp. 171-186
Author(s):  
Olivia J. Rickman ◽  
M. Auður Sigurbjörnsdóttir ◽  
Oddur Vilhemsson
Keyword(s):  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Cold Environments ◽  
Specific Pcr ◽  
Xylanolytic Activity ◽  
Cold Active ◽  
Rrna Gene Sequencing ◽  
Stenotrophomonas Rhizophila

Nine xylanolytic bacterial strains were isolated from fen and heath soils in northern Iceland. They were found by 16S rRNA gene sequencing to belong to the genera Paenibacillus, Bacillus, Pseudomonas, and Stenotrophomonas. Using a simple, plate-based semiquantitative assay with azo-crosslinked xylan as the substrate, it was determined that although isolated from cold environments, most of the strains displayed greater xylanolytic activity under mesophilic conditions, with only the paenibacilli displaying markedly cold-active xylanolytic activity. Indeed, for one isolate, Paenibacillus castaneae OV2122, xylanolytic activity was only detected at 15°C and below under the conditions tested. Of the nine strains, Paenibacillus amylolyticus OV2121 displayed the greatest activity at 5°C. Glycohydrolase family-specific PCR indicated that the paenibacilli produced multiple xylanases of families 10 and 11, whereas a family 8 xylanase was detected in Pseudomonas kilonensis AL1515, and a family 11 xylanase in Stenotrophomonas rhizophila AL1610.

Mechanism of boron tolerance in soil bacteria

2010 ◽  
Vol 56 (1) ◽  
pp. 22-26 ◽  
Author(s):  
Iftikhar Ahmed ◽  
Toru Fujiwara
Keyword(s):  
Soil Bacteria ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Soil Samples ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Tolerance Mechanisms ◽  
Boron Tolerance ◽  
Rrna Gene Sequencing ◽  
Comparative Phylogenetic Analysis

Boron (B) is toxic to living cells at levels above a certain threshold. We isolated several B-tolerant bacterial strains from soil samples and studied them for possible mechanisms of B tolerance. 16S rRNA gene sequencing and comparative phylogenetic analysis demonstrated that the isolates belong to the following 6 genera: Arthrobacter , Rhodococcus , Lysinibacillus , Algoriphagus , Gracilibacillus , and Bacillus . These isolates exhibited B-tolerance levels of 80, 100, 150, 300, 450, and 450 mmol/L, respectively, whilst maintaining a significantly lower intracellular B concentration than in the medium. Statistical analysis showed a negative correlation between the protoplasmic B concentration and the degree of tolerance to a high external B concentration. The kinetic assays suggest that the high B efflux and (or) exclusion are the tolerance mechanisms against a high external B concentration in the isolated bacteria.

scholarly journals Animal fat and glycerol bioconversion to polyhydroxyalkanoate by produced water bacteria

e-Polymers ◽  
2020 ◽  
Vol 20 (1) ◽  
pp. 92-102
Author(s):  
Rafeya Sohail ◽  
Nazia Jamil ◽  
Iftikhar Ali ◽  
Sajida Munir
Keyword(s):  
Produced Water ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Ftir Analysis ◽  
Bacterial Strains ◽  
Future Studies ◽  
Animal Fat ◽  
Bacillus Tequilensis ◽  
Rrna Gene Sequencing

AbstractOil reservoirs contain large amounts of hydrocarbon rich produced water, trapped in underground channels. Focus of this study was isolation of PHA producers from produced water concomitant with optimization of production using animal fat and glycerol as carbon source. Bacterial strains were identified as Bacillus subtilis (PWA), Pseudomonas aeruginosa (PWC), Bacillus tequilensis (PWF), and Bacillus safensis (PWG) based on 16S rRNA gene sequencing. Similar amounts of PHA were obtained using animal fat and glycerol in comparison to glucose. After 24 h, high PHA production on glycerol and animal fat was shown by strain PWC (5.2 g/ L, 6.9 g/ L) and strain PWF (12.4 g/ L, 14.2 g/ L) among all test strains. FTIR analysis of PHA showed 3-hydroxybutyrate units. The capability to produce PHA in the strains was corroborated by PhaC synthase gene sequencing. Focus of future studies can be the use of lipids and glycerol on industrial scale.

scholarly journals Direct Link between Toluene Degradation in Contaminated-Site Microcosms and a Polaromonas Strain

2009 ◽  
Vol 76 (3) ◽  
pp. 956-959 ◽  
Author(s):  
Weimin Sun ◽  
Shuguang Xie ◽  
Chunling Luo ◽  
Alison M. Cupples
Keyword(s):  
Fragment Length Polymorphism ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Stable Isotope Probing ◽  
Contaminated Site ◽  
Rrna Gene ◽  
Toluene Degradation ◽  
Soil Microcosms ◽  
Rrna Gene Sequencing ◽  
Degrading Microorganism

ABSTRACT Stable isotope probing (SIP) was used to identify the aerobic toluene-degrading microorganism in soil microcosms. Several approaches (terminal restriction fragment length polymorphism, 16S rRNA gene sequencing, and quantitative PCR) provided evidence that the microorganism responsible was a member of the genus Polaromonas and could grow on toluene. This microorganism also transformed benzene, but not m-xylene or cis-dichloroethene.

scholarly journals Effective Removal of Alkanes and Polycyclic Aromatic Hydrocarbons by Bacteria from Soil Chronically Exposed to Crude Petroleum Oil

2021 ◽  
Author(s):  
Eman Afkar ◽  
Aly M. Hafez ◽  
Rashid I.H. Ibrahim ◽  
Munirah Aldayel
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Crude Oil ◽  
Aromatic Hydrocarbons ◽  
Oil Spills ◽  
Practical Significance ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Polycyclic Aromatic ◽  
Long Chain

Abstract In this study, two bacterial strains isolated from an oil-contaminated soil, designated as AramcoS2 and AramcoS4 were able to degrade crude oil, long-chain n-alkanes of C10 to C20; (n-decane, n-undecane, n-dodecane, n-tridecane, n-tetradecane, n-pentadecane, n-hexadecane, n-heptadecane, n-octadecane n-nonadecane, and n-eicosane) and polycyclic aromatic hydrocarbons (PAHs) including biphenyl, naphthalene, and anthracene. Gas chromatography-mass spectrometry (GC-MS) technique was conducted to analyze and identify the crude oil residues after biodegradation. AramcoS2 and AramcoS4 were able to reduce the concentration of long-chain n-alkanes of C10-C20 efficiently on average by 77% of the original concentration. Both isolates could also degrade PAHs on average by 67% of the original concentration within 7 and 14 days of incubation at 30ºC, pH=6.8±0.2. The 16S rRNA gene sequences of AramcoS2 and S4 classified these isolates as Actinobacteria; well-known alkanes and PAHs degraders. The nucleotide sequences of AramcoS2 and AramcoS4 were submitted to the GenBank database under the accession numbers MN142506 and MN142551, respectively. Both isolates can be used to restore the environments contaminated with crude oil components. They should be of great practical significance both in bioremediation of soil contaminated with crude oil and bio-treatment of oil spills on surface water.

scholarly journals Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing

2017 ◽  
Author(s):  
Anuradha Ravi ◽  
Ekaterina Avershina ◽  
Inga Leena Angell ◽  
Jane Ludvigsen ◽  
Prashanth Manohar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reduced Genome ◽  
Functional Understanding ◽  
Rrna Gene Sequencing ◽  
Metagenome Sequencing ◽  
Mother To Child ◽  
Metagenome Sequence

ABSTRACTThe genetic diversity and sharing of the mother-child associated microbiota remain largely unexplored. This severely limits our functional understanding of gut microbiota transmission patterns. The aim of our work was therefore to use a novel reduced metagenome sequencing in combination with shotgun and 16S rRNA gene sequencing to determine both the metagenome genetic diversity and the mother-to-child sharing of the microbiota. For a cohort of 17 mother-child pairs we found an increase of the collective metagenome size from about 100 Mbp for 4-day-old children to about 500 Mbp for mothers. The 4-day-old children shared 7% of the metagenome sequences with the mothers, while the metagenome sequence sharing was more than 30% among the mothers. We found 15 genomes shared across more than 50% of the mothers, of which 10 belonged to Clostridia. Only Bacteroides showed a direct mother-child association, with B. vulgatus being abundant in both 4-day-old children and mothers. In conclusion, our results support a common pool of gut bacteria that are transmitted from adults to infants, with most of the bacteria being transmitted at a stage after delivery.

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