scholarly journals Molecular Dynamics of Emiliania huxleyi and Cooccurring Viruses during Two Separate Mesocosm Studies

2006 ◽  
Vol 73 (2) ◽  
pp. 554-562 ◽  
Author(s):  
Joaquín Martínez Martínez ◽  
Declan C. Schroeder ◽  
Aud Larsen ◽  
Gunnar Bratbak ◽  
William H. Wilson
Keyword(s):  
Calcium Binding ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Emiliania Huxleyi ◽  
Sequencing Analysis ◽  
Gene Encoding ◽  
Binding Motifs ◽  
Mesocosm Experiments ◽  
Virus Genotypes ◽  
Gradient Gel Electrophoresis ◽  
Genotypic Richness

ABSTRACT In this study we used denaturing gradient gel electrophoresis, sequencing analysis, and analytical flow cytometry to monitor the dynamics and genetic richness of Emiliania huxleyi isolates and cooccurring viruses during two mesocosm experiments in a Norwegian fjord in 2000 and 2003. We exploited variations in a gene encoding a protein with calcium-binding motifs (GPA) and in the major capsid protein (MCP) gene to assess allelic and genotypic richness within E. huxleyi and E. huxleyi-specific viruses (EhVs), respectively. To our knowledge, this is the first report that shows the effectiveness of the GPA gene for analysis of natural communities of E. huxleyi. Our results revealed the existence of a genetically rich, yet stable E. huxleyi and EhV community in the fjordic environment. Incredibly, the same virus and host genotypes dominated in separate studies conducted 3 years apart. Both E. huxleyi-dominated blooms contained the same six E. huxleyi alleles. In addition, despite the presence of at least six and four EhV genotypes at the start of the blooms in 2000 and 2003, respectively, the same two virus genotypes dominated the naturally occurring infections during the exponential and termination phases of the blooms in both years.

scholarly journals Virus Succession Observed during an Emiliania huxleyi Bloom

2003 ◽  
Vol 69 (5) ◽  
pp. 2484-2490 ◽  
Author(s):  
Declan C. Schroeder ◽  
Joanne Oke ◽  
Matthew Hall ◽  
Gillian Malin ◽  
William H. Wilson
Keyword(s):  
Gel Electrophoresis ◽  
Protein Gene ◽  
Major Capsid Protein ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Emiliania Huxleyi ◽  
Capsid Protein Gene ◽  
Western Norway ◽  
Virus Genotypes ◽  
Gradient Gel Electrophoresis ◽  
Major Capsid Protein Gene

ABSTRACT Denaturing gradient gel electrophoresis was used as a molecular tool to determine the diversity and to monitor population dynamics of viruses that infect the globally important coccolithophorid Emiliania huxleyi. We exploited variations in the major capsid protein gene from E. huxleyi-specific viruses to monitor their genetic diversity during an E. huxleyi bloom in a mesocosm experiment off western Norway. We reveal that, despite the presence of several virus genotypes at the start of an E. huxleyi bloom, only a few virus genotypes eventually go on to kill the bloom.

scholarly journals Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

1999 ◽  
Vol 65 (2) ◽  
pp. 396-403 ◽  
Author(s):  
George A. Kowalchuk ◽  
Zinaida S. Naoumenko ◽  
Piet J. L. Derikx ◽  
Andreas Felske ◽  
John R. Stephen ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Transformations ◽  
Rt Pcr ◽  
Gene Encoding ◽  
Specific Pcr ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Almost All

ABSTRACT Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteriain a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms.

scholarly journals Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva

2009 ◽  
Vol 3 (1) ◽  
pp. 80-84 ◽  
Author(s):  
F Gu ◽  
Y Li ◽  
C Zhou ◽  
D.T.W Wong ◽  
C.M Ho ◽  
...  
Keyword(s):  
Liquid Phase ◽  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pearson Correlation ◽  
Operational Taxonomic Unit ◽  
Human Saliva ◽  
Oral Bacteria ◽  
Oral Microbiota ◽  
Sequencing Analysis ◽  
Gradient Gel Electrophoresis

Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of saliva. Random sequencing analysis of forty PCR amplicons from the cell-free phase of saliva led to 15 operational taxonomic unit (OTU) groups. Furthermore, using denaturing gradient gel electrophoresis (DGGE), we compared 16S rRNA/rDNA profiles derived from liquid phases and cellular phases of saliva samples, and found positive correlations (Pearson Correlation=0.822,P<0.001) between these sample groups. These findings indicate that the liquid phase of saliva contains numerous bacterial 16S rRNA/rDNA molecules that have correlations with bacteria existing in the cellular phase.

scholarly journals Assessing the role of APNH, a gene encoding for a human amiloride-sensitive Na+/H+ antiporter, on the interindividual variation in red cell Na+/Li+ countertransport.

1991 ◽  
Vol 2 (4) ◽  
pp. 937-943
Author(s):  
C R Dudley ◽  
L A Giuffra ◽  
A E Raine ◽  
S T Reeders
Keyword(s):  
Linkage Analysis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Single Gene ◽  
Analytical Techniques ◽  
Complex Trait ◽  
Interindividual Variation ◽  
Red Cell ◽  
Gene Encoding ◽  
Intermediate Phenotypes ◽  
Gradient Gel Electrophoresis

The "reverse genetic" approach to essential hypertension is complicated by the fact that blood pressure is a heterogeneous, quantitative, complex trait. One strategy is to use "intermediate phenotypes" that are not only associated with hypertension but that also have a simple mode of inheritance, compatible with the action of a single gene. Red cell sodium-lithium countertransport (SLC) is one of the best characterized intermediate phenotypes for hypertension. The similarity in stoichiometry and kinetics between SLC and Na+/H+ exchange has led to the proposal that the gene encoding the Na+/H+ antiporter (APNH) may be responsible for the individual variance in SLC. We have tested this hypothesis by both an association study and Haseman and Elston's sib pair method of linkage analysis, by using a polymorphism at the APNH locus detected by denaturing gradient gel electrophoresis. Both analytical techniques were performed before and after correction of SLC values for known covariates. There was no significant association between mean SLC values and any of the three possible genotypes of the APNH locus either before or after regressing out covariates (F = 0.64 and P greater than 0.52; F = 0.63 and P greater than 0.53, respectively). Linkage analysis similarly failed to demonstrate a relationship between the squared difference in SLC values and the identity by descent status for APNH as well as other loci that map close to APNH (D1S57, RH, and ALPL). Taking these results together, we conclude that mutations at the APNH locus are not responsible for the observed variation in SLC values.

scholarly journals Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil

2001 ◽  
Vol 67 (8) ◽  
pp. 3426-3433 ◽  
Author(s):  
Tamar Oved ◽  
Avi Shaviv ◽  
Tal Goldrath ◽  
Raphi T. Mandelbaum ◽  
Dror Minz
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Ammonium Concentration ◽  
Ammonia Oxidizing Bacteria ◽  
Gene Encoding ◽  
Α Subunit ◽  
Irrigation Period ◽  
Effluent Irrigation ◽  
Gradient Gel Electrophoresis ◽  
And Function

ABSTRACT The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the α-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein.

Diversity of ammonia oxidising bacteria in a vertical flow constructed wetland

2007 ◽  
Vol 56 (3) ◽  
pp. 241-247 ◽  
Author(s):  
A. Tietz ◽  
R. Hornek ◽  
G. Langergraber ◽  
N. Kreuzinger ◽  
R. Haberl
Keyword(s):  
Constructed Wetlands ◽  
Municipal Wastewater ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wastewater Treatment Plants ◽  
Cold Season ◽  
Vertical Flow ◽  
Gene Encoding ◽  
Α Subunit ◽  
Gradient Gel Electrophoresis ◽  
Ammonia Oxidising Bacteria

Vertical flow constructed wetlands (VFCWs) with intermittent loading are very suitable for nitrification. Ammonia oxidising bacteria (AOB) are the limiting step of nitration. Therefore the AOB community of a full-scale VFCW, receiving municipal wastewater, was investigated within this study. The diversity of the functional gene encoding the α–subunit of the ammonia monooxygenase (amoA), present only in AOB, was assessed by denaturing gradient gel electrophoresis (DGGE). Only very few amoA sequence types dominated the wetland filter substrate; nevertheless a stable nitrification performance could be observed. During the cold season the nitrification was slightly reduced, but it has been shown that the same AOB could be identified. No spatial AOB pattern could be observed within the filter body of the VFCW. The most prominent bands were excised from DGGE gels and sequenced. Sequence analyses revealed two dominant AOB lineages: Nitrosomonas europaea/“Nitrosococcus mobilis” and Nitrosospira. Species of the Nitrosomonas lineage are commonly found in conventional wastewater treatment plants (WWTPs). In contrast, members of the Nitrosospira lineage are rarely present in WWTPs. Our observations indicate that the AOB community in this VFCW is similar to that found in horizontal flow constructed wetlands, but differs from common WWTPs regarding the presence of Nitrosospira.

Allelopathic and Medicinal plant. 26. Millettia speciosa

2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji
Keyword(s):  
Community Structure ◽  
Medicinal Plant ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wiener Index ◽  
Pseudomonas Spp ◽  
Evenness Index ◽  
Gradient Gel Electrophoresis ◽  
Rhizosphere Pseudomonas

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.

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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