Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the northwestern Mediterranean Sea

Article Abstract:

Research was conducted to examine the differences between the types of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria associated with particulate material and planktonic samples derived from the northwestern Mediterranean Sea. The amplification of 16S rRNA genes from extracted DNA was carried out using a nested PCR procedure performed with ammonia oxidizer-selective primers. Results suggest that Nitrosomas species and Nitrosospira species may occupy at least two distinct environmental niches in marine environments.

Environmental aspects, Mediterranean Sea, Nitrification, Nitrogen cycle, Bacteria, Nitrifying, Nitrobacteraceae, Plankton populations

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Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments

Article Abstract:

Denaturing gradient gel electrophoresis (DGGE) was assessed as a tool for determining ammonia oxidizing bacteria of the beta-subdivision of the Proteobacteria based on the mobility of PCR-amplified 16S rDNA fragments. DGGE was also employed for the analysis of mixtures of PCR products from this group produced by selective PCR of DNA extracted from coastal sand dunes. Degenerate PCR primers, CTO189f-GC and CTO654r, incorporating a 5' GC clamp, were developed to amplify a 465-bp 16S rDNA region spanning the V-2 and V-3 variable domains.

Bacteria

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Detection and characterization of fungal infections of Ammophila arenaria (Marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA

Article Abstract:

A method is proposed for cultivation-independent indentification and characterization of Ammophila arenaria root fungal infections. The approach is based on specifically amplified 18S rDNA denaturing gradient gel electrophoresis (DGGE). The DGGE patterns generated demonstrate the accuracy of the method in detecting plant-infecting fungi. The approach also detected fungal diversity not identified by other culture-based methods.

Genetic aspects, Fungi, Recombinant DNA, Diseases and pests, Grasses

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