Université de Neuchâtel

Effect of salinity on cyanobacterial community composition along a transect from Fuliya spring into the water of Lake Kinneret, Israel

Junier, Pilar ; Kim, Ok-Sun ; Imhoff, Johannes F ; Witzel, Karl-Paul ; Hadas, Ora

In: Fundamental and Applied Limnology, 2013, vol. 182, no. 2, p. 99-107

Cyanobacterial community composition was studied along a salinity gradient from the saline Spring Fuliya towards the water column of Lake Kinneret. The samples included a gradient of salinities ranging from 4270 mg Cl L–1 (Saline Spring) to 239 mg Cl L–1 (Lake Kinneret). Denaturing gradient gel electrophoresis (DGGE) and cloning of the 16 S rRNA gene, as well as cloning...

Université de Neuchâtel

Methane- and ammonia-oxidizing bacteria at the chemocline of Lake Kinneret (Israel)

Junier, Pilar ; Kim, Ok-Sun ; Eckert, Werner ; Casper, Peter ; Imhoff, Johannes F ; Witzel, Karl-Paul ; Hadas, Ora

In: Aquatic microbial ecology, 2010, vol. 58, no. 3, p. 241-248

The vertical distribution of methane- and ammonia-oxidizing bacteria (MOB and AOB, respectively), and the physicochemical conditions in the chemocline of Lake Kinneret (Israel) were studied at a resolution of 10 cm from 16.2 to 17.7 m depth. Profiles of the chemical parameters indicated decreasing concentrations of methane (from 22.4 to 0.11 μmol l–1) and ammonia (from 14.2 to 8.4...

Université de Neuchâtel

TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets

Junier, Pilar ; Junier, Thomas ; Witzel, Karl-Paul

In: Applied and Environmental Microbiology, 2008, vol. 74, no. 20, p. 6452–6456

We describe TRiFLe, a freely accessible computer program that generates theoretical terminal restriction fragments (T-RFs) from any user-supplied sequence set tailored to a particular group of organisms, sequences from clone libraries, or sequences from specific genes. The program allows a rapid identification of the most polymorphic enzymes, creates a collection of T-RFs for the data set, and...

Université de Neuchâtel

Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

Kim, Ok-Sun ; Imhoff, Johannes F ; Witzel, Karl-Paul ; Junier, Pilar

In: Aquatic ecology, 2011, vol. 45, no. 1, p. 99-112

We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment–water interface in lakes Plußsee and Schöhsee, and a near-shore site in the Baltic Sea in Germany. Although environmental changes induced by the stratification of the water column in marine environments are known to affect specific populations of denitrifying...

Université de Neuchâtel

Evaluation of PCR Primer Selectivity and Phylogenetic Specificity by Using Amplification of 16S rRNA Genes from Betaproteobacterial Ammonia-Oxidizing Bacteria in Environmental Samples

Junier, Pilar ; Kim, Ok-Sun ; Hadas, Ora ; Imhoff, Johannes F ; Witzel, Karl-Paul

In: Applied Microbiology and Biotechnology, 2008, vol. 74, no. 16, p. 5231-5236

The effect of primer specificity for studying the diversity of ammonia-oxidizing betaproteobacteria (βAOB) was evaluated. βAOB represent a group of phylogenetically related organisms for which the 16S rRNA gene approach is especially suitable. We used experimental comparisons of primer performance with water samples, together with an in silico analysis of published sequences and a literature...