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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...

Université de Neuchâtel

Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment–water interface of two lakes and the Baltic Sea

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

In: FEMS Microbiology Ecology, 2008, vol. 66, no. 2, p. 367–378

The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment–water interface of the two freshwater lakes Plußsee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger...

Université de Neuchâtel

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

Junier, Pilar ; Molina, Verónica ; Dorador, Cristina ; Hadas, Ora ; Kim, Ok-Sun ; Junier, Thomas ; Witzel, Karl-Paul ; Imhoff, Johannes F

In: Applied Microbiology and Biotechnology, 2010, vol. 85, no. 3, p. 425-440

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and...

Université de Neuchâtel

Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel

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

In: Aquatic Microbial Ecology, 2008, vol. 51, p. 129-140

The community composition of denitrifying bacteria was studied in the stratified water column of Lake Kinneret. The nitrite reductase genes nirS and nirK were amplified by PCR from water samples taken at 1, 14, 19 and 22 m depth, which represent the epi-, meta- and hypolimnion of the lake. The PCR products were analyzed with terminal restriction fragment length polymorphism (T-RFLP)...

Université de Neuchâtel

Genetic diversity of cyanobacterial communities in Lake Kinneret (Israel) using 16S rRNA gene, psbA and ntcA sequence analyses

Junier, Pilar ; Witzel, Karl-Paul ; Hadas, Ora

In: Aquatic Microbial Ecology, 2007, vol. 49, no. 3, p. 233-241

The genetic diversity of cyanobacterial communities was studied at various depths in Lake Kinneret (Israel). Denaturing gradient gel electrophoresis (DGGE) of specific 16S rRNA gene PCR products showed significant differences in the cyanobacterial community structure between epi- and hypolimnetic waters. Sequences of clone libraries prepared from 16S rRNA gene PCR products from epi- and...