Vignette d'image

Junier, Pilar

Nom
Junier, Pilar
Affiliation principale
Fonction
Professeure assistante
Email
pilar.junier@unine.ch
Identifiants
https://libra.unine.ch/handle/123456789/362
_
0000-0002-8618-3340

Résultat de la recherche

Filtres

13
13
Réinitialiser les filtres

Paramètres

Voici les éléments 1 - 10 sur 13
  • Publication
    Accès libre
    Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment–water interface of two lakes and the Baltic Sea
    (2008)
    Ok-Sun, Kim
    ;
    Junier, Pilar 
    ;
    Imhoff, Johannes F
    ;
    Witzel, Karl-Paul
    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 part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plußsee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plußsee and from rice roots in Nitrosospira -like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments.
  • Publication
    Accès libre
    Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia?oxidizing bacteria
    (2008)
    Junier, Pilar 
    ;
    Kim, Ok-Sun
    ;
    Molina, Verónica
    ;
    Limburg, Petra
    ;
    Junier, Thomas
    ;
    Imhoff, Johannes F
    ;
    Witzel, Karl-Paul
  • Publication
    Accès libre
    Resuscitation of ten-year VBNC Klebsiella oxytoca
    (2008)
    Dhiaf, Amel
    ;
    Junier, Pilar 
    ;
    Bakhrouf, Amina
    ;
    Witzel, Karl-Paul
  • Publication
    Accès libre
    Ammonia-oxidizing beta-proteobacteria from the oxygen minimum zone off northern Chile
    (2007-4-15)
    Molina, Verónica
    ;
    Ulloa, Osvaldo
    ;
    Farías, Laura
    ;
    Urrutia, Homero
    ;
    Ramírez, Salvador
    ;
    Junier, Pilar 
    ;
    Witzel, Karl-Paul
  • Publication
    Accès libre
    Genetic diversity of cyanobacterial communities in Lake Kinneret (Israel) using 16S rRNA gene, psbA and ntcA sequence analyses
    (2007)
    Junier, Pilar 
    ;
    Witzel, Karl-Paul
    ;
    Hadas, Ora
    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 hypolimnion revealed the presence of at least 11 different groups of cyanobacteria. Clones related to the unicellular cyanobacteria (Chroococcales and picocyanobacteria) dominated the clone libraries from both depths. New primers to amplify the gene coding for the photosystem II reaction centre (psbA) and the nitrogen regulator gene (ntcA) of cyanobacteria were developed and used for further characterization of the cyanobacterial communities from the lake. Sequences of psbA amplicons clustered with those from 2 different groups of marine Synechococcus and Chroococcales. Cloned ntcA amplicons from the lake were closely related and did not cluster with sequences from cultured cyanobacteria or other environmental sequences from this gene. All the molecular markers analyzed here showed similarity to sequences from some groups of cyanobacteria in the lake and those so far found in marine habitats.
  • Publication
    Accès libre
    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
    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 producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.
  • Publication
    Accès libre
    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
    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) and clone libraries. The highest diversity of nirS denitrifying communities was observed at 1 m depth. According to the T-RFLP profiles and clone libraries of nirS products, 2 groups of denitrifiers were common to and dominant in all depths. Deduced protein sequences from one of these groups displayed low identity (77%) with other nirS sequences reported in GenBank. Denitrifying bacterial communities with nirK were most diverse at 22 m and showed highest similarity to those at 19 m depth. Sequences unrelated to nirK dominated the clone libraries from 1 m depth, suggesting that denitrifying bacteria with copper-containing nitrite reductase were less frequent at this depth. The results suggest that microorganisms with nirK and those with nirS respond differently to the environmental conditions in the stratified water column of Lake Kinneret.
  • Publication
    Accès libre
    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
    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 review of clone libraries made with four specific PCR primers for the βAOB 16S rRNA gene. With four aquatic samples, the primers NitA/NitB produced the highest frequency of ammonia-oxidizing-bacterium-like sequences compared to clone libraries with products amplified with the primer combinations βAMOf/βAMOr, βAMOf/Nso1255g, and NitA/Nso1225g. Both the experimental examination of ammonia-oxidizing-bacterium-specific 16S rRNA gene primers and the literature search showed that neither specificity nor sensitivity of primer combinations can be evaluated reliably only by sequence comparison. Apparently, the combination of sequence comparison and experimental data is the best approach to detect possible biases of PCR primers. Although this study focused on βAOB, the results presented here more generally exemplify the importance of primer selection and potential primer bias when analyzing microbial communities in environmental samples.
  • Publication
    Accès libre
    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
    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 and sequencing of the psbA gene, were used to characterize cyanobacterial community composition. Despite the differences in salinity, similar cyanobacterial communities were observed in the lake and the saline spring, the only exception being the highest salinity sample (4270 mg Cl L–1). Both, DGGE patterns and results of the clone libraries revealed the dominance of cyanobacteria with colonial Gloeocapsa and unicellular Synechococcus as the closest known cultured relatives, independently of the salinity. These results suggest that cyanobacterial populations inhabiting this freshwater lake and its saline sources can adapt to a wide range of salinities.