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Junier, Pilar

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

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  • Publication
    Accès libre
    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
    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 μmol l–1) towards the water surface and in close proximity to the chemocline. The disappearance of methane coincided with methane oxidation that could be corroborated throughout this layer with highest rates at 17.4 to 17.6 m. Disappearance of ammonia could not be linked to ammonia oxidation exclusively. The genes pmoA and the homologous amoA (coding for subunit α of the methane and ammonia monooxygenase, respectively) were amplified by PCR. The products were analyzed by terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries. The results demonstrated that different MOB and AOB communities are established along the concentration gradient within the narrow layer of the metalimnetic chemocline. Changes in the intensity of the T-RFLP peaks and the frequency of different groups of alpha- and gammaproteobacterial MOB, and betaproteobacterial AOB, coincided with the concentration gradients of methane, ammonia, nitrate, and oxygen in the chemocline. This suggests that different communities of MOB, and to a lesser extent AOB, contribute to the formation of chemical gradients of their particular substrates in the chemocline.
  • 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.
  • 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
    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.