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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
_
0000-0002-8618-3340

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  • Publication
    Accès libre
    Physical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells
    (2016)
    Wunderlin, Tina 
    ;
    Junier, Thomas
    ;
    Paul, Christophe 
    ;
    Jeanneret, Nicole 
    ;
    Junier, Pilar 
    Endospore formation is a survival strategy found among some bacteria from the phylum Firmicutes. During endospore formation, these bacteria enter a morpho-physiological resting state that enhances survival under adverse environmental conditions. Even though endospore-forming Firmicutes are one of the most frequently enriched and isolated bacterial groups in culturing studies, they are often absent from diversity studies based on molecular methods. The resistance of the spore core is considered one of the factors limiting the recovery of DNA from endospores. We developed a method that takes advantage of the higher resistance of endospores to separate them from other cells in a complex microbial community using physical, enzymatic and chemical lysis methods. The endospore-only preparation thus obtained can be used for re-culturing or to perform downstream analysis such as tailored DNA extraction optimized for endospores and subsequent DNA sequencing. This method, applied to sediment samples, has allowed the enrichment of endospores and after sequencing, has revealed a large diversity of endospore-formers in freshwater lake sediments. We expect that the application of this method to other samples will yield a similar outcome.
  • Publication
    Accès libre
    Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species
    (2015)
    Filippidou, Sevasti 
    ;
    Jaussi, Marion
    ;
    Junier, Thomas
    ;
    Wunderlin, Tina 
    ;
    Roussel-Delif, Ludovic 
    ;
    Jeanneret, Nicole 
    ;
    Vieth-Hillebrand, Andrea
    ;
    Vetter, Alexandra
    ;
    Regenspurg, Simona
    ;
    Johnson, Shannon
    ;
    McMurry, Kim
    ;
    Gleasner, Cheryl D.
    ;
    Lo, Chien-Chi
    ;
    Li, Po-E
    ;
    Vuyisich, Momchilo
    ;
    Chain, Patrick S.
    ;
    Junier, Pilar 
    Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium isolated from filter deposits in a geothermal site. This novel species has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species, and it possesses genes that support its phenotypic metabolic characterization and suggest an intriguing link to metals.
  • Publication
    Accès libre
    Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir
    (2015)
    Filippidou, Sevasti 
    ;
    Jaussi, Marion
    ;
    Junier, Thomas
    ;
    Wunderlin, Tina 
    ;
    Jeanneret, Nicole 
    ;
    Regenspurg, Simona
    ;
    Li, Po-E
    ;
    Lo, Chien-Chi
    ;
    Johnson, Shannon
    ;
    McMurry, Kim
    ;
    Gleasner, Cheryl D.
    ;
    Vuyisich, Momchilo
    ;
    Chain, Patrick S.
    ;
    Junier, Pilar 
    The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera.
  • Publication
    Accès libre
    Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent
    (2015)
    Filippidou, Sevasti 
    ;
    Wunderlin, Tina 
    ;
    Junier, Thomas
    ;
    Jeanneret, Nicole 
    ;
    Johnson, Shannon
    ;
    McMurry, Kim
    ;
    Gleasner, Cheryl D.
    ;
    Lo, Chien-Chi
    ;
    Li, Po-E
    ;
    Vuyisich, Momchilo
    ;
    Chain, Patrick S.
    ;
    Junier, Pilar 
    Bacillus alveayuensis strain 24KAM51 was isolated from a marine hydrothermal vent in Milos, Greece. Its genome depicts interesting features of halotolerance and resistance to heavy metals.
  • 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
    Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.)
    Bergottini, Veronica M
    ;
    Filippidou, Sevasti 
    ;
    Junier, Thomas 
    ;
    Johnson, Shannon
    ;
    Chain, Patrick S
    ;
    Otegui, Monica B
    ;
    Zapata, Pedro D
    ;
    Junier, Pilar 
    Kosakonia radicincitans strain YD4 is a rhizospheric isolate from yerba mate (Ilex paraguariensis St. Hill.) with plant growth-promoting effects on this crop. Genes involved in different plant growth-promoting activities are present in this genome, suggesting its potential as a bioinoculant for yerba mate.
  • Publication
    Accès libre
    Bacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria
    Sauvain, Loïc 
    ;
    Bueche, Matthieu 
    ;
    Junier, Thomas 
    ;
    Masson, Matthieu
    ;
    Wunderlin, Tina
    ;
    Kohler-Milleret, Roxane
    ;
    Gascon Diez, Elena
    ;
    Loizeau, Jean-Luc
    ;
    Tercier-Waeber, Mary-Lou
    ;
    Junier, Pilar 
    Lake sediments in areas close to the outlet of wastewater treatment plants are sinks for pollutants. Bacterial communities in sediments are likely affected by the released effluents, but in turn they might modify the distribution and bioavailability of pollutants. On the shore of Lake Geneva, Switzerland, wastewater from the City of Lausanne is treated and discharged into the lake via an outlet pipe in the Vidy Bay. The objectives of this study were to assess (1) the impact of the treated wastewater release on the bacterial communities in the Vidy Bay sediments and (2) the potential link between bacterial communities and trace metal sediment content. Bacterial community composition and abundance were assessed in sediments collected in three areas with different levels of contamination. The main factors affecting bacterial communities were inferred by linking biological data with chemical analyses on these sediments. Near to the outlet pipe, large quantities of bacterial cells were detected in the three upper most cm (3.2 × 109 cells assessed by microscopy and 1.7 × 1010 copies of the 16S rRNA gene assessed by quantitative PCR, per gram of wet sediment), and the dominant bacterial groups were those typically found in activated sludge (e.g. Acidovorax defluivii and Hydrogenophaga caeni). Three samples in an area further away from the outlet and one sample close to it were characterized by 50 % of endospore-forming Firmicutes (Clostridium spp.) and a clear enrichment in trace metal content. These results highlight the potential role of endospore-forming Firmicutes on transport and deposition of trace metals in sediments.
  • 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
    The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1
    Junier, Pilar 
    ;
    Junier, Thomas 
    ;
    Podell, Sheila
    ;
    Sims, David R
    ;
    Detter, John C
    ;
    Lykidis, Athanasios
    ;
    Han, Cliff S
    ;
    Wigginton, Nicholas S
    ;
    Gaasterland, Terry
    ;
    Bernier-Latmani, Rizlan
    Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens; strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens;, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H2-evolving and H2-consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H2 cycling in the bacterium. The mechanism of metal reduction remains unknown.
  • Publication
    Accès libre
    Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes
    Wunderlin, Tina
    ;
    Junier, Thomas 
    ;
    Roussel-Delif, Ludovic 
    ;
    Jeanneret, Nicole 
    ;
    Junier, Pilar 
    In this study, we developed and validated a cultureindependent method for diversity surveys to specifically detect endospore-forming Firmicutes. The global transcription regulator of sporulation (spo0A) was identified as a gene marker for endosporeforming Firmicutes. To enable phylogenetic classification, we designed a set of primers amplifying a 602 bp fragment of spo0A that we evaluated in pure cultures and environmental samples. The amplification was positive for 35 strains from 11 genera, yet negative for strains from Alicyclobacillus and Sulfobacillus. We also evaluated various DNA extraction methods because endospores often result in reduced yields. Our results demonstrate that procedures utilizing increased physical force improve DNA extraction. An optimized DNA extraction method on biomass pre-extracted from the environmental sample source (indirect DNA extraction) followed by amplification with the aforementioned primers for spo0A was then tested in sediments from two different sources. Specifically, we validated our cultureindependent diversity survey methodology on a set of 8338 environmental spo0A sequences obtained from the sediments of Lakes Geneva (Switzerland) and Baikal (Russia). The phylogenetic affiliation of the environmental sequences revealed a substantial number of new clades within endospore-formers. This novel culture-independent approach provides a significant experimental improvement that enables exploration of the diversity of endospore-forming Firmicutes.