Université de Neuchâtel

Under-detection of endospore-forming Firmicutes in metagenomic data

Filippidou, Sevasti ; Junier, Thomas ; Wunderlin, Tina ; Lo, Chien-Chi ; Li, Po-E ; Chain, Patrick S ; Junier, Pilar

In: Computational and Structural Biotechnology Journal, 2015, vol. 13, p. 299-206

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes...

Université de Neuchâtel

Diversity of endospore-forming bacteria in sediment as a proxy for environmental lake history

Wunderlin, Tina ; Junier, Pilar (Dir.)

Thèse de doctorat : Université de Neuchâtel, 2013.

Les lacs une grande importance écologique et économique, mais ils sont aussi très vulnérables aux pressions anthropogéniques (pollution; surpêche), aux changements climatiques et à l'eutrophisation (hautes concentrations de nutriments). Pour une gestion environnementale et la mise en place de mesures de conservation, les dynamiques des écosystèmes lacustres doivent être connues et les...

Université de Neuchâtel

Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva (Switzerland–France)

Wunderlin, Tina ; Corella, Juan Pablo ; Junier, Thomas ; Bueche, Matthieu ; Loizeau, Jean-Luc ; Girardclos, Stéphanie ; Junier, Pilar

In: Aquatic sciences, 2014, vol. 76, no. S1, p. 103-116

Measurements of chemical composition and biological parameters of sediment cores are used as proxies for changes in past environmental conditions and more recently the human impact on ecosystem health. In this study, endospore-forming bacteria are proposed as a new biological proxy for such paleoecological reconstructions. A sediment core providing a record for the past 90 years (137Cs...

Université de Neuchâtel

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

In: Aquatic sciences, 2014, vol. 76, no. 1S, p. 33-46

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...

Université de Neuchâtel

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: Environmental Microbiology Reports, 2013, vol. 5, no. 6, p. 911-924

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...

Université de Neuchâtel

Quantification of Endospore-Forming Firmicutes by Quantitative PCR with the Functional Gene spo0A

Bueche, Matthieu ; Wunderlin, Tina ; Roussel-Delif, Ludovic ; Junier, Thomas ; Sauvain, Loïc ; Jeanneret, Nicole ; Junier, Pilar

In: Applied and Environmental Microbiology, 2013, vol. 79, no. 17, p. 5302-5312

Bacterial endospores are highly specialized cellular forms that allow endospore-forming Firmicutes (EFF) to tolerate harsh environmental conditions. EFF are considered ubiquitous in natural environments, in particular, those subjected to stress conditions. In addition to natural habitats, EFF are often the cause of contamination problems in anthropogenic environments, such as industrial...