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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

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

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

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...

Université de Neuchâtel

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon

Junier, Pilar ; Kim, Ok-Sun ; Junier, Thomas ; Ahn, Tae-Seok ; Imhoff, Johannes F ; Witzel

In: Applied Microbiology and Biotechnology, 2009, vol. 83, no. 1, p. 175-188

The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the...

Université de Neuchâtel

Protection of metal artifacts with the formation of metal–oxalates complexes by Beauveria bassiana

Joseph, Edith ; Cario, Sylvie ; Simon, Anaële ; Wörle, Marie ; Mazzeo, Rocco ; Junier, Pilar ; Job, Daniel

In: Frontiers in microbiology, 2011, vol. 2, no. 270, p. 1-8

Several fungi present high tolerance to toxic metals and some are able to transform metals into metal-oxalate complexes. In this study, the ability of Beauveria bassiana to produce copper oxalates was evaluated. Growth performance was tested on various copper-containing media. B. bassiana proved highly resistant to copper, tolerating concentrations of up to 20 g L-1,...

Université de Neuchâtel

Fungi, bacteria and soil pH : the oxalate–carbonate pathway as a model for metabolic interaction

Martin, Gaëtan ; Guggiari, Matteo ; Bravo, Daniel ; Zopfi, Jakob ; Cailleau, Guillaume ; Aragno, Michel ; Job, Daniel ; Verrecchia, Eric ; Junier, Pilar

In: Environmental Microbiology, 2012, vol. 14, no. 11, p. 2960-2970

The oxalate–carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria,...

Université de Neuchâtel

Experimental calcium-oxalate crystal production and dissolution by selected wood-rot fungi

Guggiari, Matteo ; Bloque, Raphael ; Aragno, Michel ; Verrecchia, Eric ; Job, Daniel ; Junier, Pilar

In: International Biodeterioration & Biodegradation, 2011, vol. 65, no. 6, p. 803-809

Twenty-six species of white-rotting Agaricomycotina fungi (Basidiomycota) were screened for their ability to produce calcium-oxalate (CaOx) crystals in vitro. Most were able to produce CaOx crystals in malt agar medium in the absence of additional calcium. In the same medium enriched with Ca2+, all the species produced CaOx crystals (weddellite or whewellite). Hyphae of...

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...

Université de Neuchâtel

Use of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity

Bravo, Daniel ; Braissant, Olivier ; Solokhina, Anna ; Clerc, Martin ; Daniels, Alma U. ; Verrecchia, Eric ; Junier, Pilar

In: FEMS Microbiology Ecology, 2011, vol. 78, no. 2, p. 266–274

Isothermal microcalorimetry (IMC) has been used in the past to monitor metabolic activities in living systems. A few studies have used it on ecological research. In this study, IMC was used to monitor oxalotrophic activity, a widespread bacterial metabolism found in the environment, and particularly in soils. Six model strains were inoculated in solid angle media with K-oxalate as the sole carbon...