Bueche, Matthieu

, Bueche, Matthieu, Junier, Pilar

A unique geochemical setting in Lake Cadagno, Switzerland, has led to the accumulation of insoluble metal sulphides in the sedimentary record as the result of past airborne pollution. This offers an exceptional opportunity to study the effect of these metals on the bacterial communities in sediments, and in particular to investigate further the link between metal contamination and an increase in the populations of endospore-forming bacteria observed previously in other metal-contaminated sediments. A decrease in organic carbon and total bacterial counts was correlated with an increase in the numbers of endospores in the oldest sediment samples, showing the first environmental evidence of a decrease in nutrient availability as a trigger of sporulation. Proteobacteria and Firmicutes were the two dominant bacterial phyla throughout the sediment, the former in an area with high sulphidogenic activity, and the latter in the oldest samples. Even though the dominant Firmicutes taxa were stable along the sediment core and did not vary with changes in metal contamination, the prevalence of some molecular species like Clostridium sp. was positively correlated with metal sulphide concentration. However, this cannot be generalized to all endospore-forming species. Overall, the community composition supports the hypothesis of sporulation as the main mechanism explaining the dominance of endospore formers in the deepest part of the sediment core, while metal contamination in the form of insoluble metal sulphide deposits appears not to be linked with sporulation as a mechanism of metal tolerance in this sulphidogenic ecosystem.

, Bueche, Matthieu, Junier, Pilar

Two components: Endospore-forming Firmicutes are well known for their capacity to survive under harsh environmental conditions through the formation of strong and persistent structures called endospores. Sediments of the Bay of Vidy (Lake Geneva), that are well known for their heavy metal pollution. The question was: Are endospore-forming Firmicutes predominant members of the bacterial communities in the most impacted sediments? The co-occurrence of these two components was effectively observed, and four particular strains of Clostridia were identified as dominant. However, their presence could be related to a combination of a dysfunction of the waste water treatment plant infrastructure and their survival in the state of an endospore. Episodic flooding events in the waste water treatment plant is effectively strongly suspected and supported by the data collected during this thesis. At the end of this work, the dominance of this particular group of bacteria does not seem to be uniquely related to their resistance to high concentrations of heavy metals, but also to the environmental changes occurring during the waste water treatment process and/or during the burial of bacterial communities in sediments.

, 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.

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

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 and magnetic susceptibility dating) was retrieved from the Rhone Delta of Lake Geneva. X-ray fluorescence was analyzed at a 0.2-cm resolution, while DNA extracts, elemental geochemistry and grain size were obtained at 4-cm intervals. The total number of bacteria and endospore-forming bacteria were quantified by qPCR using the 16S rRNA gene and the endosporulation-specific spo0A gene. Furthermore, a spo0A fragment was subjected to amplicon sequencing to define OTUs (operational taxonomic units) and the phylogenetic affiliation of the endospore formers. The results showed that despite the fact that the quantity of extracted DNA decreased with the age of the sediment, the abundance of endospore-forming bacteria remained constant. However, the diversity of this group of bacteria changed significantly, reflecting the eutrophication of the lake from 1960 to 1990. The shift in community composition was linked to the dominance of anaerobic clostridia-like endospore formers. This trend has reversed in the last 10 years of the record, suggesting a recovery after perturbation. This study shows that the abundance and diversity of endospore-forming bacteria can be used as proxies to reconstruct lake history. We hereby successfully introduce a new strategy for paleoecology that could also be applied to ocean sediments and long sediment cores.

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

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 production plants or hospitals. It is therefore desirable to assess their prevalence in environmental and industrial fields. To this end, a high-sensitivity detection method is still needed. The aim of this study was to develop and evaluate an approach based on quantitative PCR (qPCR). For this, the suitability of functional genes specific for and common to all EFF were evaluated. Seven genes were considered, but only spo0A was retained to identify conserved regions for qPCR primer design. An approach based on multivariate analysis was developed for primer design. Two primer sets were obtained and evaluated with 16 pure cultures, including representatives of the genera Bacillus, Paenibacillus, Brevibacillus, Geobacillus, Alicyclobacillus, Sulfobacillus, Clostridium, and Desulfotomaculum, as well as with environmental samples. The primer sets developed gave a reliable quantification when tested on laboratory strains, with the exception of Sulfobacillus and Desulfotomaculum. A test using sediment samples with a diverse EFF community also gave a reliable quantification compared to 16S rRNA gene pyrosequencing. A detection limit of about 10⁴ cells (or spores) per gram of initial material was calculated, indicating this method has a promising potential for the detection of EFF over a wide range of applications.