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Metabolic capabilities of spore-forming microorganisms

English title Metabolic capabilities of spore-forming microorganisms
Applicant Junier Pilar Eugenia
Number 132358
Funding scheme Project funding
Research institution Laboratoire de Microbiologie Institut de Biologie Université de Neuchâtel
Institution of higher education University of Neuchatel - NE
Main discipline Experimental Microbiology
Start/End 01.10.2010 - 31.12.2013
Approved amount 288'000.00
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All Disciplines (3)

Discipline
Experimental Microbiology
Environmental Research
Molecular Biology

Keywords (5)

Spores; Microorganisms; Metagenomics; Extremophiles; Metabolic reconstruction

Lay Summary (English)

Lead
Lay summary
Microbial spores are highly resistant resting states developed by certain bacteria to tolerate unfavorable environmental conditions. Research in spore-forming bacteria has been carried out mainly in the medical field, while the environmental role and metabolic diversity of spore-forming bacteria have remained relatively unexplored. Recently, spore-forming bacteria have been detected as dominant members of the microbial communities in heavy metal-contaminated sites. There is emerging evidence in the literature of metal reduction by groups of spore-forming microorganisms (e.g. Desulfotomaculum spp., Clostridium spp., Desulfosporosinus spp., and Alkaliphilus metalliredigens), supporting the idea that spore-formers contribute to the metabolism of heavy metals. Additionally, spore-forming bacteria (Desulfotomaculum spp., Carboxydothermus hydrogenoformans Z-2901, and Candidatus Desulforudis audaxviator) have been detected in microbial communities inhabiting extreme environments such as deep mines or geothermal systems. This suggests that spore-forming bacteria are not only more phylogenetically diverse than previously thought, but also that they should display a metabolic repertory that allow them to dominate microbial communities in environments with extreme conditions (e.g. high temperature, lack of electron donors, varying conditions of oxygen and moisture, high levels of hazardous elements). In addition to this, spore-forming microorganisms have been recently found dominating microbial fuel cells, which are an exciting new field of research into sustainable energy resources. Despite the contribution of spore-forming bacteria to the microbial communities in contaminated or extreme environments, and their biotechnological potential, they have been largely overlooked by traditional and molecular techniques used in microbial ecology. The aim of this proposal is to characterize the metabolic capabilities of spore-forming microorganisms in environments in which the production of spores could result in an advantage for survival (e.g. at contaminated subsurface or at high enthalpy geothermal sites). We propose to start by the isolation of spores, followed by the analysis of their metabolic capabilities through environmental genomics. Additionally, we propose to isolate and cultivate spore-forming bacteria. In both cases we expect to discover new metabolic properties that can contribute to explain the role of spore-formers in environmental samples.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments Endospore-forming enrichment
Wunderlin Tina, Junier Thomas, Roussel-Delif Ludovic, Jeanneret Nicole, Junier Pilar (2014), Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments Endospore-forming enrichment, in Environmental Microbiology Reports, 6(6), 631-639.
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 (2014), Bacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria, in Aquatic Sciences, 76(S1), 33-46.
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 (2014), Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva (Switzerland–France), in Aquatic Sciences, 76(S1), 103-116.
Quantification of endospore-forming Firmicutes by qPCR with the functional gene spo0A
Bueche Matthieu, Wunderlin Tina, Roussel-Delif Ludovic, Junier Thomas, Sauvain Loic, Jeanneret Nicole, Junier Pilar (2013), Quantification of endospore-forming Firmicutes by qPCR with the functional gene spo0A, in Applied and Environmental Microbiology, 79(17), 5302-5312.
Stage 0 sporulation gene A (spo0A) as a molecular marker to study diversity of endospore-forming Firmicutes
Wunderlin Tina, Junier Thomas, Roussel-Delif Thomas, Jeanneret Nicole, Junier Pilar (2013), Stage 0 sporulation gene A (spo0A) as a molecular marker to study diversity of endospore-forming Firmicutes, in Environmental Microbiology Reports, 5, 911-924.
Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva, (Switzerland-France)
Wunderlin Tina, Corella Juan Pablo, Junier Thomas, Bueche M., Loizeau Jean-Luc, Giradclos Steffanie, Junier Pilar, Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva, (Switzerland-France), in Aquatic Sciences.

Collaboration

Group / person Country
Types of collaboration
Los Alamos National Laboratory (LANL) United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Antofagasta University Chile (South America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
EPF Lausanne Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
GFZ Postdam Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Institute Forel of University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
DNA watch conference Talk given at a conference Endospores in sediment as a proxy for 20th century environmental lake history 04.12.2013 Frasne, France Junier Pilar Eugenia; Junier Thomas;
5th Swiss Microbial Ecology Meeting Talk given at a conference Paleolimnology of Lake Geneva using endospore-forming bacteria 04.02.2013 Murten, Switzerland Junier Thomas; Roussel-Delif Ludovic; Junier Pilar Eugenia;
5th Swiss Microbial Ecology Meeting Talk given at a conference New molecular method for the quantification of endospore-forming bacteria 04.02.2013 Murten, Switzerland Junier Pilar Eugenia; Junier Thomas;
5th Swiss Microbial Ecology Meeting Talk given at a conference Microbial communities in geothermal sites. Are endospore-forming bacteria favored? 04.02.2013 Murten, Switzerland Junier Pilar Eugenia; Junier Thomas;
ISME meeting 2012 Poster Endospore-forming bacteria highly under-represented 19.08.2012 Copenhagen, Denmark Junier Thomas; Junier Pilar Eugenia; Roussel-Delif Ludovic;
SSM meeting 2012 Poster Endospore-forming bacteria highly under-represented 21.06.2012 Saint-Gall, Switzerland Roussel-Delif Ludovic; Junier Pilar Eugenia; Junier Thomas;
4th congress of european microbiologist, FEMS society Poster Improving genome annotation: a tool for identifying errors in the annotation of genome sequences 26.06.2011 Geneva, Switzerland Junier Thomas; Junier Pilar Eugenia;
4th congress of european microbiologist, FEMS society Poster Metagenomics on a microbial sub-population: new selective methods to target endospore-forming bacteria 26.06.2011 Geneva, Switzerland Roussel-Delif Ludovic; Junier Thomas; Junier Pilar Eugenia;
I workshop in microbial ecology: new advances and challenges Individual talk Endospore-forming bacteria in extreme environments 14.04.2011 Antofagasta, Chile, Chile Roussel-Delif Ludovic; Junier Pilar Eugenia; Junier Thomas;


Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions MICROORGANISMES ET METAUX: PROBLEMES ET SOLUTIONS Western Switzerland 2014

Associated projects

Number Title Start Funding scheme
152972 Determinants of the adaptation of endospore-forming bacteria to extreme environments 01.05.2014 Project funding
126330 Metabolic capabilities of spore-forming microorganisms 01.11.2009 Ambizione
151112 Evaluation of an alternative to Escherichia coli as an indicator of faecal pollution in the Antarctic Environment 01.09.2013 International short research visits
126330 Metabolic capabilities of spore-forming microorganisms 01.11.2009 Ambizione

Abstract

Microbial spores, highly resistant resting states able to tolerate harsh conditions, are believed to have evolved as a mechanism for spatial and temporal escape from unfavorable environmental conditions. However, research in spore-forming bacteria has been mainly focused in the associated diseases (e.g., anthrax), and more recently in food-biotechnology (e.g., probiotics), while the environmental role and metabolic diversity of spore-forming bacteria have remained relatively unexplored. Recently, spore-forming bacteria have been detected as dominant members of the microbial communities in heavy metal-contaminated sites, suggesting that these microorganisms might play an important role in metal decontamination. As an example of this, our characterization of Desulfotomaculum reducens MI-1, an environmentally-relevant spore-forming bacterium, has revealed its ability to reduce a variety of metals and/or anthropogenic contaminants including Fe(III), Cr(VI), Se(IV), As(V), Te(IV), and U(VI). There is also emerging evidence in the literature of metal reduction by other groups of spore-forming microorganisms (e.g. Clostridium spp., Desulfosporosinus spp., and Alkaliphilus metalliredigens), supporting the idea that spore-formers contribute to the metabolism of heavy metals. Additionally, spore-forming bacteria (Desulfotomaculum spp., Carboxydothermus hydrogenoformans Z-2901, and Candidatus Desulforudis audaxviator) have been detected in microbial communities inhabiting extreme environments such as deep mines or geothermal systems. This suggests that spore-forming bacteria are not only more phylogenetically diverse than previously thought, but also that they should display a wide metabolic repertory that allow them to dominate microbial communities in environments with extreme conditions (e.g. high temperature, lack of electron donors, varying conditions of oxygen and moisture, high levels of hazardous elements). In addition to this, spore-forming microorganisms have been recently found dominating microbial fuel cells, which are an exciting new field of research into sustainable energy resources. Despite the contribution of spore-forming bacteria to the microbial communities in contaminated or extreme environments, and their biotechnological potential, they have been largely overlooked by traditional and molecular techniques used in microbial ecology. Although new molecular approaches have started to reveal the extent of the microbial diversity in different environments, this is not the case for spore-forming bacteria because DNA-based techniques do not capture spore-forming bacteria if they are found in the form of a spore. The aim of this proposal is to characterize the metabolic capabilities of spore-forming microorganisms in environments in which the production of spores could result in an advantage for survival (e.g. at contaminated subsurface or at high enthalpy geothermal sites). We propose to start by the isolation of spores, followed by the analysis of their metabolic capabilities through environmental genomics. Additionally, we propose to isolate and cultivate spore-forming bacteria. In both cases we expect to discover new metabolic properties that can contribute to explain the role of spore-formers in environmental samples.
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