Project

Back to overview

Paleoecological indicators in lake sediments based on a multidisciplinary approach of endospore-forming Firmicutes and the chemical and isotopic composition of sediments and organic matter

English title Paleoecological indicators in lake sediments based on a multidisciplinary approach of endospore-forming Firmicutes and the chemical and isotopic composition of sediments and organic matter
Applicant Junier Pilar Eugenia
Number 162810
Funding scheme Interdisciplinary projects
Research institution Laboratoire de Microbiologie Institut de Biologie Université de Neuchâtel
Institution of higher education University of Neuchatel - NE
Main discipline Other disciplines of Environmental Sciences
Start/End 01.12.2015 - 30.11.2019
Approved amount 583'046.00
Show all

All Disciplines (5)

Discipline
Other disciplines of Environmental Sciences
Environmental Research
Other disciplines of Earth Sciences
Geology
Experimental Microbiology

Keywords (7)

Endospores; Paleolimnology; Geochemistry; Sediments; Isotopes; Paleoecology; Environmental prospection

Lay Summary (French)

Lead
La paleo-écologie est l’étude de l’histoire des écosystèmes à l’aide de relevés sédimentaires ou d’autres archives naturelles. L’analyse de la composition chimique, isotopique et biologique des sédiments fournit des indices sur les conditions environnementales passées d’un écosystème particulier. Les sédiments lacustres contiennent aussi une variété de micro-organismes pouvant servir d’indicateurs biologiques pour des études paléo-écologiques. Pour être utilisé comme indicateur paléo-écologique, un organisme, ou du moins une structure reconnaissable (p. ex. grains de pollen ou thèques) ou un élément de composition chimique et isotopique lié à celui-ci (p. ex. des lipids), doit être préservé dans les sédiments pour de longues périodes. Alors que la composition minéralogique, chimique et isotopique des sédiments est déjà utilisée comme traceur des conditions paléo-écologiques et paléo-environnementales, les endospores bactériennes n’ont été que récemment envisagées en tant que tel.
Lay summary

Contenu et objectifs du travail de recherche 

Le but de ce projet est de valider l’application de une approche inédite par l’utilisation des endospores, en comparaison d’autres méthodes complémentaires utilisées pour l’interprétation paléo-écologique et paléo-environnementale des systèmes aquatiques. Pour cela, trois objectives spécifiques ont été fixés: i) valider l’utilisation des endospores parallèlement à d’autres indicateurs biologiques plus « traditionnels » ; ii) évaluer le potentiel d’une généralisation de l’approche combinée endospores/méthodes chimiques complémentaires à des lacs aux conditions environnementales diverses ; iii) examiner expérimentalement le rôle de l’état de dormance/germination sur l’établissement de communautés spécifiques de Firmicutes endosporulantes, en réponse à des changements environnementaux.

Direct link to Lay Summary Last update: 13.10.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
Bacterial spores, from ecology to biotechnology
Paul Christophe, Filippidou Sevasti, Jamil Isha, Kooli Wafa, House Geoffrey L., Estoppey Aislinn, Hayoz Mathilda, Junier Thomas, Palmieri Fabio, Wunderlin Tina, Lehmann Anael, Bindschedler Saskia, Vennemann Torsten, Chain Patrick S.G., Junier Pilar (2019), Bacterial spores, from ecology to biotechnology, in Advances in Applied Microbiology, 106, 79-111.
Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater
Paul Christophe, Bayrychenko Zhanna, Junier Thomas, Filippidou Sevasti, Beck Karin, Bueche Matthieu, Greub Gilbert, Bürgmann Helmut, Junier Pilar (2018), Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater, in PeerJ, 6, e4989-e4989.
A historical legacy of antibiotic utilization on bacterial seed banks in sediments
Madueño Laura, Paul Christophe, Junier Thomas, Bayrychenko Zhanna, Filippidou Sevasti, Beck Karin, Greub Gilbert, Bürgmann Helmut, Junier Pilar (2018), A historical legacy of antibiotic utilization on bacterial seed banks in sediments, in PeerJ, 6, e4197-e4197.

Collaboration

Group / person Country
Types of collaboration
School of Biotechnology, KIIT University India (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Chilika Development Authority India (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Group of Surface Waters, EAWAG Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Vital-IT group, Swiss Institute of Bioinformatics Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Los Alamos National Laboratory United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Department of Earth Sciences, University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
University of Lausanne 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
EGU General Assembly 2019 Poster Paleoecological reconstruction of Lake Liambezi, Botswana using multidisciplinary proxies 07.04.2019 Viena, Austria Junier Pilar Eugenia; Vennemann Torsten; Lehmann Anaël; Filippidou Sevasti;
16th Swiss Geoscience Meeting Poster Reconstruction of ecological evolution of lakes based on multidisciplinary proxies: the case of Lake Liambezi, Botswana 30.11.2018 Bern, Switzerland Junier Pilar Eugenia; Filippidou Sevasti; Vennemann Torsten; Lehmann Anaël;
EGU General Assembly 2017 Poster Origin of sediment bacteria: water versus soil 23.04.2017 Viena, Austria Filippidou Sevasti; Vennemann Torsten; Ariztegui Daniel; Junier Thomas; Junier Pilar Eugenia; Lehmann Anaël;


Associated projects

Number Title Start Funding scheme
169911 Swiss membership in the International Scientific Continental Drilling Program ICDP 01.01.2017 Research Infrastructure
179297 Lessons from bacterial dormancy: mechanisms, diversity, ecology, and evolution 01.04.2018 Project funding (Div. I-III)
166308 Establishing stable IRON isotopes of laminated LAKE sediments as novel palaeoclimate proxy (IRONLAKE) 01.12.2016 Project funding (Div. I-III)
191631 The Dark and Bright side of the force: using microbes for science education and communication 01.03.2020 Agora

Abstract

Paleoecology is the study of ecosystem history using sedimentary records or other natural archives. This scientific approach allows for a better understanding of the relationship between timeline land-usage and its impact on the health and structure of the ecosystem. Analyses of the chemical, isotopic, and biological composition of sediments provide clues on the past environmental conditions of a particular ecosystem. Lake sediments not only contain fossil organic and inorganic matter but also a variety of microorganisms that can be used as biological indicators for paleoecological studies. In order to be useful as a tracer, a paleoecological proxy, an organism, or at least a recognizable structure or chemical and isotopic composition linked to it (e.g. pollen grains or tests), must be preserved in sediments for long periods of time. While the mineralogical, chemical, and isotopic composition of sediments has been successfully used as a tracer of the paleoecological and paleoenvironmental conditions, bacterial endospores have only recently been examined as such tracers. Bacterial endospores are highly specialized cellular forms that allow bacterial groups able to produce them to tolerate harsh environmental conditions while conserving their genetic information. This type of structure has been reported only for Firmicutes (Gram-positive low G+C content bacteria). Because spores are able to survive in a dormant state for extended periods of time, these cellular forms can also be considered as potential proxies for paleoecological and paleoenvironmental studies of sediment samples. In the past several years specific molecular methods have been developed that allows for the study of endospore-forming Firmicutes in a culture-independent manner. This is a major advantage because cultivation is a highly biased methodological approach, since it requires the revival of the dormant microorganism, and in many cases the conditions to achieve this are unknown. In particular, the genetic markers that can be used to study endospore-forming bacteria directly from environmental samples have been identified. The gene encoding for the master regulator of the genetic cascade leading to endospore formation (spo0A) has proven to be a specific molecular marker for this bacterial group. Using this molecular approach a correlation between community structure in sediment and the paleolimnological history of Lake Geneva has been demonstrated. Variations in community structure can be linked to eutrophication, sulfate metabolism or changes in the inputs of terrestrial organic matter, which in turn may be related to changes in climate. A treatment allowing the separation of endospores from vegetative cells and the sequencing of the endospore fraction allows to assess the effect of disturbance on active versus dormant populations in response to changes in environmental conditions. This information, in addition to that obtained from the more “classical” approach of using the mineralogical, chemical, and isotopic composition (carbon, nitrogen and/or oxygen of organic matter and inorganic carbonate or phosphatic fossil material) can be used in conjunction so as to improve and refine the paleoecological interpretations. The aim of this proposal is to validate the application of this novel approach of using endospores, in comparison to other complimentary methods used for paleoecological and paleoenvironmental interpretations of aquatic systems. For this three specific objectives will be set: i) to validate the use of endospores in comparison to more traditional biological proxies; ii) to evaluate the potential of generalizing the combined approach endospores and complimentary chemical methods to lakes of diverse environmental settings; and, iii) to assess experimentally the role of dormancy/germination on the establishment of specific communities of endospore-forming Firmicutes in response to environmental changes.
-