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Lessons from bacterial dormancy: mechanisms, diversity, ecology, and evolution

English title Lessons from bacterial dormancy: mechanisms, diversity, ecology, and evolution
Applicant Junier Pilar Eugenia
Number 179297
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 01.04.2018 - 31.10.2022
Approved amount 700'000.00
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All Disciplines (5)

Discipline
Experimental Microbiology
Molecular Biology
Environmental Research
Genetics
Ecology

Keywords (7)

Stress responses; Cell Envelope; Biodiversity; Evolution; Dormancy; Genomics ; Spores

Lay Summary (French)

Lead
La dormance, mécanisme de résistance aux conditions environnementales défavorables, est probablement plus répandue et diversifiée chez les bactéries que ce qui est admis à l’heure actuelle. Vu l’importance écologique des bactéries et le contexte de changements climatiques, une meilleure compréhension des réponses bactériennes aux stress environnementaux est souhaitable. Tel est le but du projet.
Lay summary
Contenu et Objectifs

Confrontés à divers facteurs de stress, les microorganismes ont développé différentes stratégies leur permettant de résister à des conditions défavorables. L’une d’elles est la dormance, durant laquelle la croissance est remplacée par la formation de structures résistantes mais métaboliquement inactives, souvent appelées spores.

Seuls quelques groupes de bactéries sont connus pour former des spores, mais nous avons récemment découvert des spores chez cinq souches appartenant à d’autres groupes, et dans deux cas suivant un mode de développement jusqu’ici inconnu.

Ces souches nous serviront pour trois axes d’étude: 1°) nous étudierons la spore de l’une d’elles, dont l’enveloppe est unique en son genre, ce qui éclaircira certains aspects de l’évolution des bactéries ; 2°) nous réaliserons une description complète des spores et du mécanisme de dormance chez trois autres souches ; 3°) nous identifierons de nouvelles espèces capables de dormance.

Contexte scientifique et social

Notre planète sera probablement confrontée à des épisodes de plus en plus sévères de stress environnemental. Etant donné le rôle primordial des bactéries dans le fonctionnement des écosystèmes, l’étude de la dormance comme modèle de réponse naturelle aux changements environnementaux est un pas vers une meilleure capacité à prévoir la réponse de la biosphère aux changements climatiques.

Direct link to Lay Summary Last update: 08.04.2018

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Associated projects

Number Title Start Funding scheme
162810 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 01.12.2015 Interdisciplinary projects
198524 Cryo-focused ion beam scanning electron microscope to prepare cells for visualising their molecular architecture by electron cryo-tomography 01.11.2021 R'EQUIP

Abstract

To cope with various stresses, microorganisms have evolved various strategies to withstand environmental conditions that limit active growth and plunges them in a viable but non-growing or dormant state to endure the harsh stress and resume growth once the stress subsides. Dormancy often involves the formation of a specialized morphotype, referred to here as a dormant cell (DC) (also known spore or spore-like cell). Studying DCs in selected genetically tractable models has provided the foundation for understanding the genetic bases of DC development, and subsequently allowed the biochemical characterization of the underlying mechanism. However, DC studies are not only important for understanding mechanisms of differentiation and their regulation in response to environmental cues, but it also as recently shown to provide insight into when and how the breakpoint between monoderm (classically called Gram-positive) bacteria and diderm (Gram-negative) bacteria occurred in evolution,Prior studies claimed that DC are restricted to a few bacterial clades. However, given the diversity of microbial ecosystems, there is a significant chance that alternative pathways based on different genes and generating uncharacterized DCs remain to be discovered. Indeed, we recently found evidence for spore-like DCs in five strains belonging to additional bacterial clades. In two of these clades, the production of the spore-like (phase bright) DCs is based on novel differentiation pathways and underlying genes. The five strains were all collected at geothermal locations, which are habitats highly selective for the ability to form DCs. We will use these new strains to explore dormancy in three complementary ways. First, we will explore DCs formed by the genus Kurthia, which posses a unique cell envelope and morphogenesis program that provides new insights into bacterial evolution. Second, we will provide complete descriptions of the spore-like cells and mechanisms of dormancy in the three uncharacterized strains. Specifically, we will use electron cryotomography to describe the morphology of the specialized cell. We will also generate genomic, transcriptomic, and proteomic data, during entry and exit of the DC developmental program to get clues on the underlying genetic determinants that drive this process.Third using these genetic DC markers, we will identify new DC-forming species to demonstrate the widespread importance of this ecological survival strategy. Since most current detection methods used in molecular ecology are limited, we will develop a suite of novel methods to detect and study DC diversity in natural communities. We will extend the application of tailored metagenomic sequencing to identify the more abundant spore-forming species in the environment. The long-term goal is to develop a method for genomic sequencing of single spore-like cells in order to unveil rare DC-forming species in natural communities.Our planet is expected to undergo increasing episodes of environmental stress. Given the primordial role of bacteria for ecosystem functioning, studying microbial dormancy as a model of a natural response to changing environmental conditions could constitute a stepping-stone to improve our ability to predict the response of the biosphere to climate change.
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