Plasticity of the stress response in "Kurthia" spp.: a study highlighting the challenges to work with non-standard bacterial model species

Abstract

Natural environments represent an unstable habitat for living organisms with suitable periods for growth and reproduction alternating with suboptimal periods. Accordingly, organisms have to withstand the suboptimal periods, and for this they have developed various survival strategies. Microorganisms, including bacteria, are the most diverse and abundant groups of organisms in natural environments and they evolved really diverse survival strategies. One of the most extreme of these survival strategies is dormancy. During this process, upon the detection of unfavourable environmental conditions, microbes enter in a dormant state with a reversible interruption of growth or/and metabolism. Once conditions improve, dormant structures return to an active state and resume growth and reproduction. Several forms of dormancy exist, but the most well-known until now is sporulation. Sporulation is a complex cell differentiation process ending with the production of resistant dormant spores. Spores were observed in different bacterial phyla, and among them, endospores formed by the Firmicutes are usually considered as the reference. However, because endosporulation, as well as other dormancy strategies, are complex and costly for cells, not all bacterial cells are able to enter in these processes. Accordingly, alternative survival strategies may exist outside the well described spore-formers groups and to investigate those, the use of non-standard models is required. The aim of this thesis was to investigate resistance strategies in the non-standard bacterial model Kurthia sp. str. 11kri321. Because this environmental strain was initially isolated from an extreme environment, it represents a promising model to explore survival strategies. We cultivated Kurthia sp. str. 11kri321 under challenging growth conditions in the laboratory and observed its response through different approaches, including light microscopy, cryo-electron microscopy, genomics, and transcriptomics. Our results show the plasticity of the stress response in Kurthia sp. str. 11kri321. The strain was observed under challenging conditions to produce alternative resistant structures to spores (i.e., cryptospores), but also to modify its cell morphology and to shutdown essential molecular processes such as translation and transcription. In addition to possess a variety of survival strategies, Kurthia sp. str. 11kri321 adapted quickly to laboratory conditions and changed at the genomic level, which might explain the observed decreased production of cryptospores and reduced heat resistance. Further investigations would be necessary to confirm that the responses displayed by Kurthia sp. str. 11kri321 under challenging conditions provide a survival benefit to the strain. However, this might be quite challenging regarding the instability of the strain when maintained in the laboratory. To conclude, despite the challenges of working with a poorly known environmental species, this thesis paves the way for using non-standard bacterial models to investigate alternative survival strategies. Because bacterial survival strategies impact largely several pressing societal issues, such as the on-going antibiotics resistance crisis and global climate change, this work opens the field of research around alternative survival strategies in environmental bacteria.