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