Hidden life · Host-microbe interactions involving microbial dark matter: Biology and evolution of a ubiquitous group of intracellular bacteria.

Host-microbe interactions involving microbial dark matter: Biology and evolution of a ubiquitous group of intracellular bacteria.

The kingdom Bacteria represents the most widespread and diverse life form on Earth, and is playing major roles, from regulation of biogeochemical cycles, to pathogenesis. The vast majority of bacterial representatives are yet unculturable, being thus considered “microbial dark matter” (MDM). While metagenomics investigations have provided insights into MDM diversity and possible importance for ecosystems functioning, its ecology and biology remains largely unexplored. Indubitably, there is a raising interest for questions asked by MDM presence in the environment. The understanding and characterization of MDM is of primary concern in the field of bacteriology and microbial ecology. MDM representatives are thought to represent a large –if not the major– fraction of bacterial diversity, yet their ecology, biology and role in different ecosystems has been barely investigated. Therefore, MDM representative could have major implication in crucial processes, such as geo biochemical cycles, and pathogenicity towards humans or (micro)organisms of economic interest. TM6 is a candidate phylum standing as a prominent part of the MDM. Members of TM6, like many other MDM phyla, are described as small sized bacteria harboring reduced genomes and being unable to cultivate axenically in laboratory conditions. TM6 were first discovered in peatbogs (from the German Torf, Mittle Schicht, hence the designation TM6), but numerous subsequent studies reported TM6 occurrence worldwide in diverse environments such as soils, sediments, fresh and marine water and biofilms. In drinking water biofilms, TM6 was shown to represent up to 11% of the bacterial community, and members of this phylum were repeatedly found from drinking water distribution systems. The overall goal of the project was to uncover the ecology and biology of TM6 bacteria, as a phylum model of MDM. A targeted analysis of a range of environments enabled the assessment of TM6 ecological niches, while genomic characterisation provided useful information on the evolutionary history, as well as the biology of these poorly understood bacteria. Finally, the comprehensive analysis of the lifecycle of selected TM6 isolates uncovered original mechanisms involved in infection, replication, host interaction, and host resources subversion. This project provided the first detailed analysis of the yet-unknown life style of a major MDM phylum.

Data: CORDIS, © European Union