Understanding Ancient Microbiomes

Dear Colleagues, 

The rapidly expanding field of palaeomicrobiology—the study of ancient microorganisms—is perhaps best known for the sequencing and characterization of pathogenic bacterial, fungal, and viral agents from ancient human remains to reconstruct the history of diseases and the spread of human pandemics. Recently, ancient microbiomes are also being more widely analyzed in a variety of geologic records such as ice cores, permafrost-, peat-, and cave soils, as well as in lake and marine sediments.

The sequencing analysis of these ancient microbiomes can assist more traditional micropaleontological approaches in identifying the majority of microbial taxa that do not leave (easily) identifiable morphological remains in the fossil record and can, therefore, provide a more holistic overview of the evolution and interaction of past ecosystems such as in the context of paleoenvironmental and anthropogenic perturbations. The analysis of ancient microbiomes in the geologic record covers all domains of life: fungi and unicellular eukaryotes (protists), bacteria, archaea, bacteriophages, and protistal viruses. However, even if contamination with modern DNA can be ruled out, it can remain a challenge to determine what fraction of the microbiome in the environmental samples represents a true ancient signature from the time of death of the host organisms or from the time of burial in the geologic record. For example, subsurface bacteria (notably facultative and obligate anaerobes) are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors, and soil or sediment porosity. However, recent studies suggest that a subset of subsurface microbial taxa were present at the time of deposition and that their vertical distribution in the geologic record was shaped by the paleoenvironmental conditions that prevailed at that time. For example, downcore sedimentary 16S rRNA gene profiling revealed that Holocene sediments of Laguna Potrok Lake (Argentina) reflected a vertical stratification linked to electron acceptors’ availability, while in the late Pleistocene, samples up to 50 Ka in age, salinity, organic matter, and the depositional conditions over the last Glacial–Interglacial cycle were the most important selective pressures. As another example, shotgun metagenomic analysis revealed subseafloor bacteria that were involved in denitrification during periods of oxygen minimum zone formation in the Arabian Sea. A switch to fermentation likely explains their long-term post-depositional survival. However, further development of robust molecular approaches and bioinformatics tools is required to determine to what extent ancient microbiomes represent dead, dormant, or metabolically active communities.

For this Special Issue, we invite you to send contributions on any aspects related to the study of ancient microbiomes covering all domains of life in ancient biological remains, as well as in all varieties of geologic records. For example, this could include studies ground-truthing the feasibility of subsurface microbiomes to provide long-term records of the paleodepositional environment and/or biogeochemical cycling in the context of shifts in paleoclimate or more recent anthropogenic perturbations.

Dr. Marco Coolen
Guest Editor

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• palaeomicrobiology
• ancient DNA
• biogeochemical cycling
• palaeoclimate
• Anthropocene
• evolution of human diseases and pandemics