Permafrost microbial paleodiversity and potential for single cell survival over the last 600,000 years

• Applicant: Amedea Perfumo, Ph.D.
• Subject Area: Microbial Ecology and Applied Microbiology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 462858357

With microorganisms being a fundamental component of our ecosystem, a profound understanding of how this part of Earth’s biosphere responds to the fast-changing environmental and climate conditions is urgently needed. Looking to the past, from hundreds to millions of years ago to present time, provides us with a key to better understand the interplays of microorganisms, environment and climate. Digging into the permafrost of the Batagay megaslump (Siberia), a treasure trove of information of the last 600,000 years of ecosystem’s history, I set out to reconstruct the microbial paleodiversity – how it was and how it changed along with environmental (and climatic) changes – and to assess the physiological state of the buried microorganisms – whether they are dead, dormant, or alive and active. For long, these scientific questions could not be accurately addressed, mostly due to a lack of appropriate analytical methods. Today, our scientific toolbox with DNA Next Generation Sequencing technologies and new nano-spectroscopy approaches allows us to break through such boundaries. In the first part of this project, I will perform shotgun metagenomics on ancient DNA (aDNA) extracted from the permafrost chronosequence to obtain a blueprint of the microbial community composition, hence infer on changing dynamics. In the second part, I will apply our newly developed approach of nanospectroscopy combined with stable isotope probing (SIP-nanoFTIR) as well as nanoscale secondary ion mass spectrometry (nanoSIMS) to pinpoint active microbial cells, quantify their metabolism and identify ongoing bioprocesses (e.g. protein synthesis) at in-situ conditions over geological time. Then, the various research perspectives and the information contained in them will be integrated to conclude on microbial community’s changing patterns in the light of the paleoenvironment, the age and the organismic long-term survival. This will be one of the very first studies of environmental microbial paleogenomics and will contribute establish this emerging new field. When applied to paleoclimate reconstruction, it will open new research directions, demonstrating and promoting the use of microbial proxies for environmental changes. Furthermore, this study will showcase a new method, born from the successful marriage between microbiology and biophysics, to probe and visualize microbial activity at the single-molecule level. Overall, this project will bring microbial ecology into the spotlight of paleo-science research, contributing novelty at multiple levels, and will demonstrate that knowledge at the microbial-scale is essential to our understanding of ecosystem changes.

• DFG Programme: Research Grants