Name: Dr. Simonetta Gribaldo

Institution: Institut Pasteur

Location: Paris, France

Website: https://research.pasteur.fr/en/team/group-simonetta-gribaldo/

E-mail: simonetta.gribaldo@pasteur.fr

Twitter: @SGribaldo

Tell me a bit about how you came to be interested in Archaea and what your work entails.

During my training at the University of Catania in Sicily I was very fond of zoology, botany, systematics. I turned to microbiology later in my studies. I therefore came to know about the Archaea only in 1996 when I attended the annual meeting of the Society for General Microbiology in the UK as a young master student in molecular epidemiology. There, during a session on the evolution of microbial life, researchers were not only talking about these microorganisms looking so different from anything else I knew, but were also showing their unique placement in the Tree of Life as our closest prokaryotic cousins. It was love at first sight. I looked up for a PhD in molecular evolution and my scientific career really started at that moment.

Since then, my research has focused on the ancient evolution of microorganisms across the whole Tree of Life, which I investigate by using the information stored in present day sequences. In my group, we are particularly interested in determining the evolutionary relationships among microbial lineages, highlighting new ones, and reconstructing the evolution of fundamental microbial processes, which provide functional inferences for experimental validation. The overarching goal of these analyses is to resolve major evolutionary transitions in the history of life. For these types of studies, the Archaea are a central piece of the puzzle. 

Looking back at the last 40 years, what would you describe as the most exciting areas of research linked to the study of the Archaea? And where do you see the field headed in the next decade?

A lot of landmark research ought to be mentioned, but I would definitely underline genomics. Sequence data from uncultured archaeal lineages has increased tenfold over the last five years. This has opened unprecedented opportunities to study the evolution of the Archaea and to obtain key insights into their biology.

I think that the next decade of archaeal research will progressively move beyond sequences and explore further the biology of these new lineages. This implies of course a stronger effort in isolation and the development of genetic tools. Also, while many colleagues have already provided tremendous insights into archaeal molecular biology, much remains to be learned on fundamental elements of archaeal cell biology.

Another research area that is receiving growing attention is that of Archaea in the human microbiome. The fact that they are so different from Bacteria in many cellular and molecular aspects is an important element that should be taken into consideration. How do the Archaea interact with the resident bacterial flora and the host? What is their role in health and disease? How did they adapt to the human environment?

Finally, there are still many important unanswered questions concerning the evolutionary history of the Archaea. There is currently an important (and understandable) interest on the role of the Archaea in the origin of Eukaryotes. However, one other major issue goes even further back in time, to the very origin of the Archaea. How did the first archaeon came into being, what did it look like and where did it live? Why are Archaea so different from Bacteria in fundamental cellular processes? Answering these questions will inevitably lead us to know more about the earliest steps of life on our planet.

What would you like the public (and general microbiological audience) to appreciate about Archaea?

I am always surprised by the number of people, including scientists from other fields, who still do not know much about the Archaea. The widespread misconception that they are just curious microorganisms living in extreme environments is hard to dismantle. Another common idea is that the absence of identified pathogens in the Archaea makes them less interesting to study. However, the Archaea are an important fraction of microbial diversity and play important roles in a wide variety of environments, including our own body.  

Finally, the unique characteristics of the Archaea make them fundamental models for microbial biology that cannot be neglected. Compared to Bacteria, there is a lot that remains to be done. 

Are there any particular papers that you feel are absolute must reads for those that aren’t necessarily familiar with the field (and briefly, why)?

It’s a very difficult choice. I will skip the most obvious references that other scientists might have already suggested and instead pick up the three below for various reasons:

Iwabe, N. et al. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci U S A. 86(23):9355-9 (1989) and Gogarten, J.P. et al. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci U S A. 86(17):6661-5 (1989).

http://www.pnas.org/content/86/23/9355.long and http://www.pnas.org/content/86/17/6661.long

These two seminal papers succeeded in elegantly solving the problem of rooting the tree of life by using ancient and universal couples of duplicated genes. By doing so, they showed the close evolutionary relationships between Archaea and Eukaryotes. Considering the very limited taxonomic sampling available at the time, these analyses are stunning. They were confirmed and extended in the past few years by using new phylogenetic approaches and an increased sampling of archaeal diversity.

Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417(6884):63-7 (2002).

https://www.nature.com/nature/journal/v417/n6884/full/417063a.html

This paper identified for the first time a curious form of life in the Archaea. Nanoarchaeum equitans forms very tiny cells and lives attached to the surface of its host, another archaeon, in hyperthermophilic environments. Who could expect that fifteen years later we would come to realize that this is by no means an isolated case: the existence of nanosized lineages with very small genomes and potential parasitic/symbiotic lifestyles is a widespread phenomenon not only in Archaea but also in Bacteria, which has been totally overlooked.

Adam, P.S. et al. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J. 11(11):2407-2425 (2017).

https://www.nature.com/ismej/journal/v11/n11/full/ismej2017122a.html

This is a comprehensive review on archaeal diversity, evolution and ecology that we published last summer. It was exciting to incorporate in an updated phylogeny of the Archaea the deluge of new genomes from uncultured lineages that have come out over the last two years, and we had fun giving names for the first time to many branches of the ever-growing archaeal tree. Archaeal diversity has been vastly underappreciated for decades, we might be seeing only the tip of the iceberg.