Nature Microbiology

Snapshot: Dr. Thijs Ettema

Dr. Thijs Ettema of the Uppsala University in Sweden shares his experiences in working with Archaea.

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Nov 01, 2017
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Name: Dr. Thijs Ettema

Institution: Uppsala University 

Location: Uppsala, Sweden

Websitehttp://www.ettemalab.org/

E-mail: thijs.ettema@icm.uu.se

Twitter: @ettema_lab

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

I became intrigued by archaea during my Biology masters at Wageningen University (The Netherlands) in the late 1990’s. Here, I was reading about the work from Carl Woese and Karl Stetter, about these ‘strange organisms’ with their obscure biology. I decided to do a graduation project in the Laboratory of Microbiology and, guided by the first available archaeal genome sequences, started cloning and characterizing metabolic enzymes from hyperthermophilic archaea, such as Pyrococcus furiosus and Sulfolobus solfataricus. I liked doing this so much that I eventually ended up doing my PhD in this lab (at Wageningen University). Over the years, my interests have become focused on broader questions related to microbial evolution and diversity – still with a keen interest in archaea of course. One topic that has been centrally embedded in my research group entails the evolutionary relation between archaea and eukaryotes. In 2015, we had a major breakthrough when we discovered a new group of archaea, the Lokiarchaeota, that turned out to represent the closest prokaryotic relatives of eukaryotes. The genomes of these Lokiarchaeota turned out to encode several proteins that were previously thought to be specific to eukaryotes. The recent discovery of many additional Lokiarchaeota-related lineages, collectively referred to as the Asgard archaea, has provided several new insights into the origin of the eukaryotic cell and several of its complex features. Inspired by these findings, my lab will continue to look for new archaeal lineages that might shed light in the process of eukaryogenesis. Apart from generating more genomic data, our research will also aim to cultivate new archaeal lineages in order to provide the much-needed insight in their cell biology, metabolism and ecological role.


Part of a hydrothermal vent field along the Arctic Mid-Ocean Ridge closely located to where Lokiarchaeota were sampled. This picture was taken close to the sampling site from which the DNA samples used to recover the genome of Lokiarchaeota were isolated. The image shown was kindly provided by Rolf B. Pedersen, Centre for Geobiology, University of Bergen. 


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?

Personally, I find the recent years, during which cultivation-independent genomics approaches such as metagenomics and single cell genomics have been used to uncover a plethora of genome data of uncultivated archaeal lineages, most exiting. The scientific community has witnessed a true explosion of archaeal diversity, with many new archaeal lineages with unexpected features. Apart from the Asgard archaea already mentioned above (with relevance for understanding eukaryotic origins), we have seen a tremendous expansion of the so-called DPANN archaea – a diverse group of archaea typically with small cell size and reduced genome size. In addition, several unexpected traits have recently been discovered in archaeal lineages belonging to ‘old’ archaeal phyla, the Cren- and Euryarchaeota. For example, newly discovered euryarchaea referred to as Syntrophoarchaea were shown to perform anaerobic butane oxidation, and novel methanogenesis-related metabolism was revealed in the crenarchaea-affiliated group Verstraetearchaeota, and also in members of the newly proposed archaeal phylum Bathyarchaeota.

Clearly, the metagenomic discovery of all these new archaeal lineages has been tremendously important for uncovering many pivotal aspects of the diversity, evolution and ecology of archaea, but of course – genomes can only tell us so much! In the years to come, I foresee that the field will witness a transition. Generation of genome data will continue to be important, but in order to gain new insights into the biology of all these new archaeal  lineages, genomics data will need to be complemented with additional experimental analyses that are informative about their metabolism, their cell biology, etc. And, ultimately, we would not only like to understand the biology of single archaeal organisms, but also how they function in the context of the microbial community they are part of.


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

That, according to the most recent insights, eukaryotes (and that includes us, humans) evolved from an archaeal lineage (that was related to Asgard archaea) that took up a bacterium (from which mitochondria evolved). This finding implies that, in the strict phylogenetic sense, we, humans (and all other eukaryotes) are Archaea!

 

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)?

(Assuming this relates to work produced by my lab)

Zaremba-Niedzwiedzka, K., et al., Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017)

https://www.nature.com/nature/journal/v541/n7637/full/nature21031.html

This paper extends the previous discovery of the Lokiarchaeota by describing the Asgard archaea, a diverse clade of archaea that represent the closest prokaryotic relatives of eukaryotes. The genomes of Asgard archaea encode many features that were previously regarded as specific to eukaryotes.


Eme, L., Spang, A., Lombard, J., Stairs, C.W., and Ettema, T.J.G., Archaea and the origin of eukaryotes. Nature Reviews Microbiology 15, 711–723 (2017)

https://www.nature.com/nrmicro/

This review paper presents a comprehensive overview regarding the current view of how eukaryotes have evolved from an archaeal ancestor.


Spang, A., Caceres, E.F. and Ettema, T.J.G., Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357 (6351) eaaf3883 (2017)

http://science.sciencemag.org/content/357/6351/eaaf3883.long

This review paper outlines, from a historical perspective, how cultivation and cultivation-independent genomics approaches have over the years contributed new insights into the diversity, ecology, and evolution of the archaeal domain of life.

Go to the profile of Claudio Nunes-Alves

Claudio Nunes-Alves

Senior Editor, Nature Microbiology

I'm a senior editor at Nature Microbiology, interested in all things bacteria, virus, archaea, fungi and parasites (but I mostly handled articles focusing on bacterial physiology, evolution, parasites and archaea). Before joining Nature, I studied biochemistry at the University of Porto, Portugal, as an undergrad; and was a grad student and post-doc in the labs of Margarida Correia-Neves (ICVS, Braga, Portugal), Sam Behar (Brigham and Women's Hospital and Harvard Medical School, Boston, MA, and then at UMass Medical School, Worcester, MA) and Christophe Benoist (at Harvard Medical School, Boston, MA), where I studied multiple aspects of immunity to tuberculosis.

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