Nature Microbiology

Snapshot: Dr. Tanja Woyke

Dr. Tanja Woyke of the Department of Energy Joint Genome Institute in the US shares her experiences in working with Archaea.

Go to the profile of Claudio Nunes-Alves
Nov 01, 2017
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Name: Dr. Tanja Woyke

Institution: Department of Energy Joint Genome Institute

Location: Walnut Creek, California, USA

Websitehttps://jgi.doe.gov/our-science/scientists-jgi/single-cells/

E-mail: twoyke@lbl.gov

Twitter: @twoyke


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

My interest in Archaea began when working on the Microbial Dark Matter I project in 2013. This was a follow-on study to the Genomic Encyclopedia of Archaea and Bacteria (GEBA) project spearheaded by Joint Genome Institute (JGI) scientists and Jonathan Eisen from UC Davis, aimed at filling the branches in the genome tree of life with phylogenetically diverse representatives. For the first GEBA pilot project JGI sequenced 53 bacterial and 3 archaeal genomes from isolates. JGI meanwhile expanded this effort and generated more than 1000 type strain reference genomes, 29 of which are archaeal.

The majority of the planet’s microbial diversity remains uncultivated, yet this diversity is a treasure trove of discovery. The genes and metabolic functions of these yet undiscovered microbes enable them to live in a wide range of environments, have potential applications in fields relevant to the U.S. Department of Energy and the Joint Genome Institute’s mission interests, which range from sourcing enzymes for improved biofuels production to understanding terrestrial nutrient cycling. 

For the Microbial Dark Matter phase I project we used single-cell sequencing to generate reference genomes from phylum-level candidate lineages and among them were 35 archaeal single-cell data sets. What we found were unique predicted metabolic traits. For example, we identified genes for complete bacteria-like sigma factors in the archaeal domain, as encoded within representatives of the archaeal DPANN superphylum, a monophyletic group proposed in this study. The bacterial sigma factor encoding genomes also had the TATA-binding protein gene regulation apparatus normally found in Archaea, which made us hypothesize that sigma factors serve a more specialized purpose of gene regulation or some completely different function. Another surprise was lytic murein transglycosylase genes encoded in Nanoarchaeota, the exact biological role of which yet has to be determined.

We’ve been continuing this effort in a phase II project in collaboration with the Bigelow Laboratory for Ocean Sciences and a larger community of scientists around the globe, who have provided valuable samples for this study. Sampling sites are focused on deep subsurface ecosystems. Thus far we have generated ~100 novel archaeal single-cell genomes, which are currently in sequence analysis.  

Dewar Creek sampling site in British Columbia, currently under investigation for the MDM phase II project with Peter Dunfields lab.  Photo credit: Steve Grasby

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?

Coming from a sequencing center, one of the exciting times in archaeal research to me was the sequencing of the first archaeal genome, Methanococcus (now Methanocaldococcus) jannaschii, in 1996, illustrating that most translation, transcription and DNA replication related genes are more similar to genes from Eukarya. Following genome papers of novel Archaea were equally exciting. For example, in 2002 the Stetter lab cultivated and sequenced a hyperthermophilic Nanoarchaea symbiont from a vent environment revealing the smallest genome of any cellular organism at the time. More recent genome studies, specifically from uncultivated archaeal clades, have shaken the tree of life in exciting and interesting ways.

In the next decade I see technologies continuing to improve and as a consequence, many new discoveries made. I do believe that the DNA-based methods we currently use are somehow still missing big pieces in the archaeal tree of life. Not even 5% of all non-eukaryote genomes sequenced belong to Archaea, SSU rRNA gene primer mis-match analyses show large biases in the Archaea and I believe that even shotgun data under-represents these microorganisms. It might be a combination of the difficulty to cultivate Archaea and limited access to their genomic material even in environmental samples that challenge a more complete picture of archaeal diversity.

  

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

Archaea make profound contributions to critical geochemical processes that shape our planet so it’s easy to see how they inspire our appreciation as researchers. Their unique adaptations, among some of the archaeal clades, to extreme environmental conditions such as high temperatures or high salt concentrations, or low pH, make them prime targets for biotechnological and medical applications, which the public can appreciate. We know now that Archaea have a much more wide-spread distribution, not limited to extreme habitats, as previously assumed. There are few habitats and niches where we haven’t found them yet and I believe this may just be a result of the limitations and biases in our detection methods. 

 

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)?

Bult CJ, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058–1073 (1996).

http://science.sciencemag.org/content/273/5278/1058.long

First archaeal genome sequence leading to first genomic insights.

 

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

Nanoarchaea with, at the time, the smallest genomes of any cellular organism.

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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