Surprises from the hidden world of Asgard archaea

Hidden beneath our feet, in the muddy soil of a vernal pool, lies a microscopic world teeming with secrets. As we collected samples from this unassuming site in Lake County, California, little did we know that we were about to embark on a journey of discovery that would challenge our understanding of life’s origins.
Our journey into the hidden world of Asgard archaea began in a vernal pool on Jill Banfield’s property in Lake County, California. This site has been a treasure trove of microbial discoveries for our lab over the past five years, yielding huge phages, Borgs, mini Borgs, and other archaeal extrachromosomal elements. As we collected samples with various lab members over the years, little did we know that we were about to uncover a whole new lineage of Asgard archaea, literally from Jill’s backyard.
Asgard archaea, first described in 2015, have transformed our understanding of the tree of life and the origin of eukaryotes 1-3. While the diversity and distribution of Asgard archaea have expanded significantly since their initial discovery4, their roles in environmental processes, particularly in terrestrial ecosystems, remain largely unexplored. 

Photograph of the vernal pool that was sampled for metagenomics analyses in this study, in Lake County, California, USA

When we first started analyzing the archaeal in these soil samples, we were struck by the incredible diversity. One group of archaeal genomes were dissimilar to any known references. Initial investigations suggested they might be related to Lokiarchaeota, but when we constructed a phylogenetic tree, they seemed to represent potentially new candidate lineage within Asgard, a group widely believed to share a common ancestor with Eukaryotes.

The photo of Luis E. Valentin-Alvarado, Valerie De Andaand Kathryn Appler at the  ISME18, Switzerland 2013.

Excited by this possibility, Jill and I reached out to Brett Baker, a former lab member who studies archaea ecology and evolution. When Brett’s lab ran the phylogenetic analysis with their extensive reference database, it confirmed our suspicions – we were looking at two new, previously undescribed lineages. This became a collaborative study involving Brett Baker’s lab, with a major role played by Valerie De Anda and Katherine (Katy) Appler, who was ultimately listed as the co-first author. 

The moment we finished the two genomes and Jill asked me what we should name them was both thrilling and daunting. Naming a new archaeal lineage is no small task! Most of the names in the Asgard realm were already taken, so Jill suggested we consider a Puerto Rican goddess. I loved this idea, as it would allow me to connect my cultural background with my scientific work.

Cartoon showing Atabey as a new character inspired in the Puerto Rican Taino culture. 

After a quick literature search, I found Atabey, the goddess of water and soil fertility in Taíno mythology. It was perfect – not only did it reflect the wetland environment where we discovered these archaea, but it also gave me a way to tie my cultural heritage to my research. This connection is particularly meaningful to me, as it allows me to inspire students in Puerto Rico when I give talks there, encouraging them to pursue careers in genomics by showing how science can connect to their own cultural backgrounds.
As we inspected the genomes more deeply, we uncovered metabolic capabilities related to carbon cycling and hydrogen metabolism. They appear to be non-methanogenic acetogens, capable of breaking down various carbon compounds and potentially influencing the availability of substrates for methane-producing microbes.
The availability of complete genomes facilitates more accurate comparative genomics, phylogenetic analyses, and evolutionary studies. As we continue to uncover more complete genomes from diverse environments, we will be better equipped to understand the full spectrum of metabolic diversity within the Asgard archaea and their roles in global biogeochemical cycles.
Our exploration of the hidden world of soil microbes reminds us of how much remains to be discovered. The wetlands beneath our feet harbor complex communities of microorganisms crucial to global carbon cycling. Understanding these communities isn’t just scientific curiosity – it’s essential for predicting and potentially mitigating the impacts of climate change. The journey continues, and we’re eager to see where it leads us next.
References:

Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173-179 (2015).

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

Eme, L., Tamarit, D., Caceres, E.F. et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 618, 992–999 (2023). 

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553-557 (2021).