Dr Anja Spang, Senior Scientist:
Slowly sneaking on to our common ancestor
“Until about forty years ago, archaea were thought to be ‘just’ a special kind of bacteria”
What did the common ancestor of all cellular life forms and the ancestor of bacteria and archaea look like? And how did these cells evolve through time into the large biodiversity we see on Earth today? These are some of the fundamental questions that Dr Anja Spang at the Marine Microbiology & Biogeochemistry department is working on.
In August 2020, in a publication in Nature Communications, Spang and her NIOZ-colleague Dr Nina Dombrowski, plus an international team of collaboration partners, were able to put one more piece of the jigsaw puzzle on the right spot. To put it more precisely: Spang and colleagues unraveled a previously unknown, potentially symbiotic group of archaea that allowed to re-assess the deepest branches in the tree of the Archaea. It also revealed how separate organisms, symbionts and hosts, exchanged genes. Skewed image of the tree of life “Until about forty years ago, archaea were thought to be ‘just’ a special kind of bacteria”, Spang explains. “It was reasoned: ‘they look a lot like bacteria, so they must be a kind of bacteria’. However, in 1977, Carl Woese and co-workers described the archaea as a separate domain of life, based on fundamental differences in a part of their cells, the ribosomes. Since then, and thanks to the use of molecular tools to study microbial diversity, it has become clear that archaea are widespread and diverse.” “However, even in the early days of genomics, our image of the tree of life was still rather skewed”, Spang recalls. “We could only investigate those organisms that we could culture. But most organisms cannot be cultured in the lab easily! It was not until the advent of metagenomics, which is the sequencing and reconstruction of genomes of all organisms from a particular environmental sample, that we could analyze the genomes of uncultivated organisms. That’s when things really started to change in microbiology and evolutionary genomics.”
Depiction of the tree of life including DPANN
“We unraveled a previously unknown, potentially symbiotic group of archaea”
“We could show that these archaea frequently exchange genetic material with their hosts”
We are archaea The discovery of a large diversity of archaeal groups and the study of their genomes has completely changed our view on the tree of life and also shed new lights onto the origin of organisms with complex cells: the eukaryotes. The discovery of a completely new group of the archaea in 2015 by Spang and co-workers, allowed to update our model on how eukaryotic cells evolved: an ancestral archaeal cell likely merged with an ancestral bacterium about two billion years ago. In other words: all eukaryotic organisms, like ourselves, are the product of the merging of an archaeal cell plus bacterial cells! “But the jigsaw puzzle is much bigger than that”, Spang stresses. “If you look at the evolutionary tree of all life forms, the branches with for example all animals are tiny compared to the branches within the bacteria and archaea. To me, one of the most puzzling questions is: what did the common ancestor of all the archaea, eukaryotes and bacteria look like? In our Nature Communications paper, we describe a specific group of archaea - the Undinarchaeota - that originally seemed to be placed near the base of the archaeal branch in the tree of life. We could show that these organisms have limited metabolic capabilities, suggesting that they depend on other organisms for growth and survival, perhaps through symbiosis. They did, for example, not have the possibility to synthesize essential amino acids or vitamins. On top of that, we could show that these archaea frequently exchange genetic material with their hosts. This makes the phylogenetic jigsaw puzzle even more complicated!” These and related archaeal symbionts will be further studied by Spang, using two grants that were awarded to her and two distinct international research consortia by the Gordon and Betty Moore Foundation and Simmons Foundation, respectively. Spang: “For example, the Symbiosis Model Systems award by the Moore Foundation was granted to our consortium to study the symbiosis between Nanoarchaeaum equitans and its host Ignicoccus hospitalis. These microbes were isolated from marine hydrothermal vent systems north of Iceland by our colleague of the University of Regensburg, Dr Huber in 2002. These organisms have taught us a lot already about symbiosis of archaea and, with this grant, will hopefully teach us a lot more.”
There are two basic types of cells, prokaryotic and eukaryotic cells
“All eukaryotic organisms, like ourselves, are the product of the merging of an archaeal cell plus bacterial cells”
Prestigious grant and collaboration Apart from the genomic studies of archaea and their placement in the tree of life, Spang also studies archaea in the laboratory. For example, she received a prestigious grant from the European Research Council, ERC, in 2020. “With this grant, we will culture archaea in the lab together with the hosts they depend on. That way, we may be able to better understand their co-evolutionary patterns. We also want to investigate the genomes of these symbionts in their natural environment to better understand their place in the microbial food web.” Furthermore, Spang has started a cooperation with researchers at Utrecht University, NIOZ and University of Liège, Belgium to study the diversification of eukaryotic metabolic diversity through deep geologic time. Spang: “Together with professor Dr Berend Snel and professor Dr Paul Mason (Utrecht), professor Emmanuelle Javaux (Liege), Dr Rick Hennekam (NIOZ), we will try to trace the sources and subsequent diversification of eukaryotic enzymes relative to geological events, such as the appearance of oxygen in the atmosphere.”
“We will culture archaea in the lab together with the hosts they depend on”