The humble ancestors of almost every living thing

Archaea. Few people know of their existence. Yet these micro-organisms are one of the three types of life on earth. They are everywhere. They formed the basis of the cells of all plants, fungi and animals – the basis of us.

Archaea. /ɑːrˈkiːə/ Singular: archaeon. If you’re not a biologist you’ve probably never even heard of them. Nevertheless, archaea form one of the three main groups of life on earth. Eukaryotes (“cells with a nucleus”), bacteria, archaea.

Archaea are micro-organisms. Under a microscope they resemble bacteria, but they actually are as distantly related to bacteria as we are. In 1977, American microbiologist Carl Woese was the first to designate archaea as the “third domain” of life. This insight was so groundbreaking it took a long time before it was taken seriously.

Archaea are omnipresent. In our bowels, in the sea, in the ground. They play a main role in evolution’s plot. The indications of them being our ancestors, in a broad sense, are becoming stronger and stronger. samIt seems like the much larger and more complex eukaryotes have derived from the humble archaea. Eukaryotes are the cells of animals, plants, fungi and of all protists from malaria parasites to paramecium.

Photo ANP/Science Photo

The hitherto most spectacular discovery regarding this evolutionary role of the archaea was made last year. Thijs Ettema, a Dutch biologist with his own research group at Uppsala Universitet, published in Nature about the discovery of an archaeon of unprecedented complexity in the sea off Norway, which he named Lokiarchaeum.

“These fellows are the eukaryotes’ sister group”, he tells me in his study in the Swedish university town. Ettema (1977) has worked there since 2006. His lab currently counts eighteen researchers – almost everyone of them under 35.
“Bergen University had provided us with seabed samples collected around a hydrothermal vent, a submarine hot spring near Norway called Loki’s Castle. There were indications that interesting archaea could be found there.”

He didn’t find “Loki” very close to this hot spring, but some 10 or 15 kilometers further, inside the cold seabed. “The very first sample was spot on.”
With postdoc Anja Spang as first author, Ettema’s Swedish/Norwegian team reconstructed Lokiarchaeum’s DNA-package from this seabed sample. Ettema: “Once we held the genome, we noticed it contains eukaryotic-like genes.”

There is no photo of Loki on these pages, for it cannot be cultured inside a laboratory. Loki wouldn’t even be put under a microscope. This is not uncommon: the past decade, virtually all discoveries about bacteria and archaea have been made exclusively by isolating their DNA from seabed or water samples.
As of recently it’s even possible to filter out DNA from one species and jigsaw it back together on the computer. This way the Scandinavian team got a picture of Loki, an organism that must be leading a sluggish existence in the oligotrophic, anoxic seabed. It has around 5,500 genes.

Approximately 175 of these genes are similar to eukaryotic cells. Their counterparts in animals and amoebas shape the cells and facilitate transport of molecules through the cell. Ettema: “By now, we have also found genes which eukaryotic cells form vesicles with.” These are distinguishing features of eukaryotic cells.

“After our discovery of Loki we have found a handful of ‘brothers’”, Ettema says after he’s made espresso with the research group’s very own barista machine – his response to the weak Swedish filter coffee. Ettema named the sorts after Norwegian gods like Thor and Odin. “We don’t just find them in deep sea, but also in hot springs in Yellowstone, in river sediments, on the coast. We are able to detect Loki’s unique eukaryotic features in those other archaea as well.”

Round or flat

Under a microscope, archaea cannot be distinguished from bacteria. They are both invisibly small (say 1 to 3 thousandth of a millimeter) and look like grains. There are round, flat, or long ones, sometimes with a flagellum. By lack of a nucleus, their ring-shaped DNA is contained loosely inside the cell.
However, a schism gapes from Earth’s deepest history. Bacteria and archaea differ from each other in the most fundamental cellular processes, such as reading DNA and producing proteins.

As suggested last year by British biochemist Nick Lane in his book The vital question, the genetic material of bacteria and archaea may already have been different from each other, even before the very first cells came into existence around 3.5 billion years ago. One thing is certain: in the following one and a half billion years – roughly until 2 billion years ago – life on earth existed of these tiny scrabblers, the “prokaryotes” (cells without nuclei).
Then, suddenly there was the cell-with-nucleus that would form the basis for everything from cyclamen to cicada, and in no way resembling the micro-organisms that existed before. Eukaryotic cells are ten to ten thousand times the size of prokaryotes. Their DNA is not ring-shaped but exists of long chromosomes. Also, eukaryotic cells contain numerous elements prokaryotes don’t have. A nucleus containing DNA. A bulging cytoskeleton. A complex “parcel delivery system”.

Archeon Sulfolobus seen through an electron microscope. Foto ANP/Science Photo

The origin of eukaryotic cells remains a big question mark. The origin of merely one crucial element of the eukaryotic cell is properly known. The mitochondria, tiny cellular organs supplying energy, originated from engulfed bacteria. This “endosymbiosis” must literally have been the motor supplying all these new elements with energy. So how did the rest come about?

There is no trace of gradual evolution. All modern life is either prokaryotic or eukaryotic. A transitional form, a missing link, has never been found. Since a number of years though, genetic trees which are becoming better and more complete, have been pointing out where to look for this ancestor: in the archaea. “As the fit of the model to the data is improved, a shift [towards such an evolutionary tree] is observed”, Irish bio-computer scientist James McInerney wrote in Nature Reviews Microbiology in June, 2014.

The way it stands, Thijs Ettema’s team seems to have come closest to this transitional form with Loki and the other Norwegian gods. In September 2015 he designated six new archaea in Philosophical Transactions B. They are not closely related to each other, but they are all close to eukaryotes in the evolutionary tree of life.

And they all carry genes for something similar to a cytoskeleton and cellular parcel delivery. “These data contain unique things”, Ettema said just this week. “We are writing it down right down.”

Sediments

There are two big questions waiting to be answered. Firstly: what are the Loki-like doing with these genes? Do these “eukaryotic” genes in archaea behave the same way they do in actual eukaryotes? Ettema: “To figure this out, you need to culture them. With the original Loki, this poses a problem”.

Ettema’s Norwegian colleague Steffen Jørgensen is trying to isolate Loki from the seabed. However, the number of cells within the seabed is extremely low, and the soil parts are as tiny as the cells. It’s like looking for a needle in a haystack. Ettema: “And then there’s the chance of the cells being destroyed through exposure to oxygen after the seabed drillings.”

Cultivation is even trickier. It is estimated that cells inside the cold seabed will divide only once a year. “So it has a terribly slow growth. That’s why I expect more from the Lokis from warmer places. We are in the process of organizing that.”

The second question seems like the first step into a dark forest .

When a biologist is able to discover entirely new organisms by making some well-aimed grabs in sea and fresh waterbeds – what does it mean?

In his September 2016 article, Ettema spoke of “microbial dark matter”. It turned out the Lokis could not be detected through the “universal” standard methods for multiplying DNA from soil or water samples. If Ettema hadn’t thought of using another method, they’d never been found.

There are more such examples. In Nature of July 2015, American microbiologists reported the discovery of an entirely new group of bacteria – a group which may represent up to 15 per cent of all types of bacteria on earth – also by using an alternative detection method.

Even more curious is the EM-photo of a mysterious cell, published by the Journal of Electron Microscopy in September 2012. It was hidden between the bristles of a bristle worm from a submarine hot spring near Japan. The thing is too large to be a bacterium or archaeon. It has some indistinct cell structures – like something resembling but not quite a nucleus. There is no DNA-information available, and that was it for the past three years.

“There is more than we know about, for sure”, Thijs Ettema concludes. “But it isn’t easy to find.”

Translation: Welmoed Smith