Download The humble ancestors of almost every living thing

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.
Hester van Santen
January 16, 2016
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.
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 ringshaped 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”.
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.”
Three things you should know about archaea
1. Archaea have only been taken seriously for the last
twenty years
In 1977, the theory of a certain category of “bacteria” forming a completely separate main
group of life came out of nowhere. In this year Proceedings of the National Academy of
Sciences published a paper by microbiologist Carl Woese from the University of Illinois and
his postdoc George Fox. Woese had conducted genetic research (technically spoken
extremely complicated at the time) which proved there were three “domains of life”:
eukaryotes, bacteria and archaea.
Woese was laughed at. The genetic data were limited, and had been won with a technique
mastered by hardly anyone. It didn’t help much that Woese himself had a withdrawn
personality. The influential evolutionary biologist Ernst Mayr persisted until his dying day
that Woese was speaking “gibberish”. In the nineties, when an increasing amount of DNAinformation became available, Carl Woese was proven right. By now, his division is
commonplace in the field of Biology. Yet, after his passing on December 30, 2012, not a
single Dutch newspaper published his obituary about him.
2. The majority of archaea do not exist in salt lakes or
hot springs
Biology textbooks – by now pervaded by the archaea – mention they are most common in
extreme conditions, but this is outdated.
Stress tolerance in Archaea is higher than in bacteria. Much more archaea than bacteria will
immerse themselves in boiling hot springs, the earth’s crust containing hardly any food, brine
pools and acid mining waste. These extreme environments are where they were first
discovered.
Over the past twenty years, archaea have been found in all kinds of environments really, from
lakes to coastal areas and the cold deep sea, and from rice fields to pastures. They are
particularly successful in the sea: archaea make out an estimated 20 to 30 per cent of the
ocean’s micro-organisms.
They occur in nearly all researched soils as well, albeit in fewer numbers and less diverse than
bacteria: on average, archaea make out 2 per cent of the soil’s micro-organisms. Yet, they
seem to break down more ammonia than bacteria do (Nature, August 2006).
3. Archaea don’t make people ill.
Archaea love people. They live in everyone’s bowels. They are fewer in number than bowel
bacteria, but their influence is noticeable. People with a lot of bowel-archaea spread
measurable amounts of methane through their flatulence. There are people who gas out 100
milliliters of methane a day through their farts. All of the methane spread by cows and other
animals through burping and farting originates from archaea.
Just like bacteria, archaea dwell in other parts of our bodies as well. They are in dental plaque,
in the vagina. And archaea can enter into cells – there are protists containing archaea. As a
matter of fact, there’s nothing to keep archaea from making people or animals ill.
Yet, an archaeon causing sickness has never been found. Two reviews on the subject (from
2001 and 2003) stated it hadn’t been researched thoroughly enough, but fifteen years on, not a
single archaeon-illness has been acknowledged.
Archaea-researchers mock disappointment over this: pathogenic archaea would be fruitful for
getting research grants. Thijs Ettema: “At conferences, we sometimes joke about creating
some ourselves.”