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 A New Branch of Life

The Mystery of Crenarchaeota

Deploying a sequencing sediment trap in Lake Superior, which will collect particles that sink to the bottom of the lake for six months.

Trapping the Archaea Organism
Since 2005, a funnel-like device has been anchored in the middle of Lake Superior, quietly trapping microscopic particles as they drift through the water column. The particles contain mysterious single-celled microorganisms called Archaea, which caught scientists by surprise in the 1990s when they were first found to be present in the cool, oxygen-rich waters and sediments of oceans and great lakes.

A proposal in 1977 that the Archaea were different from bacteria caused nothing less than a paradigm shift in the biological world, and a major redrawing of the tree of life in 1990. Archaeal microorganisms were found, through studying their RNA, to be nothing less than a major new “branch” of life. (The other two major branches or “domains” are the Bacteria and the Eukarya — the branch that leads to plants and animals.)

“It was first thought that Archaea could only live in freakish environments, very hot water, super saline habitats, or places devoid of oxygen on our planet,” said Josef Werne, associate professor at the Large Lakes Observatory (LLO) and UMD’s Department of Chemistry and Biochemistry. They were pegged the “extremists” of the natural world.

The Crenarchaeota, a kingdom within the Archaea dominated by thermophilic cells that thrive at very high temperatures, caused another ripple across the scientific world in 1992 when DNA from non-thermophilic forms of these microbes was discovered in the world’s oceans, then in large freshwater lakes, and eventually, in many aquatic and terrestrial ecosystems. “Now we know that they live everywhere.” Werne said.

The non-thermophilic Crenarchaeota species, especially their living cells, are elusive. So far, only one laboratory in the world has been able to isolate a single species representative of these microorganisms and keep it alive. “Basically, the only things we know about them are from molecules we find in the environment like their DNA or compounds they leave behind when they die,” said Randall Hicks, director of UMD’s Center for Freshwater Research and a professor of biology. “It’s as if a new animal were discovered, but it is invisible.”

Werne and Hicks are seeking answers to several important questions about the Crenarchaeota in Lake Superior and other large lakes. Their studies are showing that these microorganisms contain a gold mine of information: their “fossils” hold information about temperature change over millennia, and some of the living microbes appear to play a key role in cycling nitrogen.

Crenarchaea: The studies
of Werne and Hicks
are showing that these
microorganisms contain
a gold mine of information:
their “fossils”
hold information about
temperature change over
millennia, and
some of the living microbes
appear to play a key role
in cycling nitrogen.


UMD’s Large Lakes Observatory made scientific news when it found Crenarchaeota in Lake Superior and other large lakes in the U.S., Africa and Kyrgyzstan. Archaeal microorganisms were found, through studying their RNA, to be nothing less than a major new “branch” of life. The other two major branches or “domains” are the Bacteria and the Eukarya — the branch that leads to plants and animals.

UMD, the Netherlands, and Large Lakes of the World
UMD is at the forefront in the research about these elusive microorganisms in great lakes. Both Werne and Hicks are on a quest to find answers.

Werne participated in early research on chemical compounds produced by crenarchaeons at the Netherlands Institute for Sea Research. After arriving at UMD in 2002, he was eager to continue his biogeochemical research into the “paleoenvironmental questions that can enhance our understanding of the evolution of the earth.” Scientists have known that chemical clues can provide a way to measure climate change, but the quest has been to find a reliable temperature “proxy” — something that reacts to temperature change and leaves behind a record. From Werne’s research, it looked like lipids found in the cell membranes of the Crenarchaeota might provide that proxy.

“The compounds in the membrane surrounding archaeal cells have been called ‘molecular fossils,’ ” Werne explained. “They allow us to look at life that we can’t look at any other way — both ancient and modern.”

Randall Hicks
Joe Werne
Postdoctoral investigator Brent Dalzell filters water collected from different depths that will be used to extract DNA from aquatic microorganisms.
Graduate student Jason Kish extracts microbial DNA from filters to identify crenarchaeal microorganisms and compare archaeal communities from different depths in Lake Superior.

Partnering again with the Netherlands Institute, Werne and Ph.D. student Lindsay Powers conducted a preliminary study that analyzed sediments from four large lakes: Superior, Michigan, Malawi in East Africa, and Issyk-Kul in Kyrgyzstan. Lipids from crenarchaeotal cell membranes were found in the sediments of all four lakes. They published the results of this research in 2004, reporting that the diversity of these microbial compounds in sediments — the proxy — were found to correlate “very strongly” with the annual mean surface temperatures of lakes. They suggested that these compounds might provide a way to reconstruct past temperatures in continental systems around the globe.

Werne has been studying the Crenarchaeota in Lake Malawi, East Africa, and Elk Lake in Itasca State Park, Minnesota. The Lake Malawi work has already resulted in a reconstruction of temperatures 700 years ago, 25,000 years ago, and 70,000 years ago.

“We’re pushing this back 200,000 years to compare the temperatures with the history of human evolution and migration in the East African Rift Valley,” he said. Studies continue in other East African lakes such as Lake Turkana, Lake Victoria, and Lake Albert, as well as some lakes in Mexico, but the Lake Superior location is the only place where sediment traps are being used.

Back to Large Lake Superior's Crenarchaeota
In the fall of 2004, Werne teamed up with Hicks to conduct research exploring Crenarchaeota ecology in Lake Superior to learn more about why and how the molecular fossils left behind by these microbes reflect lake surface temperatures from the past. They also want to find out what roles these microbes play in freshwater environments — in other words, what are their “jobs?” They hope to answer important, basic questions about these microbes: When during the year are they produced? Where do they live and grow in lakes — in the surface water, in the middle, or near the bottom? Do cold bodies of water contain as great a diversity of the Crenarchaeota as warm water ecosystems?

Werne and Hicks began an NSF-funded research project, Linking Archaeal Membrane Lipids and Ecology in Great Lakes, in 2005. Each May and September, a group of six scientists, including undergraduate science majors, master’s and doctoral candidates, and professors from UMD, visit their research site in the middle of Lake Superior — a spot halfway between the Apostle Islands and Isle Royale — to collect microbes from the water and materials from the sediment traps.

“The sediment traps are essentially big funnels,” Werne said. One sediment trap is submerged in the lake at 145 meters (about 475 feet), while another is sent down to 60 meters (about 197 feet) and left there to collect samples. Eighty-four samples are collected each year by the sediment traps.

Once the samples are brought back to the lab, portions of each are prepared for different analyses. A doctoral candidate, Martijn Woltering, travels to the Netherlands twice a year to process samples through their liquid chromatograph/mass spectrometer, which generates data about the lipid compounds found in the cell membranes. While back at UMD, graduate student Jason Kish and undergraduates process DNA samples in Hicks’ lab that were extracted from microbes in the water and trap samples.

A breakthrough in understanding the Crenarchaeota’s role or “job” came in 2005, according to Hicks. Evidence from studies in three different marine ecosystems suggested that at least some of these microbes might be oxidizing ammonia — catalyzing the conversion of ammonia to nitrate. Hicks and his students have found the crenarchaeotal gene that catalyzes this conversion in their Lake Superior samples.

“That’s a pathway we didn’t know about because this conversion was something scientists once thought only bacteria could do.” he said. “We need to understand how the Crenarchaeota are influencing the lake nitrogen cycle, and ultimately, their role in the global nitrogen cycle.” All organisms on earth use nitrogen to create proteins, a major chemical building block of their bodies.

A continuous, century-long increase of nitrate in Lake Superior’s waters was discovered by other researchers and a recent study suggested that most of the nitrate may be accumulating from biological processes within the lake and not from new inputs of nitrogen. UMD and LLO scientists hope continued research will show why.

Ground-Truthing Stage
The discovery of Crenarchaeota in colder aquatic systems has opened abundant opportunities for research within the scientific disciplines of geology, chemistry, and biology.

“We’re been searching for a good temperature proxy for lakes, and we think we’ve found it. Right now, we’re at the early, ‘ground truthing’ stage,” Werne said.
“One of the signs of a good science project is you generate as many questions as answers. There’s more than a career’s worth of work here,” Hicks added.

The Center for Freshwater Research and Policy

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