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Posted by baalke on December 13, 2006, 1:59 pm
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http://www.stanford.edu/dept/news/pr/2006/pr-archaea2-011007.html
Stanford University
NEWS RELEASE
December 7, 2006
Contact:
Mark Shwartz, News Service: (650) 723-9296, mshwartz@stanford.edu
Comment: Chris Francis, Department of Geological and Environmental
Sciences: (650) 724-0301, caf@stanford.edu
Editor Note: The symposium, "Archaea in the Earth System II," will be
held at 1:30 p.m. PT Dec. 11 at the American Geophysical Union's annual
meeting in San Francisco at Moscone Center South, Room 256. For
details,
visit http://www.agu.org/meetings/fm06.
Relevant Web URLs:
Introduction to the Archaea
<http://www.ucmp.berkeley.edu/archaea/archaea.html>
Microbial Life <http://serc.carleton.edu/microbelife/>
Chris Francis Website <http://pangea.stanford.edu/~caf/>
>From hot springs to rice farms, scientists reveal new insights into the
secret lives of archaea
In the world of microbes, as in politics, some groups just can't seem
to
shake the label "extremist." So it is with archaea (ar-KEY-uh), a
collection of bacteria-like microorganisms whose unique genetics and
chemical structure separate them from all other living things.
For years, biologists have pigeonholed archaea as
extremophiles - creatures that live in extreme conditions. Indeed, many
species of archaea thrive in environments that would kill other
organisms, from Yellowstone hot springs to the hyper-salty Dead Sea to
streams polluted by mining waste where the pH level is equivalent to
battery acid. Archaea even inhabit the warm, dark environs of our
intestines and mouth.
While extremophiles have been the subject of intense research,
scientists are just now beginning to focus on the large number of
archaeal species that inhabit more mundane environments, including
soils
and seawater.
At 1:30 p.m. PT Monday, Dec. 11, an international panel of researchers
will present new findings about the extreme and not-so-extreme world of
archaea during the annual meeting of the American Geophysical Union
(AGU) in San Francisco's Moscone Center South, Room 256. The session
will be moderated by Chris Francis, assistant professor of geological
and environmental sciences at Stanford University, and David Valentine,
associate professor of Earth science at the University of
California-Santa Barbara.
"Archaea have been a pretty hot topic for a number of years in the
microbial ecology and physiology realm," Francis said, noting that most
biology textbooks now divide life into three domains - Archaea,
Bacteria
and Eukarya, a category that includes plants, animals, fungi, algae and
protozoa.
Scientists believe that the most recent common ancestor of all three
domains was a single-cell organism that lived in extreme conditions
when
the Earth was very young and very hot, and the atmosphere contained
large amounts of methane instead of oxygen. Although similar in size
and
shape to bacteria, genetic analysis reveals that archaea are actually
more closely related to humans and other eukaryotes.
Ancient origins
Although archaea are believed to be among the oldest organisms on
Earth,
finding paleontological evidence of these ancient microbes has proven
elusive. At the AGU session, G. Todd Ventura of the University of
Illinois-Chicago will describe what may be the earliest archaean fossil
evidence yet discovered - rock samples that are 2.71 billion to 2.65
billion years old that were collected from a deep underground gold mine
in Ontario, Canada. Ventura and his colleagues discovered that the
rocks
contained a type of lipid, or oily compound, found only in archaeal
cell
membranes. This finding indicates that an archaean community may have
inhabited the region more than 2.65 billion years ago when the area was
submerged and inundated with hydrothermal vents that eventually
produced
a gold deposit in what is now modern Ontario.
In another AGU presentation, Roger Summons of the Massachusetts
Institute of Technology will report on the discovery of novel organic
compounds recently extracted from the lipids of contemporary archaea.
It
is likely that many of these compounds have "chemical structures that
are new to science," he said.
Karyn Rogers of the Woods Hole Oceanographic Institution will discuss
the effect of temperature and chemistry on archaeal communities
inhabiting marine hydrothermal vents on the island of Vulcano, Italy.
Several species of thermophilic archaea live in these shallow waters,
where temperatures sometimes approach the boiling point. Rogers found
that there were more than twice as many archaeal species at relatively
moderate temperatures of 59 C (38 F) than at hotter vents where the
thermometer reached 94 C (201 F).
Climate change
Three AGU presentations will focus on surprising new findings about the
significant impact of archaea on global climate and nutrition. In
recent
years, scientists have discovered that methanogenic archaea play an
important role in the build-up of methane gas in the atmosphere.
According to the Environmental Protection Agency, methane is about 20
times more efficient at trapping atmospheric heat than carbon dioxide,
the more famous greenhouse gas. A United Nations panel also found that
methane levels in the atmosphere have increased by 150 percent since
1750.
It turns out that the international demand for rice is one of the main
drivers of methane production on the planet. Studies have shown that
rice farming contributes between 10 and 25 percent of global methane
emissions, thanks in large part to methanogenic archaea, which crank
out
tons of methane gas when they break down organic matter in flooded rice
fields. AGU panelist Ralf Conrad of the Max-Planck-Institute for
Terrestrial Microbiology in Germany will describe a group of archaea
known as Rice Cluster I, which he and his coworkers have identified as
the predominant methane producers in rice paddies worldwide. Last July,
Max-Planck-Institute researchers were the first to map the genome of
Rice Cluster I species. This gene sequencing effort may one day help
scientists find a way to reduce agricultural-based methane emissions
through genetic engineering.
Non-extremophiles everywhere
"For many years, we always thought of archaea as
extremophiles - halophiles [salt-loving], thermophiles [heat-loving],
acidophiles [acid-loving] or methanogens [methane producers]," Francis
said. Indeed, some Crenarchaeota are truly extreme. The species
Pyrolobus fumarii holds the world temperature record for surviving in
waters of 113 C or 235 F, well above the boiling point.
"However, in the early '90s, it was discovered that non-extremophilic
archaea were ubiquitous and abundant in the marine environment, but it
was unclear exactly how these organisms were making a living," Francis
said. "Then, in 2005, our understanding of what some of these organisms
are doing in the environment shifted dramatically."
That year, Francis and other scientists conducted independent studies
on
Crenarchaeota, a division of the Archaea domain that includes
thermophiles and non-extremophiles. "Crenarchaeota are everywhere - in
soils, sediments, the deep subsurface and the ocean," he said. "They
are
potentially the most abundant organism on Earth, yet we really had no
idea how they survive in the ocean."
Non-extremophilic Crenarchaeota are fascinating, according to Francis,
in large part because of their potentially vital role in cycling the
global supply of nitrogen. All living things need nitrogen to make
proteins, DNA and other biomolecules. Nearly 80 percent of the
atmosphere consists of nitrogen gas, which, unlike oxygen, cannot be
absorbed by most organisms. Getting usable nitrogen turns out to be a
complicated biological process. First, special "nitrogen-fixing"
bacteria in the environment convert atmospheric nitrogen into ammonia,
then "nitrifying" bacteria oxidize the ammonia into nitrites and
nitrates, which are readily absorbed by plants or removed by other
microbes. Animals and people, in turn, obtain nitrogen by eating plants
and other herbivorous animals.
That was the dogma taught for decades in biology classes - until
September
2005, when David Stahl of the University of Washington showed that
bacteria do not have a monopoly on nitrification. In a unique
laboratory
experiment, Stahl and his colleagues demonstrated for the first time
that archaea - in this case, marine Crenarcheaota - also oxidize
ammonia
into nitrite.
Less than a month later, Francis and his colleagues published a paper
in
the Proceedings of the National Academy of Science (PNAS) showing that
ammonia-oxidizing Crenarchaeota are pervasive in water columns and
sediments throughout the ocean. Then in July 2006, German
microbiologist
Christa Schleper showed that nitrifying eota were up to 3,000-times
more
abundant in European soils than their bacterial counterparts.
Mexico to Iceland
At the AGU meeting, Francis and former Stanford graduate student Mike
Beman will discuss the role of marine archaea in Mexico's Gulf of
California, where nitrifying Crenarchaeota appear to be extremely
abundant, even at depths of 2,000 feet.
In Iceland, Schleper and her colleagues recently identified the first
ammonia-oxidizing extremophiles - a group of Crenarchaeota that inhabit
several acidic hot springs where temperatures reach 80 C (176 F).
"Collectively, our study provides evidence that ammonia-oxidizing
archaea are present in hot springs and are actively nitrifying," said
ecologist Andreas Richter of the University of Vienna, who will present
the group's findings at AGU.
"Ammonia-oxidizing bacteria were discovered more than 100 years ago,
and
ammonia oxidation was previously thought only to exist in the bacterial
realm," Francis said. "Nobody ever guessed that members of the Archaea
were also involved in this process. We're still figuring out how all
the
pieces fit together."
-30-
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