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New insights into the ancestors of all complex life

A team of scientists led by the University of Bristol has provided new insights into the origins of the Archaea, the group of simple cellular organisms that are the ancestors of all complex life.
The Archaea are one of the Earth's most genetically and ecologically diverse groups of micro-organisms.
They thrive in a bewildering variety of habitats, from the familiar - soils and oceans - to the inhospitable and bizarre, such as the boiling acid pools of Yellowstone National Park.

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Methane eating microbes can use iron and manganese oxides to breath
Iron and manganese compounds, in addition to sulphate, may play an important role in converting methane to carbon dioxide and eventually carbonates in the Earth's oceans, according to a team of researchers looking at anaerobic sediments. These same compounds may have been key to methane reduction in the early, oxygenless days of the planet's atmosphere.

"We used to believe that microbes only consumed methane in marine anaerobic sediment if sulphate was present. But other electron acceptors, such as iron and manganese, are more energetically favourable than sulphate" - Emily Beal, graduate student in geoscience, Penn State.

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Nickel isotope may be methane producing microbe biomarker
Nickel, an important trace nutrient for the single cell organisms that produce methane, may be a useful isotopic marker to pinpoint the past origins of these methanogenic microbes, according to Penn State and University of Bristol, UK, researchers.

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A new species of bacteria discovered living in one of the most extreme environments on Earth could yield a tool in the fight against global warming.
In a paper published on Dec. 6 in the prestigious science journal Nature, U of C biology professor Peter Dunfield and colleagues describe the methane-eating microorganism they found in the geothermal field known as Hells Gate, near the city of Rotorua in New Zealand. It is the hardiest methanotrophic bacterium yet discovered, which makes it a likely candidate for use in reducing methane gas emissions from landfills, mines, industrial wastes, geothermal power plants and other sources.

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 Microbes That 'Eat' Natural Gas
Scientists identify bacteria that convert chemicals in surprising ways
In the quest to explore the remarkable diversity of microbial life on Earth, an international team of scientists has identified marine bacteria that can eat butane and propane in natural gas, metabolising them in a way never observed beforein the absence of oxygen.
Scientists have known since the beginning of the 20th century that microbes consume hydrocarbons, a main constituent of natural gas, as efficiently as dogs chomp on meatas long as they could use oxygen in the process. In the late 1970s, scientists figured out that certain microbes can break down methane (CH4)the largest ingredient in natural gas and the simplest hydrocarbonwithout oxygen, and in the last few years, they finally found the microbes that could do it.  But what was eating the other hydrocarbons in natural gas, such as ethane (C2H6), propane (C3H8) and butane (C4H10), and how were they doing it?

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Max Planck researchers uncover the survival strategy of microorganisms responsible for the world-wide emission of methane from rice paddies

About 10 to 25 percent of the world's methane emissions come from flooded rice paddies. Methane is a greenhouse gas produced by various groups of microorganisms (methanogenic Archaea). Oxygen is usually highly toxic for these microorganisms. The major producer of methane in the roots of rice plants is what is known as "Rice Cluster I" (RC-I) Archaea. The mechanisms that give these Archaea a competitive advantage remained unexplained, because it was impossible to get a pure culture of them. Now, scientists from the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany and the Max Planck Institute for Molecular Genetics in Berlin have fully sequenced the genome of an RC-I archaeon from a methane-producing microbial mixed culture. From the genome sequence, the researchers were able to deduce the existence of a number of enzymatic mechanisms, unknown in methanogenic Archaea until now. The mechanisms help the RC-I Archaea to survive when oxygen is present. They allow the RC-I Archaea to adapt specifically to the oxygen-rich area around the roots of the rice plant. The results explain why RC-I Archaea have a selective survival advantage (Science, July 21, 2006).

In the current study, Max Planck researchers from Marburg and Berlin investigated the complete genome sequence of an RC-I archaeon that appears frequently in the mixed culture MRE50. As a rule, the starting point for analysis of a complete microbial genome is a pure culture - and its corresponding homogeneous component of genetic information. But in the case of RC-I Archaea, no pure culture was available. So all the genetic information of the mixed culture MRE 50 served as the starting point for sequencing the complete RC-I genome. Such heterogeneous genetic information, stemming from various microorganisms in the mixed culture, is called a metagenome. One particular analytical challenge was filtering out the complete, homogeneous genome of a defined RC-I archaeon from the metagenome. The researchers were able to do this using a specific bio-informatics analytical methodology.

IMAGE (209kb, 939 x 633)

The genome of the RC-I archaeon is made from 3.2 million base pairs, and codes for 3,103 proteins. The proteins can, among other things, be organized according to their methanogenic metabolism - that is, how they create methane simply by reducing carbon dioxide with hydrogen. Enzymes for the analysis of alternative methanogenic nutrients are not encoded by the RC-I genome. The RC-I archaeon can thus be categorised as hydrogenotroph Methanogenic Archaea can only produce methane, and the energy that comes from it, when oxygen is completely absent. The presence of oxygen is normally very hostile to them. However, this is not the case for RC-I Archaea - the RC-I genome codes for enzymatic mechanisms which are unique for methanogenic Archaea and make it possible for them to survive in an oxygenated environment. A whole group of enzymes belongs to this mechanism. These enzymes quickly detoxify highly reactive oxygen species, such as superoxide anion or hydrogen peroxide. These oxygen species are extremely toxic for living cells. When oxygen is present, RC-I Archaea quickly switch to a zymoma fermentative.

Sequencing the RC-I genome offers the groundwork for developing a means of monitoring the activity of RC-I Archaea in their natural environments, using molecular biological methods. It is uncertain, however, how long it will take before we can actually reduce the methane production of RC-I Archaea - and methane emissions from places like rice paddies.

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