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Research team of the HAW Hamburg reanimated ancestral microbe from the depth of the earth


Prof. Dr. Paul Scherer, Dr. Sandra Off and Master Sci. Biot. Katarina Wegner of the Faculty of Life Sciences made a successful job as “microbe hunters“. They reanimated an extremely seldom-ancestral microbe, a so called archaeon, which could be applied to convert excess electricity of wind energy farms into methane.

Our team of the university research center “Biomass Utilization Hamburg” is looking for tough and efficiently working “super microbes” which could be used as working beans for environmental biotechnologies, especially for biogas techniques, proclaims project leader and senior professor Paul Scherer.

The reanimated rod-shaped archaeon utilizes hydrogen and carbon dioxide as sole carbon and energy source to produce methane

Photo: Mark Goldenthal, scientist of the project GrassBiogas, team Prof. Scherer

If the microbes are alive and active, they show a green fluorescence

Project GrassBiogas, team Prof. Scherer/HAW Hamburg

Two temperature ranges exist in microbiology. The “mesophilic” range exists around 37°C. Example given, it will be used by “probiotic” yoghurt bacteria but unfortunately also by unwanted, potentially pathogenic bacteria. Therefore, our research team favors fermenters of the thermophilic range (around 55°C or higher) to outcompete strictly pathogenic microbes.

For industrial applications, the thermophilic temperature range is often new and therefore needs scientific research. During our work, we made a special, unexpected discovery. “We detected in two biogas fermenters fed with grass or beets an extremely seldom methanogenic archaeon. This species was only one time found in a 800m deep earth borehole of a natural gas field in Japan “, so Professor Scherer.

Archaea are presumably the most ancient living fossils of the planet earth

Microbes, which desire hot and extreme conditions, are narrow relatives of the first microbes living on the ancestral earth since more than 3.5 billion years. This scientifically accepted dogma derives from molecular genomic data. About 50% of the human genes are coming presumably from microbes. It is believed that in this ancestral, oxygen free time the young earth was covered by fervid volcanos and a just originated ancestral continent and ocean.

The ancestral atmosphere contained microbially produced methane as greenhouse gas with a temperature of about 60-70°C. Probably, the nutrients of these archaea were only hot water, volcanic hydrogen, carbon dioxide and some minerals. Photosynthesis or cells of higher living organisms did not exist. Therefore, the archaea can be regarded as the oldest living fossils of the earth. Apparently, they are still alive and produce actively bio-methane, called natural gas. Just 2015 some new “extremophilic Lokiarchaeota” were discovered in hot deep-sea springs, which were speculated to be the missing link between microbes and multicellular organisms like the humans (Spang et al., Nature 2015).

Japanese research team discovered a new archaeon species

Some years ago, the same methanogenic archaeon from Hamburg was found by Japanese microbiologists in an 800m deep hot borehole which was mined to find a deposit of methane. The Japanese researchers isolated the microbe and used an oxygen free atmosphere like in Hamburg to cultivate these organisms with hydrogen and carbon dioxide as substrate. What seeks such an extremophilic microbe in a place like Hamburg? How did it come to this location? Archaea do not form resistant spores, they can only swim. Were the rediscovered archaea in Hamburg the same ancestral organisms like in the 800m depth borehole in Japan?

Was the rediscovered archaeon of Hamburg really the same found in the Japanese borehole?

To solve this question, first Dr. Sandra Off of the university team discovered by so called PCR-techniques a genetic footprint of this only one time in Japan discovered archaeon, but now in a thermophilic biogas fermenter fed with fodder beet silage as substrate. The substrate hydrogen and carbon dioxide of this archaeon could be generated by accompanying microbes as intermediates of the biomass. However, was it really the same archaeon as in Japan?

Sandra Off und Katarina Wegner detected the same archaeon also in a thermophilic pilot biogas plant to digest anaerobically grass (company Bi.En GmbH & Co. KG, Kiel, partnership research project of the university). The alien microbe dominated the methanogenic population by 80% with a number of 1 billion cells per milliliter of biogas reactor volume. Nevertheless, the scientists of the Hamburg University were also able to manifest this genetic footprint as culture under thermophilic conditions (70-80°C). Now, it could be thoroughly investigated by “Next Generation Sequencing” (NGS), the most modern technique on this genetic field. Indeed, the “paternity test” revealed exactly the same archaeon species described worldwide only one time by the Japanese researchers to occur in an 800m deep borehole.

Occurrence of methanogenic archaea in biogas plants

Biogas plants to produce electricity and heating energy are very common in Germany. About 9000 biogas plants in Germany deliver from renewable biomass as well as agricultural and municipal biowaste 34 TWh electricity for more than 4 million inhabitants (world record 2016), together with 86 TWh by 27000 wind energy mills. The biogas plants of Germany and other countries were systematically investigated in the last 10 years by PCR, NGS and other molecular techniques, but the rediscovered methanogen from the depth of the earth was never described to occur in a biogas plant or a second time.

Could be something in common between the habitats of the Japanese borehole resident and the rediscovered archaeon in Hamburg?

“In depth earth habitats we have a salty environment”, says Prof. Paul Scherer. Such salty conditions provide also mesophilic or thermophilic biogas plants with manure, renewable biomass or grass as mono-input. The salt content is also comparable with the salt content of the Baltic Sea near the bay of Kiel. That alone is not extraordinary enough to attract such an extremophilic methanogenic organism. It should exist a special reason that the ancestral microbe was reanimated after thousands or even millions of years in the neighborhood of Hamburg.

An extraordinary high content of hydrogen sulfide could have attracted the ancestral reanimated microbe

The research team of the Hamburg University assumes that extraordinary high hydrogen sulfide concentrations might have attracted the new methanogenic archaeon found in two biogas fermenters, together with a high temperature and a high salt content. Generally, to preserve the biogas engines of electricity producing biogas plants from corrosion by hydrogen sulfide traces in the biogas, ferrous salts are added to biogas plant reactors. This was not the case in the laboratory fermenter with fodder beet and in the biogas pilot plant with grass. Accordingly, very high hydrogen sulfide contents of more than 1000 ppm (>0.1%) were measured in the outgoing bio-methane. That should have provided the unique chance of the ancestral resilient microbe to escape the dormancy after thousands or millions of years. On the other side, the alien microbe must have been present everywhere. Maureen O’Malley published 2008 already the interesting article “Everything is everywhere…” about the worldwide occurrence of microbes (Stud. Hist. Phil. Biol. & Biomed. Sci. 2008), but she found no comparable example of such an extremophilic organism.

Could derive a technical application from the ancestral rediscovered microbe?

The regulation of excess electricity by wind or solar power stations is at present under research in Germany. One of the most economical solution would be a “Power to Gas Station” to convert hydrogen generated by water electrolysis through a microbial methanogenic fermentation into methane. This methane could be fed into the gas grid system of Germany or it could be used as compressed natural gas at gas stations to gas up gas driven cars or trucks. The Energy Park in the German city Pirmasens runs at present the biggest microbial methanisation station for excess electricity in Germany. For this biotechnological process, they use already some known methanogenic microbes as working beans, but at 60°C. At the moment, they try to find new methanogenic microbes adapted to temperatures higher than 60°C as they probably will work more efficient at higher temperatures (M. Frey, Biogas Journal [German], 1/2017, p.51 or Therefore, the rediscovered depth earth resident would be an excellent candidate for such an application as his optimum reaches higher temperatures.

(Authors: Prof. Dr. Paul Scherer, Dr. Sandra Off and Master Sci. Biot. Katarina Wegner)

Further Information:

Faculty Life Sciences
Prof. Dr. Paul Scherer

Weitere Informationen:

Dr. Katharina Jeorgakopulos | idw - Informationsdienst Wissenschaft

Further reports about: archaeon biogas plant biogas plants carbon dioxide dioxide microbe natural gas sulfide

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