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Microbiology of extremely acidic terrestrial volcanic ecosystems

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Understanding bacteria that live inside volcanoes can bolster climate models

Extremophiles living in the hot, acidic soil around volcanoes are adept at cycling chemicals such as methane, offering clues for how we can capture these greenhouse gases.

Climate Change and Environment

A key aspect of climate change is the rapid rise in greenhouse gases such as methane, which is released from wetlands and thawing permafrost. Due to its abundance, methane is an attractive fuel, but remains difficult to capture. One possible solution is to look for microbes which can fix methane from the atmosphere. The EU-funded VOLCANO project searched for these, and other organisms, in the hot, acidic soils found in volcanic regions. “We are extremely interested in the cycle of elements in nature: nitrogen, carbon, sulfur, organisms that metabolise these elements, and how that works in an ecosystem,” explains project coordinator Huub Op den Camp.

Island volcanoes

To hunt for novel organisms, his team at Radboud University in the Netherlands turned to three extremophile hotspots in Italy: the Solfatara volcano near Naples, the island of Vulcano near Sicily, and the island of Pantelleria near the coast of Tunisia. “The Solfatara volcano won’t erupt, but there is still activity, with bubbling mud pots, and fumaroles, hot steam venting out of the earth,” says Op den Camp. These fumaroles supply concentrated gases such as methane and carbon dioxide, and all the sites feature soils with high temperatures – up to 100 °C at 50 cm depth – and low pH. To capture the microbes, the team drilled cores and collected samples of soil before rushing back to the hotel. “Once back at the hotel, we used the room as a lab to inoculate everything on the spot,” he adds. “We returned in 24 hours, and installed the new incubations in our laboratory.” The bacteria were identified using two techniques. In the first, Op den Camp and his team followed a metagenomics approach, extracting DNA directly from the mixed samples. A second approach involved enrichment and culturing the bacteria to finally isolate the different species present.

New discoveries

The team were able to characterise hundreds of bacterial species, including members of a new genus not previously known to science. Several of these species were methanotrophs – bacteria that feed on the methane present in the soil. “How they use atmospheric methane is an important question,” notes Op den Camp. “The concentration of methane in the atmosphere is increasing, if you could isolate an organism that can easily take it out, that could be very helpful.” He adds that a better understanding of how microbes mediate the flow of methane between the atmosphere and sources such as wetlands will help to improve climate models. Other strains of interest isolated by Op den Camp’s team include a species that was able to readily convert methane into methanol, an important precursor in the chemical industry, and a bacterium on Pantelleria that lives on a diet consisting solely of gas. “The only thing this bacterium needs is hydrogen, CO2 and oxygen,” he says. “They fix CO2 like a plant does with sunlight; except they burn hydrogen to provide the energy to do it.” Another species was shown to lose half the carbon it fixes into the surrounding medium, which could make it especially useful for producing organic compounds. Following this project, Op den Camp plans to find ways to isolate the key players in this microbial ecosystem: “Researchers are never done, there are always new questions that open up, and a lot of really interesting things that are worthwhile studying.”

Keywords

VOLCANO, mud, bacteria, methanotroph, methane, fumaroles, Solfatara, Pantelleria, Vulcano

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