The Iceland Diaries, Part 2
In June 2007, Prof. Charles Cockell, Dr. Aude Herrera, Joseph Deeks from the Geomicrobiology Research Group at the Open University and Prof. Stephen Self from the Volcano Dynamics Group at the Open University left England to spend one week in Landmannalaugar, a region near the volcano Hekla in the Southern Highlands of Iceland.
|Hot spring view in Landmannalaugar, Iceland. Click image for larger view. |
Image Credit: Charles Cockell.
Their goal was to collect volcanic rock samples in order to study the bacteria that colonize them. This work, which is funded by the Leverhulme Trust in the UK, required them to fly to Reykjavik and then drive to Landmannalaugar, with a stop on the way in Valahnukar. Aude Herrera recalls their adventures in the second part of her journal.
(Read Part 1 of this journal.)
June 13, 2007: Landmannalaugar
After spending all of yesterday collecting rhyolite samples, our objective for today is to explore a different environment: the hot springs. Hot springs are abundant in Iceland and probably were common on the early Earth.
Hot springs have extremely high temperatures and elevated sulfide concentrations, and they are an extreme environment for most living organisms. However, microorganisms previously have been reported to thrive in such springs. For example, bacteria have been described forming long streamers or mats, with a different appearance depending on the sulfide concentration, pH, temperature, and other chemical and physical factors. Many Icelandic hot springs have sulfide concentrations as high as 30 mg per liter-1 and, under such conditions; thick bacterial mats can appear spectacularly white or bright yellow due to precipitated sulfur.
Investigating these extreme environments can help us to improve our understanding of life’s emergence, and also has considerable biotechnological potential. A typical example is the history of Taq DNA polymerase, purified from the hot springs bacterium Thermus aquaticus. Roughly 10 years after the first report published by Drs Brook and Freeze in 1976, the polymerase chain reaction was developed and shortly thereafter “Taq” became a household word in molecular biology circles.
|Dr. Aude Herrera collecting samples in a hot spring in Landmannalaugar, Iceland. Click image for larger view. |
Image Credit: Charles Cockell.
Currently, the world market for Taq polymerase is in the hundreds of millions of dollars each year. The recent interest in biotechnology, coupled with the discovery of novel thermophiles, have prompted studies on the utilization of these unique organisms and their enzymes for industrial purposes.
Motivated by this double “fundamental and applied” purpose, we have walked through a valley near the hut until reaching a majestic hot spring, and we are now collecting samples. As we expected, the steam from the spring is really hot and smells strongly of sulfide.
I’m anxious to identify the microbial communities present in our samples and compare them with previous reports. Generally, two different approaches can be used to access the microbial communities living in environmental samples: culture- or molecular-based approaches.
The culture approaches are based on detailed biochemical characterisations of pure-cultured microorganisms, and provide valuable information on their potential roles in the environmental processes. However, more than 95 percent of microbes will not grow in laboratory culture due to the selectivity of growth media and culture conditions.
The molecular techniques are able to investigate a far greater proportion of bacterial communities. They are based on two major steps: first, a DNA extraction from the environmental sample, following by the amplification, from this total DNA pool, of a gene common to all microorganisms (such as the small ribosomal subunit or SSU). This gene is a microbial signature that can be used to identify microorganisms present in samples. In our case, we will apply molecular methods to identify the microbial community living in our hot spring samples.
|View of Hekla, Iceland. Click image for larger view. |
Image Credit: Aude Herrera.
June 14, 2007: Hekla
Today we are going to explore a different lava flow from Hekla. Comparing the microbial communities inhabiting volcanic rocks from different places around the volcano can help us understand the distribution of microbial communities in the Hekla region. We then can use this knowledge to correlate the distribution with the environmental conditions.
The samples we are collecting today will be analysed by DNA extraction and microbial gene amplification, as with the hot spring. However, the rock samples are totally different from the hot spring samples. Consequently, because of the large diversity of chemically and physically complex samples we will have to analyse, extracting DNA from volcanic samples is technically challenging and we might have to adapt and optimize a method for each sample.
An interesting issue we would like to explore with the volcanic rock samples, and probably also with the rhyolite samples, is to localize the microorganisms inside the rock in order to understand their relation with the rock’s mineral composition and physical conditions. For that, a molecular approach called Fluorescence In-Situ Hybridisation (FISH) recently has been developed to directly visualize microbial cells in their natural environment.
In short, cells are fixed (i.e., the cells are not alive anymore but their DNA and RNA is preserved). The cell wall is made permeable, and this allows introduced nucleic acid probes to reach their targets. The probes are either directly labelled with a fluorochrome or the dye is introduced in a secondary detection step. The samples can then be analysed by epifluorescence or laser scanning microscopy. The classic FISH technique relied solely on rRNA as probe target. The rRNA is an ideal target because it is present in all living cells in relatively high numbers. Furthermore, since it is traditionally used as a phylogenetic marker, a lot of sequence data is available for probe design.
|Prof. Charles Cockell collecting rock samples from Hekla. Click image for larger view. |
Image Credit: Aude Herrera.
Since its origins some 20 years ago, this technique has become an invaluable tool for environmental microbiologists and has spawned numerous variations. The reasons for this popularity are obvious: FISH allows the detection of cells regardless of our ability to grow them in the lab, and detecting cells in-situ provides insight into the structure of microbial communities, and may help unveil their ecological function.
In order to apply this method to our rock samples in the near future, some of our samples have been introduced directly in a formamide solution. This fixes the cells in their natural environments and avoids changing their location inside the rock.
June 15, 2007: Last day in Iceland
Before returning to England, Prof. Steve Self, from the Volcano Dynamics Group at the Open University, desperately wants to show us a few amazing Icelandic sights, such as a canyon where you can enjoy a fantastic view over the Laki lava eruption of 1783.
We are now on the top of the canyon, and the view is even more astonishing than I expected. From here, you can admire the “lava sea” covering a large area. You can imagine hot lava flowing and devastating everything in its way.
|Canyon near the Laki lava eruption, Iceland. Click image for larger view. |
Image Credit: Aude Herrera.
However, as dedicated microbiologists, we were more excited by the microbial traces we found in this environment. At one point, to Prof Self’s dismay, our interest was caught by a strange biofilm growing inside a river near the canyon, and we completely forgot the Laki lava after few minutes! Volcanologists might not even notice the presence of this dirty color in the water.
This sort of thing unfortunately often happens when geologists and microbiologists try to work together. We don’t always speak the same language and don’t see the same things. However, being in the field during this last week has taught me a lot about volcanic rocks. I also enjoyed discovering Iceland; it’s a wonderful place for scientists investigating life’s emergence on Earth. I can’t wait to analyse all the samples we collected — I can almost hear the bacteria inside our rocks calling out to us, ready to reveal all their secrets!
Postscript: Since last June, we have investigated the microbial community living in the obsidian sample collected from the Dómadalshraun lava flow. The DNA extracted from this sample served to amplify the SSU genes that we used like a microbial signature. The sequencing of these genes allowed us to identify the microorganisms present in the sample. The results revealed a diverse eubacterial assemblage inhabiting the obsidian, including a group of unknown bacteria. These microorganisms could potentially form a new bacterial division adapted to live in extreme conditions.
The presence of bacteria living in the obsidian rock also was confirmed by the FISH experiments. By using this technique, we were able to visualise the cells in the interior rock, mainly in the periphery of the cavities and cracks. Other experiments to cultivate the bacteria living in the obsidian rock and investigate their metabolisms are still in progress.