Probing the depths of the biosphere

Rarely do I read papers whose title really sums up exactly what is so cool about the study in a succinct way, free of jargon. I think that "First Investigation of the Microbiology of the Deepest Layer of Ocean Crust" does just that. It isn't trying to be sexy... it just is!

Examining the microbial communities in the so-called "deep subsurface biosphere" is a relatively new field. Until recently people didn't think there was much, or really any, life deep in Earth's crust. As with many scientific assumptions made before scientists had the opportunity to actually study a new environment... these were clearly wrong!

If you will allow a slight non-microbial tangent... in the mid 19th century Edward Forbes noticed that organisms appeared to become "impoverished" with depth. This led him to postulate the notorious Azoic Theory that there was an ocean depth (300 fathoms or about 550 meters) below which, no life was possible. This hypothesis was logical given what was known at the time about ecological zonation and the deep sea, but has since been disproven time and time again. But I digress...

Often, initial studies of microbial diversity in previously uncharacterized environments discover, roughly, who is present. This is, of course, useful information, but it is limited since more than 99% of all microbes have not been grown in the lab (and we therefore know virtually nothing about them). This means that simply documenting which microbes are present in a new environment doesn't explain much about what is happing in these ecosystems. The study I am writing about today goes a step farther and also looks at what metabolic genes are present. Metabolic genes are genes that code for proteins that are involved in specific chemical reactions that are part of specific metabolic pathways. One example (found in these samples) is mmo. mmo is the code for methane monooxygenase, which is an enzyme that breaks the carbon-hydrogen bond in methane, allowing it to be oxidized (forming carbon dioxide). This type of information allows insights about what the microbial community might be doing. I say might because the presence of a gene doesn't, necessarily, mean that it is active, but that is a story for another day.

Oceanic crust covers about 70% of Earth's surface, and most of it is made of a relatively low silica rock, black called Basalt. For this study basalt samples were collected from below the Atlantis Massif at depths up to almost 1400 meters below the sea floor (mbsf) on an Integrated Ocean Drilling Program (IODP) cruise. At their deepest sample (1392 mbsf) the temperature was 102°C, which is approaching the known upper limit to life (currently accepted as around 122°C). This temperature is simply due to the heat conduction from Earth's core. One of the reasons this type of study has not been completed until now is the technical difficulties associated with drilling this deep into the crust. This type of drilling is technically similar to the drilling done for offshore oil, but is done at a much smaller scale and therefore has many fewer environmental consequences.

The study concluded that these rock samples were fairly low in bacterial diversity (compared with previous analyses of shallower rocks of the same type from other areas), and very little evidence of Archaea. Diversity was correlated with how much "alteration" the rock had undergone. Rock alteration is a geologic term that refers to changes in rock composition due to heat, pressure, and other chemical processes. More altered samples tended to have higher diversity, implying that something about the alteration process opens up new niches for microbial colonization.

The study reached some interesting conclusion about the types of microbes that were present. They found that many seemed to be more closely related to hydrocarbon degrading microbes (know from non-crustal environments) than they were to other microbes known from similar crustal rock. This may offer insight into unanswered questions about how widespread these organisms are, and the extent to which the crustal reservoir interacts with the overlying ocean waters.

To further support this, genes know to be involved in hydrocarbon degradation were found in these rock samples. Genes involved in aerobic methane oxidation as well as methane production (interestingly in roughly equal frequencies... possibly implying that these processes are coupled; one type of microbe producing methane, and another type breaking it down). The carbon fixation genes might also tie in here, because methane is broken down into carbon dioxide, which is then converted into organic materian during carbon fixation. Carbon fixation is an autotrophic process is typically thought of in terms of photosynthesis, but in the deep sea it is not photosynthesis, but chemosynthesis (specifically chemolithoautotrophy - this just means they make their own food from an inorganic carbon source, without light, and without releasing oxygen) that is responsible for the conversion of inorganic carbon (carbon dioxide) into sugars (which later become food for other deep sea organisms that can't make their own food).

These processes are particularly interesting to me because the role of the deep sea in the global carbon cycle is unknown, and knowing the extent and rates of processes like this would help us to better understand what impact the deep sea has on this cycle (how big of a carbon sink is it, for example).

Finally aerobic toluene oxidation genes were also found in some of the samples. With the diversity and phylogenetic analyses, the presence of toluene and methane oxidation genes implies that hydrocarbon oxidation is occurring in the deep subsurface. Genes involved in carbon fixation were also found.

While this study is a very early look into this environment, it is one of the first steps into trying to understand the role that crustal communities play in global biogeochemical cycles. Because this environment represents an immense volume it is important that we better understand the virtually unknown microbial communities present there. The authors also point out that given the recent discovery of methane being produced on Mars and the fact that it is unknown whether or not that is biological in origin, the subsurface environment on Earth may be an important analog site.

The authors (one of whom I got to meet at a recent conference) conclude with the following:

Our results raise the intriguing possibility that hydrocarbons in very deep ocean rocks support microbial communities. Additionally, we show that the genetic potential for novel metabolic processes, such as carbon and nitrogen fixation, is present within an unexplored layer of ocean crust. Our findings, particularly regarding the presence of genes coding for methane cycling, have implications not only for Earth's subsurface, but also for other planets such as Mars. Methane on Mars is concentrated in some equatorial regions of the atmosphere, which suggests that it is derived from localized geological sources. Although the exact mechanism by which methane forms on Mars is not known, serpentinization reactions in the Martian subsurface have recently been proposed. Therefore, similar to the Atlantis Massif, the Martian subsurface may harbor methane-consuming prokaryotes. Future efforts should be directed towards quantifying the role endolithic prokaryotes play in methane cycling and in determining the sources of methane, and other hydrocarbons in marine crust. These findings will undoubtedly focus attention on obtaining more information on the geochemistry of formation fluids from deep ocean rocks, which are technically challenging to acquire requiring different sampling technologies than those used in the design of this exploratory study.

Mason OU, Nakagawa T, Rosner M, Van Nostrand JD, Zhou J, et al. 2010 First Investigation of the Microbiology of the Deepest Layer of Ocean Crust. PLoS ONE 5(11): e15399. doi:10.1371/journal.pone.0015399

This article is available freely (!) online here


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Sweet! Quick question though - what percentage of these DNA sequences can't be aligned with any known genes? I mean, are these guys just using known metabolic processes in a different environment or are there new enzymes out there that we know absolutely nothing about?

Considering we know almost nothing about the microbes that inhabit our own guts, it's pretty incredible that we're starting to scratch the surface of these mostly inaccessible microbial communities.

Kevin, that's a great question. However, this study can't provide an answer because they didn't sequence all of the DNA from the samples. As I am sure you know, that's called Metagenomics, and is something I will certainly write more about in the future because its the kind of work we do in my lab. In this study they used a microarray (called GeoChip) which had probes for all sorts of known relevant environmental genes on it. They add their samples to the chip, see where parts of their DNA binds with the probes, and know that gene is present in their sample. Because of this, there really isn't any information about the quantity of genes with unknown function.