An Ecosystem in Deep, Ancient Mud
Scientists have found microorganisms, including archaea, bacteria and eukaryotes, living more than 500 feet beneath the ocean floor in sediment estimated to be 5 million years old. The team identified the organisms by studying messenger RNA (mRNA) in samples collected in 2002 off the coast of Peru during Leg 201 of the Ocean Drilling Program. The study marks the first time that total mRNA, or the “metatranscriptome,” was successfully extracted from the deep biosphere. mRNA in living cells delivers information from DNA to ribosomes, which is a critical step in the production of proteins necessary for life. When cells die, mRNA quickly degrades. This means that the presence of mRNA in samples indicates that organisms are alive and functioning.
The research team identified members of all three domains of life – archaea, bacteria, and eukaryotes (specifically fungi). They also found evidence of cell division in all three of these domains. Previously, scientists have suggested that organisms in the deep subsurface were trapped there long ago and survive only by repairing damage. However, the new study shows that these organisms are actively dividing and creating new cells.
Finally, evidence indicates that some of the mRNA in samples is coding for enzymes used by cells in sulfate reduction and nitrate reduction. These are processes that cells can use to generate energy in the absence of sunlight. Sulfate reduction has been seen in the deep subsurface before, but the new research shows that nitrate reduction may also be significant in these environments.
“This type of examination shows active cells. We knew that all of these cells were buried, but we didn’t know if they were doing anything.”
– Jennifer F. Biddle (co-author), assistant professor of marine biosciences, University of Delware College of Earth, Ocean, and Environment
Some facts about the deep biosphere:
“Until recently, the fungi in deep sediments have been ignored. The fact that fungi are metabolically active in deep sediments refines our understanding of the extent of the deep biosphere.”
– William (Bill) Orsi (lead author), Woods Hole Oceanographic Institution
Why is this research important to Astrobiology?
Studying how life survives in isolated, extreme environments on Earth is a primary goal of the Astrobiology Program at NASA. The evolutionary mechanisms that cells use to live in the deep subsurface, and independent from the Sun’s energy, can teach us a great deal about the potential for life in beneath the surface of other worlds.
Where can you read more about this research?
The paper, "Gene expression in the deep biosphere," was published in the journal Nature under lead author William D. Orsi, doi:10.1038/nature12230. Click here to view the abstract.
Astrobiology Magazine contacted lead author William Orsi of the Woods Hole Oceanographic Institution and co-author Jennifer Biddle of the University of Delaware with some additional questions:
Astrobiology Magazine (AM): Was 500 feet (below the sea floor) the final drilling depth for the 2002 ODP drilling off the coast of Peru, or was this greatest depth at which you found evidence of microbial communities?
William Orsi: This was just the deepest cores we analyzed. The sediments at this site are actually miles thick.
Jennifer Biddle: The drilling at this site went all the way to basalt, and microbes were seen along the entire depth. We went to 159 meters only due to funding limitations for this study!
AM: Are you performing the same analysis on samples from other drilling efforts?
William Orsi: Additional analyses of the same type are currently being done by Jennifer Biddle’s graduate student Joseph Russell from the recent drilling cruise to the Iberian margin.
Jennifer Biddle: Yes, we are currently comparing a site on the Iberian Margin that should be a good comparison to Site 1229 on the Peru Margin.
AM: Do you think the results of this research bode well for life’s potential below the seafloor of oceans on other worlds like Jupiter’s moon Europa?
William Orsi: Yes, I think so. Our work shows that life is still thriving even after being isolated from the surface world for millions of years.
Jennifer Biddle: One of the very surprising thing that happened is that life in this environment depends a great deal on previously fixed organic carbon. So it raises the question, what potential is there for carbon cycling on Europa? We still have many questions, the least of which is how cells colonize the subseafloor – I think it’s too soon to say anything definitive on Europa, except that we need to think of how carbon and nitrogen work on planets without photosynthesis.
AM: Have you ever come across environments in your work where life on Earth does not find a way to survive?
Jennifer Biddle: Yes, at the hydrothermal vents of Guaymas Basin, we never saw life above 100-ish degrees C. Most other places, there is something!
William Orsi: Yes – in hydrothermal systems where temperatures reach over ~130 degrees Celsius there is no life found anymore.
AM: What form of contamination control did you employ to ensure that foreign material did not enter samples from the drill core during the retrieval process?
Jennifer Biddle: These cores were collected using microbead techniques and chemical tracers. There’s a good indication that none of these entered the core (see House et al. 2003, Smith et al. (2000)*). As far as the molecular study, we always run lab controls – those were all clean in our tests. It’s definitely a hard part about this work to avoid all the microbes in the air and on surfaces, and even in reagents. This is why we were very excited to see the good correlations with porosity and depth, it’s helpful confirmation we are seeing a correct signal.
William Orsi: During the coring process there are fluorescent microbeads that are a put into the drilling apparatus to see if any of the beads are visible inside of the cores. Also, we do all of our mRNA extractions on "blanks" as well as experimental samples. The blank is an extraction that is done on the sterile water that we are using in the extraction protocol. We validated that no mRNA was amplifiable from the blank, and thus we are confident that contamination was reduced to levels insignificant for the mRNA amplification protocol that we used.
*House, CH et. al. (2003). Drilling contamination tests during ODP Leg 201 using chemical and particulate tracers. Proceedings of the Ocean Drilling Program, Initial Reports Volume 201
Smith, D.C. et. al. (2000) Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiology Journal, 17:207–219.
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