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Discover the Earth:Live microorganisms in a geological layer from 460,000 years ago

The scientific drilling vessel CHIKYU recovered samples from a subseafloor geological layer dating back 460,000 years, off the coast of Hachinohe on the Shimokita Peninsula. The microorganisms in these samples were found to be living. At the time these microorganisms were discovered it was extremely difficult to investigate their living activities, making it impossible to determine whether they were alive or not. However, Dr. Yuki Morono, a senior scientist at the Kochi Institute for Core Sample Research’s Geomicrobiology Group, together with his colleagues, has been able to demonstrate for the first time —using a nano-scale secondary ion mass spectrometer (NanoSIMS)—that these subseafloor microorganisms taking up nutrients.
(Published in April 2012)

Dr. Yuki Morono Interviewee:
Dr. Yuki Morono
Senior Scientist
Geomicrobiology Group
Kochi Institute for Core Sample Research

Saving energy for survival

 It has become clear that many microorganisms live just under the subseafloor in the deep ocean. There are considerably more of these microorganisms under the seafloor than on the surface of the earth that we inhabit; it is said that nearly one-third of all living creatures on earth exist below the sea floor. However, very little has been known about the nature of these subseafloor microorganisms and their activities. Moreover, it was not even known whether these microorganisms were alive when they were discovered in a subseafloor geological layer dating back 460,000 years ago, off the coast of Hachinohe on the Shimokita Peninsula. However, Dr. Morono and his colleagues managed to verify that the microorganisms were indeed taking up glucose and other nutrients, and also undergoing division, thereby demonstrating that they are alive. “We have been assuming that majority were probably dead or in extremely starved dormant state” Dr. Morono explains, “but in fact we found that 76% of them could take up nutrients we fed.”

Percentage of microorganisms taking up various nutrients and the number of cell divisions. A maximum of 76% of the microorganisms were taking up nutrients (when glucose and ammonia are included).   NanoSIMS image of cell that has taken up glucose labeled with stable carbon isotope (13C). The amounts taken up are shown in different colors.

Percentage of microorganisms taking up various nutrients and the number of cell divisions. A maximum of 76% of the microorganisms were taking up nutrients (when glucose and ammonia are included).

 

NanoSIMS image of cell that has taken up glucose labeled with stable carbon isotope (13C). The amounts taken up are shown in different colors.

 It was found that the rate at which these microorganisms take up nutrients is very slow (less than one ten-thousandth the rate of Escherichia coli) and their metabolism also proceeds at a slow pace. “Subseafloor microorganisms are at the very edge between life and non-life,” Dr. Morono points out. “They are in a state of metabolic activity lower than that of animals in hibernation. They are thought to have survived by dividing at an extremely slow rate—only about once every thousand or ten thousand years.” There are almost no nutrients below the seafloor. It is a very harsh environment for living organisms, with high pressure and a low temperature. For microorganisms to survive in such an environment they must minimize their metabolism, using as little energy as possible.

 In comparing the uptake of carbon and nitrogen, two essential elements for sustaining life, it was found that the ratio of incorporation of nitrogen into subseafloor microorganisms exceeded the ratio for carbon in vitro condition. Nitrogen is necessary for life, but its uptake requires energy. Microorganisms that need to conserve energy would find it difficult to expend energy in order to take up nitrogen, as Dr. Morono explains: “Nitrogen uptake is suppressed below the seafloor since microorganisms are in a starved state, then the uptake activity was stimulated by the addition of energy-generating substrates.” Microorganisms, in this manner, control their nitrogen uptake and conserve energy in order to survive.

Images were created from the results of NanoSIMS analysis in which uptake of glucose labeled with stable carbon isotope (13C) is shown in red and uptake of ammonia labeled with stable nitrogen isotope (15N) is shown in green. These images are superimposed here.   In the image to the left of the graph above, the uptakes of carbon and of nitrogen by each of the cells (surrounded by the white dotted lines) is indicated. The graph shows that the percentage of nitrogen uptake is high in all of the analyzed cells (positioned in lower right of graph). This means that much nitrogen was taken up when microorganisms are placed in a test tube containing energy-generating nutrients. From this we can surmise that the native environment is nitrogen-poor. However, a considerable amount of nitrogen actually exists, as ammonium, in the subseafloor environment, raising the question of why the microorganisms do not take up this nitrogen? Because a living organism requires energy in order to incorporate ammonium in their metabolic pathway, Dr. Morono speculates that the subseafloor microorganisms suppress nitrogen incorporation as a means of conserving their energy.

Images were created from the results of NanoSIMS analysis in which uptake of glucose labeled with stable carbon isotope(13C)is shown in red and uptake of ammonia labeled with stable nitrogen isotope (15N)is shown in green. These images are superimposed here.

 

In the image to the left of the graph above, the uptakes of carbon and of nitrogen by each of the cells (surrounded by the white dotted lines) is indicated. The graph shows that the percentage of nitrogen uptake is high in all of the analyzed cells (positioned in lower right of graph). This means that much nitrogen was taken up when microorganisms are placed in a test tube containing energy-generating nutrients. From this we can surmise that the native environment is nitrogen-poor. However, a considerable amount of nitrogen actually exists, as ammonium, in the subseafloor environment, raising the question of why the microorganisms do not take up this nitrogen? Because a living organism requires energy in order to incorporate ammonium in their metabolic pathway, Dr. Morono speculates that the subseafloor microorganisms suppress nitrogen incorporation as a means of conserving their energy.