Tuesday, July 31, 2012

Carbon Dioxide Fixation in the Dark Ocean

Cells require both a source of energy and a source of building blocks for synthesis of organic (carbon-containing) molecules. Some of the most interesting species are those that only need inorganic molecules to survive. They can make all their carbon compounds from carbon dioxide (CO2) by "fixing" it into more complex molecules like sugars.

These species are called "autotrophs'" The most familiar are the plants. As most of you know, plants can grow quite successfully in a glass of water (with minerals). Animals are the most obvious example of "heterotrophs," species that need to be supplied with complex organic molecules in order to survive. We can't survive on water alone. We need to get sugars and a host of other compounds from eating other (mostly dead) species.

Plants and algae are autotrophs that get much of their energy from light. Photosynthesis is the process where light energy is converted to chemical energy in the form of ATP and other "high energy" cofactors. Plants and algae are called "photoautotrophs" because they combine the ability to fix carbon dioxide with the ability to use light as a source of energy.

Most people think that these two processes are closely linked. They have been taught that photosynthesis is the process where light energy is used to fix CO2 to make carbohydrates (sugars). That's not correct (see: The Photosynthesis Song and a Pet Peeve ).1

There are many species that can efficiently fix CO2 but can't carry out photosynthesis. They get their energy from the oxidation of inorganic molecules like hydrogen (H2), iron (Fe2⊕), nitrite (NO2), hydrogen sulfide (H2S), or sulphur (S). These species are called "chemoautotrophs" and they are very interesting organisms because the first forms of life were probably chemoautotrophs.

Chemoautotrophs can survive in the dark. They are common in the deep ocean below 200m where light does not penetrate. That's probably where life began.

Swan et al. (2011) were interested in how these dark ocean bacteria fix carbon dioxide. There are many possibilities but it has been difficult to study their biochemistry because most of the deep ocean species can't be cultured in the lab.

Swan et al. decided to isolate single cells from the deep ocean and sequence parts of their genomes to see what enzymes they could make. It turns out that many of these species use the Calvin cycle, the same pathway used by plants, algae, and photosynthetic bacteria (Calvin cycle). The chemoautrophic bacteria use energy supplied by oxidation of inorganic molecules and CO2 fixation by rubisco (ribulose 1,5-bisphosphate carboxylase-oxygenase) [Fixing Carbon: the Rubisco Reaction].

Rubisco and the Calvin cycle evolved long before photosynthesis. Carbon dioxide fixation to produce sugars does not require photosynthesis. Furthermore, in photosynthetic bacteria and algae most of the energy captured from sunlight is used to make nucleic acids, proteins, and lipids, not carbohydrates.

It's about time we stopped thinking of photosynthesis as a pathway for the production of carbohydrates.


1. Potato plants use light energy to make ATP, which is then used to make glucose, which is then stored in the roots as starch. Thus, poutine is an excellent source of light energy.

[Photo Credits: (top) Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. page 463 [Pearson: Principles of Biochemistry 5/E]
(bottom) Ocean Explorer: Chemoautotrophic whale-fall community, including bacteria mats, vesicomyid clams in the sediments, galatheid crabs, polynoids, and a variety of other invertebrates. The 35-ton gray whale was originally implanted on the sea floor at 1,674 m depth in the Santa Cruz Basin in 1998. This image was captured six years later by Craig Smith from the University of Hawaii. Image courtesy of Craig Smith, University of Hawaii.

Swan, B.K., Martinez-Garcia, M., Preston, C.M., Sczyrba, A., Woyke, T., Lamy, D., Reinthaler, T., Poulton, N.J., Masland, E.D., Gomez, M.L., Sieracki, M.E., DeLong, E.F., Herndl, G.J., and Stepanauskas, R. (2011) Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296-1300. [PubMed] [DOI: 10.1126/science.1203690]

1 comment:

  1. I have been reading your blog for a couple of years now. I always find something of interest here and always find the biochem articles interesting and informative. So thanks for that. Articles such as this refute at least to some extent your own contention that distance learning would be inadequate. Where will most people get this sort of mini-education otherwise? The comments add to the value at times. Certainly this doesn't duplicate the classroom experience, but for many of us it is the only possibility of contact with an expert in the field.

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