What is Rubisco doing in the deep, dark ocean?

A report published in the 2 September, 2011 issue of Science by Swan et. al suggests that bacteria in the “dark ocean”, meaning depths below 200 m, where no sunlight penetrates, contribute significantly to primary production. Previous studies indicated that carbon fixation at these depths rivals heterotrophic production, and could amount to 15-50% of the primary production that is exported from the surface. Sometimes called “marine snow“, export production is the fraction of primary production that is not metabolized to inorganic carbon by heterotrophs at the surface, but instead drifts down as organic particulates into the deep ocean. This dark ocean primary production is due in part to Crenarchaea that fix carbon via an unusual 3-hydroxypropionate pathway, but the metabolic activity of these archaea seemed inadequate to fully account for the observed rates of carbon fixation.

An international collaboration of scientists from DOE Joint Genome Institute, the Bigelow Laboratory, the Monterey Bay Aquarium Research Institute, the University of Vienna, and MIT used leading-edge single-cell genome amplification and sequencing technologies to characterize the prokaryotic communities in the dark ocean (Figure 1).

Fig. 1 Proportions of bacterial and archaeal single-cell amplified genomes

The bacterial communities at 800 m differed markedly from the surface waters (note the absence of the cyanobacterium Prochlorococcus), but were similar between the North Pacific and South Atlantic research stations. The SAR11 group of bacteria is abundant in both surface waters and deep waters. A recent phylogenomic analysis found that the SAR11 bacteria share a common ancestor with mitochondria (Thrash et al. 2011).

Screening the amplified genomes revealed that at least 12% of the dark-ocean bacteria possess genes for Rubisco. Labeling with carbon-14 bicarbonate showed that at least one of these groups of bacteria with Rubisco genes assimilates inorganic carbon (Figure 3A and 3B).

Fig. 3 Micrographs demonstrating bicarbonate uptake and aggregation around particles by Deltaproteobacteria SAR324.

So what is Rubisco doing in an environment with no light? How can the Calvin cycle operate without the products of the light reactions?

Clearly, these deep-ocean bacteria with Rubisco that assimilate inorganic carbon cannot be photoautotrophs; they must be chemoautotrophs. Most of the bacterial genomes that have genes for Rubisco also have genes for oxidation of reduced sulfur compounds. Like many anoxygenic photosynthetic bacteria, they obtain reducing power from sulfur to reduce NAD+ to NADH and drive the Calvin cycle. They are most likely mixotrophs, obtaining energy and carbon both from metabolism of organic food and from chemoautotrophic fixation of inorganic carbon.

What’s the takeaway? Rubisco is not just for photosynthesis. Rubisco is hard at work even in the deep, dark ocean, running a carbon sink that can help counteract increasing atmospheric carbon dioxide.

Questions for Intro Biology students:

1. Is the oxygenase activity of Rubisco relevant in the dark ocean? Explain.

2. What does the Calvin cycle need to fix carbon dioxide and to regenerate RuBP?

3. How are these bacteria making ATP? Examine Figure 3C – are they most likely running aerobic or anaerobic respiration? Are they making ATP mostly through oxidative phosphorylation or exclusively through substrate-level phosphorylation?

4. Where is the electron transport chain and ATP synthase in these bacteria?


Science Daily – Up from the depths: how bacteria capture carbon in the “twilight zone” http://www.sciencedaily.com/releases/2011/09/110901142054.htm

Swan et al. 2011, Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean. Science 333: 1296-1300 DOI: 10.1126/science.1203690

Thrash et al. 2011, Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific Reports 1: article 13 doi:10.1038/srep00013


About jchoigt

I'm an Associate Professor in the School of Biology at Georgia Tech, and Faculty Coordinator of the Professional MS Bioinformatics degree program.
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