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Dark Carbon Fixation in the Columbia River’s Estuarine Turbidity Maxima: Molecular Characterization of Red-Type cbbL Genes and Measurement of DIC Uptake Rates in Response to Added Electron Donors

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Abstract

Dark CO2 fixation has been shown to rival the importance of oxygenic photosynthesis in the global carbon cycle, especially in stratified environments, such as salt wedge estuaries. We investigated this process in the Columbia River estuary using a variety of techniques including functional gene cloning of cbbL (the large subunit of form I RuBisCO), quantitative real-time PCR (qPCR) estimations of cbbL abundance, and analyses of stimulated 14C-bicarbonate assimilation. A diversity of red-type cbbL genes were retrieved from clone libraries, with 28 unique operational taxonomic units determined from 60 sequences. The majority of the sequences formed two clusters that were distinct from the major clusters typically found in soil environments, revealing the presence of a unique community of autotrophic or facultatively autotrophic/mixotrophic microorganisms in the Columbia River estuary. qPCR estimates indicated that roughly 0.03–0.15 % of the microbial population harbored the cbbL gene, with greater numbers of total bacteria and cbbL gene copies found in the estuarine turbidity maxima (ETM) compared to non-ETM events. In vitro incubations with radiolabeled bicarbonate indicated maximum stimulation by thiosulfate and also suggested that a diversity of other potential electron donors may stimulate CO2 fixation, including nitrite, ammonium, and Mn(II). Taken together, these results highlight the diversity of the microbial metabolic strategies employed and emphasize the importance of dark CO2 fixation in the dynamic waters of the Columbia River estuary despite the abundance of organic material.

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Acknowledgments

The authors would like to thank the captains and crews of the R/V Barnes and R/V Forerunner for assistance with sampling. We thank the chief scientists, especially Lydie Herfort and Byron Crump, as well as the computer analysts who gave us insight into predicting and capturing samples during ETM events. We also thank Dr. Anne Pohlman and Dr. Bärbel Friedrich of Humboldt-Universität zu Berlin for their generous donation of Ralstonia eutropha H16 cultures. We also thank R. Davis for helpful discussion of RuBisCO genes. Partial support was provided through the following National Science Foundation, Division of Ocean Sciences grants: The Science and Technology Center for Coastal Margin Observation and Prediction (0424602) awarded to A. Baptista and an Ocean Sciences Postdoctoral Fellowship (0935270) awarded to S. Bräuer. Support to B. Tebo was provided by an Oregon Opportunity grant and grant no. P42ES010337 from the National Institute of Environmental Health Sciences (NIEHS).

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Authors and Affiliations

  1. Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 286080-2027, USA

    S. L. Bräuer & N. Goodson

  2. Center for Coastal Margin Observation & Prediction and Division of Environmental & Biomolecular Systems, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, OR, 97006, USA

    S. L. Bräuer, K. Kranzler, D. Murphy, H. M. Simon, A. M. Baptista & B. M. Tebo

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  1. S. L. Bräuer
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  2. K. Kranzler
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  3. N. Goodson
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  4. D. Murphy
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  5. H. M. Simon
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  6. A. M. Baptista
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  7. B. M. Tebo
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Correspondence to S. L. Bräuer.

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Bräuer, S.L., Kranzler, K., Goodson, N. et al. Dark Carbon Fixation in the Columbia River’s Estuarine Turbidity Maxima: Molecular Characterization of Red-Type cbbL Genes and Measurement of DIC Uptake Rates in Response to Added Electron Donors. Estuaries and Coasts 36, 1073–1083 (2013). https://doi.org/10.1007/s12237-013-9603-6

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  • DOI: https://doi.org/10.1007/s12237-013-9603-6

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