Beyond the Calvin cycle: autotrophic carbon fixation in the ocean.

@article{Hgler2011BeyondTC,
  title={Beyond the Calvin cycle: autotrophic carbon fixation in the ocean.},
  author={Michael H{\"u}gler and Stefan M. Sievert},
  journal={Annual review of marine science},
  year={2011},
  volume={3},
  pages={
          261-89
        }
}
Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out… 
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References

SHOWING 1-10 OF 194 REFERENCES
Autotrophic carbon fixation in archaea
TLDR
The diverse carbon fixation mechanisms that are found in archaea differ fundamentally from those of the well-known Calvin cycle, and their distribution mirrors the phylogenetic positions of the archaeal lineages and the needs of the ecological niches that they occupy.
Something from almost nothing: carbon dioxide fixation in chemoautotrophs.
TLDR
The last decade has seen significant advances in the understanding of the physiology, ecology, and molecular biology of chemoautotrophic bacteria, and the Calvin-Benson-Bassham cycle, characterized by three unique enzymatic activities: ribulose bisphosphate carboxylase/oxygenase, phosphoribulokinase, and sedoheptulosebisphosphatase.
Resourceful heterotrophs make the most of light in the coastal ocean
TLDR
In coastal systems, these mixed metabolic strategies have implications for how efficiently organic carbon is retained in the marine food web and how climatically important gases are exchanged between the ocean and the atmosphere.
Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota
TLDR
Analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism substantiate the likely global metabolic importance of Cren archaeal importance with respect to key steps in the biogeochemical transformation ofcarbon and nitrogen in marine ecosystems.
Abundance of Reverse Tricarboxylic Acid Cycle Genes in Free-Living Microorganisms at Deep-Sea Hydrothermal Vents
TLDR
Diversity, similarity matrix, and phylogenetic analyses of cloned samples and amplified gene products from autotrophic enrichment cultures suggest that the majority of autotrophs that utilize the reverse tricarboxylic acid cycle are members of the epsilon subdivision of Proteobacteria.
Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations
TLDR
This study demonstrated that there are important differences in the carbon dioxide and nitrogen fixation mechanisms among bioleaching bacteria that coexist in mining environments and provided an analysis of the potential regulatory pathways and functional networks that control carbon and nitrogenfixing in these microorganisms.
Contribution of Aerobic Photoheterotrophic Bacteria to the Carbon Cycle in the Ocean
The vertical distribution of bacteriochlorophylla, the numbers of infrared fluorescent cells, and the variable fluorescence signal at 880 nanometers wavelength, all indicate that photosynthetically
Autotrophic Carbon Dioxide Assimilation in Thermoproteales Revisited
TLDR
It is concluded that the dicarboxylate/4-hydroxybutyrate cycle is operating in CO(2) fixation in the strict anaerobic Thermoproteales as well as in Desulfurococcales.
Deciphering the evolution and metabolism of an anammox bacterium from a community genome
TLDR
This work uses environmental genomics—the reconstruction of genomic data directly from the environment—to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community, and identifies candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism.
Carbohydrate Metabolism and Carbon Fixation in Roseobacter denitrificans OCh114
TLDR
The first metabolic studies on carbohydrate utilization, CO2 assimilation, and amino acid biosynthesis in the phototrophic Roseobacteria clade bacterium Roseobacter denitrificans OCh114 are reported, and isoleucine can be synthesized from both threonine-dependent and citramalate-dependent pathways using pyruvate as the sole carbon source.
...
1
2
3
4
5
...