Halothiobacillus neapolitanus c2 is a sulfur oxidizing chemoautotroph that is the model organism for structural and functional studies of carboxysomes. These polyhedral protein "organelles" enhance the carbon sequestration ability of this bacterium.

The aerobic sulfur bacteria Halothiobacillus neapolitanus and Thiomonas intermedia are representatives of two groups of proteobacteria (gamma- and beta-, respectively). Both play important roles in the global biogeochemical carbon and sulfur cycles by virtue of their ability to satisfy their carbon and energy needs entirely with inorganic compounds (CO₂ and reduced sulfur compounds, respectively). Sulfur oxidizers like these are found in a range of different environments, some of which can be classified as "extreme", and have gained notoriety as biological agents that promote corrosion of concrete, acidification of mine tailings, and bioleaching of low-grade ores. They are also being tested in a variety of bioremediation efforts.

Of equal, if not greater, importance for the scientific community at large is their status as model organisms for the study of carboxysomes. These polyhedral "organelles," made up entirely of protein, enhance the catalytic efficiency of the CO₂-fixing enzyme they sequester, ribulose-bisphosphate carboxylase (RubisCO), and thereby play important roles in microbial CO₂ sequestration. Because all cyanobacteria have carboxysomes, and because oceanic cyanobacteria play a dominant role in CO₂ fixation, carboxysomes play a key part in the global carbon cycle. Furthermore, since the recent discovery that homologs of carboxysome genes are found in a large number of heterotrophic bacteria (i.e., bacteria that use complex organic molecules as nutrients), where in most cases they appear to be involved in the catabolism of carbon compounds, research efforts to elucidate the structure/function relationships and mechanisms of action of these "organelles" have intensified. To fully understand the advantages of sequestering RubisCO into carboxysomes, how carboxysome biogenesis is regulated, and to what extent carboxysomes contribute to carbon metabolism, all aspects of carboxysome biochemistry, molecular biology, and genetics must be understood. To gain such comprehensive understanding, researchers must know the entire gene complement of these organisms. A complete genome will aid in elucidating regulatory strategies of carbon metabolism, integration of carbon and energy-generating sulfur metabolism, and other metabolic aspects relevant to the biology of H. neapolitanus and T. intermedia.