Candidatus ruthia magnifica

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A Microbial Biorealm page on the genus Candidatus ruthia magnifica


Higher order taxa

Bacteria(Kindgdom); Proteobacteria(Phylum); Gammaproteobacteria(Class); sulfur-oxidizing symbionts(order)[1].


NCBI: Taxonomy

Candidatus Ruthia magnifica

Description and significance

R. magnifica is a chemoautotrophic bacteria that lives symbiotically in the gut of a giant clam, the Metazoan Calyptogena magnifica. It lives in an environment that may be characterized as a hydrothermal vent. It uses the chemical energy of reduced sulfur emanating from vents to provide its host with carbon and a large array of additional necessary nutrients such as essential amino acids and vitamins.[2] In return, the hosts provide the bacteria with inorganic substrates necessary for chemoautotrophic activity. R. magnifica itself lives in the gut and ciliary food groove of C. magnifica.[2] The sequencing of the R. magnifica genome is important in determining its metabolism and the compounds it is able to produce, which in turn, will give insight into the metabolism and biology of the host. R. magnifica is the first intracellular, sulfur-oxidizing endosymbiont to have its genome sequenced. It also has the largest genome of any intracellular symbiont sequenced to date and may represent an early intermediate in the evolution toward a chemoautotrophic organelle such as a chloroplast.[2]

Genome structure

R. magnifica has 1,248 genes. A single circular chromosome contains genes which are predicted to encode all the proteins necessary for all the metabolic pathways typical of free-living chemoautotrophs. Some of the major pathways are carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis.[2]

Cell structure and metabolism

Because the environment of R. magnifica cannot be replicated in the laboratory, culturing the organism is difficult; therefore, its cell structure and cellular components remain largely unknown. However, because the endosymbiont's genome can be sequence via environmental shot gun sequencing, much of its metabolic pathways are elucidated.R. magnifica fixes carbon through the Calvin Cycle, with its genome encoding RuBisCo and phosphoribulokinase. R. magnifica gains energy by sulfur oxidation through the expression of sox(sulfur oxidation) and dsr (dissimilatory sulfite reductase) genes. When there is no environmental sulfur available, it may oxidize its sulfur granules through the use of dsr homologs. R. magnifica has the potential to produce 20 amino acids and 10 vitamins and cofactors. The genome encodes a complete glycolytic pathway and the nonoxidative branch of the pentose phosphate pathway. It also encodes a tricarboxylic acid (TCA) cycle, but lacks a critical enzyme needed to break down a substrate in the cycle called alpha-ketoglutarate dehydrogenase. The lack of this enzyme has been suggested to indicate obligate autotrophy in other bacteria, allowing them to fix carbon dioxide when no other substrates are available as a carbon source. In order to gain energy via reduction, R. magnifica uses an electron transport chain that is relatively simple when compared to other microbes. It is thought that a reduced quinone transfers electrons to cytochrome c upon being oxidized via a bc1 complex, and a terminal cytochrome c then transfers these electrons to oxygen, when and if available. The energy derived from the transfer of electrons can be stored in the form of an NADH molecule. The R. magnifica genome also encodes proteins that are necessary for two nitrogen assimilation pathways. Nitrate and ammonia are transported inside the cell through the nitrate or nitrite transporter, respectively. Those compounds are then reduced via nitrate and nitrite reductase enzymes and incorporated into the cell via glutamine synthetase and glutamate synthase. R. magnifica not only uses nitrogen available from the vents, it also recycles the host's amino acid waste.[2]


R. magnifica lives in the gill tissues of C. magnifica and is transmitted vertically between generations through the clam’s eggs[3]. R. magnifica provides nutrition for its host, C. magnifica, by oxidizing sulfur in hydrothermal vents[2]. Because R. magnifica can fix carbon through the Calvin cycle, environmental carbon dioxide can be converted into a more bioavailable form that can be distributed throughout the environment when R. magnifica is eventually digested by its host [7]. Also, the assimilation of nitrate from the vents into amino acids provides its host with structural components for its proteins. R. magnifica uses an oxidized form of nitrogen that the host would not be able to use without its endosymbiont. Similarly, because C. magnifica cannot use a reduced form of sulfur such as hydrogen sulfide or the elemental form of sulfur available at the vents, R. magnifica allows its host to survive by metabolizing a compound that would not normally be used.


Due to its need for sulfur and its niche of hydrothermic vents, it is not likely to find R. magnifica in the same environment as humans. Therefore, it is not considered a pathogen and is not currently thought to cause any disease.

Application to Biotechnology

No known compounds that are useful to biotechnology are produced by R. magnifica.

Current Research

In 2003, Hortado et al. were questioning whether R. magnifica was laterally passed down from generation to generation through the egg, or if horizontal transfer occurred, where R. magnifica is taken up by the clam from the environment. The results from their experiments strongly supported the former hypothesis where lateral gene transfer occurs. Because the endosymbiont is passed on from generation to generation, it may serve as a model for the origin and evolution of eukaryotic organisms[4].

Also in 2003, Pruski et al. used C. magnifica in addition to Bathymodiolus thermophilus and Riftia pachyptila in order to find which molecules regulate the different mechanisms that are are needed for the storage and transport of sulfur. Because sulfur is a toxin to aerobic respiration, there need to be mechanisms to sequester it so that it does not interfere with aerobic respiration. Two compounds, named thiotaurine and hypotaurine, were found to be candidates in supporting a general role for sulfide metabolism in hydrothermal vent symbiotic organisms. Their precise function as to whether they transport the sulfur or aid in its storage, however, remains to be elucidated [5].

In 1998, Hart et al. used the strontium/calcium concentration of C. magnifica shells to document The East Pacific Rise 1991 and 1992 eruptive events, as well as other eruptions in the 1970s and 80s. The varying concentrations of strontium and calcium in relation to how far they were from the center of the shell provided a timeline of the events. The shells of the C. magnifica have been found to be a valuable tool in allowing the history of hydrothermal vent activity to be seen and documented [6].


[1]] NCBI Taxonomy

[2] LG Newton, T. Woyke, "The Calyptogena magnifica Chemoautotrophic Symbiont Genome". Science. 2007. Volume 315. p. 998.

[3] C. M. Cavanaugh, J. J. Robinson, "vertical transmission of chemoautotrophic symbionts". biol. bull. 1996. volume 190. p. 195.

[4] Luis A. Hurtado, Mariana Mateos, Richard A. Lutz and Robert C. Vrijenhoek "Coupling of Bacterial Endosymbiont and Host Mitochondrial Genomes in the Hydrothermal Vent Clam Calyptogena magnifica" APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 2003, Vol. 69, No. 4 p. 2058–2064

[5] Pruski AM, Fiala-Médioni A. "Stimulatory effect of sulphide on thiotaurine synthesis in three hydrothermal-vent species from the East Pacific Rise". J Exp Biol. 2003 Sep;206(Pt 17):2923-30.

[6] Stanley R. Hart, Jerzy Blusztajn, "Clams As Recorders of Ocean Ridge Volcanism and Hydrothermal Vent Field Activity" Science 8 May 1998: Vol. 280. no. 5365, pp. 883 - 886

[7] A. Fiala-Médioni, C. Métivier, A. Herry, M. Le Pennec, Mar. Biol. 92, 65 (1986)

Edited by Albert Noniyev, student of Rachel Larsen and Kit Pogliano