Chlamydomonas reinhardtii is a single celled green alga about 10 micrometres in diameter that swims with two flagella. It has a cell wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid, and an "eyespot" that senses light.
Although widely distributed worldwide in soil and fresh water, C. reinhardtii is primarily used as a model organism in biology in a wide range of subfields. When illuminated, C. reinhardtii can grow in media lacking organic carbon and chemical energy sources, and can also grow in the dark when supplied with these. C. reinhardtii is also of interest in the biopharmaceuticals field and the biofuel field, as a source of hydrogen.
The species has been spelled several different ways because of different transliterations of the name from Russian: reinhardi, reinhardii and reinhardtii all refer to the same species, C. reinhardtii Dangeard.
Model organism 
- How do cells move?
- How do cells respond to light?
- How do cells recognize one another?
- How do cells generate regular, repeatable flagellar waveforms?
- How do cells regulate their proteome to control flagellar length?
- How do cells respond to changes in mineral nutrition? (nitrogen, sulfur etc.)
There are many known mutants of C. reinhardtii. These mutants are useful tools for studying a variety of biological processes, including flagellar motility, photosynthesis or protein synthesis. Since Chlamydomonas species are normally haploid, the effects of mutations are seen immediately without further crosses.
In 2007, the complete nuclear genome sequence of C. reinhardtii was published.
Channelrhodopsin-1 and Channelrhodopsin-2, proteins that function as light-gated cation channels, were originally isolated from C. reinhardtii. These proteins and others like them are increasingly widely used in the field of optogenetics.
Vegetative cells of the reinhardtii species are haploid with 17 small chromosomes. Under nitrogen starvation, haploid gametes develop. There are two mating types, identical in appearance and known as mt(+) and mt(-), which can fuse to form a diploid zygote. The zygote is not flagellated, and it serves as a dormant form of the species in the soil. In the light the zygote undergoes meiosis and releases four flagellated haploid cells that resume the vegetative life cycle.
Under ideal growth conditions, cells may sometimes undergo two or three rounds of mitosis before the daughter cells are released from the old cell wall into the medium. Thus, a single growth step may result in 4 or 8 daughter cells per mother cell.
The cell cycle of this unicellular green algae can be synchronized by alternating periods of light and dark. The growth phase is dependent on light, whereas, after a point designated as the transition or commitment point, processes are light-independent.
The attractiveness of the alga as a model organism has recently increased with the release of several genomic resources to the public domain. The Chlre3 draft of the Chlamydomonas nuclear genome sequence prepared by Joint Genome Institute of the U.S. Dept of Energy comprises 1557 scaffolds totaling 120 Mb. Roughly half of the genome is contained in 24 scaffolds all at least 1.6 Mb in length. The current assembly of the nuclear genome is available online.
In addition to genomic sequence data there is a large supply of expression sequence data available as cDNA libraries and expressed sequence tags (ESTs). Seven cDNA libraries are available online. A BAC library can be purchased from the Clemson University Genomics Institute. There are also two databases of >50 000 and >160 000 ESTs available online.
Chlamydomonas has been used to study different aspects of evolutionary biology and ecology. It is an organism of choice for many selection experiments because (1) it has a short generation time, (2) it is both a heterotroph and facultative autotroph, (3) it can reproduce both sexually and asexually, and (4) there is a wealth of genetic information already available.
Some examples (non exhaustive) of evolutionary work done with Chlamydomonas include the evolution of sexual reproduction, the fitness effect of mutations, and the effect of adaptation to different levels of CO2.
DNA transformation techniques 
Gene transformation occurs mainly by homologous recombination in the chloroplast and heterologous recombination in the nucleus. The C. reinhardtii chloroplast genome can be transformed using microprojectile particle bombardment and the nuclear genome has been transformed with both glass bead agitation and electroporation. The biolistic procedure appears to be the most efficient way of introducing DNA into the chloroplast genome. This is probably because the chloroplast occupies over half of the volume of the cell providing the microprojectile with a large target. Electroporation has been shown to be the most efficient way of introducing DNA into the nuclear genome with maximum transformation frequencies two orders of magnitude higher than obtained using glass bead method.
Production of biopharmaceuticals 
Genetically engineered Chlamydomonas reinhardtii has been used to produce a mammalian serum amyloid protein, a human antibody protein, human Vascular endothelial growth factor, a potential malaria vaccine and a complex designer drug that could be used to treat cancer.
Clean source of hydrogen production 
In 1939 the German researcher Hans Gaffron (1902–1979), who was at that time attached to the University of Chicago, discovered the hydrogen metabolism of unicellular green algae. Chlamydomonas reinhardtii and some other green algae can, under specified circumstances, stop producing oxygen and convert instead to the production of hydrogen. This reaction by hydrogenase, an enzyme only active in the absence of oxygen, is short-lived. Over the next thirty years Gaffron and his team worked out the basic mechanics of this photosynthetic hydrogen production by algae.
To increase the production of hydrogen, several tracks are being followed by the researchers.
- The first track is decoupling hydrogenase from photosynthesis. This way, oxygen accumulation can no longer inhibit the production of hydrogen. And, if one goes one step further by changing the structure of the enzyme hydrogenase, it becomes possible to render hydrogenase insensitive to oxygen. This makes a continuous production of hydrogen possible. The flux of electrons needed for this production comes, in this case, no longer from the production of sugars, but is drawn from the breakdown of its own stock of starch.
- A second track is to interrupt temporarily, through genetic manipulation of hydrogenase, the photosynthesis process. This inhibits oxygen reaching a level where it is able to stop the production of hydrogen.
- The third track, mainly investigated by researchers in the 1950s, is chemical or mechanical methods of removal of O2 produced by the photosynthetic activity of the algal cells. These have included the addition of O2 scavengers, the use of added reductants, and purging the cultures with inert gases. However, these methods are not inherently scalable, and may not be applicable to applied systems. New research has appeared on the subject of removing oxygen from algae cultures, and may eliminate scaling problems.
- A fourth track has been investigated; namely, using copper salts to decouple hydrogenase action from oxygen production. 
- "CC-125 wild type mt+ 137c". Chlamydomonas Center core collection list.
- The Chlamydomonas Sourcebook, ISBN 978-0-12-370873-1)
- http://megasun.bch.umontreal.ca/protists/chlamy/taxonomy.html Chlamydomonas Taxonomy.
- Merchant et al.; Prochnik, SE; Vallon, O; Harris, EH; Karpowicz, SJ; Witman, GB; Terry, A; Salamov, A et al. (2007). "The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions". Science 318 (5848): 245–250. doi:10.1126/science.1143609. PMC 2875087. PMID 17932292.
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- Lagali PS, Balya D, Awatramani GB, Münch TA, Kim DS, Busskamp V, Cepko CL, Roska B (June 2008). "Light-activated channels targeted to ON bipolar cells restore visual function in retinal degeneration". Nature Neuroscience 11 (6): 667–75. doi:10.1038/nn.2117. PMID 18432197.
- Oldenhof, H, Zachleder, V. and van den Ende, H. 2006. Blue- and red-light regulation of the cell cycle in Chlamydomonas reinhardtii (Chlorophyta). Eur. J. Phycol. 41: 313 - 320
- Colegrave N. 2002. Sex releases the speed limit on evolution. Nature 420: 664-666.
- De Visser et al. 1996 The effect of sex and deleterious mutations on fitness in Chlamydomonas. Proc. R. Soc. Lond. B 263-193-200.
- Collins & Bell. 2004. Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga. Nature 431: 566-569.
- (16 May 2012) Biologists produce potential malarial vaccine from algae PhysOrg, Retrieved 15 April 2013
- (10 December 2012) Engineering algae to make complex anti-cancer 'designer' drug PhysOrg, Retrieved 15 April 2013
- Anastasios Melis, Thomas Happe (2004). "Trails of green alga hydrogen research — from Hans Gaffron to new frontiers". Photosynthesis Research 80 (1–3): 401–409. doi:10.1023/B:PRES.0000030421.31730.cb. PMID 16328836.
- Laurent Cournac, Florence Musa, Laetitia Bernarda, Geneviève Guedeneya, Paulette Vignaisb and Gilles Peltie (2002). "Limiting steps of hydrogen production in Chlamydomonas reinhardtii and Synechocystis PCC 6803 as analysed by light-induced gas exchange transients". International Journal of Hydrogen Energy 27 (11/12): 1229–1237. doi:10.1016/S0360-3199(02)00105-2.
- Anastasios Melis. "Hydrogen and hydrocarbon biofuels production via microalgal photosynthesis". Retrieved 2008-04-07.
- Kosourov, S. Tsyganov, A. Seibert, Ghirardi, M. "Sustained Hydrogen Photoproduction by Chlamydomonas reinhardtii:Effects of Culture Parameters". Retrieved 2012-04-06.
- Fernandez VM, Rua ML, Reyes P, Cammack R, Hatchikian EC. "Inhibition of Desulfovibrio gigas hydrogenase with copper salts and other metal ions.". Retrieved 2013-04-01.
Further reading 
Aoyama, H., Kuroiwa, T. and Nakamura, S. 2009. The dynamic behaviour of mitochondria in living zygotes during maturation and meiosis in Chlamydomonas reinhardtii. Eur. J. Phycol. 44: 497 - 507.
Jamers, A., Lenjou, M., Deraedt, P., van Bockstaele, D., Blust, R. and de Coen, W. 2009. Flow cytometric analysis of the cadmium-exposed green algae Chlamydomonas reinhadtii (Chlorophyceae). Eur. J. Phcol. 44: 54 - 550.
- Chlamydomonas reinhardtii resources
- The Chlamydomonas Center - genomic, genetic and bibliographic information and the Chlamydomonas culture collection.
- Chlamydomonas reinhardtii cell, life cycle, strains, mating types
- Chlamydomonas reinhardtii at the Encyclopedia of Life
- Guiry, M.D.; Guiry, G.M. (2008). "'Chlamydomonas reinhardtii'". AlgaeBase. World-wide electronic publication, National University of Ireland, Galway.