Genome analysis is available for only four unicellular algae: Chlamydomonas reinhardtii, Cyanidoschyzon merolae, Ostreococcus tauri, and Thalassiosira pseudonana (Misumi et al., 2008). Genetic modification (GM) of microalgae holds promise as a strategy to attain higher lipid yields while concurrently generating value-added products (Jin et al., 2003; Leon and Fernandez, 2007; Gressel, 2008). Although several hundred strains of microalgae have been cultured, detailed inves­tigation of cellular physiology and biochemistry is limited to fewer than thirty species. Fewer still are the algal strains that have been studied at the genomic level. Genetic transformation of microalgae has been constrained by the presence of rigid cell walls (Rosenberg et al., 2008). However, using a plethora of techniques such as bombardment, electroporation, and treatment with silicon whiskers and glass beads, several species have been modified genetically (Leon and Fernandez, 2007), including Amphidinium sp., Anabaena sp., Chlamydomonas sp., Chlorella ellipsoidea, C. kessleri, C. reinhardtii, C. sacchrophila, C. sorokiniana, C. vulgaris, Cyclotella cryptica, Cylindrotheca fusiformis, Dunaliella salina, Euglena gracilis, Haematococcus pluvialis, Navicula saprophila, Phaeodactylum tricornutum, Porphyridium sp., Symbiodinium microadriaticum, Synechocystis sp., Thalassiosira weisflogii, and Volvox carteri. The red alga Cyanidoschyzon merolae and the euglenoid Euglena gracilis have also been genetically transformed (Rosenberg et al., 2008). We agree with Pienkos et al. (2011), who suggest that through genetic engineering a few “designer algal strains” that have all the properties needed for large-scale biotechnology should be developed, and more research must be carried out in parallel with natural strains to fully understand their physiological function­ing. Such modifications can impart properties to improve yield. For instance, Li and Tsai (2008) demonstrated that the microalga Nannochloropsis oculata, which was codon-optimized to produce bovine lactoferricin (LFB) fused with a red fluorescent protein (DsRed), has bactericidal defense against V. parahaemolyticus infection in the shrimp digestive tract.

The utility of engineered microalgae for augmented lipid biosynthesis, conver­sion from autotrophy to heterotrophy, enhancing photosynthetic conversion effi­ciency and expression of recombinant proteins is gaining prominence (Rosenberg et al., 2008). While it is possible to enhance lipid synthesis through cloning acetyl — CoA carboxylase (ACC) genes in yeast, fungi, bacteria, and a few higher plants, there was no change in lipid content of a similarly engineered diatom Cyclotella cryptica (Dunahay et al., 1995; Dunahay et al., 1996). Three possible strategies exist for enhanced lipid production: biochemical engineering (BE), genetic engineering (GE), and transcription factor engineering (TFE). BE approaches are currently the most widely established in microalgal lipid production (Courchesne et al., 2009).

Radakovits et al. (2010) discussed the potential of manipulating the central car­bon metabolism in eukaryotic microalgae through genetic engineering to enhance lipid production. They suggested that it should be possible to increase production of not only carbon storage compounds, such as TAGs and starch, but also designer hydrocarbons that may be used directly as fuels.

Another possibility is to engineer the light-harvesting antennae in autotrophic algae. Smaller antennae lead to greater photosynthetic efficiency (Mitra and Melis, 2008); mutating genes that control antennae biogenesis is a possible mechanism for enhancing photosynthetic efficiency (Scott et al., 2010). Possibilities exist to improve solar energy conversion efficiency from the present the 1-4% to 8-12% to realize fully the potential of microalgal co-production systems in Chlamydomonas perigranulata, C. reinhardtii, Chlorella vulgaris, Cyclotella sp., Dunaliella salina, Scenedesmus obliquus, and Synechocystis PCC 6714 (Stephens et al., 2010).

A mechanistic model developed by Flynn et al. (2010) explores cellular chlorophyll and photosynthetic efficiency to optimize commercial algal biomass production. The model predicts that genetically modified strains with a large antenna size, indi­cated by a low Chl:C ratio, are more suitable for commercial biofuel production than strains selected from nature. However, for the generation of hydrogen and hydrocarbons as biofuels, smaller light-collecting antennae seem to be more effi­cient in Botryococcus braunii (Eroglu and Melis, 2010). Three races (Race A, B, and L) of the strain Botryococcus braunii are recognized (Banerjee et al., 2002); these races are regarded as a potential source of renewable fuel with yields of hydro­carbons reaching up to 75% of algal dry mass. A Botyrococcus Squalene Synthase (BSS) gene from a Race B variant of B. braunii has been sequenced, amplified as a 1,403-bp fragment, and expressed as a heterologous protein in E. coli BL21 cells. Following Isopropyl-P-D-thiogalactoside (IPTG) induction, recombinant squalene synthase activity was detected, suggesting that a key hydrocarbon synthesis gene from a commercial alga can be isolated and cloned into a heterologous expression system. This opens the door for large-scale hydrocarbon synthesis in more amenable systems such as E. coli and may help reduce the problems associated with the vis­cous nature of Botyrococcus cultures (Banerjee et al., 2002).