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Woese et al. first proposed that life on earth is composed of three primary divisions, or domains to which all organisms belong. These domains are named Archaea (or archaebacteria), Bacteria (or eubacteria), and Eucarya (or eukaryotes), with Eucarya being relatives (or descendants) of Archaea (Woese & Fox, 1977; Woese et al., 1990). This proposal was based on 16S ribosomal RNA sequences and later confirmed by the comparison of many protein sequences (Pohlschroder et al., 1997; Scamardella, 1999; Woese & Fox, 1977; Woese et al., 1990) . This proposal is currently widely accepted, although some sequence features and phylogenies derived from many highly conserved proteins are inconsistent (Gupta, 1998).
Prokaryotes and eukaryotes differ from each other in many respects, with the most important criteria of their distinction being the type of their cells; eukaryotes’ cells contain a membrane-bounded nucleus, while prokaryotes not (Gupta, 1998). Archaea resemble morphologically with bacteria (e.g both of them are prokaryotes), but they are evolutionary distinct from them and other prokaryotes and constitute a fundamentally different form of life (i.e., life's third domain) (Gupta, 1998; Olsen & Woese, 1993; Pohlschroder et al., 1997; Woese & Fox, 1977; Woese et al., 1990).
Eukaryotes are organisms composed of one or more cells with nuclei which have inhabited Earth for approximately 1.2 billion to 1.8 billion years (Knoll et al., 2006). Eukaryotes dominate the visible landscapes of terrestrial and marine systems and are major players in biogeochemical cycling and cause numerous global diseases (e.g., malaria, African sleeping sickness, amoebic dysentery). Eukaryotes clearly differentiate from prokaryotes as all of eukaryotes share the main features of cellular architecture (e.g the complex intracellular compartmentalization) and the regulatory circuitry (Koonin, 2010). Plants, animals, fungi and protists are the most familiar eukaryotes (Tekle et al., 2009).
The small size of some of Eukaryotes has traditionally made these groups recalcitrant to study. In addition, their evolution exhibits a vast timescale that obscures evolutionary events during their origin and early diversification. However, advances in molecular techniques (e.g., multigene sequencing, genomics) are transforming our views on eukaryotic evolution (Tekle et al., 2009).
Protozoa are single-celled eukaryotes that commonly show characteristics usually associated with animals, most notably mobility and heterotrophy (Flynn et al., 2007; Pink et al., 2005). Protozoa combine cell and organism in one (Vickerman & Coombs, 1999). The kingdom Protozoa belongs to Protists that contains also algae, and lower fungi (Corliss, 2002). The term “protist” is often used instead of ”protozoa” because many protozoa have features in common with fungi or algae (Flynn et al., 2007).
They are a multiphyletic group of organisms, whose members differ in structure, morphology, biochemistry and genetics (Flynn et al., 2007; Scamardella, 1999) and their vast diversity of cellular organization provides an endless supply of material for biologists to investigate (Vickerman & Coombs, 1999). Protozoa adapt to changing environments by modifying form and function to achieve homeostasis (Vickerman & Coombs, 1999).