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The genus Symbiodinium encompasses the largest and most prevalent group of endosymbiotic dinoflagellates known to science. These unicellular algae commonly reside in the endoderm of tropical cnidarians such as corals, anemones, and jellyfish, where they translocate photosynthetic material to the host and in turn receive inorganic nutrients (e.g. CO2, NH4) for growth (Fig. 1). They are also harbored by various species of sponges, flatworms, mollusks (e.g. giant clams), foraminifera (soritids), and some ciliates. With the exception of mollusks, these dinoflagellates enter the host cell through normal phagocytosis, persist as intracellular symbionts, reproduce, and disperse. Hosts that require high densities of Symbiodinium occur mostly in warm oligotrophic (nutrient-poor) marine environments where they are often the dominant constituents of benthic communities. These dinoflagellates are therefore among the most abundant eukaryotic microbes found in coral reef ecosystems.

Symbiodinium are colloquially called "zooxanthellae" (or "zoox"), and animals symbiotic with algae in this genus are said to be "zooxanthellate". The term was loosely used to refer to any golden-brown endosymbionts, including diatoms and other dinoflagellates. Continued use of the term in the scientific literature should be discouraged because of the confusion caused by overly generalizing many disparate and taxonomically diverse symbiotic relationships.

Intracellular Symbionts
Symbiodinum are known primarily for their role as mutualistic endosymbionts. In host tissues they usually occur in high concentrations, ranging from 100s of thousands to millions per square centimeter. The successful culturing of swimming gymnodinoid cells from coral led to the discovery that “zooxanthellae were actually dinoflagellates (Fig. 2A). Each Symbiodinium cell is coccoid in hospite (living in a host cell) and surrounded by a membrane that originates from the host cell plasmalemma during phagocytosis (Figs 2B and 3). This cell membrane probably undergoes some modification to its protein content, which functions to limit or prevent phago-lysosome fusion (Fig. 2B). The vacuole structure containing the symbiont is therefore termed the symbiosome. Under normal conditions, symbiont and host cells exchange organic and inorganic molecules that enable the growth and proliferation of both partners.

Natural Services and Economic Value
Symbiodinium are among the most researched of the Dinophyceae. Their mutualistic relationships with reef-building corals form the basis of a highly diverse and productive ecosystem. Coral reefs have economic benefits – valued at hundreds of billions of dollars each year – in the form of ornamental, subsistence, and commercial fisheries, tourism and recreation, coastal protection from storms, a source of new bioactive compounds for pharmaceutical development, and more. The economic value of Symbiodinium is thus immeasurable, their continued productivity as symbionts and the functioning of tropical reef ecosystems are in serious jeopardy due to ocean warming.

Geographic distributions and patterns of diversity
Symbiodinium is a good group for studying micro-eukaryote physiology and ecology for several reasons. 1) Phylogenetic and population genetic markers are now available that allow for detailed examination of their genetic diversity over broad spatial and temporal scales. 2) Large quantities Symbiodinium cells are readily obtained through the collection of hosts that harbor them. 3) Their association with animals provides an additional axis by which to compare and contrast ecological distributions.

The earliest genetic methods for assessing Symbiodinium diversity relied on low-resolution molecular markers that separated the genus into a few evolutionarily divergent lineages, referred to as “clades” (see below). Previous characterizations of geographic distribution and dominance have focused on the clade-level of genetic resolution, however more detailed assessments of diversity at the species level are needed (Fig. 5). While members of a given clade may be ubiquitous, the species diversity within each group is potentially large, with each species often having different ecological and geographic distributions related to their dispersal ability, host biogeography, and external environmental conditions. A small number of species occur in temperate environments where few symbiotic animals occur. As a result, these high latitude associations tend to be highly specific.

Symbiodinium diversity assigned to different ecological guilds
The large diversity of Symbiodinium revealed by genetic analyses is distributed non-randomly and appears to comprise several guilds with distinct ecological habits (Fig. 6). Of the many Symbiodinium characterized genetically, most are host-specific, mutualistic, and dominate their host. Others may represent compatible symbionts that remain as low-abundance background populations because of competitive inferiority under the prevailing external environmental conditions (e.g. high light vs. low light). Some may also comprise opportunistic species that may proliferate during periods of physiological stress and displace the normal resident symbiont and remain abundant in the host’s tissues for months to years before being replaced by the original symbiont. Similarly there are those that rapidly infect and establish populations in host juveniles until being replaced by symbionts that normally associate with host adult colonies. Finally, there appears to be another group of Symbiodinium that are incapable of establishing endosymbiosis yet exist in environments around the animal or associate closely with other substrates where nutrients are available (i.e. macro-algal surfaces, surface sediment). Symbiodinium from functional groups 2, 3, and 4 are known to exist because they culture easily, however species with these life histories are difficult to study because of their low abundance in the environment (Fig. 6).

Free-living and “non-symbiotic” Symbiodinium
There are few examples of documented populations of free-living Symbiodinium (see references ). Given that most host larvae must initially acquire their symbionts from the environment, Symbiodinium cells must occur commonly outside the host. It may be that the motile phase plays an important role in the external environment and in the infection of host larvae. The use of aposymbiotic host polyps deployed as "capture vessels" and the application of molecular techniques has allowed for the detection of environmental sources of Symbiodinium. With these methods employed, investigators may resolve the distribution of different species on various benthic surfaces and cell concentrations suspended in the water column. The genetic identities of cells cultured from the environment are often dissimilar to those found in hosts. Learning more about the "private lives" of these environmental populations and their ecological function will further our knowledge about the diversity, dispersal potential, and evolution among members within this genus.

Major phylogenetic disparity among Symbiodinium “Clades”
The earliest ribosomal gene sequence data indicated that Symbiodinium was comprised of lineages whose genetic divergence was similar to differences observed among dinoflagellates from different genera, families, and even orders. This large genetic disparity among “clades” A, B, C, etc. was reconfirmed with mitochondrial gene sequences (CO1) analyzing the Dinophyceae (Fig. 7). Most of these “clade” groupings comprise numerous reproductively isolated, genetically distinct lineages (see below), exhibiting different ecological and biogeographic distributions (see above). Given the over-simplified perceptions created by using clade-level taxonomic designations for grouping Symbiodinium, future taxonomic revision of this genus is required. Most likely, many of these “clades” will be reclassified into distinct genera.

Species Diversity
The recognition of species diversity in this group remained problematic for many decades due the challenges of identifying morphological and biochemical traits useful for diagnosing species. Presently, phylogenetic, ecological, and population genetic data can be more rapidly acquired to resolve Symbiodinium into separate entities that are consistent with Biological, Evolutionary, and Ecological Species Concepts Most genetics-based measures of diversity have been estimated from the analysis of one genetic marker (e.g. LSU, ITS2, cp23S), yet in recent studies these and other markers were analyzed in combination. The high concordance found among nuclear, mitochondrial and chloroplast DNA argues that a hierarchical phylogenetic scheme, combined with ecological data, can unambiguously recognize and assign nomenclature to reproductively isolated lineages, i.e. species (Fig. 8).

When analyzed in the context of the major species concepts, ITS2 sequence data provide a good proxy for species diversity. Currently ITS2 types number in the 100’s and most communities of symbiotic cnidaria around the world still require comprehensive sampling. Furthermore, there appear to be a large number of unique species found in association with equally diverse species assemblages of soritid foraminifera, as well as many other Symbiodinium that are exclusively free-living and found in varied, often benthic, habitats. Given the potential species diversity of these ecologically cryptic Symbiodinium, the total species number may never be accurately assessed.