Variation in Symbiodinium ITS2 Sequence Assemblages among Coral Colonies

Abstract

Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.

Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals

“…(c) Statistical analysis To determine coverage of the clone libraries, and to test for equal coverage across host taxa, coverage estimates were determined following Stat et al [34], and coverage values were tested with one-way ANOVA among host genera. To compare Symbiodinium sequence assemblages among coral taxa, relative abundance data were square root-transformed, and a Bray -Curtis similarity coefficient [35] was calculated for all samples, ranging from 0 (indicating dissimilarity) to 100 (indicating identical assemblages).…”

Long-term changes in Symbiodinium communities in Orbicella annularis in St. John, US Virgin Islands

“…DGGE fingerprints) (LaJeunesse 2002, Pochon et al 2007, Sampayo et al 2009), and, while such approaches have good resolution for identifying dominant patterns, they have limited capacity to more finely resolve genetic variation or to detect rare genotypes. While interpreting the biological significance of rare Symbiodinium genotypes remains controversial in light of the presence of intra genomic variation associated with ITS2 (LaJeunesse & , Stat et al 2011, the increasing number of examples of Symbiodinium− host symbioses in which rare Symbiodinium genotypes have been found (Franklin et al 2012, Green et al 2014 argue strongly for using techniques with the resolution to detect such forms. This argument was compelling to us in the decision to expand our analytical approach to tag pyrosequencing of nrITS2 (nuclear ribosomal internal transcriber spacer 2) amplicons, as was the success of this approach in advancing other fields requiring fine-grained genetic resolution of single-celled organisms (Sogin et al 2006).…”

“…Prior work (e.g. Stat et al 2011) has recognized the inability to link an individual biological entity to individual sequences due to duplication in the ribosomal array resulting in the production of paralogs that preclude species assignment. ITS2 can, however, be utilized in a comparative approach to determine patterns in the assemblage of sequences within a given sample.…”

“…Our results showed that variation in Symbiodinium community composition in O. annularis in St. John was more strongly influenced by location on the reef on a scale of meters than by host genotype. Given the apparent spatial homogeneity of the reef where the study was conducted, we foresaw no physical driver of variation in Symbiodinium genotypes on a scale of meters, even though variation at this spatial scale has been found among colonies of Montipora capitata in Ha waii (Stat et al 2011, but see LaJeunesse & Thornhill 2011 and Acropora millepora on a single reef flat (Jones et al 2008). While discordant environmental conditions over the surface of mounding corals creates opportunities for variation in Symbiodinium genotypes (Rowan et al 1997, Garren et al 2006, such effects are unlikely to have influenced the Symbiodinium communities in the present study because care was taken to sample corals in similar locations on the upper surface of all colonies.…”

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

“…In the genus Symbiodinium, each clade contains multiple genetic types, and identification has been performed using ribosomal, mitochondrial, plastid, and nuclear DNA markers (Rowan and Powers, 1991;Wilcox, 1998;Lajeunesse, 2001;Santos et al, 2002;Takabayashi et al, 2004). Recently internal-transcribed spacer 2 (ITS-2) regions have been widely used as genetic markers (Lajeunesse, 2001(Lajeunesse, , 2002(Lajeunesse, , 2005Pochon et al, 2007;Stat et al, 2011) and databases of Symbiodinium DNA sequences, such as SYM-BLAST (https://www.auburn.edu/~santosr/symblast.htm), SymbioGBR (Tonk et al, 2013), and GeoSymbio (Franklin et al, 2012), are currently available. In this laboratory study, we developed a technique that would enable simultaneous detection and identification of coral and Symbiodinium eDNA in reefs, in order to assess distributions of corals and their symbiont types.…”