Deep-Sequencing Method for Quantifying Background Abundances of Symbiodinium Types: Exploring the Rare Symbiodinium Biosphere in Reef-Building Corals

Abstract

The capacity of reef-building corals to associate with environmentally-appropriate types of endosymbionts from the dinoflagellate genus Symbiodinium contributes significantly to their success at local scales. Additionally, some corals are able to acclimatize to environmental perturbations by shuffling the relative proportions of different Symbiodinium types hosted. Understanding the dynamics of these symbioses requires a sensitive and quantitative method of Symbiodinium genotyping. Electrophoresis methods, still widely utilized for this purpose, are predominantly qualitative and cannot guarantee detection of a background type below 10% of the total Symbiodinium population. Here, the relative abundances of four Symbiodinium types (A13, C1, C3, and D1) in mixed samples of known composition were quantified using deep sequencing of the internal transcribed spacer of the ribosomal RNA gene (ITS-2) by means of Next Generation Sequencing (NGS) using Roche 454. In samples dominated by each of the four Symbiodinium types tested, background levels of the other three types were detected when present at 5%, 1%, and 0.1% levels, and their relative abundances were quantified with high (A13, C1, D1) to variable (C3) accuracy. The potential of this deep sequencing method for resolving fine-scale genetic diversity within a symbiont type was further demonstrated in a natural symbiosis using ITS-1, and uncovered reef-specific differences in the composition of Symbiodinium microadriaticum in two species of acroporid corals (Acropora digitifera and A. hyacinthus) from Palau. The ability of deep sequencing of the ITS locus (1 and 2) to detect and quantify low-abundant Symbiodinium types, as well as finer-scale diversity below the type level, will enable more robust quantification of local genetic diversity in Symbiodinium populations. This method will help to elucidate the role that background types have in maximizing coral fitness across diverse environments and in response to environmental change.

Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals

“…In fact, the diversity reported here is almost five times greater than that reported in other recent next-generation sequencing studies on Symbiodinium diversity (Quigley et al , 2014; Thomas et al , 2014; Arif et al , 2014; Green et al , 2014; Edmunds et al , 2014b). For example, a study on Acropora coral species (Thomas et al , 2014) at another high latitude reef (Abrolhos Island, Western Australia) found a Shannon diversity of 0.145 (vs 0.620 at LHI in September 2012).…”

“…Here, we challenge this notion by exploring the Symbiodinium rare biosphere using next-generation sequencing, a cost-effective, high-throughput method that has been recently shown to accurately detect low-abundance Symbiodinium types (Quigley et al , 2014; Thomas et al , 2014; Arif et al , 2014; Green et al , 2014; Edmunds et al , 2014b). We assess Symbiodinium communities in a time-series sample set to investigate (1) the cryptic diversity of the Symbiodinium rare biosphere within two common pocilloporid species; (2) possible changes within the Symbiodinium community over a period of time that spans two successive bleaching events; and (3) whether Symbiodinium shuffling and/or switching has occurred in pocilloporid corals from a subtropical reef at Lord Howe Island (LHI), eastern Australia.…”

Rapid adaptive responses to climate change in corals

“…The generally greater diversity of Symbiodinium communities in early life-history stages compared to in adults 79 could be viewed as a bet-hedging strategy, providing juvenile corals with the opportunity to fine-tune endosymbiotic communities to suit ambient conditions. Finally, the retention of low-abundance background Symbiodinium types in adult stages of some corals 16,81 may provide further adaptive capacity to the holobiont (but see 82), facilitating future shuffling of dominant Symbiodinium types in response to changing environmental conditions 76,83 .…”

Not just who, but how many: the importance of partner abundance in reef coral symbioses

“…While their application to coral symbiont communities has only just begun, NGS approaches have the power to recover a more complete picture of community diversity, including the rare biosphere (Quigley et al, 2014), and require no prior taxonomic knowledge. However, while these approaches can estimate relative proportions of different symbiont types, these data are subject to numerous quantitative biases (Amend et al, 2010) and must still be normalized to surface area or other host parameters to quantify symbiont abundance.…”