Abstract
The association between corals and photosynthetic dinoflagellates (
Symbiodinium
spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles‘ heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host–
Symbiodinium
pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic
Symbiodinium
assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident
Symbiodinium
species to coral physiology is widely recognized, the significance of the rare and low abundant background
Symbiodinium
remains a matter of debate. In this study, we assessed how coral–
Symbiodinium
communities assemble and how rare and abundant components together constitute the
Symbiodinium
community by analyzing 892 coral samples comprising >110 000 unique
Symbiodinium
ITS2 marker gene sequences. Using network modeling, we show that host–
Symbiodinium
communities assemble in non-random ‘clusters‘ of abundant and rare symbionts.
Symbiodinium
community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the ‘rare bacterial biosphere’) has long been recognized. Importantly, the inclusion of rare
Symbiodinium
taxa in robustness analyses revealed a significant contribution to the stability of the host–symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.