The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

Abstract

Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.

Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera

“…Interestingly, we identified two phylotypes (Ralstonia and Pseudomonas) that warrant specific attention. Ralstonia has been highlighted as a 'core' member in many other coral species and has been shown to be associated with coral host cells containing dinoflagellates (Ainsworth et al 2015). Although this phylotype was dominant and stable in the majority of corals sampled in this study, it would have not fitted into the classification of 'core' based on the 90% cutoff and so may have been missed if we were solely reliant on the importance of core associates.…”

“…However, Ainsworth et al (2015), for example, showed that the core microbiome of Acropora granulosa consisted of 159 phylotypes from a total of 1508 detected (10.5%), while the Leptoseris spp. microbiome was dominated by 204 phylotypes from 1424 (14.3%) and Montipora capitata had a core microbiome consisting of 350 phylotypes out of 1433 (24.4%).…”

“…The nearby coastline supports both oyster and fish farms, and two of the bacteria detected with a high frequency on Day 2 in *4-yr-old corals have been formerly associated with shellfish farms (Fulvivirga) and fish diseases (Piscirickettsiaceae) (Nedashkovskaya et al 2007;Rozas and Enríquez 2014). It has been proposed that the microbiome can be separated into microbes that can be classed as 'transient' and more sporadic versus those that are more stable or sometimes referred to as 'core' members (Ainsworth et al 2015;Hester et al 2015;Sweet and Bulling 2017). A large proportion of the bacterial phylotypes found in this study fall into the category of 'transient' members (i.e., only present in relatively few samples with little to no consistency among replicate colonies).…”

“…These values for 'core' members are considerably higher than the examples of other organisms given above. However, Ainsworth et al (2015) used a 30% cutoff for describing the core coral microbiome (i.e., for a bacterial phylotype to be described as a core member it had to be in at least 30% of all samples). If we use the same cutoff, the percentage of core members in the community (with relation to the total number of phylotypes sequenced) is similar, i.e., there is an increase to 32 out of 162 (19.8%) and 34 out of 175 (19.4%) in *4-and *10-yr-old colonies, respectively.…”

Rapid adaptive responses to climate change in corals

“…Roles in immunity, nitrogen fixation, nutrient cycling, osmoregulation and oxidative stress responses have been suggested for bacteria associated with different microhabitats within the coral host 68 . The potential significance of specific bacterial groups is suggested by their vertical transmission 80 and common presence within the tissues of a wide range of corals 85,86 . In particular, whereas transient, highly variable communities are typically associated with external coral mucus layers, low and relatively stable numbers of 'core' types are more generally associated with host cells 85 .…”