Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial–temporally stable or species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadic symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution.

The ISME Journal (2016) 10, 1157–1169; doi:10.1038/ismej.2015.190; published online 10 November 2015 

Primary producers release oxygen as the by-product of photosynthetic light reactions during the day. However, a prevalent, globally-occurring nighttime spike in dissolved oxygen in the absence of light challenges the traditional assumption that biological oxygen production is limited to daylight hours, particularly in tropical coral reefs. Here we show: 1) the widespread nature of this phenomenon, 2) its reproducibility across tropical marine ecosystems, 3) the influence of biotic and abiotic factors on this phenomenon across numerous datasets, and 4) the observation of nighttime oxygen spikes in vitro from incubations of coral reef benthic organisms. The data from this study demonstrate that in addition to physical forcing, biological processes are likely responsible for increasing dissolved oxygen at night. Additionally, we demonstrate an association between these nighttime oxygen spikes and measures of both net community calcification and net community production. These results suggest that nighttime oxygen spikes are likely a biological response associated with increased respiration and are most prominent in communities dominated by calcifying organisms.