Corals at the lower limits of mesophotic habitats are likely to have unique photosynthetic adaptations that allow them to persist and dominate in these extreme low light ecosystems. We examined the host–symbiont relationships from the dominant coral genus Leptoseris in mesophotic environments from Hawai'i collected by submersibles across a depth gradient of 65–125 m. Coral and Symbiodinium genotypes were compared with three distinct molecular markers including coral (COX1–1-rRNA intron) and Symbiodinium (COI) mitochondrial markers and nuclear ITS2. The phylogenetic reconstruction clearly resolved five Leptoseris species, including one species (Leptoseris hawaiiensis) exclusively found in deeper habitats (115–125 m). The Symbiodinium mitochondrial marker resolved three unambiguous haplotypes in clade C, which were found at significantly different frequencies between host species and depths, with one haplotype exclusively found at the lower mesophotic extremes (95–125 m). These patterns of host–symbiont depth specialization indicate that there are limits to connectivity between upper and lower mesophotic zones, suggesting that niche specialization plays a critical role in host–symbiont evolution at mesophotic extremes.

Despite widespread climate-driven reductions of coral cover on tropical reefs, little attention has been paid to the possibility that changes in the geographic distribution of coral recruitment could facilitate beneficial responses to the changing climate through latitudinal range shifts. To address this possibility, we compiled a global database of normalized densities of coral recruits on settlement tiles (corals m −2) deployed from 1974 to 2012, and used the data therein to test for latitudinal range shifts in the distribution of coral recruits. In total, 92 studies provided 1253 records of coral recruitment, with 77% origi nating from settlement tiles immersed for 3−24 mo, herein defined as long-immersion tiles (LITs); the limited temporal and geographic coverage of data from short-immersion tiles (SITs; deployed for < 3 mo) made them less suitable for the present purpose. The results from LITs show de clines in coral recruitment, on a global scale (i.e. 82% from 1974 to 2012) and throughout the tropics (85% reduction at < 20°latitude), and in creases in the sub-tropics (78% increase at > 20°latitude). These trends indicate that a global decline in coral recruitment has occurred since 1974, and the persistent reduction in the densities of recruits in equatorial latitudes, coupled with increased densities in subtropical latitudes, suggests that coral recruitment may be shifting poleward.

Reef-building corals inhabiting the mesophotic zone (30−150 m) not only survive but thrive in light-limiting environments. Similar to shallow corals, mesophotic corals also exhibit coral fluorescence. Because fluorescent proteins (FPs) absorb high-energy light and emit lowerenergy light, FPs could play an important role in mesophotic coral physiology and ecology. For 4 species of the Hawaiian mesophotic reef-building coral Leptoseris (65−125 m), we investigated the abundance of fluorescent morphs, types of FPs, fluorescence emission phenotypes, and the physiological relationship between coral fluorescence and endosymbiotic Symbiodinium (dinoflagellate; Dinophyta). Cyan/green coral fluorescence emission was widespread in mesophotic Leptoseris spp.; more than 70% of corals fluoresced, yet fluorescent and nonfluorescent corals cooccurred at all depths investigated. Coral fluorescence was attributed to 2 proteins, a cyan fluorescent protein (CFP, λ ex = 424 nm, λ em = 490 nm) and a green fluorescent protein (GFP, λ ex = 478 nm, λ em = 502 nm). The type of FP in Leptoseris colonies was correlated with depth; CFP was dominant in corals from shallower depths (65−85 m), GFP was dominant in corals from deeper depths (96−125 m), and CFP and GFP were present in corals from middle depths (86−95 m). Coral FP emission was primarily localized in the coenosarc and/or the oral disc. Symbiodinium from corals with and without fluorescence emission had similar genotypes, abundances, photosynthetic pigments, photosynthetic efficiencies, photosynthetic rates, and chlorophyll excitation spectra. As such, it is unlikely that these FPs play a significant role in enhancing symbiont photosynthesis. The high abundance of fluorescent morphs (> 70%) dominating this energetically limited environment may suggest that FPs play an integral and conserved physiological role in corals.

Compiled abundances of juvenile corals revealed no change over time in the Pacific, but a decline in the Caribbean. Using these analyses as a rationale, we explored recruitment and post-settlement success in determining coral cover using studies in the Caribbean (St John, Bonaire) and Pacific (Moorea, Okinawa). Juvenile corals, coral recruits, and coral cover have been censused in these locations for years, and the ratio of juvenile (J) to recruiting (R) corals was used to measure post-settlement success. In St John and Bonaire, coral cover was stable but different between studies, with the CSIRO PUBLISHING Marine and Freshwater Research, 2015, 66, 609-622 http://dx.doi.org/10.1071/MF14139 Journal compilation Ó CSIRO 2015 www.publish.csiro.au/journals/mfrratio of the density of juveniles to density of recruits (J : R) ,0.10; in Moorea, declines in coral cover were followed by recovery that was related to the density of juvenile corals 3 years before, with J : R ,0.40; and in Okinawa, a decline in coral cover in 1998 was followed by a slow recovery with J/R ,0.01. Coral cover was associated positively with juvenile corals in St John, and in Okinawa, the density of juvenile corals was associated positively with recruits the year before. J : R varied among studies, and standardised densities of juvenile corals declined in the Caribbean, but increased in the Pacific. These results suggest that differences in the post-settlement success may drive variation in coral community structure.

The microbiomes of tropical reef-building corals are actively studied using 16S rRNA gene amplicons to understand microbial roles in coral health, metabolism, and disease resistance. However, primers targeting bacterial and archaeal 16S rRNA genes may additionally amplify organelle rRNA genes from the coral, associated microbial eukaryotes, and encrusting organisms. In this manuscript, we show that standard workflows using SILVA or Greengenes taxonomies under-annotate mitochondrial sequences in 1 272 short-read coral microbiomes from the Earth Microbiome Project. This under-annotation prevents even domain-level annotation of >95% of reads in some samples. Worse, mitochondrial under-annotation varies from species to species and across anatomy, biasing comparisons of α- and β-diversity. By supplementing existing taxonomic references with diverse mitochondrial rRNA sequences, we resolve ~97% of unique unclassified sequences as mitochondrial, without increasing misannotation in mock communities. We recommend using these extended taxonomies for coral microbiome analysis, and encourage vigilance regarding similar issues in other hosts.