Coral reefs are undergoing degradation due to overexploitation, pollution, and climate change. Management and restoration efforts require that we gain a better understanding of the complex interactions between corals, their microbiomes, and their environment. For this purpose, Varadero Reef near Cartagena, Colombia, serves as an informative study system located at the entrance of the Bay of Cartagena adjacent to the Canal del Dique, which carries turbid and polluted water into the bay. Varadero’s survival under poor environmental conditions makes it a great study site for investigating the relationship between the microbiome and coral resistance to environmental stressors. To determine whether the microbiomes of Varadero corals differ from those in less impacted sites, we conducted a reciprocal transplant experiment by relocating coral fragments from Varadero as well as a geographically proximate reef that is less affected by plume dynamics (Rosario) across a gradient of turbidity (low, medium, and high). After 6 months of acclimatization, transplanted corals developed site-specific microbiomes that differed significantly from pre-transplant microbiomes, and corals transplanted to the highly impacted site from both Varadero and Rosario site saw higher mortality and an increase in overall microbial diversity. In combination with physiology and survivorship outcomes pointing to a limit in the corals’ photoacclimative capacity, our results indicate that, rather than surviving, Varadero Reef is experiencing a slow decline, and its corals are likely on the brink of dysbiosis. With continued anthropogenic interference in marine environments, sites such as Varadero will become increasingly common, and it is imperative that we understand how corals and their microbial symbionts are changing in response to these new environmental conditions.

Degradation of water optical properties due to anthropogenic disturbances is a common phenomenon in coastal waters globally. Although this condition is associated with multiple drivers that affect corals health in multiple ways, its effect on light availability and photosynthetic energy acquisition has been largely neglected. Here, we describe how declining the water optical quality in a coastal reef exposed to a turbid plume of water originating from a man-made channel compromises the functionality of the keystone coral species Orbicella faveolata. We found highly variable water optical conditions with significant effects on the light quantity and quality available for corals. Low-light phenotypes close to theoretical limits of photoacclimation were found at shallow depths as a result of reduced light penetration. The estimated photosynthetically fixed energy depletion with increasing depth was associated with patterns of colony mortality and vertical habitat compression. A numerical model illustrates the potential effect of the progressive water quality degradation on coral mortality and population decline along the depth gradient. Collectively, our findings suggest that preserving the water properties seeking to maximize light penetration through the water column is essential for maintaining the coral reef structure and associated ecosystem services.

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Forest pests drive tree mortality through disruption of functional traits linked to nutrient acquisition, growth and reproduction. The impacts of attack by individual or multiple above‐ground herbivores on root functional traits critical to tree health have received little attention. This is especially true for exotic herbivores, organisms often found in disturbed forests. We excavated whole‐root systems from eastern hemlock (Tsuga canadensis) individuals experimentally infested with hemlock woolly adelgid (HWA: Adelges tsugae) and elongate hemlock scale (EHS: Fiorina externa) individually, or in combination, for periods of 2 and 4 years. Below‐ground root biomass, functional traits and storage nutrients were measured to assess impacts of herbivory. We also quantified ectomycorrhizal fungal (EMF) colonisation of fine roots and used culture‐independent methods to examine EMF diversity. Trees infested with HWA had a greater root mass fraction (root to total biomass ratio), although feeding had no observable effects on root functional traits (e.g. specific root length) or on resource allocation to roots. HWA feeding did significantly reduce EMF colonisation of hemlock fine roots, though surprisingly, EMF diversity and that of other fungal associates were unaffected. In contrast to HWA, EHS (alone or in conjunction with HWA) feeding had no observable effect on below‐ground traits or EMF colonisation alone; however, its presence mediated HWA effects when trees were co‐infested. Simultaneous infestation within the same year yielded significant reductions in EMF colonisation, whereas prior EHS attack weakened HWA effects. Our results collectively suggest that prior EHS attack dampens the impact of HWA on below‐ground functional traits. This highlights how the timing and sequence of herbivore arrival can alter plant‐mediated interactions between herbivores and their effects on above–below‐ground linkages and associated tree health. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12910/suppinfo is available for this article.

Degradation of water optical properties due to anthropogenic disturbances is a common phenomenon in coastal waters globally. Although this condition is associated with multiple drivers that affect corals health in multiple ways, its effect on light availability and photosynthetic energy acquisition has been largely neglected. Here, we describe how declining the water optical quality in a coastal reef exposed to a turbid plume of water originating from a man-made channel compromise the functionality of the keystone coral species Orbicella faveolata. We found highly variable water optical conditions with significant effects on the light quantity and quality available for corals. Reduction of light penetration into the water column elicits the development of low-light phenotypes close to theoretical limits of photoacclimation despite their occurrence at shallow depths. Predicted photosynthetic energy depletion with increasing depth is associated with patterns of colony mortality and contraction of the habitable space for the population. A numerical model illustrates the potential effect the progressive degradation of water optical properties on the gradual mortality and population decline of O. faveolata. Our findings suggest that preserving the water optical properties seeking to maximize light penetration into the water column may have an extraordinary impact on coral reefs conservation, mostly toward the deeper portions of reefs.

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the corals Orbicella annularis and O. franksi , two young species with contrasting vertical distribution in the Caribbean. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation and low mortality, and maintained a consistent bacterial community. By contrast, O. annularis experienced high mortality and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

From 1913 to 1980, two zinc smelters in Palmerton, Pennsylvania, emitted large quantities of atmospheric pollutants nearly eliminating forests along a ridge above the town. In 2008, a remediation treatment was applied to the land above one of the smelters that included the planting of several locally adapted plant species. It also included mineral fertilization and mycorrhizal inoculation. One of the species, the Pitch pine (Pinus rigida, Mill.), is a native tree that is both tolerant of metalliferous soils and obligatorily ectomycorrhizal. This report summarizes the results of two observational studies conducted 5 years after the remediation treatment. The first study's objective was to compare ectomycorrhizal communities on treated Pitch pine saplings, with communities on naturally regenerating saplings in an adjacent non-remediated area. The second study's objective was to determine if the composition of the fungal communities on root tips of naturally regenerating Pitch pine saplings differed with distance from the smelters. Fungal community compositions were determined using internal transcribed spacer rRNA sequences. Comparisons of sequences from the remediated and non-remediated sites revealed that communities at the remediated sites had lower taxonomic diversity and were dominated by members of a genus in the remediation inoculant. The results of the smelter-proximity study indicated that although fungal diversity did not differ markedly with distance from the smelters, the relative abundances of some taxa were greater on saplings growing directly above the smelters, where the soils contained highest concentrations of zinc and cadmium.

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the Caribbean corals Orbicella annularis and O. franksi. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation, low mortality, and maintained a consistent bacterial community. In contrast, O. annularis experienced higher mortality, and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.