There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO ⁻ ₃ ) and phosphate (PO ³⁻ ₄ ) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: (i) NCC rates declined in response to nutrient addition in all substrate types, (ii) the mixed community switched from net calcification to net dissolution under medium and high nutrient conditions, (iii) nutrients augmented pH variability through modified photosynthesis and respiration rates, and (iv) nutrients disrupted the relationship between NCC and aragonite saturation state documented in ambient conditions. These results indicate that the negative effect of NO ⁻ ₃ and PO ³⁻ ₄ addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion.

Significance: Marine dissolved organic matter (DOM) is one of the most complex and abundant chemical mixtures on earth, comprising thousands of different molecules. The molecular structure of these compounds is one factor structuring the community of microorganisms that metabolize them; in turn, this microbial metabolism mediates the composition of DOM. Decades of coral reef research has established the fundamental importance of microbial biogeochemistry in ecosystem function. This study unveils coral reef DOM by identifying a myriad of specific metabolite classes released into the surrounding waters by reef-building corals and algae, further characterizing their energetic and nutrient content and providing a foundation for linking benthic ecology with microbial processes that influence both the livelihood and demise of coral reefs.

On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night samples collected from the same site than between day or night samples collected across geographically distant reefs. Diel community differentiation is largely driven by the flux ofPsychrobactersp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species ofRoseobacter,Halomonas, andAlteromonasencoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.

The widespread loss of stony reef-building coral populations has been compounded by the low settlement and survival of coral juveniles. To rebuild coral communities, restoration practitioners have developed workflows to settle vulnerable coral larvae in the laboratory and outplant settled juveniles back to natural and artificial reefs. These workflows often make use of natural biochemical settlement cues, which are presented to swimming larvae to induce settlement. This paper establishes the potential for inorganic cues to complement these known biochemical effects. Settlement substrates were fabricated from calcium carbonate, a material present naturally on reefs, and modified with additives including sands, glasses, and alkaline earth carbonates. Experiments with larvae of two Caribbean coral species revealed additive-specific settlement preferences that were independent of bulk surface properties such as mean roughness and wettability. Instead, analyses of the substrates suggest that settling coral larvae can detect localized topographical features more than an order of magnitude smaller than their body width and can sense and positively respond to soluble inorganic minerals such as silica (SiO₂) and strontianite (SrCO₃). These findings open a new area of research in coral reef restoration, in which composite substrates can be designed with a combination of natural organic and inorganic additives to increase larval settlement and perhaps also improve post-settlement growth, mineralization, and defense.

Reef-building crustose coralline algae (CCA) are known to facilitate the settlement and metamorphosis of scleractinian coral larvae. In recent decades, CCA coverage has fallen globally and degrading environmental conditions continue to reduce coral survivorship, spurring new restoration interventions to rebuild coral reef health. In this study, naturally produced chemical compounds (metabolites) were collected from two pantropical CCA genera to isolate and classify those that induce coral settlement. In experiments using four ecologically important Caribbean coral species, we demonstrate the applicability of extracted, CCA-derived metabolites to improve larval settlement success in coral breeding and restoration efforts. Tissue-associated CCA metabolites induced settlement of one coral species,Orbicella faveolata, while metabolites exuded by CCA (exometabolites) induced settlement of three species:Acropora palmata,Colpophyllia natansandOrbicella faveolata. In a follow-up experiment, CCA exometabolites fractionated and preserved using two different extraction resins induced the same level of larval settlement as the unfractionated positive control exometabolites. The fractionated CCA exometabolite pools were characterized using liquid chromatography tandem mass spectrometry, yielding 145 distinct molecular subnetworks that were statistically defined as CCA-derived and could be classified into 10 broad chemical classes. Identifying these compounds can reveal their natural prevalence in coral reef habitats and facilitate the development of new applications to enhance larval settlement and the survival of coral juveniles.

Dissolved organic matter (DOM) composition influences microbial community metabolism and benthic primary producers are a source of DOM in coral reefs. As reef benthic communities change, in part due to nutrient pollution, understanding impacts on reef microbial processes requires knowledge of DOM sources and composition. We conducted a multi‐week mesocosm experiment dosing four coral reef benthic constituents with three levels of nitrate and phosphate to contrast exudate composition and quantify the effects of nutrient enrichment on exudate release. Moderate nutrient enrichment enhanced bulk dissolved organic carbon exudation by all producers. Corals exuded rapidly accumulating DOM with a markedly high concentration of aromatic amino acid‐like fluorescent DOM components that clearly distinguishes them from algal exudates, which were dominated by humic‐like fluorescent components and did not accumulate significantly. Our results indicate that corals and algae release DOM of different quality and the quantity of DOM release increases with inorganic nutrient availability.