Water column contributions to coral reef productivity: overcoming challenges of context dependence

Coral reefs are declining at an unprecedented rate. Effective management and conservation initiatives necessitate improved understanding of the drivers of production because the high rates found in these ecosystems are the foundation of the many services they provide. The water column is the nexus of coral reef ecosystem dynamics, and functions as the interface through which essentially all energy and nutrients are transferred to fuel both new and recycled production. Substantial research has described many aspects of water column dynamics, often focusing on specific components because water column dynamics are highly spatially and temporally context dependent. Although necessary, a cost of this approach is that these dynamics are often not well linked to the broader ecosystem or across systems. To help overcome the challenge of context dependence, we provide a comprehensive review of this literature, and synthesise it through the perspective of ecosystem ecology. Specifically, we provide a framework to organise the drivers of temporal and spatial variation in production dynamics, structured around five primary state factors. These state factors are used to deconstruct the environmental contexts in which three water column sub-food webs mediate 'new' and 'recycled' production. We then highlight critical pathways by which global change drivers are altering coral reefs via the water column. We end by discussing four key knowledge gaps hindering understanding of the role of the water column for mediating coral reef production, and how overcoming these could improve conservation and management strategies. Throughout, we identify areas of extensive research and those where studies remain lacking and provide a database of 84 published studies. Improved integration of water column dynamics into models of coral reef ecosystem function is imperative to achieve the understanding of ecosystem production necessary to develop effective conservation and management strategies needed to stem global coral loss.

Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses

The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.

Bacterioplankton communities reveal horizontal and vertical influence of an Island Mass Effect

Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized 16S rRNA gene metabarcoding as a biological tracer to elucidate horizontal and vertical influence of an IME around the islands of Mo'orea and Tahiti, French Polynesia. We show that those nearshore oceanic stations with elevated chlorophyll a included bacterioplankton found in high abundance in the reef environment, suggesting advection of reef water is the source of altered nearshore biogeochemistry. We also observed communities in the nearshore deep chlorophyll maximum (DCM) with enhanced abundances of upper euphotic bacterioplankton that correlated with intrusions of low-density, O₂ rich water, suggesting island influence extends into the DCM.

Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals

Metabolites exuded by primary producers comprise a significant fraction of marine dissolved organic matter, a poorly characterized, heterogenous mixture that dictates microbial metabolism and biogeochemical cycling. We present a foundational untargeted molecular analysis of exudates released by coral reef primary producers using liquid chromatography-tandem mass spectrometry to examine compounds produced by two coral species and three types of algae (macroalgae, turfing microalgae, and crustose coralline algae [CCA]) from Mo'orea, French Polynesia. Of 10,568 distinct ion features recovered from reef and mesocosm waters, 1,667 were exuded by producers; the majority (86%) were organism specific, reflecting a clear divide between coral and algal exometabolomes. These data allowed us to examine two tenets of coral reef ecology at the molecular level. First, stoichiometric analyses show a significantly reduced nominal carbon oxidation state of algal exometabolites than coral exometabolites, illustrating one ecological mechanism by which algal phase shifts engender fundamental changes in the biogeochemistry of reef biomes. Second, coral and algal exometabolomes were differentially enriched in organic macronutrients, revealing a mechanism for reef nutrient-recycling. Coral exometabolomes were enriched in diverse sources of nitrogen and phosphorus, including tyrosine derivatives, oleoyl-taurines, and acyl carnitines. Exometabolites of CCA and turf algae were significantly enriched in nitrogen with distinct signals from polyketide macrolactams and alkaloids, respectively. Macroalgal exometabolomes were dominated by nonnitrogenous compounds, including diverse prenol lipids and steroids. This study provides molecular-level insights into biogeochemical cycling on coral reefs and illustrates how changing benthic cover on reefs influences reef water chemistry with implications for microbial metabolism.

Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives

Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.

Intracellular competition for nitrogen controls dinoflagellate population density in corals

The density of dinoflagellate microalgae in the tissue of symbiotic corals is an important determinant for health and productivity of the coral animal. Yet, the specific mechanism for their regulation and the consequence for coral nutrition are insufficiently understood due to past methodological limitations to resolve the fine-scale metabolic consequences of fluctuating densities. Here, we characterized the physiological and nutritional consequences of symbiont density variations on the colony and tissue level in Stylophora pistillata from the Red Sea. Alterations in symbiont photophysiology maintained coral productivity and host nutrition across a broad range of symbiont densities. However, we demonstrate that density-dependent nutrient competition between individual symbiont cells, manifested as reduced nitrogen assimilation and cell biomass, probably creates the negative feedback mechanism for symbiont population growth that ultimately defines the steady-state density. Despite fundamental changes in symbiont nitrogen assimilation, we found no density-related metabolic optimum beyond which host nutrient assimilation or tissue biomass declined, indicating that host nutrient demand is sufficiently met across the typically observed range of symbiont densities under ambient conditions.

Mercury Biomagnification Through a Coral Reef Ecosystem

Total mercury (Hg) and stable isotopes of nitrogen and carbon were determined in the muscle tissue of 50 species of fishes and invertebrates collected at two sites along the Florida reef tract from April 2012 to December 2013. The objective was to test the hypothesis that high biodiversity in coral reefs leading to complex food webs with increased lateral links reduces biomagnification. However, Hg levels ranged as high 6.84 mg/kg. Interestingly, it was not highest in great barracuda (Sphyraena barracuda), considered the top predatory fish, but instead in small porkfish (Anisotremus virginicus), possibly due to their role as a cleaner fish. Trophic magnification slopes (TMS; from regression of log Hg on δ¹⁵N) as a measure of biomagnification did not differ between sites, ranging from 0.155 ± 0.04 (± 95% CI) to 0.201 ± 0.07. These TMS also were within the ranges of slopes reported for food webs in other ecosystems; thus, biomagnification of Hg in muscle tissue was not reduced in the system.

Fishing down nutrients on coral reefs

Fishing is widely considered a leading cause of biodiversity loss in marine environments, but the potential effect on ecosystem processes, such as nutrient fluxes, is less explored. Here, we test how fishing on Caribbean coral reefs influences biodiversity and ecosystem functions provided by the fish community, that is, fish-mediated nutrient capacity. Specifically, we modelled five processes of nutrient storage (in biomass) and supply (via excretion) of nutrients, as well as a measure of their multifunctionality, onto 143 species of coral reef fishes across 110 coral reef fish communities. These communities span a gradient from extreme fishing pressure to protected areas with little to no fishing. We find that in fished sites fish-mediated nutrient capacity is reduced almost 50%, despite no substantial changes in the number of species. Instead, changes in community size and trophic structure were the primary cause of shifts in ecosystem function. These findings suggest that a broader perspective that incorporates predictable impacts of fishing pressure on ecosystem function is imperative for effective coral reef conservation and management.

Molecular trophic markers in marine food webs and their potential use for coral ecology

Notable advances in ecological genomics have been driven by high-throughput sequencing technology and taxonomically broad sequence repositories that allow us to accurately assess species interactions with great taxonomic resolution. The use of DNA as a marker for ingested food is particularly relevant to address predator-prey interactions and disentangle complex marine food webs. DNA-based methods benefit from reductionist molecular approaches to address ecosystem scale processes, such as community structure and energy flow across trophic levels, among others. Here we review how molecular trophic markers have been used to better understand trophic interactions in the marine environment and their advantages and limitations. We focus on animal groups where research has been focused, such as marine mammals, seabirds, fishes, pelagic invertebrates and benthic invertebrates, and use case studies to illustrate how DNA-based methods unraveled food-web interactions. The potential of molecular trophic markers for disentangling the complex trophic ecology of corals is also discussed.

Fringing reefs exposed to different levels of eutrophication and sedimentation can support similar benthic communities

Benthic communities are sensitive to anthropogenic disturbances which can result in changes in species assemblages. A spatio-temporal survey of environmental parameters was conducted over an 18-month period on four different fringing reefs of Moorea, French Polynesia, with unusual vs. frequent human pressures. This survey included assessment of biological, chemical, and physical parameters. First, the results showed a surprising lack of a seasonal trend, which was likely obscured by short-term variability in lagoons. More frequent sampling periods would likely improve the evaluation of a seasonal effect on biological and ecological processes. Second, the three reef habitats studied that were dominated by corals were highly stable, despite displaying antagonistic environmental conditions through eutrophication and sedimentation gradients, whereas the reef dominated by macroalgae was relatively unstable. Altogether, our data challenge the paradigm of labelling environmental parameters such as turbidity, sedimentation, and nutrient-richness as stress indicators.

Among-species variation in the energy budgets of reef-building corals: scaling from coral polyps to communities

The symbiosis between corals and dinoflagellates promotes the rapid growth of corals in shallow tropical oceans, and the high overall productivity of coral reefs. The aim of this study was to quantify and understand variation in carbon acquisition and allocation among coral species. We measured multiple physiological traits (including symbiont density, calcification, photosynthesis and tissue composition) for the same coral fragments to facilitate direct comparisons between species (Stylophora pistillata, Pocillopora damicornis, Galaxea fascicularis, Turbinaria reniformis and Acropora sp.). Tissue protein content was highly sensitive to the availability of particulate food, increasing in fed colonies of all species. Despite among-species variation in physiology, and consistent effects of feeding on some traits, overall energy allocation to tissue compared with skeleton growth did not depend on food availability. Extrapolating from our results, estimated whole-assemblage carbon uptake varied>20 fold across different coral assemblages, but this variation was largely driven by differences in the tissue surface area of different colony morphologies, rather than to differences in surface-area specific physiological rates. Our results caution against drawing conclusions about reef productivity based solely on physiological rates measured per unit tissue surface area. Understanding the causes and consequences of among-species variation in physiological energetics provides insight into the mechanisms that underlie in the fluxes of organic matter within reefs, and between reefs and the open ocean.

Consistent nutrient storage and supply mediated by diverse fish communities in coral reef ecosystems

Corals thrive in low nutrient environments and the conservation of these globally imperiled ecosystems is largely dependent on mitigating the effects of anthropogenic nutrient enrichment. However, to better understand the implications of anthropogenic nutrients requires a heightened understanding of baseline nutrient dynamics within these ecosystems. Here, we provide a novel perspective on coral reef nutrient dynamics by examining the role of fish communities in the supply and storage of nitrogen (N) and phosphorus (P). We quantified fish-mediated nutrient storage and supply for 144 species and modeled these data onto 172 fish communities (71 729 individual fish), in four types of coral reefs, as well as seagrass and mangrove ecosystems, throughout the Northern Antilles. Fish communities supplied and stored large quantities of nutrients, with rates varying among ecosystem types. The size structure and diversity of the fish communities best predicted N and P supply and storage and N : P supply, suggesting that alterations to fish communities (e.g., overfishing) will have important implications for nutrient dynamics in these systems. The stoichiometric ratio (N : P) for storage in fish mass (~8 : 1) and supply (~20 : 1) was notably consistent across the four coral reef types (but not seagrass or mangrove ecosystems). Published nutrient enrichment studies on corals show that deviations from this N : P supply ratio may be associated with poor coral fitness, providing qualitative support for the hypothesis that corals and their symbionts may be adapted to specific ratios of nutrient supply. Consumer nutrient stoichiometry provides a baseline from which to better understand nutrient dynamics in coral reef and other coastal ecosystems, information that is greatly needed if we are to implement more effective measures to ensure the future health of the world's oceans.

Coral reef primary productivity. A hierarchy of pattern and process

The abundance of interdisciplinary studies of coral reef metabolism means that coral reefs are amongst the best understood of marine benthic communities in terms of the determinants of primary production and nutrient fluxes, and their variation, at different levels of integration. Recent work has extended our understanding of the variation in coral reef productivity at different spatial and temporal scales. Nutrient limitation of production at scales ranging from the organism to the ecosystem is one of the most important topics of research at present, the relevance of which extends well beyond the tropics.

New directions in coral reef microbial ecology

Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate.

Coral Gas: Oxygen Production in Millepora on the Great Barrier Reef

Large volumes of a gas consisting of 69 percent molecular oxygen and 31 percent molecular nitrogen with trace amounts of carbon monoxide, carbon dioxide, and methane have been found trapped inside skeletons of the common hydrozoan Millepora. Volumes were low in the morning and reached a maximum by late afternoon. The oxygen was probably produced by the endolithic (boring) algae, with which the Millepora skeletons are very heavily infested. Oxygen production by endolithic algae in Millepora and in other substrates could influence estimates of reef productivity based on measurements of dissolved gases.

Nitrogen Fixation in a Coral Reef Community

Algal reef flats at Enewetak Atoll, Marshall Islands, fix atmospheric nitrogen at rates comparable to those in managed agriculture. The dominant nitrogen fixer appears to be the blue-green alga Calothrix crustacea. Since this nutrient enrichment contributes to the high productivity of adjacent coral reefs and undoubtedly to atoll lagoons, it is recommended that the algal reef flats receive increased conservation priority.

Tropical Agroecosystems

I have listed some of the ways in which the lowland tropics are not such a warm and wonderful place for the farmer, some of the reasons why it may be unreasonable to expect him to cope with the problems, and some of the ways in which the temperate zones make his task more difficult. The tropics are very close to being a tragedy of the commons on a global scale (69, 103), and it is the temperate zone's shepherds and sheep who are among the greatest offenders (31). Given that the temperate zones have some limited amount of resources with which they are willing to repay the tropics, how can these resources best be spent? The first answer, without doubt, is education, and the incorporation of what is already known about the tropics into that education. Second should be the generation of secure psychological and physical resources for governments that show they are enthusiastic about the development of an SYTA. Third should be support of intensive research needed to generate the set of site-specific rules for specific, clearly identified SYTA's. The subject matter of youths' cultural programming is presumably determined by what they will need during the rest of their lives. A major component of this programming should be the teaching of the socioeconomic rules of a sustained-yield, nonexpanding economy, tuned to the concept of living within the carrying capacity of the country's or region's resources. Incorporating such a process into tropical school systems will cause a major upheaval, if for no other reason than that it will involve an evaluation of the country's resources, what standard of living is to be accepted by those living on them, and who is presently harvesting them. Of even greater impact, it will have to evaluate resources in terms of their ability to raise the standard of living by Y amount for X proportion of the people in the region, rather than in terms of their cash value on the world market. For such a change to be technologically successful, it will require a great deal of pantropical information exchange. This information exchange will cost a great deal of resource, not only in travel funds and support of on-site study, but in insurance policies for the countries that are willing to take the risk of trying to change from an exploitative agroecosystem to an SYTA. For such an experiment to be sociologically successful, it will require a complete change in tropical educational systems, from emphasizing descriptions of events as they now stand, to emphasizing analysis of why things happen the way they do. This will also be very expensive, not only in retreading the technology and mind-sets of current teaching programs, but in gathering the facts on why the tropics have met their current fate. There is a surfeit of biological and agricultural reports dealing with ecological experiments and generalities which suggest that such and such will be the outcome if such and such form of resource harvest is attempted. It is clear that human desiderata regarding a particular site are often radically different from the needs of the "average" wild animals and plants that formed the basis for such experiments and generalities. A finely tuned SYTA will come close to providing a unique solution for each region. The generalities that will rule it are highly stochastic. The more tropical the region, the more evenly weighted the suboutcomes will be, and thus the more likely each region will be to have a unique overall outcome. For example, it is easy to imagine four different parts of the tropics, each with the same kind of soil and the same climate, with four different, successful SYTA's, one based on paddy rice, one on shelterwood forestry, one on tourism, and one on shifting maize culture. A regional experiment station working holistically toward an SYTA is potentially one of the best solutions available. As currently structured, however, almost all tropical experiment stations are inadequate for such a mission. Most commonly they are structured around a single export crop such as coffee, sugar, rubber, cotton, cacao, or tea. A major portion of their budgets comes directly or indirectly from the industry concerned. This industry can hardly be expected to wish to see its production integrated with a sustained-yield system that charges real costs for its materials. When an experiment station is centered around a major food crop, such as rice or maize, the goal becomes one of maximizing production per acre rather than per unit of resource spent; this goal may often be translated into one of generating more people. More general experiment stations tend to be established in the most productive regions of the country and, therefore, receive the most funding. Such regions (islands, intermediate elevations, areas with severe dry seasons) need experiment stations the least because they can often be successfully farmed with only slightly modified temperate zone technologies and philosophies. The administrators of tropical experiment stations often regard their job as a hardship post and tend to orient their research toward the hand that feeds them, which is certainly not the farming communities in which they have been placed. The tropics do not need more hard cash for tractors; they need a program that will show when, where, and how hand care should be replaced with draft animals, and draft animals with tractors. The tropics do not need more randomly gathered, esoteric or applied agricultural research: they need a means to integrate what is already known into the process of developing SYTA's. The tropics do not need more food as much as a means of evaluating the resources they have and generating social systems that will maximize the standard of living possible with those resources, whatever the size. The tropics need a realistic set of expectations.