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ABSTRACT High molecular weight (HMW; >1 kDa) carbohydrates are a major component of dissolved organic matter (DOM) released by benthic primary producers. Despite shifts from coral to algae dominance on many reefs, little is known about the effects of exuded carbohydrates on bacterioplankton communities in reef waters. We compared the monosaccharide composition of HMW carbohydrates exuded by hard corals and brown macroalgae and investigated the response of the bacterioplankton community of an algae-dominated Caribbean reef to the respective HMW fractions. HMW coral exudates were compositionally distinct from the ambient, algae-dominated reef waters and similar to coral mucus (high in arabinose). They further selected for opportunistic bacterioplankton taxa commonly associated with coral stress (i.e., Rhodobacteraceae, Phycisphaeraceae, Vibrionaceae, and Flavobacteriales) and significantly increased the predicted energy-, amino acid-, and carbohydrate-metabolism by 28%, 44%, and 111%, respectively. In contrast, HMW carbohydrates exuded by algae were similar to those in algae tissue extracts and reef water (high in fucose) and did not significantly alter the composition and predicted metabolism of the bacterioplankton community. These results confirm earlier findings of coral exudates supporting efficient trophic transfer, while algae exudates may have stimulated microbial respiration instead of biomass production, thereby supporting the microbialization of reefs. In contrast to previous studies, HMW coral and not algal exudates selected for opportunistic microbes, suggesting that a shift in the prevalent DOM composition and not the exudate type (i.e., coral vs algae) per se, may induce the rise of opportunistic microbial taxa.IMPORTANCEDissolved organic matter (DOM) released by benthic primary producers fuels coral reef food webs. Anthropogenic stressors cause shifts from coral to algae dominance on many reefs, and resulting alterations in the DOM pool can promote opportunistic microbes and potential coral pathogens in reef water. To better understand these DOM-induced effects on bacterioplankton communities, we compared the carbohydrate composition of coral- and macroalgae-DOM and analyzed the response of bacterioplankton from an algae-dominated reef to these DOM types. In line with the proposed microbialization of reefs, coral-DOM was efficiently utilized, promoting energy transfer to higher trophic levels, whereas macroalgae-DOM likely stimulated microbial respiration over biomass production. Contrary to earlier findings, coral- and not algal-DOM selected for opportunistic microbial taxa, indicating that a change in the prevalent DOM composition, and not DOM type, may promote the rise of opportunistic microbes. Presented results may also apply to other coastal marine ecosystems undergoing benthic community shifts.

Abstract The mucus surface layer serves vital functions for scleractinian corals and consists mainly of carbohydrates. Its carbohydrate composition has been suggested to be influenced by environmental conditions (e.g., temperature, nutrients) and microbial pressures (e.g., microbial degradation, microbial coral symbionts), yet to what extend the coral mucus composition is determined by phylogeny remains to be tested. To investigate the variation of mucus carbohydrate compositions among coral species, we analyzed the composition of mucosal carbohydrate building blocks (i.e., monosaccharides) for five species of scleractinian corals, supplemented with previously reported data, to discern overall patterns using cluster analysis. Monosaccharide composition from a total of 23 species (belonging to 14 genera and 11 families) revealed significant differences between two phylogenetic clades that diverged early in the evolutionary history of scleractinian corals (i.e., complex and robust; p = 0.001, R2 = 0.20), mainly driven by the absence of arabinose in the robust clade. Despite considerable differences in environmental conditions and sample analysis protocols applied, coral phylogeny significantly correlated with monosaccharide composition (Mantel test: p

Abstract Seagrass meadows form highly productive and diverse ecosystems in coastal areas worldwide, where they are increasingly exposed to ocean acidification (OA). Efficient nitrogen (N) cycling and uptake are essential to maintain plant productivity, but the effects of OA on N transformations in these systems are poorly understood. Here we show that complete N cycling occurs on leaves of the Mediterranean seagrass Posidonia oceanica at a volcanic CO2 vent near Ischia Island (Italy), with OA affecting both N gain and loss while the epiphytic microbial community structure remains largely unaffected. Daily leaf-associated N2 fixation contributes to 35% of the plant’s N demand under ambient pH, while it contributes to 45% under OA. Nitrification potential is only detected under OA, and N-loss via N2 production increases, although the balance remains decisively in favor of enhanced N gain. Our work highlights the role of the N-cycling microbiome in seagrass adaptation to OA, with key N transformations accelerating towards increased N gain.

Mass bleaching events and local anthropogenic influences have changed the benthic communities of many coral reefs with pronounced spatial differences that are linked to resilience patterns. The Gulf of Thailand is an under-investigated region with only few existing datasets containing long-term developments of coral reef communities using the same method at fixed sites. We thus analyzed benthic community data from seven reefs surrounding the island of Koh Phangan collected between 2014 and 2022. Findings revealed that the average live hard coral cover around Koh Phangan increased from 37% to 55% over the observation period, while turf algae cover decreased from 52% to 29%, indicating some recovery of local reefs. This corresponds to a mean increased rate of coral cover by 2.2% per year. The increase in live hard coral cover was mainly driven by plate-like corals, which quadrupled in proportion over the last decade from 7% to 28% while branching corals decreased in proportion from 9% to 2%. Furthermore, the hard coral genus richness increased, indicating an increased hard coral diversity. While in other reefs, increasing live hard coral cover is often attributed to fast-growing, branching coral species, considered more susceptible to bleaching and other disturbances, the reefs around Koh Phangan recovered mainly via growth of plate-like corals, particularly of the genus Montipora. Although plate-like morphologies are not necessarily more bleaching tolerant, they are important for supporting reef fish abundance and structural complexity on reefs, aiding reef recovery and sturdiness. Hence, our findings indicate that the intensity of local stressors around Kho Phangan allows reef recovery driven by some hard coral species.

In the Mediterranean, the fleshy, mat-forming red alga Phyllophora crispa creates high-biodiversity habitats that influence light availability, water movement, and temperature. However, knowledge about its influence on other key environmental parameters, such as oxygen availability, chlorophyll, and turbidity, is missing. Therefore, we conducted an in situ study in the Western Mediterranean Sea using multiparameter probes that were placed multiple times on algal P. crispa mats, in adjacent Posidonia oceanica seagrass meadows, and on bare hard bottoms. We acquired a total of 17 full diel measurements for dissolved oxygen (DO), chlorophyll, and turbidity in September and October 2019. Results showed that P. crispa mats influence the investigated parameters differently when compared to P. oceanica meadows and that a monthly effect was observed. In September, general DO patterns measured for P. crispa mats and P. oceanica meadows follow the daily cycle depending on light availability, with the measured DO being lower in the P. oceanica meadows compared to the P. crispa mats and the hard-bottom habitats. In October, however, no significant difference in DO concentrations was observed between P. crispa mats and P. oceanica meadows. Results of this study corroborate that P. crispa mats can be viewed as an ecosystem engineering species, influencing environmental parameters and, hence, providing a habitat for outstanding associated biodiversity.

Marine fishes can substantially contribute to the inorganic carbon cycle through the excretion of intestinally precipitated carbonates, but the underlying drivers remain largely unknown. This study identifies the environmental factors and fish traits that predict carbonate excretion rate and mineralogical composition in tropical reef fishes.

Abstract Both global and local factors affect coral reefs worldwide, sometimes simultaneously. An interplay of these factors can lead to phase shifts from hard coral dominance to algae or other invertebrates, particularly soft corals. However, most studies have targeted the effects of single factors, leaving pronounced knowledge gaps regarding the effects of combined factors on soft corals. Here, we investigated the single and combined effects of phosphate enrichment (1, 2, and 8 μM) and seawater temperature increase (26 to 32 °C) on the soft coral Xenia umbellata by quantifying oxygen fluxes, protein content, and stable isotope signatures in a 5-week laboratory experiment. Findings revealed no significant effects of temperature increase, phosphate enrichment, and the combination of both factors on oxygen fluxes. However, regardless of the phosphate treatment, total protein content and carbon stable isotope ratios decreased significantly by 62% and 7% under temperature increase, respectively, suggesting an increased assimilation of their energy reserves. Therefore, we hypothesize that heterotrophic feeding may be important for X. umbellata to sustain their energy reserves under temperature increase, highlighting the advantages of a mixotrophic strategy. Overall, X. umbellata shows a high tolerance towards changes in global and local factors, which may explain their competitive advantage observed at many Indo-Pacific reef locations.

A weaker ocean gyre in the Pine Island Bay, suppressed by higher sea-ice concentration over the ocean near the Thwaites Eastern Ice Shelf, allows more meltwater to enter the sub-ice-shelf cavity. This increases the ocean temperature beneath the ice.

Abstract The resistance of hard corals to warming can be negatively affected by nitrate eutrophication, but related knowledge for soft corals is scarce. We thus investigated the ecophysiological response of the pulsating soft coral Xenia umbellata to different levels of nitrate eutrophication (control = 0.6, medium = 6, high = 37 μM nitrate) in a laboratory experiment, with additional warming (27.7 to 32.8 °C) from days 17 to 37. High nitrate eutrophication enhanced cellular chlorophyll a content of Symbiodiniaceae by 168%, while it reduced gross photosynthesis by 56%. After additional warming, polyp pulsation rate was reduced by 100% in both nitrate eutrophication treatments, and additional polyp loss of 7% d−1 and total fragment mortality of 26% was observed in the high nitrate eutrophication treatment. Warming alone did not affect any of the investigated response parameters. These results suggest that X. umbellata exhibits resistance to warming, which may facilitate ecological dominance over some hard corals as ocean temperatures warm, though a clear negative physiological response occurs when combined with nitrate eutrophication. This study thus confirms the importance of investigating combinations of global and local factors to understand and manage changing coral reefs.

Abstract The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.

IntroductionCoral bleaching immediately impacts the reef benthos, but effects on fish communities are less well understood because they are often delayed and confounded by anthropogenic interactions.MethodsWe assessed changes in fish abundance, biomass and community composition before and after the 2015/16 coral bleaching event at Aldabra Atoll, Seychelles, where local human impacts are minimal, but reefs suffered 50% bleaching-induced coral mortality. We monitored 12 shallow (2–5 m water depth) and nine deep (15 m water depth) permanent survey sites using two survey methods: indicator surveys recording 84 taxa over six years (pre-: 2014; post-bleaching: 2016–2019, 2021), sizing fish based on six size-class categories, and extended fish surveys recording 198 taxa over two years (pre-: 2015; post-bleaching: 2020) with size estimates to the nearest cm (excluding fish < 8 cm).ResultsDuring indicator surveys, mean fish abundance did not change on deep reefs. However, abundance increased by 77% on shallow reefs between 2014 and 2016, which was mainly driven by increases in herbivores and omnivores, likely as a response to elevated turf algae cover following coral mortality. Overall (and functional group-specific) indicator fish biomass did not differ between 2014 and 2016 and remained at or above pre-bleaching levels throughout 2016–2021. In contrast, extended fish surveys in 2015 and 2020 showed a 55–60% reduction in overall abundance on shallow and deep reefs, and a 69% reduction in biomass on shallow reefs, with decreases in biomass occurring in all functional groups. Biomass on deep reefs did not differ between 2015 and 2020. Multivariate analysis of both data sets revealed immediate and long-lasting differences between pre- and post-bleaching fish community compositions, driven largely by herbivorous, omnivorous and piscivorous taxa.DiscussionResults from the indicator surveys suggest that the bleaching event had limited impact on fish abundance and biomass, while the extended surveys recorded changes in abundance and biomass which would otherwise have gone undetected. Our findings improve understanding of the shift a broad community of fish undergoes following a mass coral bleaching event and highlights the value of survey methods that include the full suite of species to detect ecological responses to environmental drivers.

Eutrophication with organic carbon (OC) can be harmful for corals and their reefs due to its stimulating effects on associated and sedimentary microbes, leading to oxygen deficits. Mitigation measures require real-time monitoring of wastewater pulses close to coral reefs, where biogenic carbonate sands act as biocatalytic filters for OC. Microbial fuel cells (MFCs) where the anode is deployed in sediments and the cathode is in contact with the overlying water can directly generate electricity from the microbial degradation of OC in sediments, but their application in coral reefs has not yet been tested. During a laboratory experiment, we thus investigated if MFCs, vertically deployed in coral reef sands, can be used as indicator tools for eutrophication with artificial wastewater (AW, prepared from organic compounds and chemicals) at OC concentrations of 20, 40, or 52 mg C L-1 higher than controls. AW pulses were repeated three times at every concentration, with five weeks between the first and second pulse, and six months between the second and third pulse. Results revealed significant increases in current densities in all AW treatments (means up to 11, 36, and 39 mA m−2, respectively), while controls remained stable and low (-1 to 3 mA m−2). Current densities and OC concentrations correlated significantly (rrm = 0.64), and the slope of the correlation increased with each consecutive AW pulse. This highlights the functionality of the MFC as a qualitative indicator tool for OC pulses even months after deployment. The response time of the MFCs was fast (

Upwelling events can change the sea water conditions within few hours during several months on a seasonal regimen. These events are predicted to intensify due to climate change, exposing shallow benthic organisms to hypoxia and thermal stress, among other extreme conditions. Some coral reefs in the Eastern Tropical Pacific (ETP) recurrently experience upwelling events. Coral reefs off Gorgona Island, Colombia, are exposed to lower oxygen concentrations (3.0 - 3.7 mg O2 L-1) and lower temperatures (17 - 24°C) from mid-January to mid-April, when upwelling develops, compared to the rest of the year (4.9 ± 0.7 mg O2 L-1, 28.4 ± 0.3°C, mean ± SD). While no visible signs of stress have been reported for corals during upwelling, it can be hypothesized that corals would be negatively affected by these changes. Therefore, the objectives of this study were to (1) identify the effects of temperature and hypoxia on the metabolic rate (MO2) of Pocillopora corals under lab conditions, and (2) to examine the changes in skeletal growth and Symbiodiniaceae density of Pocillopora in the field between upwelling and non-upwelling seasons. Findings revealed that MO2 was significantly reduced by 20% at 24°C and significantly increased by 10% at 32°C compared to 28°C. During the upwelling season, Pocillopora corals exhibited a 52% increase in Symbiodiniaceae density, but the growth rate decreased by 50% compared to the non-upwelling season. Fast changes in water conditions during the upwelling strongly affects the metabolism of Pocillopora corals. Although conditions during upwelling were not lethal, they compromised the energy of the coral for their vital functions, indicating that upwelling pushes them toward their physiological limit. Consequently, predicted increases in upwelling events in combination with ocean warming and deoxygenation may be particularly critical for upwelling-exposed corals and the reefs they build in the Eastern Tropical Pacific.

One mechanism giving fleshy algae a competitive advantage over corals during reef degradation is algal-induced and microbially-mediated hypoxia (typically less than 69.5 µmol oxygen L−1). During hypoxic conditions oxygen availability becomes insufficient to sustain aerobic respiration in most metazoans. Algae are more tolerant of low oxygen conditions and may outcompete corals weakened by hypoxia. A key question on the ecological importance of this mechanism remains unanswered: How extensive are local hypoxic zones in highly turbulent aquatic environments, continuously flushed by currents and wave surge? To better understand the concert of biological, chemical, and physical factors that determine the abundance and distribution of oxygen in this environment, we combined 3D imagery, flow measurements, macro- and micro-organismal abundance estimates, and experimentally determined biogenic oxygen and carbon fluxes as input values for a 3D bio-physical model. The model was first developed and verified for controlled flume experiments containing coral and algal colonies in direct interaction. We then developed a three-dimensional numerical model of an existing coral reef plot off the coast of Curaçao where oxygen concentrations for comparison were collected in a small-scale grid using fiberoptic oxygen optodes. Oxygen distribution patterns given by the model were a good predictor for in situ concentrations and indicate widespread localized differences exceeding 50 µmol L-1 over distances less than a decimeter. This suggests that small-scale hypoxic zones can persist for an extended period of time in the turbulent environment of a wave- and surge- exposed coral reef. This work highlights how the combination of three-dimensional imagery, biogenic fluxes, and fluid dynamic modeling can provide a powerful tool to illustrate and predict the distribution of analytes (e.g., oxygen or other bioactive substances) in a highly complex system.

Comparative analyses of fleshy red algae mats and seagrass meadows highlight their value in fostering sessile invertebrate biodiversity.

Abstract Ocean Acidification (OA), due to rising atmospheric CO2, can affect the seagrass holobiont by changing the plant's ecophysiology and the composition and functioning of its epiphytic community. However, our knowledge of the role of epiphytes in the productivity of the seagrass holobiont in response to environmental changes is still very limited. CO2 vents off Ischia Island (Italy) naturally reduce seawater pH, allowing to investigate the adaptation of the seagrass Posidonia oceanica L. (Delile) to OA. Here, we analyzed the percent cover of different epiphytic groups and the epiphytic biomass of P. oceanica leaves, collected inside (pH 6.9–7.9) and outside (pH 8.1–8.2) the CO2 vents. We estimated the contribution of epiphytes to net primary production (NPP) and respiration (R) of leaf sections collected from the vent and ambient pH sites in laboratory incubations. Additionally, we quantified net community production (NCP) and community respiration (CR) of seagrass communities in situ at vent and ambient pH sites using benthic chambers. Leaves at ambient pH sites had a 25% higher total epiphytic cover with encrusting red algae (32%) dominating the community, while leaves at vent pH sites were dominated by hydrozoans (21%). Leaf sections with and without epiphytes from the vent pH site produced and respired significantly more oxygen than leaf sections from the ambient pH site, showing an average increase of 47 ± 21% (mean ± SE) in NPP and 50 ± 4% in R, respectively. Epiphytes contributed little to the increase in R; however, their contribution to NPP was important (56 ± 6% of the total flux). The increase in productivity of seagrass leaves adapted to OA was only marginally reflected by the results from the in situ benthic chambers, underlining the complexity of the seagrass community response to naturally occurring OA conditions.

Nitrogen limitation is the foundation of stable coral-algal symbioses. Diazotrophs, prokaryotes capable of fixing N2 into ammonia, support the productivity of corals in oligotrophic waters, but could contribute to the destabilization of holobiont functioning when overstimulated. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress increases diazotroph abundance and activity, thereby increasing nitrogen availability and destabilizing the coral-algal symbiosis. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (via relative quantification of nifH gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral Xenia umbellata and the more autotrophic gorgonian Pinnigorgia flava, under (i) labile DOC enrichment for 21 days, followed by (ii) combined labile DOC enrichment and heat stress for 24 days. Without heat stress, relative diazotroph abundances in X. umbellata and P. flava were unaffected by DOC enrichment. During heat stress, DOC enrichment (20 and 40 mg glucose l−1) increased the relative abundances of diazotrophs by sixfold in X. umbellata and fourfold in P. flava, compared with their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals by stimulating diazotroph proliferation. Ultimately, the disruption of nitrogen cycling may further compromise octocoral fitness by destabilizing symbiotic nutrient cycling. Therefore, improving local wastewater facilities to reduce labile DOC input into vulnerable coastal ecosystems may help octocorals cope with ocean warming.

Dissolved organic carbon (DOC) enrichment and ocean warming both negatively affect hard corals, but studies on their combined effects on other reef organisms are scarce. Octocorals are likely to become key players in future reef communities, but they are still highly under-investigated with regard to their responses to global and local environmental changes. Thus, we evaluated the individual and combined effects of DOC enrichment (10, 20 and 40 mg L−1 DOC, added as glucose) and warming (stepwise from 26 to 32 °C) on the widespread Indo-Pacific gorgonian Pinnigorgia flava in a 45-day laboratory experiment. Oxygen fluxes (net photosynthesis and respiration), as well as Symbiodiniaceae cell density and coral growth were assessed. Our results highlight a differential ecophysiological response to DOC enrichment and warming as well as their combination. Individual DOC addition did not significantly affect oxygen fluxes nor Symbiodiniaceae cell density and growth, while warming significantly decreased photosynthesis rates and Symbiodiniaceae cell density. When DOC enrichment and warming were combined, no effect on P. flava oxygen fluxes was observed while growth responded to certain DOC conditions depending on the temperature. Our findings indicate that P. flava is insensitive to the individual effect of DOC enrichment, but not to warming and the two stressors combined. This suggests that, if temperature remains below certain thresholds, this gorgonian species may gain a competitive advantage over coral species that are reportedly more affected by DOC eutrophication. However, under the expected increasing temperature scenarios, it is also likely that this octocoral species will be negatively affected, with potential consequences on community structure. This study contributes to our understanding of the conditions that drive phase shift dynamics in coastal coral reef ecosystemds.

Coral reefs may experience lower pH values as a result of ocean acidification (OA), which has negative consequences, particularly for calcifying organisms. Thus far, the effects of this global factor have been mainly investigated on hard corals, while the effects on soft corals remain relatively understudied. We therefore carried out a manipulative aquarium experiment for 21 days to study the response of the widespread pulsating soft coral Xenia umbellata to simulated OA conditions. We gradually decreased the pH from ambient (~8.3) to three consecutive 7-day long pH treatments of 8.0, 7.8, and 7.6, using a CO2 dosing system. Monitored response variables included pulsation rate, specific growth rate, visual coloration, survival, Symbiodiniaceae cell densities and chlorophyll a content, photosynthesis and respiration, and finally stable isotopes of carbon (C) and nitrogen (N) as well as CN content. Pulsation decreased compared to controls with each consecutive lowering of the pH, i.e., 17% at pH 8.0, 26% at pH 7.8 and 32% at pH 7.6, accompanied by an initial decrease in growth rates of ~60% at pH 8.0, not decreasing further at lower pH. An 8.3 ‰ decrease of δ13C confirmed that OA exposed colonies had a higher uptake and availability of atmospheric CO2. Coral productivity, i.e., photosynthesis, was not affected by higher dissolved inorganic C availability and none of the remaining response variables showed any significant differences. Our findings suggest that pulsation is a phenotypically plastic mechanism for X. umbellata to adjust to different pH values, resulting in reduced growth rates only, while maintaining high productivity. Consequently, pulsation may allow X. umbellata to inhabit a broad pH range with minimal effects on its overall health. This resilience may contribute to the competitive advantage that soft corals, particularly X. umbellata, have over hard corals.

Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution. Due to ocean warming and eutrophication, the ocean is deoxygenating. In the Eastern Tropical Pacific (ETP), deep waters with low DO (20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora. Because DO concentrations in coral reefs of Gorgona Island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.

Hard corals are in decline as a result of the simultaneous occurrence of global (e.g., ocean warming) and local (e.g., inorganic eutrophication) factors, facilitating phase shifts towards soft coral dominated reefs. Yet, related knowledge about soft coral responses to anthropogenic factors remains scarce. We thus investigated the ecophysiological response of the pulsating soft coral Xenia umbellata to individual and combined effects of phosphate enrichment (1, 2, and 8 μM) and ocean warming (26 to 32°C) over 35 days. Throughout the experiment, we assessed pulsation, mortality, Symbiodiniaceae density, and cellular chlorophyll a content. Simulated ocean warming up to 30°C led to a significant increase in polyp pulsation and by the end of the experiment to a significant increase in Symbiodiniaceae density, whereas cellular chlorophyll a content significantly decreased with warming, regardless of the phosphate treatment. The combination of phosphate enrichment and simulated ocean warming increased pulsation significantly by 41 – 44%. Warming alone and phosphate enrichment alone did not affect any of the investigated response parameters. Overall, X. umbellata displayed a high resilience towards ocean warming with no mortality in all treatments. Phosphate enrichment enabled soft corals to significantly increase their pulsation under increasing temperatures which may enhance their resilience towards ocean warming. This, in turn, could further facilitate their dominance over hard corals on future reefs.

The upside-down jellyfish Cassiopea increasingly occurs in many (sub-) tropical coastal habitats such as mangrove forests, seagrass meadows, and coral reefs. Its mixotrophic lifestyle and ecophysiological plasticity as well as a high regenerative capacity may be reasons for its success. While the regeneration of umbrella tissue and body structures (i.e. rhopalia and oral arms) was already demonstrated, it remains unclear whether a fully functioning medusa can regenerate from only umbrella tissue. In this study, we thus investigated the regeneration of umbrella fragments over time. We conducted a laboratory experiment for which we used 18 Cassiopea medusae of three different size classes that were cut into two pieces each, one fragment with oral arms and one without. Over a total observation period of 5 weeks, we regularly monitored survival, pulsation behavior, growth and the regeneration pattern of fragments. Findings revealed that 100% of the fragments with oral arms and 88% of the fragments without oral arms survived. Pulsation behavior occurred in all fragments and lasted until the end of the experiment in 94% of all fragments. The umbrella area of fragments without oral arms showed a significantly higher decrease in the first two weeks compared to fragments with oral arms. A complete regeneration of umbrella tissue was observed in all fragments, with and without oral arms alike, and 50% of all fragments even regenerated rhopalia or oral arms as body structures after 33 days. These results suggest an outstanding regenerative capacity of Cassiopea jellyfish after fragmentation. This may contribute to (i) explain the currently observed success of upside-down jellyfish and (ii) extend our knowledge about its regeneration process, which might even act as an asexual reproduction mode in Cassiopea.

Abstract Coral reefs experience phase shifts from coral- to algae-dominated benthic communities, which could affect the interplay between processes introducing and removing bioavailable nitrogen. However, the magnitude of such processes, i.e., dinitrogen (N2) fixation and denitrification levels, and their responses to phase shifts remain unknown in coral reefs. We assessed both processes for the dominant species of six benthic categories (hard corals, soft corals, turf algae, coral rubble, biogenic rock, and reef sands) accounting for > 98% of the benthic cover of a central Red Sea coral reef. Rates were extrapolated to the relative benthic cover of the studied organisms in co-occurring coral- and algae-dominated areas of the same reef. In general, benthic categories with high N2 fixation exhibited low denitrification activity. Extrapolated to the respective reef area, turf algae and coral rubble accounted for > 90% of overall N2 fixation, whereas corals contributed to more than half of reef denitrification. Total N2 fixation was twice as high in algae- compared to coral-dominated areas, whereas denitrification levels were similar. We conclude that algae-dominated reefs promote new nitrogen input through enhanced N2 fixation and comparatively low denitrification. The subsequent increased nitrogen availability could support net productivity, resulting in a positive feedback loop that increases the competitive advantage of algae over corals in reefs that experienced a phase shift.

Abstract Documenting post-bleaching trajectories of coral reef communities is crucial to understand their resilience to climate change. We investigated reef community changes following the 2015/16 bleaching event at Aldabra Atoll, where direct human impact is minimal. We combined benthic data collected pre- (2014) and post-bleaching (2016–2019) at 12 sites across three locations (lagoon, 2 m depth; seaward west and east, 5 and 15 m depth) with water temperature measurements. While seaward reefs experienced relative hard coral reductions of 51–62%, lagoonal coral loss was lower (− 34%), probably due to three-fold higher daily water temperature variability there. Between 2016 and 2019, hard coral cover did not change on deep reefs which remained dominated by turf algae and Halimeda, but absolute cover on shallow reefs increased annually by 1.3% (east), 2.3% (west) and 3.0% (lagoon), reaching, respectively, 54%, 68% and 93% of the pre-bleaching cover in 2019. Full recovery at the shallow seaward locations may take at least five more years, but remains uncertain for the deeper reefs. The expected increase in frequency and severity of coral bleaching events is likely to make even rapid recovery as observed in Aldabra’s lagoon too slow to prevent long-term reef degradation, even at remote sites.

Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.

In the Mediterranean Sea, the fleshy red alga Phyllophora crispa forms dense mats of up to 15 cm thickness, mainly located on rocky substrates in water depths below 20 m. Because of the observed density of these mats and some first observations, we hypothesize that P. crispa is a yet undescribed ecosystem engineer that provides a multitude of ecological niches for associated organisms along small-scale environmental gradients. Therefore, we conducted an in-situ pilot study in the Western Mediterranean Sea to assess potential influence of the algae mats on the key environmental factors water movement, temperature and light intensity. We comparatively and simultaneously measured in P. crispa mats, in neighboring Posidonia oceanica seagrass meadows, on neighboring bare rocky substrates without algae mats, and in the directly overlying water column. We used several underwater logging sensors and gypsum clod cards. Findings revealed that P. crispa significantly reduced water movement by 41% compared to the overlying water column, whereas water movement was not affected by P. oceanica meadows and bare rocky substrates. Surprisingly, P. crispa increased the water temperature by 0.3°C relative to the water column, while the water temperature in P. oceanica and on bare rocky substrates was reduced by 0.5°C. Light intensity inside the red algae mats was reduced significantly by 69% compared to the water column. This was similar to measured light reduction of 77% by P. oceanica. These findings highlight the strong influence of the dense red algae mats on some key environmental factors. Their influence is obviously similar or even higher than for the well-known seagrass ecosystem engineer. This may be a factor that facilitates associated biodiversity similarly as described for P. oceanica.

Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.

Recent research suggests that nitrogen (N) cycling microbes are important for coral holobiont functioning. In particular, coral holobionts may acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove excess N via denitrification activity. However, our understanding of environmental drivers on these processes in hospite remains limited. Employing the strong seasonality of the central Red Sea, this study assessed the effects of environmental parameters on the proportional abundances of N cycling microbes associated with the hard corals Acropora hemprichii and Stylophora pistillata. Specifically, we quantified changes in the relative ratio between nirS and nifH gene copy numbers, as a proxy for seasonal shifts in denitrification and N2 fixation potential in corals, respectively. In addition, we assessed coral tissue-associated Symbiodiniaceae cell densities and monitored environmental parameters to provide a holobiont and environmental context, respectively. While ratios of nirS to nifH gene copy numbers varied between seasons, they revealed similar seasonal patterns in both coral species, with ratios closely following patterns in environmental nitrate availability. Symbiodiniaceae cell densities aligned with environmental nitrate availability, suggesting that the seasonal shifts in nirS to nifH gene abundance ratios were probably driven by nitrate availability in the coral holobiont. Thereby, our results suggest that N cycling in coral holobionts probably adjusts to environmental conditions by increasing and/or decreasing denitrification and N2 fixation potential according to environmental nitrate availability. Microbial N cycling may, thus, extenuate the effects of changes in environmental nitrate availability on coral holobionts to support the maintenance of the coral–Symbiodiniaceae symbiosis.

The Eastern Tropical Pacific (ETP) is one of the most isolated and least studied regions in the world. This particularly applies to the coast of El Salvador, where the only reef between Guatemala and Nicaragua, called Los Cóbanos reef, is located. There is very little published information about the reef’s biodiversity, and to our knowledge, no research on its ecology and responses to anthropogenic impacts, such as overfishing, has been conducted. The present study, therefore, described the benthic community of Los Cóbanos reef, El Salvador, using the Line-Point-Intercept-Transect method and investigated changes in the benthic community following the exclusion of piscine macroherbivores over a period of seven weeks. Results showed high benthic algae cover (up to 98%), dominated by turf and green algae, and low coral cover (0–4%). Porites lobata was the only hermatypic coral species found during the surveys. Surprisingly, crustose coralline algae (CCA) showed a remarkable total cover increase by 58%, while turf algae cover decreased by 82%, in experimental plots after seven weeks of piscine macroherbivore exclusion. These findings apparently contradict the results of most previous similar studies. While it was not possible to ascertain the exact mechanisms leading to these drastic community changes, the most likely explanation is grazing on turf by small grazing macroherbivores that had access to the cages during the experiment and clearing of CCA initially covered by epiphytes and sediments. A higher CCA cover would promote the succesful settlement by corals and prevent further erosion of the reef framework. Therefore it is crucial to better understand algal dynamics, herbivory, and implications of overfishing at Los Cóbanos to avoid further reef deterioration. This could be achieved through video surveys of the fish community, night-time observations of the macroinvertebrate community, exclusion experiments that also keep out herbivorous macroinvertebrates, and/or experimental assessments of turf algae/CCA interactions.

Coral recruitment and successive growth are essential for post-disturbance reef recovery. As coral recruit and juvenile abundances vary across locations and under different environmental regimes, their assessment at remote, undisturbed reefs improves our understanding of early life stage dynamics of corals. Here, we first explored changes in coral juvenile abundance across three locations (lagoon, seaward west and east) at remote Aldabra Atoll (Seychelles) between 2015 and 2019, which spanned the 2015/16 global coral bleaching event. Secondly, we measured variation in coral recruit abundance on settlement tiles from two sites (lagoon, seaward reef) during August 2018–August 2019. Juvenile abundance decreased from 14.1 ± 1.2 to 7.4 ± 0.5 colonies m-2 (mean ± SE) during 2015–2016 and increased to 22.4 ± 1.2 colonies m-2 during 2016–2019. Whilst juvenile abundance increased two- to three-fold at the lagoonal and seaward western sites during 2016–2018 (from 7.7–8.3 to 17.3–24.7 colonies m-2), increases at the seaward eastern sites occurred later (2018–2019; from 5.8–6.9 to 16.6–24.1 colonies m-2). The composition of coral recruits on settlement tiles was dominated by Pocilloporidae (64–92% of all recruits), and recruit abundance was 7- to 47-fold higher inside than outside the lagoon. Recruit abundance was highest in October–December 2018 (2164 ± 453 recruits m-2) and lowest in June–August 2019 (240 ± 98 recruits m-2). As Acroporid recruit abundance corresponded to this trend, the results suggest that broadcast spawning occurred during October–December, when water temperature increased from 26 to 29°C. This study provides the first published record on coral recruit abundance in the Seychelles Outer Islands, indicates a rapid (2–3 years) increase of juvenile corals following a bleaching event, and provides crucial baseline data for future research on reef resilience and connectivity within the region.

Biological imaging is an essential tool to visualise and obtain reference data. In this context, the programme ImageJ has been widely used in many disciplines to determine the surface areas of planar biological samples in marine and aquatic experimental biology. Despite its range of advantages, ImageJ is relatively time-consuming, because of the need to manually select the target areas for quantification. Hence, we here evaluated the freeware programme Photopea as a potential alternative by comparing the accuracy and time required for the surface area quantification of exemplary algae compared with established ImageJ analysis. Our results show that Photopea is equally accurate as ImageJ, but 45% more time efficient. This time efficiency originates from using colour contrast that reduces the time needed to analyse each picture. Photopea thus offers an accurate, rapid, and cost-free tool to easily obtain reference data from field and laboratory experiments. This tool is particularly useful for experiments with an extensive sample size of specimens and thus can increase the power of study results.

With its geographically isolated location and geological history, the Mediterranean Sea harbors well-known biodiversity hotspots, such as Posidonia oceanica seagrass meadows. Recently, long-living mats formed by the fleshy red alga Phyllophora crispa have been described to be associated with a high diversity of sessile invertebrates in the Tyrrhenian Sea. One of the key taxa among these sessile invertebrates are bryozoans: their abundance, diversity, and spatial distribution in P. crispa mats represent a gap in scientific knowledge. Thus, we conducted a pilot study on bryozoan assemblages associated with P. crispa mats around Giglio Island (Tuscan Archipelago, Italy) in 2018, followed by a comparative study on four sites distributed around the island in the subsequent year, 2019. We compared these findings to bryozoan abundance and diversity on P. oceanica shoots and leaves during the second expedition. The findings revealed more than 46 families, with a significantly higher number of taxa identified in P. crispa mats (33) than in P. oceanica meadows (29). The Shannon diversity index was similar between P. crispa and P. oceanica shoots, while Pielou’s evenness index was lower in P. crispa mats. The most abundant families reported across all habitats were Crisiidae, Aetidae, and Lichenoporidae; but the most abundant family on P. crispa was Chlidoniidae (Chlidonia pyriformis). The assemblages associated with P. crispa differed among sites, with higher abundances but lower diversity on the exposed southernmost site. The total bryozoan abundance was significantly higher on P. crispa (average 2.83 × 106 ± 1.99 × 106 colonies per m2 seafloor) compared to P. oceanica meadows (average 0.54 × 106 ± 0.34 × 106 colonies per m2 seafloor). Our results show a high diversity of bryozoans on P. crispa thalli compared to P. oceanica meadows, which was consistent throughout the study. These findings confirm the value of the red alga-generated habitat for associated bryozoans and may have implications for future biodiversity assessments and conservation measures.

Human activities are changing ecosystems at an unprecedented rate, yet large-scale studies into how local human impacts alter natural systems and interact with other aspects of global change are still lacking. Here we provide empirical evidence that local human impacts fundamentally alter relationships between ecological communities and environmental drivers. Using tropical coral reefs as a study system, we investigated the influence of contrasting levels of local human impact using a spatially extensive dataset spanning 62 outer reefs around inhabited Pacific islands. We tested how local human impacts (low versus high determined using a threshold of 25 people km−2 reef) affected benthic community (i) structure, and (ii) relationships with environmental predictors using pre-defined models and model selection tools. Data on reef depth, benthic assemblages, and herbivorous fish communities were collected from field surveys. Additional data on thermal stress, storm exposure, and market gravity (a function of human population size and reef accessibility) were extracted from public repositories. Findings revealed that reefs subject to high local human impact were characterised by relatively more turf algae (>10% higher mean absolute coverage) and lower live coral cover (9% less mean absolute coverage) than reefs subject to low local human impact, but had similar macroalgal cover and coral morphological composition. Models based on spatio-physical predictors were significantly more accurate in explaining the variation of benthic assemblages at sites with low (mean adjusted-R2 = 0.35) rather than high local human impact, where relationships became much weaker (mean adjusted-R2 = 0.10). Model selection procedures also identified a distinct shift in the relative importance of different herbivorous fish functional groups in explaining benthic communities depending on the local human impact level. These results demonstrate that local human impacts alter natural systems and indicate that projecting climate change impacts may be particularly challenging at reefs close to higher human populations, where dependency and pressure on ecosystem services are highest.

Nitrogen (N) cycling in coral reefs is of key importance for these oligotrophic ecosystems, but knowledge about its pathways is limited. While dinitrogen (N2) fixation is comparably well studied, the counteracting denitrification pathway is under-investigated, mainly because of expensive and relatively complex experimental techniques currently available. Here, we combined two established acetylene-based assays to one single setup to determine N2-fixation and denitrification performed by microbes associated with coral reef substrates/organisms simultaneously. Accumulating target gases (ethylene for N2-fixation, nitrous oxide for denitrification) were measured in gaseous headspace samples via gas chromatography. We measured N2-fixation and denitrification rates of two Red Sea coral reef substrates (filamentous turf algae, coral rubble), and demonstrated, for the first time, the co-occurrence of both N-cycling processes in both substrates. N2-fixation rates were up to eight times higher during the light compared to the dark, whereas denitrification rates during dark incubations were stimulated for turf algae and suppressed for coral rubble compared to light incubations. Our results highlight the importance of both substrates in fixing N, but their role in relieving N is potentially divergent. Absolute N2-fixation rates of the present study correspond with rates reported previously, even though likely underestimated due to an initial lag phase. Denitrification is also presumably underestimated due to incomplete nitrous oxide inhibition and/or substrate limitation. Besides these inherent limitations, we show that a relative comparison of N2-fixation and denitrification activity between functional groups is possible. Thus, our approach facilitates cost-efficient sample processing in studies interested in comparing relative rates of N2-fixation and denitrification.

Recent research indicates that hard corals in a process that is termed phase shift are often replaced by soft corals in reefs. The simultaneous occurrence of local (i.e. organic eutrophication as highly under-investigated parameter) and global (i.e. ocean warming) factors may facilitate these phase shifts as hard corals are negatively affected by both ocean warming and organic eutrophication. Knowledge about soft coral responses to environmental change remains incomplete, although these organisms are becoming important players in reefs. The present study thus investigated the individual and combined effects of organic eutrophication (as glucose addition) and warming on the ecological data of the pulsating soft coral Xenia umbellata. We assessed health status, growth and pulsation rates of soft corals in a 45 day aquarium experiment, with first manipulation of organic eutrophication (no, low, medium and high glucose addition) over 21 days followed by step-wise increases in water temperature from 26 to 32 °C over 24 days. Findings revealed that glucose addition did not affect health status, growth and pulsation rates of the investigated soft corals. Under simulated ocean warming, soft corals that had experienced organic eutrophication before, maintained significantly higher pulsation rates (averaging 22 beats per minute—bpm) and no mortality compared to the controls that showed a decrease of 56% (averaging 15 bpm) in pulsation rates and mortality of 30% at water temperatures of 32 °C compared to 26 °C. This apparently positive effect of organic eutrophication on the ecological data of soft corals under an ocean warming scenario decreased with increasing water temperature. This study thus indicates that (a) organic eutrophication as additional energy source up to a certain threshold may increase the resistance of soft corals to ocean warming and (b) pulsation rates of soft corals may be used as inexpensive, easily detectable, and non-invasive early warning indicator for ocean warming effects on benthic reef communities. When comparing findings of this study for soft corals with previous results for hard corals, it can be assumed that soft corals under the predicted increases of organic eutrophication and warming gain more and more competitive advantages. This may further facilitate phase shifts from hard to soft corals in warming reefs.

While various sources increasingly release nutrients to the Red Sea, knowledge about their effects on benthic coral reef communities is scarce. Here, we provide the first comparative assessment of the response of all major benthic groups (hard and soft corals, turf algae and reef sands—together accounting for 80% of the benthic reef community) to in-situ eutrophication in a central Red Sea coral reef. For 8 weeks, dissolved inorganic nitrogen (DIN) concentrations were experimentally increased 3-fold above environmental background concentrations around natural benthic reef communities using a slow release fertilizer with 15% total nitrogen (N) content. We investigated which major functional groups took up the available N, and how this changed organic carbon (Corg) and N contents using elemental and stable isotope measurements. Findings revealed that hard corals (in their tissue), soft corals and turf algae incorporated fertilizer N as indicated by significant increases in δ15N by 8%, 27% and 28%, respectively. Among the investigated groups, Corg content significantly increased in sediments (+24%) and in turf algae (+33%). Altogether, this suggests that among the benthic organisms only turf algae were limited by N availability and thus benefited most from N addition. Thereby, based on higher Corg content, turf algae potentially gained competitive advantage over, for example, hard corals. Local management should, thus, particularly address DIN eutrophication by coastal development and consider the role of turf algae as potential bioindicator for eutrophication.

Abstract The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host‐microbe associations under adverse environmental conditions. To gain insight into the stability of coral host‐microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora‐associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.

The Mediterranean Sea comprises habitats such as Posidonia oceanica seagrass meadows that exhibit high associated biodiversity of sessile organisms. Recent pilot research indicates that benthic mats formed by the scarcely investigated fleshy red alga Phyllophora crispa also host a high diversity of benthic fauna. Among the key taxa found in these mats in the recent pilot studies are benthic foraminifera that live as epiphytes on the red algae thalli. Knowledge about their abundance and species richness associated with this habitat in relation to reference habitats is missing. We thus carried out a comparative assessment focusing on foraminifera within samples from P. crispa mats and neighboring P. oceanica meadows on five different sampling sites around Giglio Island in the Tuscan Archipelago (Tyrrhenian Sea, Italy). A total of 104 different foraminiferal taxa were identified, of which a total of 85 taxa were found in P. crispa samples (46 exclusively in this habitat). This biodiversity was higher compared to other studies on phytal habitats in the Mediterranean Sea. The number of foraminiferal taxa associated with P. crispa was significantly higher (average 27.5 ± 8.1 taxa) compared to P. oceanica (leaves average 7.0 ± 3.6, shoots average 7.9 ± 3.4 taxa). The abundance of foraminifera (12,000 individuals m−2 surface area of P. crispa mat) was also higher than in the neighboring P. oceanica meadows (7792 individuals m−2 leaf and 8171 individuals m−2 shoot surface area). The most frequently found taxa across habitats were Miniacina miniacea, Lobatula lobatula, and Sejunctella sp. (24%, 20%, and 6% of the total population, respectively). Our results imply that P. crispa mats host an exceptional diversity of associated foraminifera that is even higher than those associated with seagrass meadows. Red algae mats built by P. crispa may thus be considered as potential refuge habitats and biodiversity reservoirs in management and conservation.

Microbial dinitrogen (N2) fixation (diazotrophy) is a trait critical for coral holobiont functioning. The contribution of N2 fixation to holobiont nitrogen (N) supply likely depends on the ecological niche of the coral holobiont. Consequently, coral-associated diazotroph communities may exhibit distinct activity patterns across a water depth gradient. We thus compared relative abundances of diazotrophs in the tissues of two common hard coral species, Podabacia sp. and Pachyserisspeciosa, along their water depth distribution (10–30 m and 30–50 m, respectively) in the Central Red Sea. The relative gene copy numbers of the nifH gene (i.e., referenced against the eubacterial 16S rRNA gene), as a proxy for N2 fixation potential, were assessed via quantitative PCR. We hypothesized that relative nifH gene copy numbers would decrease with water depth, assuming a related shift from autotrophy to heterotrophy. Findings confirmed this hypothesis and revealed that nifH gene abundances for both corals decreased by ∼97% and ∼90% from the shallowest to the deepest collection site. However, this result was not significant for Pachyserisspeciosa due to high biological variability. The observed decrease in nifH gene abundances may be explained by the relative increase in heterotrophy of the coral animal at increasing water depths. Our results underline the importance of interpreting microbial functions and associated nutrient cycling processes within the holobiont in relation to water depth range reflecting steep environmental gradients.

Observations of coral–algal competition can provide valuable information about the state of coral reef ecosystems. Here, we report contact rates and apparent competition states for six shallow lagoonal reefs in Fiji. A total of 81.4% of examined coral perimeters were found to be in contact with algae, with turf algae (54.7%) and macroalgae of the genus Lobophora (16.8%) representing the most frequently observed contacts. Turf algae competitiveness was low, with 21.8% of coral–turf contacts being won by the algae (i.e. overgrowth or bleaching of coral tissue). In contrast, Lobophora competitiveness against corals was high, with 62.5% of contacts being won by the alga. The presence of epiphytic algae on Lobophora was associated with significantly greater algal competitiveness against corals, with 75.8% and 21.1% of interactions recorded as algal wins in the presence and absence of epiphytes, respectively. Sedimentation rate, herbivorous fish biomass, and coral colony size did not have a significant effect on Lobophora–coral interactions. This research indicates a novel and important role of epiphytes in driving the outcome of coral–algal contacts.

The Mediterranean Sea harbors more than 17,000 eukaryotic marine species, with several ecosystems recognized as biodiversity hotspots, such as Posidonia oceanica meadows. Recent research indicates that benthic mats formed by the fleshy red alga Phyllophora crispa are also associated with high species richness. Among key groups found in these mats are sessile polychaetes, which live as epiphytes on the red algae thalli. Knowledge of abundance, species richness, and spatial variation of polychaetes associated with these habitats is still scarce. We carried out a comparative assessment focusing on serpulid polychaetes within samples from P. crispa mats and neighboring P. oceanica meadows at six different sampling sites around Giglio Island (Tyrrhenian Sea, Italy). A total of 17 serpulid taxa were identified. The abundance of serpulids (5665 individuals m−2 of P. crispa mat) were similar to neighboring P. oceanica meadows (2304 individuals m−2 leaves and 5890 individuals m−2 shoots). The number of serpulid taxa was significantly higher in P. crispa mats (average 6.63 ± 1.32 taxa) compared to P. oceanica beds (average 1.56 ± 0.63 and 1.84 ± 1.04 taxa in leaves and shoots, respectively). Within habitat type, there were no significant differences in species richness between sites. The most abundant species found was Josephella marenzelleri (61% of individuals), while Vermiliopsis spp. and Bathyvermilia sp. were exclusively found in P. crispa samples. Our results highlight that P. crispa mats host an exceptional diversity and that these habitats should be included in conservation strategies. Further research should focus on the significance of other important taxonomic groups within these mats and evaluate the distribution of P. crispa in different regions of the Mediterranean Sea.

Coral reef resilience is greatly influenced by herbivory. There is a need to identify key fish species fulfilling this critical function in biogeographically distinct regions. This experimental in situ study investigated fish herbivory in coral reefs of the lower Gulf of Thailand characterized by a considerably low herbivorous fish biomass and diversity, but high live coral and low macroalgal cover. This provided an intriguing situation for macroalgal browsing research. Visual census techniques assessed the abundance of local herbivorous fish species, and filmed single-choice assays using the macroalga Turbinaria evaluated mass-standardized bites (ms-bites) and biomass removal. Multiple-choice assays offering four locally abundant macroalgae identified specific biomass removal and ms-bites to uncover selection and avoidance patterns of observed fish species. The rabbitfish Siganusvirgatus constituted only 39% of herbivore biomass but accounted for 90% of ms-bites. In multiple-choice assays, fishes took most (61%) bites on Sargassum, followed by Padina (28%) and Turbinaria (11%), while Lobophora was avoided. S. virgatus exhibited the most generalized browsing pattern of all species observed. Coinciding with recent studies, our findings suggest that S. virgatus plays a key functional role in reefs characterized by low diversity of herbivores and low functional redundancy.

In 2005, an extreme heatwave hit the Wider Caribbean, followed by 13 hurricanes (including hurricanes Emily and Wilma) that caused significant loss in hard coral cover. However, the drivers of the potential recovery are yet to be fully understood. Based on recent findings in the literature of coral cover recovery in the Mexican Caribbean after the mass bleaching event and associated hurricanes in 2005, this study analyzed, through random-effects meta-analysis, the hard coral and macroalgae benthic development and potential drivers of change between 2005 and 2016 in the Mexican Caribbean. Therefore, we tested the relative effect of sea surface temperature (SST), chlorophyll-a water concentration, coastal human population development, reef distance to shore, and geographical location on both hard coral and macroalgae cover over time. Findings revealed increases of both hard coral (by 6%) and algae cover (by ca. 14%, i.e., almost three times the increase of corals) over 12 years. Although our findings confirm the partial coral recovery after the 2005 Caribbean mass coral mortality event, they also indicate rapid colonization of algae across the region. Surprisingly, only SST correlated negatively with changes in coral cover. Contrary to expectations, there was a significantly greater algae cover increase in the Central section of the Mexican Caribbean, which is characterized by a low population density. However, a constant discharge of nutrient-rich freshwater may have facilitated algae growth there. This study reports partial regional reef recovery, but it also indicates that local factors, particularly eutrophication, facilitate algae growth at a speed that is much faster than coral recovery.

Recent research indicates that synchronicity of sexual reproduction in coral spawning events is breaking down, leading to aging populations and decreased recruitment success. In this perspective, we develop a hypothesis that this phenomenon could be caused by ongoing ocean acidification (OA). We hypothesize, that the underlying physiological machinery could be the carbon concentrating mechanism (CCM). The endosymbiotic zooxanthellae of corals could use this mechanism to sense calm water motion states in a comparable way to that known from macroalgae. In macroalgae, it is well-established that dissolved inorganic carbon (DIC) acts as the trigger for signaling low water motion. Hence, evolutionarily developed signals of low water motion, suited for gamete-release, may be misleading in the future, potentially favoring opportunistic species in a broad range of marine organisms.

The northern Red Sea experiences strong annual differences in environmental conditions due to its relative high-latitude location for coral reefs. This allows the study of regulatory effects by key environmental parameters (i.e., temperature, inorganic nutrient, and organic matter concentrations) on reef primary production and dinitrogen (N2) fixation, but related knowledge is scarce. Therefore, this study measured environmental parameters, primary production and N2 fixation of phytoplankton groups in the water overlying a coral reef in the Gulf of Aqaba. To this end, we used a comparative approach between mixed and stratified water column scenarios in a full year of seasonal observations. Findings revealed that inorganic nutrient concentrations were significantly higher in the mixed compared to the stratified period. While gross photosynthesis and N2 fixation rates remained similar, net photosynthesis decreased from mixed to stratified period. Net heterotrophic activity of the planktonic community increased significantly during the stratified compared to the mixed period. While inorganic nitrogen (N) availability was correlated with net photosynthesis over the year, N2 fixation only correlated with N availability during the mixed period. This emphasizes the complexity of planktonic trophodynamics in northern Red Sea coral reefs. Comparing mixed and stratified planktonic N2 fixation rates with those of benthic organisms and substrates revealed a close seasonal activity similarity between free-living pelagic and benthic diazotrophs. During the mixed period, N2 fixation potentially contributed up to 3% of planktonic primary production N demand. This contribution increased by ca. one order of magnitude to 21% during the stratified period. Planktonic N2 fixation is likely a significant N source for phytoplankton to maintain high photosynthesis under oligotrophic conditions in coral reefs, especially during stratified conditions.

Sea cucumbers play an important role in the recycling and remineralization of organic matter (OM) in reef sands through feeding, excretion, and bioturbation processes. Growing demand from Asian markets has driven the overexploitation of these animals globally. The implications of sea cucumber fisheries for shallow coastal ecosystems and their management remain poorly understood. To address this knowledge gap, the current study manipulated densities of Holothuria scabra within enclosures on a reef flat in Fiji, between August 2015 and February 2016, to study the effects of sea cucumber removal on sedimentary function as a biocatalytic filter system. Three treatments were investigated: (i) high density (350 g m−2 wet weight; ca. 15 individuals); (ii) natural density (60 g m−2; ca. 3 individuals); and (iii) exclusion (0 g m−2). Quantity of sediment reworked through ingestion by H. scabra, grain size distribution, O2 penetration depth, and sedimentary oxygen consumption (SOC) were quantified within each treatment. Findings revealed that the natural population of H. scabra at the study site can rework ca. 10,590 kg dry sediment 1,000 m−2 year−1; more than twice the turnover rate recorded for H. atra and Stichopus chloronotus. There was a shift towards finer fraction grains in the high treatment. In the exclusion treatment, the O2 penetration depth decreased by 63% following a 6 °C increase in water temperature over the course of two months, while in the high treatment no such change was observed. SOC rates increased ca. two-fold in the exclusion treatment within the first month, and were consistently higher than in the high treatment. These results suggest that the removal of sea cucumbers can reduce the capacity of sediments to buffer OM pulses, impeding the function and productivity of shallow coastal ecosystems.

Pollution, fishing, and outbreaks of predators can heavily impact coastal coral reef ecosystems, leading to decreased water quality and benthic community shifts. To determine the main environmental drivers of coral reef status in the Spermonde Archipelago, Indonesia, we monitored environmental variables and coral reef benthic community structure along an on-to-offshore gradient annually from 2012 to 2014. Findings revealed that concentrations of phosphate, chlorophyll a-like fluorescence, suspended particulate matter, and light attenuation significantly decreased from on-to-offshore, while concentrations of dissolved O2 and values of water pH significantly increased on-to-offshore. Nitrogen stable isotope signatures of sediment and an exemplary common brown alga were significantly enriched nearshore, identifying wastewater input from the city of Makassar as primary N source. In contrast to the high temporal variability in water quality, coral reef benthic community cover did not show strong temporal, but rather, spatial patterns. Turf algae was the dominant group next to live coral, and was negatively correlated to live coral, crustose coralline algae (CCA), rubble and hard substrate. Variation in benthic cover along the gradient was explained by water quality variables linked to trophic status and physico-chemical variables. As an integrated measure of reef status and structural complexity, the benthic index, based on the ratio of relative cover of live coral and CCA to other coral reef organisms, and reef rugosity were determined. The benthic index was consistently low nearshore and increased offshore, with high variability in the midshelf sites across years. Reef rugosity was also lowest nearshore and increased further offshore. Both indices dropped in 2013, increasing again in 2014, indicating a period of acute disturbance and recovery within the study and suggesting that the mid-shelf reefs are more resilient to disturbance than nearshore reefs. We thus recommend using these two indices with a selected number of environmental variables as an integral part of future reef monitoring.

The Spermonde Archipelago is a complex of ~70 mostly populated islands off Southwest Sulawesi, Indonesia, in the center of the Coral Triangle. The reefs in this area are exposed to a high level of anthropogenic disturbances. Previous studies have shown that variation in the benthos is strongly linked to water quality and distance from the mainland. However, little is known about the fish assemblages of the region and if their community structure also follows a relationship with benthic structure and distance from shore. In this study, we used eight islands of the archipelago, varying in distance from 1 to 55 km relative to the mainland, and 3 years of surveys, to describe benthic and fish assemblages and to examine the spatial and temporal influence of benthic composition on the structure of the fish assemblages. Cluster analysis indicated that distinct groups of fish were associated with distance, while few species were present across the entire range of sites. Relating fish communities to benthic composition using a multivariate generalized linear model confirmed that fish groups relate to structural complexity (rugosity) or differing benthic groups; either algae, reef builders (coral and crustose coralline algae) or invertebrates and rubble. From these relationships we can identify sets of fish species that may be lost given continued degradation of the Spermonde reefs. Lastly, the incorporation of water quality, benthic and fish indices indicates that local coral reefs responded positively after an acute disturbance in 2013 with increases in reef builders and fish diversity over relatively short (1 year) time frames. This study contributes an important, missing component (fish community structure) to the growing literature on the Spermonde Archipelago, a system that features environmental pressures common in the greater Southeast Asian region.

Coral reefs persist in an accretion-erosion balance, which is critical for understanding the natural variability of sediment production, reef accretion, and their effects on the carbonate budget. Bioerosion (i.e. biodegradation of substrate) and encrustation (i.e. calcified overgrowth on substrate) influence the carbonate budget and the ecological functions of coral reefs, by substrate formation/consolidation/erosion, food availability and nutrient cycling. This study investigates settlement succession and carbonate budget change by bioeroding and encrusting calcifying organisms on experimentally deployed coral substrates (skeletal fragments of Stylophora pistillata branches). The substrates were deployed in a marginal coral reef located in the Gulf of Papagayo (Costa Rica, Eastern Tropical Pacific) for four months during the northern winter upwelling period (December 2013 to March 2014), and consecutively sampled after each month. Due to the upwelling environmental conditions within the Eastern Tropical Pacific, this region serves as a natural laboratory to study ecological processes such as bioerosion, which may reflect climate change scenarios. Time-series analyses showed a rapid settlement of bioeroders, particularly of lithophagine bivalves of the genus Lithophaga/Leiosolenus (Dillwyn, 1817), within the first two months of exposure. The observed enhanced calcium carbonate loss of coral substrate (>30%) may influence seawater carbon chemistry. This is evident by measurements of an elevated seawater pH (>8.2) and aragonite saturation state (Ωarag >3) at Matapalo Reef during the upwelling period, when compared to a previous upwelling event observed at a nearby site in distance to a coral reef (Marina Papagayo). Due to the resulting local carbonate buffer effect of the seawater, an influx of atmospheric CO2 into reef waters was observed. Substrates showed no secondary cements in thin-section analyses, despite constant seawater carbonate oversaturation (Ωarag >2.8) during the field experiment. Micro Computerized Tomography (μCT) scans and microcast-embeddings of the substrates revealed that the carbonate loss was primarily due to internal macrobioerosion and an increase in microbioerosion. This study emphasizes the interconnected effects of upwelling and carbonate bioerosion on the reef carbonate budget and the ecological turnovers of carbonate producers in tropical coral reefs under environmental change.