Coral reef benthic community changes in the Anthropocene: Biogeographic heterogeneity, overlooked configurations, and methodology

Coral high molecular weight carbohydrates support opportunistic microbes in bacterioplankton from an algae-dominated reef

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.

IMPORTANCE

Dissolved 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.

Drivers of coastal benthic communities in a complex environmental setting

Analyzing the environmental factors affecting benthic communities in coastal areas is crucial for uncovering key factors that require conservation action. Here, we collected benthic and environmental (physical-chemical-historical and land-based) data for 433 transects in Taiwan. Using a k-means approach, five communities dominated by crustose coralline algae, turfs, stony corals, digitate, or bushy octocorals were first delineated. Conditional random forest models then identified physical, chemical, and land-based factors (e.g., light intensity, nitrite, and population density) relevant to community delineation and occurrence. Historical factors, including typhoons and temperature anomalies, had only little effect. The prevalent turf community correlated positively with chemical and land-based drivers, which suggests that anthropogenic impacts are causing a benthic homogenization. This mechanism may mask the effects of climate disturbances and regional differentiation of benthic assemblages. Consequently, management of nutrient enrichment and terrestrial runoff is urgently needed to improve community resilience in Taiwan amidst increasing challenges of climate change.

Shifts in dominance of benthic communities along a gradient of water temperature and turbidity in tropical coastal ecosystems

Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (<31 °C, 31-32 °C, and >32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes <31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4-18.8% hard coral, 3.5-26.3% CCA, and 15-15.5% turf algae, respectively), while the higher temperature marine lakes (31-32 °C and >32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (>31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant.

Depth variation in benthic community response to repeated marine heatwaves on remote Central Indian Ocean reefs

Coral reefs are increasingly impacted by climate-induced warming events. However, there is limited empirical evidence on the variation in the response of shallow coral reef communities to thermal stress across depths. Here, we assess depth-dependent changes in coral reef benthic communities following successive marine heatwaves from 2015 to 2017 across a 5-25 m depth gradient in the remote Chagos Archipelago, Central Indian Ocean. Our analyses show an overall decline in hard and soft coral cover and an increase in crustose coralline algae, sponge and reef pavement following successive marine heatwaves on the remote reef system. Our findings indicate that the changes in benthic communities in response to elevated seawater temperatures varied across depths. We found greater changes in benthic group cover at shallow depths (5-15 m) compared with deeper zones (15-25 m). The loss of hard coral cover was better predicted by initial thermal stress, while the loss of soft coral was associated with repeated thermal stress following successive warming events. Our study shows that benthic communities extending to 25 m depth were impacted by successive marine heatwaves, supporting concerns about the resilience of shallow coral reef communities to increasingly severe climate-driven warming events.

Diversification of refugia types needed to secure the future of coral reefs subject to climate change

Identifying locations of refugia from the thermal stresses of climate change for coral reefs and better managing them is one of the key recommendations for climate change adaptation. We review and summarize approximately 30 years of applied research focused on identifying climate refugia to prioritize the conservation actions for coral reefs under rapid climate change. We found that currently proposed climate refugia and the locations predicted to avoid future coral losses are highly reliant on  excess heat metrics, such as degree heating weeks. However, many existing alternative environmental, ecological, and life-history variables could be used to identify other types of refugia that lead to the desired diversified portfolio for coral reef conservation. To improve conservation priorities for coral reefs, there is a need to evaluate and validate the predictions of climate refugia with long-term field data on coral abundance, diversity, and functioning. There is also the need to identify and safeguard locations displaying resistance toprolonged exposure to heat waves and the ability to recover quickly after thermal exposure. We recommend using more metrics to identify a portfolio of potential refugia sites for coral reefs that can avoid, resist, and recover from exposure to high ocean temperatures and the consequences of climate change, thereby shifting past efforts focused on avoidance to a diversified risk-spreading portfolio that can be used to improve strategic coral reef conservation in a rapidly warming climate.

Precision and accuracy of common coral reef sampling protocols revisited with photogrammetry

The rapid decline of coral reefs calls for cost-effective benthic cover data to improve reef health forecasts, policy building, management responses and evaluation. Reef monitoring has been largely based on divers' observations along transects, and secondarily on quadrat-based protocols, video and photographic records. However, the accuracy and precision of the most common sampling approaches are not yet fully understood. Here, we compared benthic cover estimates from three common sampling protocols: Reef Check (RC), Atlantic and Gulf Rapid Reef Assessment (AGRRA) and photoquadrats (PQ). The reef cover of two contrasting sites was reconstructed with ∼450 m2 orthomosaics built with high resolution Structure-from-Motion (SfM) photogrammetry, which were used as references for comparisons among protocols. In addition, we explored sample size requirements for each protocol and provided cost-effectiveness comparisons. Our results evidenced between-reef differences in the accuracy and precision of estimates with the different protocols. The three protocols performed similarly in the reef with low macroalgal cover (<0.5%), but PQ were more accurate and precise in the reef with relatively high (∼20%) macroalgal cover. The sample size for estimating coral cover with a 20% error margin and a 0.05 significance level was lower for PQ, followed by AGRRA and RC. Considering performance, cost surrogates and equipment needs, cost-effectiveness was higher for PQ. We also discuss costs, limitations and advantages/disadvantages of SfM photogrammetry as a sampling approach for coral reef monitoring.

Mass mortality event of the giant barrel sponge Xestospongia sp.: population dynamics and size distribution in Koh Phangan, Gulf of Thailand

Marine sponges are prominent organisms of the benthic coral reef fauna, providing important ecosystem services. While there have been increasing reports that sponges are becoming one of the dominant benthic organisms in some locations and ecoregions (e.g. Caribbean), they can be impacted by changing environmental conditions. This study presents the first documentation of a mass mortality event of the barrel sponge Xestospongia sp. in the lower Gulf of Thailand and its consequences on population dynamics and size distribution. Two anthropogenic impacted reefs (Haad Khom and Mae Haad) of the island Koh Phangan and two anthropogenic non-impacted reefs of the islands Koh Yippon and Hin Yippon within the Mu Ko Ang Thong Marine National Park were surveyed in the years 2015 and 2016. The results showed a strong shift in population densities at Koh Phangan. Fatal "bleaching" ending up in mass mortality was observed for these reefs in 2015. Xestospongia sp. abundance decreased from 2015 to 2016 by 80.6% at Haad Khom and by 98.4% at Mae Haad. Sponges of all sizes were affected, and mortality occurred regardless of the survey depth (4 and 6 m). However, Xestospongia population densities in the Marine Park were at a constant level during the surveys. The abundances in 2015 were 65% higher at the Marine Park than at Koh Phangan and 92% higher in 2016. The most likely causes of the mass mortality event was a local harmful algal bloom event, pathogens, undetected local higher water temperatures, or a combination of these factors, whereas sea surface temperature analyses showed no marine heatwave during the observed mass mortality event in 2015. Considering the ecological importance of sponges such as Xestospongia sp., long-term monitoring of reefs and their environmental parameters should be implemented to prevent such mass die-offs.

Heatwave hit phase shifted coral reefs: Zoantharian mass mortality record

Phase shift is characterized by an abrupt change in the structure of a community in response to a disturbance that can break its resistance, displacing it from its natural variation. This phenomenon has been recognized in several ecosystems and often points to human activities as the main cause. However, reactions of shifted communities to anthropogenic impacts have been less studied. In recent decades, heatwaves resulting from climate change have strongly affected coral reefs. Mass coral bleaching events are recognized as the main cause of coral reef phase shifts on a global scale. In 2019, an unprecedented heatwave hit the southwest Atlantic Ocean causing mass coral bleaching in non-degraded and phase-shifted reefs of Todos os Santos Bay, at an intensity never recorded in a 34-year historical series. We analyzed the effects of this event on the resistance of phase-shifted reefs, dominated by the zoantharian Palythoa cf. variabilis. Using benthic coverage data from 2003, 2007, 2011, 2017, and 2019, we analyzed three non-degraded reefs and three phase-shifted reefs. We estimated the coverage and bleaching of corals and P. cf. variabilis on each reef. There was a reduction in coral coverage in non-degraded reefs before the 2019 mass bleaching event (i.e., heatwave). However, there was no significant coral coverage variation after the event and the structure of non-degraded reef communities did not change. In phase-shifted reefs the coverage of zoantharians did not change significantly before the 2019 event, however, after the mass bleaching, there was a significant reduction in the coverage of these organisms. Here we revealed that the resistance of the shifted community was broken, and its structure was altered, indicating that reefs in this condition were more susceptible to bleaching disturbance than non-degraded reefs.

Turbidity shapes shallow Southwestern Atlantic benthic reef communities

Southwestern Atlantic reefs (Brazilian Province) occur along a broad latitudinal range (∼5°N-27°S) and under varied environmental conditions. We combined large-scale benthic cover and environmental data into uni- and multivariate regression tree analyses to identify unique shallow (<30 m) benthic reef communities and their environmental drivers along the Brazilian Province. Turbidity was the leading environmental driver of benthic reef communities, with the occurrence of two main groups: clear-water (dominated by fleshy macroalgae) and turbid (dominated by turf algae). Seven out of 14 scleractinian coral species were more abundant in the turbid group, thus corroborating the photophobic nature of some Brazilian corals. The most abundant scleractinian in Brazil (Montastraea cavernosa), largely dominated (71-93% of total coral cover) both, the shallow turbid and deeper clear-water reefs. Because these habitat types are widely recognized as potential climate refuges, local threats (e.g. pollution, overfishing) should be averted.

Benthic composition changes on coral reefs at global scales

Globally, ecosystems are being reconfigured by a range of intensifying human-induced stressors. Coral reefs are at the forefront of this environmental transformation, and if we are to secure their key ecosystem functions and services, it is important to understand the likely configuration of future reefs. However, the composition and trajectory of global coral reef benthic communities is currently unclear. Here our global dataset of 24,468 observations spanning 22 years (1997-2018) revealed that particularly marked declines in coral cover occurred in the Western Atlantic and Central Pacific. The data also suggest that high macroalgal cover, widely regarded as the major degraded state on coral reefs, is a phenomenon largely restricted to the Western Atlantic. At a global scale, the raw data suggest decreased average (± standard error of the mean) hard coral cover from 36 ± 1.4% to 19 ± 0.4% (during a period delineated by the first global coral bleaching event (1998) until the end of the most recent event (2017)) was largely associated with increased low-lying algal cover such as algal turfs and crustose coralline algae. Enhanced understanding of reef change, typified by decreased hard coral cover and increased cover of low-lying algal communities, will be key to managing Anthropocene coral reefs.

Movement, Space Use, and the Responses of Coral Reef Fish to Climate Change

Anthropogenic climate change and other localized stressors have led to the widespread degradation of coral reefs, characterized by losses of live coral, reduced structural complexity, and shifts in benthic community composition. These changes have altered the composition of reef fish assemblages with important consequences for ecosystem function. Animal movement and space use are critically important to population dynamics, community assembly, and species coexistence. In this perspective, I discuss how studies of reef fish movement and space use could help us to elucidate the effects of climate change on reef fish assemblages and the functions they provide. In addition to describing how reef fish space use relates to resource abundance and the intrinsic characteristics of reef fish (e.g., body size), we should begin to take a mechanistic approach to understanding movement in reef fish and to investigate the role of movement in mediating species interactions on coral reefs. Technological advances in animal tracking and biotelemetry, as well as methodological advances in the analysis of movement, will aid in this endeavor. Baseline studies of reef fish movement and space use and their effect on community assembly and species coexistence will provide us with important information for predicting how climate change will influence reef fish assemblages.

The widely distributed soft coral Xenia umbellata exhibits high resistance against phosphate enrichment and temperature increase

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.

Benthic cyanobacterial mat formation during severe coral bleaching at Lizard Island: The mediating role of water currents

Cyanobacterial mats are increasingly recognised as a symptom of coral reef change. However, the spatial distribution of cyanobacterial mats during coral bleaching has received limited attention. We explored cyanobacterial mat distribution during a bleaching event at Lizard Island and considered hydrodynamics as a potential modifier. During bleaching cyanobacterial mats covered up to 34% of the benthos at a transect scale, while some quadrats (1 m2) were covered almost entirely (97.5%). The spatial distribution of cyanobacterial mats was limited to areas with slower water currents. Coral cover declined by 44% overall, although cyanobacterial mats were not spatially coupled to the magnitude of coral loss. Overall, the marked increase in cyanobacterial mat cover was an ephemeral spike, not a sustained change, with cover returning to 0.4% within 6 months. Cyanobacterial mats clearly represent dynamic space holders on coral reefs, with a marked capacity to rapidly exploit change, if conditions are right.

A critical evaluation of benthic phase shift studies on coral reefs

Coral reef decline has accelerated in the last two decades resulting in substantial research into the phenomenon of 'phase shifts' or 'regime shifts'. However, the conclusions drawn from this research have been varied. Some of this variability may stem from methodological approaches, although the extent to which these factors have shaped our understanding remain largely unexplored. To examine this, we conducted a systematic review of the literature. In doing so, we revealed marked variability in the approaches used for studying phase shifts. Notably, very few studies clearly defined what they meant by phase shifts. Therefore, we developed a clarified definition of phase shifts, which specifically defined persistence and dominance. The applicability of this definition was tested on multi-decadal benthic composition data on the Great Barrier Reef. The number of shifts depended critically on the definition selected, suggesting that this may be a primary reason underpinning the variability in past results.