A Protocol for Extracting Structural Metrics From 3D Reconstructions of Corals

The 3D structure of individual coral colonies provides insights into their ecological functioning. While structure from motion techniques make it possible to reconstruct 3D models of coral colonies based on overlapping images, the extraction of relevant metrics of complexity in a reproducible way remains challenging. We present a method and associated scripts for the 3D reconstruction of coral colonies from in-situ images and the automatic extraction of eleven structural complexity metrics, designed to be run in widely-used software packages. The metrics are designed to capture aspects of complexity relating to the colony’s size and shape that are related to their ecological function. We explored the potential ecological applications of some of these metrics using linear models, comparing aspects of complexity among colonies of different size and morphotaxa (combined information on morphology and taxa). Our results showed that a metric as simple as colony diameter explained 95% of the variation in shelter provisioning capability when paired with information on colony morphotaxa. Further, the habitat provisioning of colonies of comparable size was similar among the six of the seven morphotaxa examined. During the current period of rapid uptake of photogrammetry among ecologists, the results of our study provide a basis to use data derived from 3D models to further explore the nuances of the relationship between structure and function of corals at the colony scale in a replicable and standardised way

Macroalgal browsing on a heavily degraded, urbanized equatorial reef system

The removal of macroalgal biomass is critical to the health of coral reef ecosystems. Previous studies on relatively intact reefs with diverse and abundant fish communities have quantified rapid removal of macroalgae by herbivorous fishes, yet how these findings rel ate to degraded reef systems where fish diversity and abundance are markedly lower and algal biomass substantially higher, is unclear. We surveyed roving herbivorous fish communities and quantified their capacity to remove the dominant macroalga Sargassum ilicifolium on seven reefs in Singapore; a heavily degraded urbanized reef system. The diversity and abundance of herbivorous fishes was extremely low, with eight species and a mean abundance ~1.1 individuals 60 m -2 recorded across reefs. Consumption of S. ilicifolium varied with distance from Singapore's main port with consumption being 3- to 17-fold higher on reefs furthest from the port (Pulau Satumu: 4.18 g h -1 ; Kusu Island: 2.38 g h -1 ) than reefs closer to the port (0.35-0.78 g h -1 ). Video observations revealed a single species, Siganus virgatus, was almost solely responsible for removing S. ilicifolium biomass, accounting for 83% of the mass-standardized bites. Despite low herbivore diversity and intense urbanization, macroalgal removal by fishes on some Singaporean reefs was directly comparable to rates reported for other inshore Indo-Pacific reefs

Settlement patterns of corals and other benthos on reefs with divergent environments and disturbances histories around the northeastern Arabian Peninsula

Larval supply is a principal factor determining the establishment, structure, and diversity of sessile benthic assemblages on coral reefs. Benthic reef communities in north-eastern Arabia have been subject to recurrent disturbances in recent years, and subsequent recovery will be, in part, driven by variation in the supply of available colonists. Using settlement tiles deployed seasonally over 1 year at eight sites encompassing three environmentally divergent regions (southern Arabian Gulf, the Musandam Peninsula in the Strait of Hormuz, and the Sea of Oman) we assessed spatial and seasonal variability in settlement of benthic reef organisms. There was strong spatial variation in composition of new colonists among regions, mainly driven by the high abundance of coralline algae in the Arabian Gulf, colonial ascidians on the Musandam Peninsula and barnacles in the Sea of Oman. Seasonal differences in composition of new colonists were less important than regional differences, with seasonal variation in settlement not consistent among regions. The number of corals settling to the tiles was low compared to those reported for other regions, with mean densities ranging from 0 corals m -2 year -1 in the Sea of Oman to 30 (± 0.6 SE) and 38 (± 0.5 SE) in Musandam and the Arabian Gulf, respectively. Peak coral settlement abundance in the Gulf occurred in summer and autumn and in Musandam in spring (averaging 82 and 70 settlers m -2 year -1 , respectively, during the peak settlement season). This work provides the first record of large-scale spatial and seasonal patterns of settlement in north-eastern Arabia and provides valuable information on the supply of settlers available to recolonize heavily disturbed reefs in this region. The extremely low rates of coral settlement suggest that these marginal reefs are likely to be extremely slow to recover from on-going and future disturbances

Fear effects and group size interact to shape herbivory on coral reefs

Fear of predators (‘fear effects’) is an important determinant of foraging decisions by consumers across a range of ecosystems. Group size is one of the main behavioural mechanisms for mitigating fear effects while also providing foraging benefits to group members. Within coral reef ecosystems, fear effects have been shown to influence the feeding rates of herbivorous fishes, a key functional group that prevents macroalgal overgrowth. Yet, how fear effects and group size interact to shape macroalgal removal on coral reefs remains unclear. Here, we conducted field-based experiments using models of a common piscivorous fish, the leopard coral grouper Plectropomus leopardus and a series of macroalgal Sargassum ilicifolium assays positioned at increasing distances from the models (1, 2, 3 and 4 m) on two coral reefs in Singapore to investigate how acute fear effects shape the intensity of herbivory, and whether these effects were influenced by variation in the group size of herbivorous fishes feeding on the assays. We found acute fear effects strongly influenced the foraging behaviour of herbivorous fishes over small spatial scales. Rates of Sargassum biomass removal, feeding rates and the total number of individual feeding events were all lower near the predator model. These effects dissipated rapidly with increasing distance from the predator model and were undetectable at a distance of 4 m. We also found generally larger group sizes of herbivorous fishes further from the predator model, presumably reflecting decreased risk. Furthermore, the number of individual bites/event increased significantly with increasing group size for two common browsing fishes, Siganus virgatus and Siganus javus. Our findings highlight that acute fear effects influence the distribution and intensity of herbivory over small spatial scales. Fear effects also interacted with herbivore group size resulting in changes in the number of individual feeding events and bite rates that collectively shape the realized ecosystem function of macroalgal removal on coral reefs. Group size is an important context-dependent factor that should be considered when examining fear effects on coral reefs. A free Plain Language Summary can be found within the Supporting Information of this article

Fear effects and group size interact to shape herbivory on coral reefs

Fear of predators (‘fear effects’) is an important determinant of foraging decisions by consumers across a range of ecosystems. Group size is one of the main behavioural mechanisms for mitigating fear effects while also providing foraging benefits to group members. Within coral reef ecosystems, fear effects have been shown to influence the feeding rates of herbivorous fishes, a key functional group that prevents macroalgal overgrowth. Yet, how fear effects and group size interact to shape macroalgal removal on coral reefs remains unclear. Here, we conducted field-based experiments using models of a common piscivorous fish, the leopard coral grouper Plectropomus leopardus and a series of macroalgal Sargassum ilicifolium assays positioned at increasing distances from the models (1, 2, 3 and 4 m) on two coral reefs in Singapore to investigate how acute fear effects shape the intensity of herbivory, and whether these effects were influenced by variation in the group size of herbivorous fishes feeding on the assays. We found acute fear effects strongly influenced the foraging behaviour of herbivorous fishes over small spatial scales. Rates of Sargassum biomass removal, feeding rates and the total number of individual feeding events were all lower near the predator model. These effects dissipated rapidly with increasing distance from the predator model and were undetectable at a distance of 4 m. We also found generally larger group sizes of herbivorous fishes further from the predator model, presumably reflecting decreased risk. Furthermore, the number of individual bites/event increased significantly with increasing group size for two common browsing fishes, Siganus virgatus and Siganus javus. Our findings highlight that acute fear effects influence the distribution and intensity of herbivory over small spatial scales. Fear effects also interacted with herbivore group size resulting in changes in the number of individual feeding events and bite rates that collectively shape the realized ecosystem function of macroalgal removal on coral reefs. Group size is an important context-dependent factor that should be considered when examining fear effects on coral reefs

Limited cross-shelf variation in the growth of three branching corals on Australia's Great Barrier Reef

Pronounced differences exist in the biodiversity and structure of coral reef assemblages with increasing distance from shore, which may be expected given marked cross-shelf gradients in environmental conditions. Cross-shelf variation in the abundance of coral reef organisms is likely to be caused, at least in part, by differences in demography (e.g., growth and survival), though this has rarely been tested. This study quantified growth of three distinct branching coral taxa (Acropora nasuta, Pocillopora spp. and Stylophora pistillata) at six locations on Australia's Great Barrier Reef (GBR), encompassing inshore, mid-shelf and outer-shelf reefs. Replicate colonies (0–15 colonies per species, per reef) were stained using Alizarin Red in December 2015 and retrieved one year later to quantify linear extension on replicate branches for each colony. Annual linear extension varied within and among coral taxa, with pronounced differences among reefs. For A. nasuta. and S. pistillata, growth rates were highest at one of the inshore reefs, Orpheus Island. However, inter-reef differences in linear extension were not explained by shelf position. Based on differences in skeletal density, which did vary according to shelf position, branching corals at the inshore sites may actually have higher rates of calcification compared to conspecifics on mid-and outer-shelf reefs. This study shows that growth of branching corals is not lower at inshore sites (and perhaps even higher) compared to sites at mid-shelf and outer reefs, despite generally higher levels of sedimentation and turbidity

Ocean warming has greater and more consistent negative effects than ocean acidification on the growth and health of subtropical macroalgae

Macroalgae are the major habitat-forming organisms in many coastal temperate and subtropical marine systems. Although climate change has been identified as a major threat to the persistence of macroalgal beds, the combined effects of ocean warming and ocean acidification on algal performance are poorly understood. Here we investigate the effects of increased temperature and acidification on the growth, calcification and nutritional content of 6 common subtropical macroalgae; Sargassum linearifolium, Ulva sp., Amphiroa anceps, Corallina officinalis, Delisea pulchra and Laurencia decussata. Algae were reared in a factorial cross of 3 temperatures (23°C [ambient], 26°C and 28°C) and 3 pH levels (8.1 [ambient], 7.8 and 7.6) for 2 wk. The highest (28°C) temperature decreased the growth of all 6 macroalgal species, irrespective of the pH levels. In contrast, the effect of decreased pH on growth was variable. The growth of Ulva sp. and C. officinalis increased, L. decussata decreased, while the remaining 3 species were unaffected. Interestingly, the differential responses of macroalgae to ocean acidification were unrelated to whether or not a species was a calcifying alga, or their carbon-uptake mechanism—2 processes that are predicted to be sensitive to decreased pH. The growth of the calcifying algae (C. officinalis and A. anceps) was not affected by reduced pH but calcification of these 2 algae was reduced when exposed to a combination of reduced pH and elevated temperature. The 3 species capable of uptake of bicarbonate, S. linearifolium, L. decussata and Ulva sp., displayed positive, negative and neutral changes in growth, respectively, in response to reduced pH. The C:N ratio for 5 of the 6 species was unaffected by either pH or temperature. The consistent and predictable negative effects of temperature on the growth and calcification of subtropical macroalgae suggests that this stressor poses a greater threat to the persistence of subtropical macroalgal populations than ocean acidification under ongoing and future climate change

Growth impacts in a changing ocean: insights from two coral reef fishes in an extreme environment

Determining the life-history consequences for fishes living in extreme and variable environments will be vital in predicting the likely impacts of ongoing climate change on reef fish demography. Here, we compare size-at-age and maximum body size of two common reef fish species (Lutjanus ehrenbergii and Pomacanthus maculosus) between the environmentally extreme Arabian/Persian Gulf (‘Arabian Gulf’) and adjacent comparably benign Oman Sea. Additionally, we use otolith increment width profiles to investigate the influence of temperature, salinity and productivity on the individual growth rates. Individuals of both species showed smaller size-at-age and lower maximum size in the Arabian Gulf compared to conspecifics in the less extreme and less variable environment of the Oman Sea, suggesting a life-history trade-off between size and metabolic demands. Salinity was the best environmental predictor of interannual growth across species and regions, with low growth corresponding to more saline conditions. However, salinity had a weaker negative effect on interannual growth of fishes in the Arabian Gulf than in the Oman Sea, indicating Arabian Gulf populations may be better able to acclimate to changing environmental conditions. Temperature had a weak positive effect on the interannual growth of fishes in the Arabian Gulf, suggesting that these populations may still be living within their thermal windows. Our results highlight the potential importance of osmoregulatory cost in impacting growth, and the need to consider the effect of multiple stressors when investigating the consequences of future climate change on fish demography

New branched Porolithon species (Corallinales, Rhodophyta) from the Great Barrier Reef, Coral Sea, and Lord Howe Island

Porolithon is one of the most ecologically important genera of tropical and subtropical crustose (non-geniculate) coralline algae growing abundantly along the shallow margins of coral reefs and functioning to cement reef frameworks. Thalli of branched, fruticose Porolithon specimens from the Indo-Pacific Ocean traditionally have been called P. gardineri, while massive, columnar forms have been called P. craspedium. Sequence comparisons of the rbcL gene both from type specimens of P. gardineri and P. craspedium and from field-collected specimens demonstrate that neither species is present in east Australia and instead resolve into four unique genetic lineages. Porolithon howensis sp. nov. forms columnar protuberances and loosely attached margins and occurs predominantly at Lord Howe Island; P. lobulatum sp. nov. has fruticose to clavate forms and free margins that are lobed and occurs in the Coral Sea and on the Great Barrier Reef (GBR); P. parvulum sp. nov. has short (<2 cm), unbranched protuberances and attached margins and is restricted to the central and southern GBR; and P. pinnaculum sp. nov. has a mountain-like, columnar morphology and occurs on oceanic Coral Sea reefs. A rbcL gene sequence of the isotype of P. castellum demonstrates it is a different species from other columnar species. In addition to the diagnostic rbcL and psbA marker sequences, the four new species may be distinguished by a combination of features including thallus growth form, margin shape (attached or unattached), and medullary system (coaxial or plumose). Porolithon species, because of their ecological importance and sensitivity to ocean acidification, need urgent documentation of their taxonomic diversity

Body Size and Substrate Type Modulate Movement by the Western Pacific Crown-Of-Thorns Starfish, Acanthaster solaris

The movement capacity of the crown-of-thorns starfishes (Acanthaster spp.) is a primary determinant of both their distribution and impact on coral assemblages. We quantified individual movement rates for the Pacific crown-of-thorns starfish (Acanthaster solaris) ranging in size from 75–480 mm total diameter, across three different substrates (sand, flat consolidated pavement, and coral rubble) on the northern Great Barrier Reef. The mean (±SE) rate of movement for smaller (diameter) A. solaris was 23.99 ± 1.02 cm/ min and 33.41 ± 1.49 cm/ min for individuals \u3e350 mm total diameter. Mean (±SE) rates of movement varied with substrate type, being much higher on sand (36.53 ± 1.31 cm/ min) compared to consolidated pavement (28.04 ± 1.15 cm/ min) and slowest across coral rubble (17.25 ± 0.63 cm/ min). If average rates of movement measured here can be sustained, in combination with strong directionality, displacement distances of adult A. solaris could range from 250–520 m/ day, depending on the prevailing substrate. Sustained movement of A. solaris is, however, likely to be highly constrained by habitat heterogeneity, energetic constraints, resource availability, and diurnal patterns of activity, thereby limiting their capacity to move between reefs or habitats