Rocky Reefs Research Articles

Coral reef & temperate coastal soundscape features evident in directional and omnidirectional passive acoustic time series

Biologically complex coastal environments, such as coral reefs, demonstrate an equally rich ambient soundscape. Bioacoustic features of coastal soundscapes are closely tied with relative ecosystem health, functional groups present, and can be linked with specific behaviors. Biological contributions to ambient soundscapes have distinctive qualities as compared to sound associated with physical processes (i.e. wind and wave noise). While some biological components are readily identifiable, such as marine mammal or fish calls, the background noise associated with hundreds of thousands of biological clicks, snaps, and pops is not as well studied but contains a wealth of information about the ecosystem. A 64-element line array with 4.5 kHz design frequency was deployed for several field experiments off the coast of Kona, Hawaii in 2019 and 2020. Soundscape data from Hawaii were compared with comparable omnidirectional time series from Bermuda (2020) and coastal New England rocky reefs (2020–2021). Similarities in certain spectral features associated with biological sound sources were found between these unique ecosystems. The characteristic coral reef evening chorus, or significant increase in sound levels immediately prior to sunset, was consistent in Hawaii and Bermuda with comparable crepuscular changes in coastal New England.

Seascape connectivity of temperate fishes between estuarine nursery areas and open coastal reefs

Abstract While estuaries are considered valuable nurseries for many harvested fish species, little quantitative data exist about the spatial scales over which estuaries supply individuals to coastal reefs and how this influences coastal metapopulations. Quantifying this connectivity between estuaries and coastal reefs will assist the sustainable management of fisheries and key fish habitat. This information is particularly pertinent considering estuaries world‐wide are experiencing degradation and habitat loss. We examine how the relative abundance and body length of three exploited fishes (Chrysophrys auratus, Pseudocaranx georgianus and Nemadactylus douglasii) varied in relation to the proximity and size of the nearest estuary, predicting that estuarine dependent species (i.e. C. auratus) would be smaller and more abundant on reefs close to large estuaries. As a network of ‘no‐take’ marine reserves exist across the study area, we also assessed for reserve effects and if these were influenced by the proximity and size of estuaries. Fish assemblages were surveyed using baited remote underwater video systems deployed on 629 rocky reefs across 417 km of coastline in south‐eastern Australia. As predicted, C. auratus were smaller and more abundant on reefs adjacent to estuaries (<8.5 km), which is consistent with the species being heavily reliant on estuaries as nursery habitats. Neither the length nor abundance of N. douglasii and P. georgianus were influenced by the proximity or size of estuaries. Marine reserves consistently had higher abundances and larger C. auratus, regardless of their proximity to estuaries. However, reserve effects were more variable for both N. douglasii and P. georgianus. Synthesis and applications. Our results suggest that the dispersal of subadult Chrysophrys auratus from estuarine nurseries to coastal reefs occurs across relatively small spatial scales, highlighting that conserving the ecological functioning of estuaries is paramount to sustaining recruitment to nearby coastal fisheries. Estuary size and proximity had little influence on populations of both Nemadactylus douglasii and Pseudocaranx georgianus as these species are not greatly dependent on estuaries. We also found that the proximity to estuaries did not enhance reserve effects, instead these effects were consistent across the study area.

An evaluation of fish spawning on degraded and remnant reefs in Saginaw Bay, Lake Huron

Saginaw Bay is a shallow, nutrient-rich embayment in Lake Huron that historically had a complex network of natural rocky reefs. These reef habitats were used as spawning and nursery areas for a variety of fish species, but decades of land-use related sedimentation caused many of these reefs to be degraded. Our study objectives were to analyze abiotic and biotic conditions on degraded and remnant reefs and describe spawning patterns of walleye (Sander vitreus) and lake whitefish (Coregonus clupeaformis) at these sites to determine the potential for increased utilization following reef restoration. During fall and spring 2014–2016, we evaluated water quality and egg predation at four sites with varying levels of reef degradation. Further, we documented reproductive utilization through capture of spawning adults and quantification of egg deposition. Walleye and lake whitefish utilized multiple sites for reproduction; however, densities of spawners and deposited eggs were low, suggesting that they were not utilizing study sites as major spawning locations. Walleye and lake whitefish eggs were eaten by multiple fish species, including larger fish such as channel catfish (Ictalurus punctatus). Dissolved oxygen levels were adequate (i.e., >7 mg 02 L−1) during spring walleye egg incubation; however, bottom dissolved oxygen levels became very low at some sites during winter ice cover, coinciding with lake whitefish egg incubation. As restoration of rocky reefs proceeds in the Bay, evidence of remnant reef spawning fish bodes well for long-term success, though potential limiting factors such as low dissolved oxygen, sedimentation, and egg predation require continued monitoring.

Alternative state transition control by regulating the spatial arrangement of organisms using a lattice model

AbstractEcological systems can exist under multiple stable states for a specific set of environmental conditions. Perturbations can shift ecosystems to alternative stable states, and these changes are difficult to reverse. This is a concept known as hysteresis. Current management methods for system recovery require considerable effort. A model for system recovery that requires small changes in a target community would be of high value for ecosystem restoration. In this study, we focused on rocky reefs that exhibit two alternative stable states: one dominated by macroalgae and another dominated by sea urchins and crustose coralline algae. Community recovery requires a state shift. To better understand the state shift, we simulated the ecosystem using a lattice model incorporating local interactions, rather than equations representing homogenized spaces. Using spatial information and simulating conditions in the target ecosystem, we concluded that a shift to an alternative stable state is possible by adjusting the spatial arrangement of the organisms. These results indicate that spatial arrangements are significant in systems exhibiting hysteresis and that the spatial manipulation of organisms may be useful for ecosystem management and restoration.

A comparison of stereo-videos and visual census methods for assessing subtropical rocky reef fish assemblage

A comparison of stereo-videos and visual census methods for assessing subtropical rocky reef fish assemblage

Sea Urchin Removal as a Tool for Macroalgal Restoration: A Review on Removing “the Spiny Enemies”

Kelp and macroalgal forests provide the ecological foundations of many temperate rocky reef ecosystems, but have regionally declined, often due to sea urchin overgrazing and the formation of urchin barrens. Sea urchin removal has long been used to investigate kelp-sea urchin dynamics and is increasingly being promoted for kelp forest restoration. In this review, we assess the methods and outcomes of sea urchin removal experiments to evaluate their potential use and feasibility as a tool for restoring macroalgal forests. Seventy-nine sea urchin removal projects were reviewed from temperate subtidal rocky reef systems between 1975 and 2020. Removal methods were often not reported (35%), but included manual culling, including crushing (25%) and chemical application (quicklime, 9%), or relocating sea urchins (13%). Only a small percentage of removals were large in scale (16% > 10 ha) and 92% of these utilized culling. Culling is often the most practical method of urchin removal, but all methods can be effective and we encourage development of new approaches that harvest and utilize low-quality urchins. Urchin removal led to an increase in macroalgae in 70% of studies, and a further 21% showed partial increases (e.g., at one or more sites or set of conditions). Restoration effectiveness is increased by removing essentially all sea urchins from discrete areas of urchin barrens. Sea urchin removal provides a simple, relatively cheap, and effective method that promotes kelp recovery within urchin barrens. However, sea urchin removal does not address the underlying cause of elevated sea urchin populations and is unlikely to provide a long-term solution to restore kelp forests and full ecosystem function on its own. We therefore suggest that if sea urchin removal is considered as a tool for kelp forest restoration, it should be incorporated with other management measures that aim to increase kelp forest resilience and biodiversity (e.g., marine protected areas, predator protection or enhancement). This will ensure that kelp restoration efforts have the greatest ecological, socio-economic and cultural outcomes in the long-term.

Data and code : Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: environmental DNA metabarcoding complements underwater visual census

Data and code : Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: environmental DNA metabarcoding complements underwater visual census

Connectivity Shapes Functional Diversity and Maintains Complementarity in Surf Zones on Exposed Coasts

Habitat complexity and connectivity can influence the number of species and their diversity across a landscape. For the surf zones of ocean-exposed beaches, globally one of the longest habitat interfaces, the assumed low structural complexity, and apparent homogeneity, of the sandy seafloor habitats predicts low taxonomic and functional diversity. Here, we assessed how the configuration of the seascape and the context of different beach structure functional diversity and functional niche space of fish assemblages in surf zones. We expected that beaches that were well connected with highly productive and complex estuarine and reef habitats would support a greater level of functional diversity, and a greater degree of functional complementarity within different niches. We sampled surf zones at twenty-five beaches along 50 km of coastline in southeast Queensland, Australia. We calculated functional diversity and functional niche space using variation in the functional traits of fish assemblages. We found that increased proximity with nearby subtidal rocky reefs was the key feature of the coastline shaping functional diversity and functional niche space in surf zone fishes. These effects resulted in increased functional complementarity within a number of fish functional group niches when rocky reefs were nearby. We provide empirical evidence that habitat proximity can structure functional diversity and complementarity in the surf zones of ocean beaches, a system traditionally viewed as having low habitat heterogeneity. Our results highlight the focus management must take in conserving these highly connected ecosystems to avoid negative functional consequences.

Depth-related drivers of benthic community structure on shallow subtidal rocky reefs

Knowing how benthic distribution responds to depth variation is necessary as future changes will alter species’ distributions. This study, carried out on tropical rocky reefs in the southeast Atlantic (Brazil), investigated how subtidal benthic communities vary over depth and which drivers were responsible. Communities were sampled at three sites over four depths as were a proxy for grazing intensity and several environmental drivers. Temperature, water movement and water clarity decreased with depth, while sediment cover and salinity on reefs increased. Communities differed across depth ranges, organized into a clear vertical zonation driven mostly by temperature and grazing intensities. Palythoa caribaeorum was the most important taxon/functional group in the shallows while Jania sp. were mostly associated with the mesohabitat at the base of the reefs. This study contributes to conservation planning by fixing a baseline to better predict changes in benthic communities.

Organic contaminants in imported salmon feed and their effects on reef ecosystems in New Zealand

Organic matter from salmon farms has been shown to be assimilated by soft sediment and rocky reef communities within the ecological footprint of salmon farms. Given these findings, another question arises – What other chemicals in salmon feed may be assimilated into wild communities via organic waste from salmon farms? Here we measured a suite of organic contaminants in salmon feed, in organisms used in a controlled feeding experiment, and in reef species collected within the depositional footprint of salmon farms. Gas Chromatography-Tandem Mass Spectrometry was used to quantify trace concentrations of polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and current-use (CPUs) and historic-use pesticides (HUPs) in salmon feed imported to New Zealand. The effect of assimilation of farm-derived organic matter on contaminant profiles differed among species during the controlled feeding experiment and demonstrated that migration of individuals to a farm-associated site has the potential to increase or decrease organic contaminant concentrations. Concentrations of PCBs in Parapercis colias (blue cod), a highly resident, long-lived fish, were significantly higher at farm sites than at reference sites. While these concentrations were relatively low in a global context, this result presents blue cod as an important candidate for future monitoring of organic contaminants around point sources. PCBs and PBDEs measured in wild marine species were all below limits set by the European Union, whereas concentrations of certain HUPs, specifically dichlorodiphenyltrichloroethane (DDT) and its degradation products and endosulfan, may be of concern as a consequence of alternative anthropogenic activities. Overall, feed imported to New Zealand had relatively low levels of most organic contaminants that, at current levels, are unlikely to result in significant ecological effects to wild communities in adjacent habitats.

Biomass calibration of nine dominant native and non-native Levantine seaweeds

Seaweeds provide important ecosystem functions in shallow temperate rocky reefs including carbon uptake. The macroalgae communities in shallow reefs off the south-eastern Mediterranean shores have shifted dramatically due to bioinvasions and possibly ocean warming over the past few decades. These changes have likely caused and will continue to shift the ecosystem functionality and carbon sequestration capacity of these reefs. In order to assess the potential changes in carbon sequestration capacity, it is important to determine the organic reservoir contained in the biomass of the native as well as the increasingly dominant alien algal species, for which biometric relationships can serve as good proxies. Between 2017 and 2020, we collected samples of nine species of native and non-native seaweeds that currently dominate the hard substrate of shallow reefs along the northern Israeli Levantine coast. For each species, we provide the biometric relationships between wet weight, dry weight and ash-free dry weight and report the equations for the conversions between the different mass-calibrations. Comparison between species, indicate that organic matter content in Ochrophyta is generally greater than Rhodophyta. Furthermore, seasonality was detected in some metrics of the tested species. Our results provide basic tools for assessing the impacts of climate change and bioinvasions in terms of carbon sequestration potential in shallow water seaweed communities of the Levantine and possibly other regions.

Shelf Transport Pathways Adjacent to the East Australian Current Reveal Sources of Productivity for Coastal Reefs

The region where the East Australian Current (EAC) separates from the coast is dynamic and the shelf circulation is impacted by the interplay of the western boundary current and its eddy field with the coastal ocean. This interaction can drive upwelling, retention or export. Hence understanding the connection between offshore waters and the inner shelf is needed as it influences the productivity potential of valuable coastal rocky reefs. Near urban centres, artificial reefs enhance fishing opportunities in coastal waters, however these reefs are located without consideration of the productivity potential of adjacent waters. Here we identify three dominant modes of mesoscale circulation in the EAC separation region (~31.5−34.5°S); the ‘EAC mode’ which dominates the flow in the poleward direction, and two eddy modes, the ‘EAC eddy mode’ and the ‘Eddy dipole mode’, which are determined by the configuration of a cyclonic and anticyclonic eddy and the relationship with the separated EAC jet. We use a Lagrangian approach to reveal the transport pathways across the shelf to understand the impact of the mesoscale circulation modes and to explore the productivity potential of the coastal waters. We investigate the origin (position and depth) of the water that arrives at the inner-mid shelf over a 21-day period (the plankton productivity timescale). We show that the proportion of water that is upwelled from below the euphotic zone varies spatially, and with each mesoscale circulation mode. Additionally, shelf transport timescales and pathways are also impacted by the mesoscale circulation. The highest proportion of upwelling (70%) occurs upstream of 32.5°S, associated with the EAC jet separation, with vertical displacements of 70–120 m. From 33 to 33.5°S, water comes from offshore above the euphotic layer, and shelf transport timescales are longest. The region of highest retention over the inner shelf is immediately downstream of the EAC separation region. The position of the EAC jet and the location of the cyclonic eddy determines the variability in shelf-ocean interactions and the productivity of shelf waters. These results are useful for understanding productivity of temperate rocky reefs in general and specifically for fisheries enhancements along an increasingly urbanised coast.

The trophic basis of fish assemblages in temperate estuarine and coastal ecosystems

More than half of the fish biomass of coastal rocky reefs depends on zooplankton; however, the trophic basis of estuarine fish assemblages remains unknown. We quantified the trophic basis (i.e. basal energy sources) of fish community biomass inhabiting three habitat types (seagrass, natural reef and artificial reef) in two estuaries, compared with two coastal rocky reef sites. Fish assemblages were surveyed with Baited Remote Underwater Video (BRUVs) and the species abundance, richness and biomass of fish were classified into nine functional feeding groups (6 teleost and 3 elasmobranch). Comparable metrics for coastal fish assemblages were obtained from published surveys using BRUVs. Using the functional feeding group biomass and the group-specific diet composition, the breakdown of energy sources was calculated using a food web analysis. Estuarine reef habitats had different species and different functional feeding group composition than seagrass habitat. The majority of fish biomass in the seagrass habitat was supported by detritus (51% in Botany Bay) or macrophytes (58% in Lake Macquarie). In contrast, zooplankton supported most fish biomass (45–59%) at the coastal reef locations, and in reef habitat in one estuary (35–43%), but not the other estuary (33–34%). Trophic pathways which support fish assemblages, are key in identifying mitigation measures which can help conserve these populations with growing urbanisation of estuaries and coasts.

Characterising epibenthic diversity and physical drivers in unconsolidated marine habitats of Algoa Bay, South Africa

Unconsolidated marine sediment habitats spatially make up the majority of global ocean seabed, yet benthic faunal patterns and their abiotic drivers remain poorly understood. Benthic research in Algoa Bay, on the south coast of South Africa, has largely focused on rocky reefs, while the dominant unconsolidated sediment habitats have been poorly studied. This study describes epibenthic assemblages associated with unconsolidated sediment in Algoa Bay, at between 30 and 100 m depth, and investigates the relationship between biotic patterns and physical drivers. Epibenthic abundance data were quantified from benthic imagery and tested against the long-term means and coefficients of variation of 12 abiotic factors, including depth, mean grain size and bottom temperature. Multivariate analyses revealed two statistically distinct epibenthic communities. This pattern was largely explained by depth, mean grain size, mean bottom temperature and mean current speed (cumulative variation of 52.49%). To a lesser extent, the long-term variability of bottom temperature, current speed and dissolved oxygen also influenced the community (cumulative variation of 34.44%). Visual classification of the substrates indicated that a mixed substrate type (i.e. sand and a low percentage of rock) significantly influences the benthic community. The findings suggest that a combination of depth and substrate type are largely responsible for the epibenthic assemblages observed.

Macrocystis pyrifera forest development shapes the physical environment through current velocity reduction

Marine forests of the giant kelp Macrocystis pyrifera create biogenic habitat spanning the water column, within which hydrodynamic conditions can differ strongly from those outside. Such flow alteration has implications for physical, chemical, and ecological processes across multiple spatial scales. At the forest-wide scale, M. pyrifera has been shown to decrease alongshore current velocities, but relatively little is known about how the attenuation of such currents evolves as new kelp forests emerge and mature. Here, we quantified alongshore current velocities outside and within a temperate rocky reef environment that twice underwent a transition from a barren state to one in which a thick surface canopy was present. We identified a threshold density during forest emergence at which much of the attenuation of alongshore depth-averaged velocity occurs—3 stipes m-2 with a surface canopy present. Incremental increases in damping occur as the forest matures, highlighting that relatively young, thin forests can induce substantially reduced flows. Additionally, the presence of a young forest’s subsurface canopy and its subsequent increase in height create a seasonally changing profile of varying velocities through the water column. These results indicate greater complexity in how canopy-forming kelp influence nearshore flow properties than has often been recognized. Importantly, emerging forests can alter the nearshore environment through modulation of current speeds shortly following initial recruitment, with consequences for the transport of larvae, nutrients, and sediment throughout the forest and adjacent habitats.

Anchor Scour from Shipping and the Defaunation of Rocky Reefs: A Quantitative Assessment

Anchor Scour from Shipping and the Defaunation of Rocky Reefs: A Quantitative Assessment

Rocky reef fish biodiversity and conservation in a Brazilian Hope Spot region

Abstract Coastal islands of Grande Rio, located south Rio de Janeiro and Maricá cities have been under multiple anthropogenic impacts. Despite these problems, these insular systems shelter a high diversity of fish species. Reef fishes are essential components of tropical marine coastal communities, also providing food and income for millions of people around the world. In this work, we generated an updated checklist from Cagarras Islands Natural Monument and surrounding areas based on fisheries data, literature records and multiple sampling techniques, including the Submersible Rotating Video technique, used for the first time in Brazil. We present an inventory of 282 fish species representing 91 different families, with 21 new records for the study area, including a non-native species (Heniochus acuminatus). In addition, our results show a moderate endemism level for the Brazilian province (approximately 6.0%), while 10.5% of species are assigned to one of IUCN’s threatened categories. Our efforts show the fish biodiversity scenario and their distribution on coastal islands more than 10 years after the Cagarras Islands Natural Monument establishment, reinforcing the importance of monitoring research programs for the management of this Marine Protected Area and surrounding waters, that play a key role for artisanal fisheries.

Habitat-specific performance of high-frequency acoustic telemetry tags in a tropical marine environment

High-frequency (>175 kHz) acoustic telemetry transmitters are increasingly being used to track the movements of small fishes and other aquatic organisms. These transmitters, which are often smaller than conventional types, have primarily been used in freshwater, yet limited information is available on their efficacy in estuarine or marine environments. This study quantified detection ranges (DR) of 180-kHz tags and potential environmental factors influencing detection probability in three different habitats within a large embayment in Costa Rica. Mangrove (DR at 50% detection efficiency; DR50 = 121.0 m ± 8.1 s.e.) and transitional estuarine (DR50 = 145.6 m ± 12.2) habitats had relatively high detection ranges, albeit smaller than similar studies in freshwater, highlighting the effectiveness of using this frequency in tropical marine environments. By contrast, performance within rocky reef habitat was poor (DR50 consistently <0 m), which may have been caused by the heterogeneous bottom structure or close proximity detection interference (CPDI) due to ambient noise. This study provides novel information on the performance of high-frequency acoustic tags in a tropical marine environment serving as an important case study as investigations of the spatial ecology of small fishes in both marine and freshwater become more common.

Comparison of video and traps for detecting reef fishes and quantifying species richness in the continental shelf waters of the southeast USA

The management of reef-associated fish species is challenging due to their life history characteristics and occurrence in rocky reef habitats that are difficult to sample using traditional sampling gears. We compared 2 common sampling gears for reef fish species, chevron traps and underwater video, using 5 yr of comprehensive paired sampling data (N = 7034) collected at reef habitats between North Carolina and Florida along the southeast United States Atlantic continental shelf. Most fish families (80%) and species (85%) were observed significantly more often on video than caught in traps, and only 2 species out of 40 (5%)—black sea bass Centropristis striata and bank sea bass C.ocyurus—were caught significantly more often in traps than observed on video. Moreover, site-specific species richness was approximately 3-4 times higher on average for video compared to traps. We also used a generalized additive model to show that the ratio of trap-caught species to video-observed species was higher in shallower waters off North and South Carolina, especially when water clarity was low. Results demonstrate that video can be an efficient gear to sample most reef fishes around the world but may provide even greater benefits when paired with traditional sampling gears like traps to leverage the strengths of each gear for estimating relative abundance and species richness with more certainty.

Giant appetites: exploring the trophic ecology of California’s largest kelp forest predator, the giant sea bass Stereolepis gigas

The recovery of endangered predators has the potential to influence the ecosystems they inhabit. After suffering severe population declines due to fishing pressure, giant sea bassStereolepis gigasin southern California, USA, are beginning to recover. As large-bodied predators often associated with the kelp forest and rocky reef environments of southern California and Baja California, Mexico, the local recovery of this species could influence trophic dynamics in these systems. Here we leverage stable isotope and gut content analysis to describe the trophic ecology of adult giant sea bass. We found that they are generalist predators, with larger individuals relying more heavily on macroalgae-derived carbon, occupying a larger trophic niche, and obtaining higher trophic positions. Using these results, we speculate about the relationship between giant sea bass and kelp forest ecosystems, a vulnerable yet key habitat, including the impact of the return of these predators, as well as how contemporary threats to kelp forests might mediate their continued recovery.