Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea

Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula

The Arabian Peninsula accounts for approximately 6% of the world's coral reefs. Some thrive in extreme environments of temperature and salinity. Using 51 Autonomous Reef Monitoring Structure (ARMS), a standardized non-destructive monitoring device, we investigated the spatial patterns of coral reef cryptobenthic diversity in four ecoregions around the Arabian Peninsula and analyzed how geographical and/or environmental drivers shape those patterns. The mitochondrial cytochrome c oxidase subunit I (COI) gene was used to identify Amplicon Sequence Variants and assign taxonomy of the cryptobenthic organisms collected from the sessile and mobile fractions of each ARMS. Cryptobenthic communities sampled from the two ecoregions in the Red Sea showed to be more diverse than those inhabiting the Arabian (Persian) Gulf and the Gulf of Oman. Geographic distance revealed a stronger relationship with beta diversity in the Mantel partial correlation than environmental distance. However, the two mobile fractions (106-500 µm and 500-2000 µm) also had a significant correlation between environmental distance and beta diversity. In our study, dispersal limitations explained the beta diversity patterns in the selected reefs, supporting the neutral theory of ecology. Still, increasing differences in environmental variables (environmental filtering) also had an effect on the distribution patterns of assemblages inhabiting reefs within short geographic distances. The influence of geographical distance in the cryptofauna assemblages makes these relevant, yet usually ignored, communities in reef functioning vulnerable to large scale coastal development and should be considered in ecosystem management of such projects.

Low diversity and abundance of predatory fishes in a peripheral coral reef ecosystem

Semi-enclosed seas are often associated with elevated local threats and distinct biogeographic patterns among marine fishes, but our understanding of how fish assemblage dynamics vary in relation to relatively small semi-enclosed seas (e.g., the Gulf of Aqaba) remains limited. Baited remote underwater video surveys (n = 111) were conducted across ~300 km of coral reef habitats in the Gulf of Aqaba and the northern Red Sea. A total of 55 predatory fish species were detected, with less than half of all species (n = 23) observed in both basins. Relative abundance patterns between the Gulf of Aqaba and the northern Red Sea were variable among taxa, but nearly twice as many predatory fish were observed per unit of effort in the northern Red Sea. In general, assemblages in both basins were dominated by three taxa (Epinephelinae, Carangidae, and Lethrinidae). Large-bodied and threatened species were recorded at very low abundances. Multivariate analysis revealed distinct assemblage structuring of coral reef predators between the Gulf of Aqaba and the northern Red Sea. Most of the species driving these differences were recorded in both basins, but occurred at varying levels of abundance. Environmental factors were largely unsuccessful in explaining variation in assemblage structuring. These findings indicate that biological assemblages in the Gulf of Aqaba are more distinct than previously reported and that reef fish assemblage structuring can occur even within a relatively small semi-enclosed sea. Despite inter-basin assemblage structuring, the overall low abundance of vulnerable fish species is suggestive of overexploitation in both the Gulf of Aqaba and the northern Red Sea of Saudi Arabia. As the region surveyed is currently undergoing large-scale coastal development, the results presented herein aim to guide spatial management and recovery plans for these coral reef systems in relation to this development.

Coral reefs in the northeastern Saudi Arabian Red Sea are resilient to mass coral mortality events

We conducted an integrated survey combining visual census and baited remote underwater video survey on the coral reefs in the northeastern Red Sea and examined their health by comparing the baseline information from two decades ago. The mean coverage of the corals of all stations was 36 %, including 32 % stony corals and 4.0 % soft corals, significantly higher and lower to previous baseline. Observed high proportion of dead corals indicated the occurrence of the events of mass mortality, and the heating events were the most likely cause. Similar levels of coral coverage compared to two decades ago indicated their resilience to past events with mass coral mortality. Small proportions of macroalgae and sea urchins indicated that they might be controlled by their predators frequently observed in both visual census and underwater video survey. Regular monitoring and careful development plans are needed to safeguard these invaluable reefs.

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013-2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.

Morphological and ecological trait diversity reveal sensitivity of herbivorous fish assemblages to coral reef benthic conditions

Herbivorous fishes play a critical role in the maintenance of coral reefs through grazing and cropping of various benthic algae types. Herbivorous fish assemblages are sensitive to changes in the reef environment and are often targeted by local fisheries. This can lead to a decline in ecosystem functions if key groups are reduced. The present study investigates the morphological and ecological trait diversity of herbivorous reef fish assemblages in habitats differing in relative benthic coverage: i) coral-dominated, ii) algae-dominated, and iii) an intermediate habitat. Trait diversity for conspicuous herbivorous fishes was measured using three trait diversity indices: trait richness, trait divergence, and trait evenness. These indices were derived from in situ community surveys and feeding observations, morphological assessment of feeding mechanics from locally collected specimens, and ecological information obtained from published data. Trait diversity, reflected in higher trait evenness and lower trait richness, was lower within algae-dominated habitats than coral-dominated habitats, suggesting that algae-dominated habitats may be compromised by the lack of essential functions provided by key species. These groups reduce algal biomass and may help facilitate the survival and growth of corals, which in turn can increase coral cover. Algae-habitats were dominated with species known to consume macroalgae (rabbitfish and surgeonfish), appearing to provide essential feeding and habitat resources. These species include browsers and croppers that are fundamental in reducing algal biomass and may help facilitate the survival and growth of corals, which in turn can promote reef health. However, this habitat lacked parrotfishes known to remove turf algae and sediments, an essential function for clearing benthic space for coral settlement and other key benthic invertebrates. This study identified several species with overlapping functional roles in the coral-dominated and intermediate habitats. Still, species that were not redundant showed high trait complementarity, suggesting that their removal may result in the loss of unique functions. Importantly, we show that algae-dominated habitats supported high numbers of juvenile fishes especially in species targeted by local artisanal fishers. We also showed that the loss of trait diversity is greater than the loss of species diversity through the comparison of taxonomic and trait β-diversity, further emphasizing the importance of trait diversity analysis in understanding ecosystem health and maintenance.

Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea

In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.

Hyperdiverse Macrofauna Communities Associated with a Common Sponge, Stylissa carteri, Shift across Ecological Gradients in the Central Red Sea

Sponges act as important microhabitats in the marine environment and promote biodiversity by harboring a wide variety of macrofauna, but little is known about the magnitude and patterns of diversity of sponge-associated communities. This study uses DNA barcoding to examine the macrofaunal communities associated with Stylissa carteri in the central Saudi Arabian Red Sea, an understudied ecosystem with high biodiversity and endemism. In total, 146 operational taxonomic units (OTUs) were distinguished from 938 successfully-sequenced macrofauna individuals from 99 sponges. A significant difference was found in the macrofaunal community composition of S. carteri along a cross-shelf gradient using OTU abundance (Bray–Curtis dissimilarity index), with more amphipods associated with offshore sponges and more brittle stars and fishes associated with inshore sponges. The abundance of S. carteri also showed a gradient, increasing with proximity to shore. However, no significant differences in macrofaunal community composition or total macrofauna abundance were observed between exposed and sheltered sides of the reefs and there was no significant change in total macrofauna abundance along the inshore–offshore gradient. As climate change and ocean acidification continue to impact coral reef ecosystems, understanding the ecology of sponges and their role as microhabitats may become more important for understanding their full ramifications for biodiversity.

Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were dominated by Porifera (sessile fraction), Arthropoda and Annelida (mobile fractions). The two primer sets detected different taxa lists, but patterns in community composition and structure were similar. While the microhabitat of the ARMS deployment affected the community structure, a clear cross-shelf gradient was observed for all fractions investigated. The partitioning of beta-diversity revealed that replacement (i.e. the substitution of species) made the highest contribution with richness playing a smaller role. Hence, different reef habitats across the shelf are relevant to regional diversity, as they harbor different communities, a result with clear implications for the design of Marine Protected Areas. ARMS can be vital tools to assess biodiversity patterns in the generally neglected but species-rich cryptic benthos, providing invaluable information for the management and conservation of hard-bottomed habitats over local and global scales.

Exploring the larval fish community of the central Red Sea with an integrated morphological and molecular approach

An important aspect of population dynamics for coral reef fishes is the input of new individuals from the pelagic larval pool. However, the high biodiversity and the difficulty of identifying larvae of closely related species represent obstacles to more fully understanding these populations. In this study, we combined morphology and genetic barcoding (Cytochrome Oxidase I gene) to characterize the seasonal patterns of the larval fish community at two sites in close proximity to coral reefs in the central-north Red Sea: one shallower inshore location (50 m depth) and a nearby site located in deeper and more offshore waters (~ 500 m depth). Fish larvae were collected using oblique tows of a 60 cm-bongo net (500 μm mesh size) every month for one year (2013). During the warmer period of the year (June-November), the larval fish stock was comparable between sampling sites. However, during the colder months, abundances were higher in the inshore than in the offshore waters. Taxonomic composition and temporal variation of community structure differed notably between sites, potentially reflecting habitat differences, reproductive patterns of adults, and/or advective processes in the area. Eleven out of a total of 62 recorded families comprised 69–94% of the fish larval community, depending on sampling site and month. Richness of taxa was notably higher in the inshore station compared to the offshore, particularly during the colder period of the year and especially for the gobiids and apogonids. Two mesopelagic taxa (Vinciguerria sp. and Benthosema spp.) comprised an important component of the larval community at the deeper site with only a small and sporadic occurrence in the shallower inshore waters. Our data provide an important baseline reference for the larval fish communities of the central Red Sea, representing the first such study from Saudi Arabian waters.