Remote reef cryptobenthic diversity: Integrating autonomous reef monitoring structures and in situ environmental parameters

Coral reef sessile organisms inhabiting cryptic spaces and cavities of the reef matrix perform vital and varied functional roles but are often understudied in comparison to those on exposed surfaces. Here, we assess the composition of cryptobenthic taxa from three remote tropical reef sites (Central Indian Ocean) alongside a suite of in situ environmental parameters to determine if, or how, significant patterns of diversity are shaped by local abiotic factors. To achieve this, we carried out a point-count analysis of autonomous reef monitoring structure (ARMS) plate images and employed in situ instrumentation to recover long-term (12 months) profiles of flow velocity, wave heights, temperature, dissolved oxygen, and salinity, and short-term (3 weeks) profiles of light and pH. We recovered distinct environmental profiles between sampling sites and observed that ocean-facing reefs experienced frequent but short-lived cooling internal wave events and that these were key in shaping in situ temperature variability. By comparing temperature and wave height profiles recovered using in situ loggers with ex situ models, we discovered that global satellite products either failed to recover site-specific profiles or both over- and underestimated actual in situ conditions. We found that site choice and recruitment plate face (top or bottom) significantly impacted the percentage cover of bryozoans, gastropods, soft and calcified tube worms, as well as crustose coralline algae (CCA) and fleshy red, brown, and green encrusting macroalgae on ARMS. We observed significant correlations between the abundance of bryozoans, CCA, and colonial tunicates with lower mean temperature and higher mean dissolved oxygen profiles observed across sites. Red and brown encrusting macroalgae abundance correlated significantly with medium-to-high flow velocities and wave height profiles, as well as higher pH and dissolved oxygen. This study provides the first insight into cryptobenthic communities in the Chagos Archipelago marine-protected area and adds to our limited understanding of tropical reef sessile communities and their associations with environmental parameters in this region. With climate change accelerating the decline of reef ecosystems, integrating analyses of cryptobenthic organisms and in situ physicochemical factors are needed to understand how reef communities, if any, may withstand the impacts of climate change

Turbid reefs experience lower coral bleaching effects in NE Borneo (Sabah, Malaysia)

The impacts of climate change are becoming more evident in recent years. Future projections suggest that heat stress events will likely be more frequent and severe over the next century, threatening the high diversity of the Coral Triangle. Shallow turbid reefs may help dampen some of these effects as several studies have shown their inherent resilience to heat stress events. Therefore, our main goal was to test this hypothesis by assessing the response of corals to the heat stress event of 2020. We conducted bleaching surveys in two contrasting habitats in Darvel Bay, Sabah: the turbid reef of Sakar, and the clear-water reef of Blue Lagoon. Relatively high coral cover (40-43%) was observed on both reefs in 2019. Underwater data loggers were used to monitor temperature and light. Coral colonies were scored from video transects of 100m at 5m and 10m depth in both localities, with an additional transect at 15m depth in Blue Lagoon. A total of 1,326 coral colonies were evaluated for bleaching presence and bleaching severity based on the six-point scoring method. Bleaching severity varied significantly between both reefs. Low bleaching impacts were observed in the high turbid reef, with an average of 9.6% of colonies having bleached. Meanwhile, the clear-water of Blue Lagoon had an average of 37.1% of coral colonies affected by bleaching. Bleaching severity also varied significantly among depth, where corals in deeper depths bleached less in Blue Lagoon. Foliose coral forms were most affected in Blue Lagoon, while massive coral forms suffered the most in Sakar reef. Bleaching responses were also significantly different among coral genera. While Ctenactis and Herpolitha were consistently resistant in both reefs, Leptoseris, Fungia and Goniopora were most affected in the 5m of Blue Lagoon. Meanwhile, Pachyseris was notably more affected in Sakar reef at 10m than in Blue Lagoon. Overall, bleaching indices within these two reefs are lower than most that were assessed around the globe during heat stress events in 2020. These outcomes support the hypothesis of turbid reefs hosting resilient coral communities in the face of climate change

Microstructure and crystallographic texture data in modern giant clam shells (Tridacna squamosa and Hippopus hippopus)

This article provides novel data on the microstructure and crystallographic texture of modern giant clam shells (Tridacna squamosa and Hippopus hippopus) from the Coral Triangle region of northeast Borneo. Giant clams have two aragonitic shell layers—the inner and outer shell layer. This dataset focuses on the inner shell layer as this is well preserved and not affected by diagenetic alteration. To prepare samples for analysis, shells were cut longitudinally at the axis of maximum growth and mounted onto thin sections. Data collection involved scanning electron microscopy (SEM) to determine microstructure and SEM based electron backscatter diffraction (EBSD) for quantitative measurement of crystallographic orientation and texture. Post-acquisition reanalysis of saved EBSD patterns to optimize data quality included changing the number of reflectors and band detection mode. We provide EBSD data as band contrast images and colour-coded orientation maps (inverse pole figure maps). Crystallographic co-orientation strength obtained with multiple of uniform density (MUD) values are derived from density distributed pole figures of indexed EBSD points. Raw EBSD data files are also given to ensure repeatability of the steps provided in this article and to allow extraction of further crystallographic properties for future researchers. Overall, this dataset provides 1. a better understanding of shell growth and biomineralization in giant clams and 2. important steps for optimizing data collection with EBSD analyses in biogenic carbonates

Limited Progress in Improving Gender and Geographic Representation in Coral Reef Science

Despite increasing recognition of the need for more diverse and equitable representation in the sciences, it is unclear whether measurable progress has been made. Here, we examine trends in authorship in coral reef science from 1,677 articles published over the past 16 years (2003–2018) and find that while representation of authors that are women (from 18 to 33%) and from non-OECD nations (from 4 to 13%) have increased over time, progress is slow in achieving more equitable representation. For example, at the current rate, it would take over two decades for female representation to reach 50%. Given that there are more coral reef non-OECD countries, at the current rate, truly equitable representation of non-OECD countries would take even longer. OECD nations also continue to dominate authorship contributions in coral reef science (89%), in research conducted in both OECD (63%) and non-OECD nations (68%). We identify systemic issues that remain prevalent in coral reef science (i.e., parachute science, gender bias) that likely contribute to observed trends. We provide recommendations to address systemic biases in research to foster a more inclusive global science community. Adoption of these recommendations will lead to more creative, innovative, and impactful scientific approaches urgently needed for coral reefs and contribute to environmental justice efforts.We acknowledge the contributions of the many unrecognized and undervalued individuals in coral reef research whose efforts have made it possible for the field to progress. These scientists have collected data, translated across languages, coordinated field work, welcomed foreign visitors to their countries, shared ideas, trained and mentored students, become friends, inspired, and built the foundation for the discipline we know today. We acknowledge the work of all coral reef scientists who continue day after day to pursue equity, inclusion, and justice in the field and for their colleagues and themselves.Ye

Miocene reef-coral diversity of Indonesia: unlocking the murky origins of the Coral Triangle

Reefs in the Coral Triangle host the richest marine diversity today. While the biodiversity gradients associated with the Coral Triangle are progressively better documented, the mechanisms responsible for the origins and maintenance of this pattern still remain obscure. Until recently, palaeontological and molecular evidence suggest that the Miocene (5-23 Ma) was an important period for diversification of corals and associated biota in this region. However, the fossil record was markedly undersampled. As part of the Throughflow Project (TF), the main objective of this research was to obtain insights into the early history of today’s Coral Triangle diversity and understand its major ecological drivers. Corals play an essential role in the diversity of this region, not only due to the richness of the group itself, but also because they are the main reef builders and coral reefs are the main ecosystem in which diversity thrives. In addition, corals possess carbonate skeletons with a high potential of fossilization. These characteristics make corals an interesting model group to carry on taxonomic, phylogenetic and palaeoecological studies. The new TF collections include tens of thousands of specimens from the rich and well-preserved Miocene fossil record of small patch reefs in the Kutai Basin (East Kalimantan, Indonesia). These reefs developed in turbid habitats. A high diversity of corals was uncovered, with a total of 234 identified morphospecies from 79 genera, including 12 globally extinct genera. Our findings have revealed that some lineages that were previously known only from the Plio-Pleistocene were already present during the Miocene in the Coral Triangle. These discoveries have a profound impact on our understanding of the origins of today’s diversity in the Coral Triangle

Unravelling the moons: review of the genera Paratetilla and Cinachyrella in the Indo-Pacific (Demospongiae, Tetractinellida, Tetillidae)

Paratetilla bacca (Selenka, 1867) and Cinachyrella australiensis (Carter, 1886) occur in a broad range of marine environments and are allegedly widely distributed species in the Indo-Pacific. We coin the term ‘moon sponges’ for these species as they are spherical in shape with numerous porocalices resembling the lunar surface. Both species have a complex taxonomic history with high synonymization, in particular by Burton (1934, 1959). An examination of the junior synonyms proposed by Burton (1934, 1959) was conducted to establish the validity of the names. More than 230 specimens from Naturalis Biodiversity Center were reviewed that belong to the genera Paratetilla and Cinachyrella from marine lakes, coral reefs, and mangroves in Indonesia. The aim of the current study was to untangle the taxonomic history, describe the collection of moon sponges from Indonesia, and develop a key. We extensively reviewed the taxonomic literature as well as holotypes of most of the species synonymized by Burton. The taxonomic history of Paratetilla spp. and Cinachyrella australiensis showed some cases of misinterpreted synonyms, misidentifications, and lack of detailed descriptions for some species. The conclusion of the revision is that there are three valid species of Paratetilla (P. arcifera, P. bacca, and P. corrugata) and four valid species of Cinachyrella (C. australiensis, C. porosa, C. paterifera, and C. schulzei) in Indonesia. This is furthermore corroborated by molecular work from previous studies. Paratetilla arcifera Wilson 1925 and C. porosa (Lendenfeld, 1888) are resurrected. A full review of taxonomic history is provided as well as a key for identification of moon sponges from Indonesia. All species are sympatric and we expect that there are undescribed species remaining within the Tetillidae from the Indo-Pacific. Our current review provides the framework from which to describe new species in the genera Paratetilla and Cinachyrella from the Indo-Pacific

Molecular machineries of ciliogenesis, cell survival, and vasculogenesis are differentially expressed during regeneration in explants of the demosponge Halichondria panicea

Sponges are interesting animal models for regeneration studies, since even from dissociated cells, they are able to regenerate completely. In particular, explants are model systems that can be applied to many sponge species, since small fragments of sponges can regenerate all elements of the adult, including the oscula and the ability to pump water. The morphological aspects of regeneration in sponges are relatively well known, but the molecular machinery is only now starting to be elucidated for some sponge species. Here, we have used an explant system of the demosponge Halichondria panicea to understand the molecular machinery deployed during regeneration of the aquiferous system. We sequenced the transcriptomes of four replicates of the 5–day explant without an osculum (NOE), four replicates of the 17–18–day explant with a single osculum and pumping activity (PE) and also four replicates of field–collected individuals with regular pumping activity (PA), and performed differential gene expression analysis. We also described the morphology of NOE and PE samples using light and electron microscopy. Our results showed a highly disorganised mesohyl and disarranged aquiferous system in NOE that is coupled with upregulated pathways of ciliogenesis, organisation of the ECM, and cell proliferation and survival. Once the osculum is formed, genes involved in “response to stimulus in other organisms” were upregulated. Interestingly, the main molecular machinery of vasculogenesis described in vertebrates was activated during the regeneration of the aquiferous system. Notably, vasculogenesis markers were upregulated when the tissue was disorganised and about to start forming canals (NOE) and angiogenic stimulators and ECM remodelling machineries were differentially expressed once the aquiferous system was in place (PE and PA). Our results are fundamental to better understanding the molecular mechanisms involved in the formation of the aquiferous system in sponges, and its similarities with the early onset of blood-vessel formation in animal evolution

Unveiling deep-sea habitats of the Southern Ocean-facing submarine canyons of southwestern Australia

We present the outcomes of the first deep-sea remotely operated vehicle study of previously unexplored submarine canyon systems along the southwest Australian continental margin. This was conducted around: (1) the Bremer Marine Park; (2) the Mount Gabi seamount and nearby slope-shelf margin at the interface of the Southern and Indian oceans; with new information from (3) the Perth Canyon Marine Park located in the SE Indian Ocean. These canyons differ from many explored around the world in having no connectivity to continental river systems, thus little detrital input, with the Bremer systems and Mount Gabi facing the Southern Ocean which plays a key role in the global ocean circulation and climate systems. Such studies in the vast deep waters around the Australian continent are rare given the lack of local ROV capability available for research, thus little is known about these environments. Using the resources of the Schmidt Ocean Institute, we characterised the submarine topography from highresolution bathymetric mapping, geology, physical and chemical oceanography, and provide an overview of these environments and fauna observed and collected. We show that these Southern Ocean-influenced environments incorporate South Indian Central Water, Subantarctic Mode Water, Antarctic Intermediate Water, and Upper and Lower Circumpolar Deep Water, with Antarctic Bottom Water present in deep water just south of the Bremer canyon systems. The richness in megabenthos, especially along the steep, rocky substrates of the canyon heads and walls around the Bremer canyon systems, contrasts to the comparatively depauperate fauna of the more northerly Perth Canyon. Various corals serve as important substrates for a range of other species and often exhibit particular faunal associations. Especially notable are distinct ecological zones including a bryozoan and sponge-dominated (animal) forest on the shelf edge, spectacular coral gardens along canyon margins, and the occurrence of solitary scleractinians well below the aragonite saturation horizon. Subfossil coral deposits were discovered across all three study areas, reflecting periodic waxing and waning of deep-water Scleractinia throughout this southwest region. Extensive pre-modern assemblages at Mount Gabi contrast markedly with the sparse populations of living species and suggest that it might have once been a major coral ‘hotspot’, or whether they reflect long-term coral aggregations is yet to be determined. Nevertheless, stark differences in both living and past coral distribution patterns across our study sites point to at least localised fluctuations in Southern Ocean-derived nutrient and/or oxygen supplies to these deep-sea communities

Allele matrix of 11 microsatellites in Plenaster craigi for 4 areas and 30 populations

The excel file has two spread-sheets: (i) "Microsatellites-4Areas" including the information of the 11 microsatellites used in the paper for the four different areas we investigated; (ii) "Microsatellites-30Populations" including the information of the 11 microsatellites used in the paper for the 30 different populations we investigated. In the two spread-sheets we include the following columns: "Number of individual" from 1 to 168; "Area" with the names of the areas or populations for every individual; "Sample Code" with the name of the sample used in the paper; "1Ple, 3Ple, 11Ple, 13Ple, 12Ple, 14Ple, 16Ple, 5Ple, 19Ple, 10Ple, and 2Ple" the name of each of the 11 microsatellites gentotyped in our study. In addition to that, we provide a small summary of the "Number of microsatellites", "Number of Individuals", "Number of Areas", "Number of Populations", and "N of individuals per area and population"