Combining environmental DNA and visual surveys can inform conservation planning for coral reefs.

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning.

Reflecting on Indonesia's young academy movement.

In the past three decades, there has been a rise in young academy movements in the Global North and South. Such movements, in at least Germany and the Netherlands, have been shown to be quite effective in connecting scientific work with society. Likewise, these movements share a common goal of developing interdisciplinary collaboration among young scientists, which contributes to the growth of a nation's-but also global-scientific endeavors. This paper focuses on the young academy movement in the fourth-largest country hosting the biggest Muslim population in the world, which is also the third-most populous democracy: Indonesia. We observe that there has been rising awareness among the young generation of scientists in Indonesia of the need to advocate for the use of sciences in responding to upcoming and current multidimensional crises. Science advocacy can be seen in their peer-based identification of Indonesia's future challenges, encompassing the fundamental areas for scientific inquiry, discovery, and intervention. We focus on the Indonesian Young Academy of Sciences (ALMI) and its network of young scientists. We describe ALMI's science communication practice, specifically SAINS45 and Science for Indonesia's Biodiversity, and how they have been useful for policymakers, media, and school engagements. The article closes with a reflection on future directions for the young academy movement in Indonesia and beyond.

Reduced small-scale structural complexity on sponge-dominated areas of Indo-Pacific coral reefs.

Corals provide a complex 3D framework that offers habitat to diverse coral reef fauna. However, future reefs are likely to experience reduced coral abundance. Sponges have been proposed as one potential winner on future coral reefs, but little is known of how they contribute to reef 3D structure. Given the ecological importance of structural complexity, it is critical to understand how changes in the abundance of structure-building organisms will affect the three-dimensional properties of coral reefs. To investigate the potentially important functional role of coral reef sponges as providers of structural complexity, we compared the structural complexity of coral- and sponge-dominated areas of an Indonesian coral reef, using 3D photogrammetry at a 4 m2 spatial scale. Structural complexity of 31 4 m2 quadrats was expressed as rugosity indicating reef contour complexity (R), vector dispersion indicating heterogeneity of angles between reef surfaces (1/k), and fractal dimension indicating geometrical complexity at five different spatial scales between 1 and 120 cm (D1-5). Quadrats were identified as high- or low-complexity using hierarchical clustering based on the complexity metrics. At high structural complexity, coral- and sponge-dominated quadrats were similar in terms of R and 1/k. However, smallest-scale refuge spaces (1-5 cm) were more abundant in coral-dominated quadrats, whereas larger scale refuge spaces (30-60 cm) were more abundant in sponge-dominated quadrats. Branching and massive corals contributed the most to structural complexity in coral-dominated quadrats, and barrel sponges in sponge-dominated quadrats. We show that smaller-scale refugia (1-5 cm) are reduced on sponge-dominated reefs at the spatial scale considered here (4 m2), with potential negative implications for smaller reef fauna.

Two centuries of sponges (phylum Porifera) taxonomic studies in Indonesia (1820-2021): checklist and bibliography.

Sponges in Indonesia have been studied since the 19th century during several historical expeditions and international collaborations. Hundreds of new species were reported from various locations, e.g., Ambon, Ternate, Sulawesi, Aru, and Kei Islands. This study aimed to create a sponge (Porifera: Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha) species checklist from Indonesia based on World Porifera Database. With a total of 731 species, our checklist comprises approximately 45 species of Calcarea, 566 species of Demospongiae, 115 species of Hexactinellida, and five species of Homoscleromorpha. The number of species are recorded from 12 marine ecoregions across the Indonesian Archipelago and freshwater habitats (Spongillida) between 1820-2021. The species composition indicates higher regional endemism or poorly studied since no other report after the original description. However, several marine ecoregions of Indonesia remain highly overlooked (e.g., Northeast Sulawesi, Papua, Southern Java, Western Sumatra), including freshwater habitats. Therefore, a taxonomic biodiversity baseline study, particularly on Porifera, is necessary to better understand the aquatic and marine biodiversity in the Indonesia Archipelago.

Docking Studies and Molecular Dynamics Simulations of Potential Inhibitors from the Brown Seaweed Sargassum polycystum (Phaeophyceae) against PLpro of SARS-CoV-2.

The COVID-19 disease is a major problem affecting human health all over the world. Consequently, researchers have been trying to find solutions to treat this pandemic-scale disease. Even if there are vaccines and approved drugs that could decrease the spread of this pandemic, multidisciplinary approaches are still needed to identify new small molecules as alternatives to combat COVID-19, especially those from nature. In this study, we employed computational approaches by screening 17 natural compounds from the tropical brown seaweed Sargassum polycystum known to have anti-viral properties that benefit human health. This study assessed some seaweed natural products that are bound to the PLpro of SARS-CoV-2. By employing pharmacophore and molecular docking, these natural compounds from S. polycystum showed remarkable scores for protein targets with competitive scores compared to X-ray crystallography ligands and well-known antiviral compounds. This study provides insightful information for advanced study and further in vitro examination and clinical investigation for drug development prospects of abundant yet underexploited tropical seaweeds.

Macroalgae exhibit diverse responses to human disturbances on coral reefs.

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human-driven disturbance. Using genus-level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats.

Fluctuating sea-level and reversing Monsoon winds drive Holocene lagoon infill in Southeast Asia.

Many lagoons surrounded by reefs are partially or completely infilled with reef-derived detrital carbonate sediment. Sediment deposits in such restricted environments are archives of prevailing environmental conditions during lagoon infill. For Indonesia, no paleoenvironmental reconstructions based on Holocene lagoon sediments exist. Here we analyze the sedimentary record obtained from five percussion cores penetrating 10 m into the unconsolidated subsurface of a reef island in the Spermonde Archipelago, Indonesia. The combined compositional, textural and chronostratigraphic analyses reveal that the sedimentary infill of the lagoon underlying the island, starting 6900 years cal BP, was interrupted between 5800 and 4400 years cal BP, when sea level was ~ 0.5 m higher than at present, and monsoon intensity was lower. After the intensity of the monsoons increased to modern levels, and sea level dropped to its present position, lagoonal sedimentation was re-initiated and created the foundation for an island that built up since 3000 years cal BP. Our study provides the first geological evidence for the strong sensitivity of detrital carbonate systems in Indonesia to fluctuations in sea level and dominant wind direction. It thus sheds light on how changing environmental conditions in the context of global warming could affect the morphological development of reef systems, and thereby also habitable coastal areas.

COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies.

Monitoring community composition of Foraminifera (single-celled marine protists) provides valuable insights into environmental conditions in marine ecosystems. Despite the efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) metabarcoding to assess the presence of multiple taxa, this has not been straightforward for Foraminifera partially due to the high genetic variability in widely used ribosomal markers. Here, we test the correctness in retrieving foraminiferal communities by metabarcoding of mock communities, bulk-DNA from coral reef sediment samples, and eDNA from their associated ethanol preservative using the recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we compared our results with large benthic foraminiferal communities previously reported from the same sampling sites. Results from our mock communities demonstrate that all species were detected in two mock communities and all but one in the remaining four. Technical replicates were highly similar in number of reads for each assigned ASV in both the mock communities and bulk-DNA samples. Bulk-DNA showed a significantly higher species richness than their associated eDNA samples, and also detected additional species to what was already reported at the specific sites. Our study confirms that metabarcoding using the foraminiferal COI marker adequately retrieves the diversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nuclear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool to assess foraminiferal community composition under the condition that the reference database is adequate to the target taxa.

Safeguarding Imperiled Biodiversity and Evolutionary Processes in the Wallacea Center of Endemism.

Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently.

The relative influence of sea surface temperature anomalies on the benthic composition of an Indo-Pacific and Caribbean coral reef over the last decade.

Rising ocean temperatures are the primary driver of coral reef declines throughout the tropics. Such declines include reductions in coral cover that facilitate the monopolization of the benthos by other taxa such as macroalgae, resulting in reduced habitat complexity and biodiversity. Long-term monitoring projects present rare opportunities to assess how sea surface temperature anomalies (SSTAs) influence changes in the benthic composition of coral reefs across distinct locations. Here, using extensively monitored coral reef sites from Honduras (in the Caribbean Sea), and from the Wakatobi National Park located in the center of the coral triangle of Indonesia, we assess the impact of global warming on coral reef benthic compositions over the period 2012-2019. Bayesian generalized linear mixed effect models revealed increases in the sponge, and hard coral coverage through time, while rubble coverage decreased at the Indonesia location. Conversely, the effect of SSTAs did not predict any changes in benthic coverage. At the Honduras location, algae and soft coral coverage increased through time, while hard coral and rock coverage were decreasing. The effects of SSTA at the Honduras location included increased rock coverage, but reduced sponge coverage, indicating disparate responses between both systems under SSTAs. However, redundancy analyses showed intralocation site variability explained the majority of variance in benthic composition over the course of the study period. Our findings show that SSTAs have differentially influenced the benthic composition between the Honduras and the Indonesian coral reefs surveyed in this study. However, the large intralocation variance that explains the benthic composition at both locations indicates that localized processes have a predominant role in explaining benthic composition over the last decade. The sustained monitoring effort is critical for understanding how these reefs will change in their composition as global temperatures continue to rise through the Anthropocene.

Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?

Ecological regime shifts in the marine realm have been recorded from a variety of systems and locations around the world. Coral reefs have been especially affected, with their benthic habitat changing from a dominance of stony corals to a dominance of other organisms such as fleshy algae. To detect changes in the benthic habitat of coral reefs, simple tools applicable on a global scale are necessary for future monitoring programs. Hence, the aim of this research is to explore the hypothesis that shifts in assemblages of large benthic foraminifera (LBF) can detect early signs of degradation in the reef benthic habitat. To do so, data on living assemblages of LBF collected between 1997 and 2018 at 12 islands in the Spermonde Archipelago (South Sulawesi, Indonesia) were analyzed. Foraminiferal specimens were morphologically identified to the species level and statistical analyses performed to assess changes in their assemblage composition. A clear temporal shift was observed. Typical foraminiferal assemblages in a coral-dominated (e.g., Amphistegina lobifera, Calcarina spengleri, Heterostegina depressa) and fleshy algae-dominated (e.g., Neorotalia gaimardi, C. mayori) reef habitats were identified and significantly linked to the substrate type. Other species (e.g., Elphidium spp., Peneroplis planatus and Sphaerogypsina globulus) seem to reflect a spatial and temporal gradient of anthropogenic pollution from local inhabited islands and ongoing urban development on the mainland. Hence communities of LBF consistently follow gradual shifts in environmental conditions. Additionally to foraminiferal assemblages being an indicator for actual reef condition, closely monitoring LBF may provide early information on reef degradation, in time to take action against identified stressors (e.g., eutrophication or intensive fishing) at local and regional scales. The circumtropical distribution of LBF is such that they can be included worldwide in reef monitoring programs, conditional to calibration to the regional species pool.

The effectiveness of 7% table salt concentration test to increase collagen in the healing process of wound.

OBJECTIVE: Table salt (sodium chloride) is an ionic compound consisting of positive ions (cations) and negative ions (anions) to form neutral compounds that can provide a healing effect on wounds. This study's purpose of seeing and test the impact of soaking 7% sodium chloride concentration on people's salt toward the wound healing process. METHOD: This study was an experimental laboratory using the One-Way ANOVA test and the Mann Whitney test conducted in the animal enclosure of the Faculty of Pharmacy, Hasanuddin University, Makassar. The study was conducted from July to August 2019. Samples of 20 mice (Mus Musculus) female swiss webster strains were sliced on the abdominal skin then divided into two groups: the treatment group (n=15) and the control group (n=5). The wound area was observed from the first day to the seventh day to see the wound closure process. RESULTS: The research shows that soaking 7% of table salt concentration can significantly accelerate the wound healing process compared to the control group, with a decrease in wound diameter on the 3rd day and completely heal on the 7th day. CONCLUSION: 7% concentration of table Salt Soaking can increase the effectiveness of wound healing.

First report of mitochondrial COI in foraminifera and implications for DNA barcoding.

Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia.

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.

The effectiveness of 7% table salt concentration test to increase collagen in the healing process of wound

Objective: Table salt (sodium chloride) is an ionic compound consisting of positive ions (cations) and negative ions (anions) to form neutral compounds that can provide a healing effect on wounds. This study's purpose of seeing and test the impact of soaking 7% sodium chloride concentration on people's salt toward the wound healing process. Method: This study was an experimental laboratory using the One-Way ANOVA test and the Mann Whitney test conducted in the animal enclosure of the Faculty of Pharmacy, Hasanuddin University, Makassar. The study was conducted from July to August 2019. Samples of 20 mice (Mus Musculus) female swiss webster strains were sliced on the abdominal skin then divided into two groups: the treatment group (n = 15) and the control group (n = 5). The wound area was observed from the first day to the seventh day to see the wound closure process. Results: The research shows that soaking 7% of table salt concentration can significantly accelerate the wound healing process compared to the control group, with a decrease in wound diameter on the 3rd day and completely heal on the 7th day. Conclusion: 7% concentration of table Salt Soaking can increase the effectiveness of wound healing. (AU)

High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef-dwelling calcifier.

Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo-West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological-scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation.

Interactions between coral restoration and fish assemblages: implications for reef management.

Corals create complex reef structures that provide both habitat and food for many fish species. Because of numerous natural and anthropogenic threats, many coral reefs are currently being degraded, endangering the fish assemblages they support. Coral reef restoration, an active ecological management tool, may help reverse some of the current trends in reef degradation through the transplantation of stony corals. Although restoration techniques have been extensively reviewed in relation to coral survival, our understanding of the effects of adding live coral cover and complexity on fishes is in its infancy with a lack of scientifically validated research. This study reviews the limited data on reef restoration and fish assemblages, and complements this with the more extensive understanding of complex interactions between natural reefs and fishes and how this might inform restoration efforts. It also discusses which key fish species or functional groups may promote, facilitate or inhibit restoration efforts and, in turn, how restoration efforts can be optimised to enhance coral fish assemblages. By highlighting critical knowledge gaps in relation to fishes and restoration interactions, the study aims to stimulate research into the role of reef fishes in restoration projects. A greater understanding of the functional roles of reef fishes would also help inform whether restoration projects can return fish assemblages to their natural compositions or whether alternative species compositions develop, and over what timeframe. Although alleviation of local and global reef stressors remains a priority, reef restoration is an important tool; an increased understanding of the interactions between replanted corals and the fishes they support is critical for ensuring its success for people and nature.

Author Correction: Growth and longevity in giant barrel sponges: Redwoods of the reef or Pines in the Indo-Pacific?

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Reproductive Biology of Three Important Threatened/Near-Threatened Groupers (Plectropomus leopardus, Epinephelus polyphekadion and Plectropomus areolatus) in Eastern Indonesia and Implications for Management.

The three grouper species most heavily fished for the live reef fish trade (LRFT) in Indonesia are Plectopomus leopardus (greatest catch volume), and two species classified as Vulnerable on the International Union for Conservation of Nature (IUCN) Red List: Plectropomus areolatus and Epinephelus polyphekadion. Understanding the reproductive biology of these fishes is essential for sustainable management, but relevant data are limited. This study aimed to determine reproductive dynamics, so as to inform management measures to maintain the reproductive capacity of these groupers. Grouper gonad samples collected from fish caught for the LRFT were analyzed histologically. Data were also collected from participatory mapping and interviews with fishermen, and underwater monitoring of three known spawning aggregation sites in the Wakatobi National Park, Eastern Indonesia. Based on observed gonad development, the respective lengths and weights at first maturity were: 37.7 cm and 759 g (P. leopardus); 36.65 cm and 771.2 g (P. areolatus); 36.95 cm and 889.9 g (E. polyphekadion). The mean weight of the groupers market-based sampled was higher than the size at first sexual maturity. Sex transition was observed in P. leopardus; sex reversal was not observed in E. polyphekadion, and the sex pattern of P. areolatus was unresolved. Based on the fisher surveys and spawning aggregation monitoring, spawning occurs around the new moon from September to April, with reproductive peaks in November and December. Fisheries management measures that are suggested to sustain grouper stocks include enforcing appropriate size limits, temporal spatial closures (spawning aggregation sites), and a trading ban during the peak spawning season (November-December).

Artisanal fish fences pose broad and unexpected threats to the tropical coastal seascape.

Gear restrictions are an important management tool in small-scale tropical fisheries, improving sustainability and building resilience to climate change. Yet to identify the management challenges and complete footprint of individual gears, a broader systems approach is required that integrates ecological, economic and social sciences. Here we apply this approach to artisanal fish fences, intensively used across three oceans, to identify a previously underrecognized gear requiring urgent management attention. A longitudinal case study shows increased effort matched with large declines in catch success and corresponding reef fish abundance. We find fish fences to disrupt vital ecological connectivity, exploit > 500 species with high juvenile removal, and directly damage seagrass ecosystems with cascading impacts on connected coral reefs and mangroves. As semi-permanent structures in otherwise open-access fisheries, they create social conflict by assuming unofficial and unregulated property rights, while their unique high-investment-low-effort nature removes traditional economic and social barriers to overfishing.