Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial.

Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.

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.

Potential of seagrass habitat restorations as nature-based solutions: Practical and scientific implications in Indonesia.

Seagrasses offer diverse ecosystem services, yet, they are among the most threatened ecosystems. When degraded or destroyed, their services are lost or reduced in the process, affecting, for instance, local communities directly dependent on their livelihood provision. The Intergovernmental Panel on Climate Change (IPCC) reported that climate change is projected to worsen over time; thus, there is an urgent need for mitigation strategies in practice and also in the longer term. This work aims to provide an alternative perspective of seagrass restoration as a nature based solution (NbS) on a global scale, yet, giving an emphasis on tropical regions such as Indonesia. We focused on seagrass restorations which are not yet well established in comparison with other restoration programs (e.g., mangroves) despite their critical roles. We present in this work how restoring seagrass meadows fits the global standard of NbS published by the International Union for Conservation of Nature (IUCN). The results of this study can serve as a basis for promoting seagrass restorations as NbS against climate change particularly in countries with a wide extent of seagrass coverage.

The success of seagrass restoration using Enhalus acoroides seeds is correlated with substrate and hydrodynamic conditions.

The extent of seagrass areas and their associated ecosystem functions and services have been declining due to many factors. Seagrass restoration is important to mitigate such declines. Seagrass restoration using seeds can be a viable method due to the high seed availability of some seagrass species and could enhance seagrass resilience to climate change stress. However, this method sometimes has low success rates due to high seed predation and seeds being washed away by wave action or substrate movement. The research was conducted to compare the settlement of Enhalus acoroides seeds and the establishment of seedlings on different sediment types (fine sand, coarse sand, and hard substrate with rubble) combined with different wave exposure levels (high and moderate). This is the first study to observe seed survival and seedling establishment of the tropical seagrass E. acoroides in the wild. On average, 64% of seeds dispersed on fine sand substrate at a moderate exposure site survived and developed into established seedlings by the end of the 40 days observation period, but the survival of seeds dispersed on coarse sand at high exposure and hard substrate at moderate exposure only remained above 50% for up to 3 days, and had declined to 2% and 1.4%, respectively, by day 40. Six years later, surviving E. acoroides sample from the coarse sand and hard substrate both had well-developed rhizomes but fewer roots than the plant from the fine sand site, these rhizome and roots characteristics were likely adaptations to increase anchoring capacity in the specific site. The results indicate that Enhalus seed settlement and seedling establishment can readily occur at sites with fine sand substrate and lower wave exposure; however, additional measures may be required at more exposed sites with mobile or hard substrates until seedlings become established.

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.

Quantification of blue carbon in seagrass ecosystems of Southeast Asia and their potential for climate change mitigation.

Seagrasses have the ability to contribute towards climate change mitigation, through large organic carbon (Corg) sinks within their ecosystems. Although the importance of blue carbon within these ecosystems has been addressed in some countries of Southeast Asia, the regional and national inventories with the application of nature-based solutions are lacking. In this study, we aim to estimate national coastal blue carbon stocks in the seagrass ecosystems in the countries of Southeast Asia including the Andaman and Nicobar Islands of India. This study further assesses the potential of conservation and restoration practices and highlights the seagrass meadows as nature-based solution for climate change mitigation. The average value of the total carbon storage within seagrass meadows of this region is 121.95 ± 76.11 Mg ha-1 (average ± SD) and the total Corg stock of the seagrass meadows of this region was 429.11 ± 111.88 Tg, with the highest Corg stock in the Philippines (78%). The seagrass meadows of this region have the capacity to accumulate 5.85-6.80 Tg C year-1, which accounts for $214.6-249.4 million USD. Under the current rate of decline of 2.82%, the seagrass meadows are emitting 1.65-2.08 Tg of CO2 year-1 and the economic value of these losses accounts for $21.42-24.96 million USD. The potential of the seagrass meadows to the offset current CO2 emissions varies across the region, with the highest contribution to offset is in the seagrass meadows of the Philippines (11.71%). Current national policies and commitments of nationally determined contributions do not include blue carbon ecosystems as climate mitigation measures, even though these ecosystems can contribute up to 7.03% of the countries' reduction goal of CO2 emissions by 2030. The results of this study highlight and promote the potential of the southeast Asian seagrass meadows to national and international agencies as a practical scheme for nature-based solutions for climate change mitigation.

Evaluating sustainable development policies in rural coastal economies.

Sustainable development (SD) policies targeting marine economic sectors, designed to alleviate poverty and conserve marine ecosystems, have proliferated in recent years. Many developing countries are providing poor fishing households with new fishing boats (fishing capital) that can be used further offshore as a means to improve incomes and relieve fishing pressure on nearshore fish stocks. These kinds of policies are a marine variant of traditional SD policies focused on agriculture. Here, we evaluate ex ante economic and environmental impacts of provisions of fishing and agricultural capital, with and without enforcement of fishing regulations that prohibit the use of larger vessels in nearshore habitats. Combining methods from development economics, natural resource economics, and marine ecology, we use a unique dataset and modeling framework to account for linkages between households, business sectors, markets, and local fish stocks. We show that the policies investing capital in local marine fisheries or agricultural sectors achieve income gains for targeted households, but knock-on effects lead to increased harvest of nearshore fish, making them unlikely to achieve conservation objectives in rural coastal economies. However, pairing an agriculture stimulus with increasing enforcement of existing fisheries' regulations may lead to a win-win situation. While marine-based policies could be an important tool to achieve two of the United Nations Sustainable Development Goals (alleviate poverty and protect vulnerable marine resources), their success is by no means assured and requires consideration of land and marine socioeconomic linkages inherent in rural economies.

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.

Social-ecological drivers and dynamics of seagrass gleaning fisheries.

Invertebrate gleaning (walking) fisheries are common within intertidal seagrass meadows globally, contributing to the food supply of hundreds of millions of people, but understanding of these fisheries and their ecological drivers are extremely limited. The present study provides a unique analysis of these fisheries using a combined social and ecological approach. Catches contained 34 species and were dominated by Bivalves, Urchins and Gastropods. CPUE in all sites varied from 0.05 to 3 kg gleaner-1 hr-1, respectively, with the majority of fishers being women and children. Landings were of major significance for local food supply and livelihoods at all sites. Local ecological knowledge suggests seagrass meadows are declining in line with other regional trends. Increasing seagrass density significantly and positively correlated with CPUE of the invertebrate gleaning (r = 0.830) highlighting the importance of conserving these threatened habitats. Understanding the complexities of these fisheries, their supporting habitats and their sustainability is important for the support of sustainable coastal livelihoods.

Indonesia's globally significant seagrass meadows are under widespread threat.

Indonesia's marine ecosystems form a fundamental part of the world's natural heritage, representing a global maxima of marine biodiversity and supporting the world's second largest production of seafood. Seagrasses are a key part of that support. In the absence of empirical data we present evidence from expert opinions as to the state of Indonesia's seagrass ecosystems, their support for ecosystem services, with a focus on fisheries, and the damaging activities that threaten their existence. We further draw on expert opinion to elicit potential solutions to prevent further loss. Seagrasses and the ecosystem services they support across the Indonesian archipelago are in a critical state of decline. Declining seagrass health is the result of shifting environmental conditions due largely to coastal development, land reclamation, and deforestation, as well as seaweed farming, overfishing and garbage dumping. In particular, we also describe the declining state of the fisheries resources that seagrass meadows support. The perilous state of Indonesia's seagrasses will compromise their resilience to climate change and result in a loss of their high ecosystem service value. Community supported management initiatives provide one mechanism for seagrass protection. Exemplars highlight the need for increased local level autonomy for the management of marine resources, opening up opportunities for incentive type conservation schemes.

Time to stop mucking around? Impacts of underwater photography on cryptobenthic fauna found in soft sediment habitats.

Scuba diving tourism is a sustainable source of income for many coastal communities, but can have negative environmental impacts if not managed effectively. Diving on soft sediment habitats, typically referred to as 'muck diving', is a growing multi-million dollar industry with a strong focus on photographing cryptobenthic fauna. We assessed how the environmental impacts of scuba divers are affected by the activity they are engaged in while diving and the habitat they dive in. To do this, we observed 66 divers on coral reefs and soft sediment habitats in Indonesia and the Philippines. We found diver activity, specifically interacting with and photographing fauna, causes greater environmental disturbances than effects caused by certification level, gender, dive experience or age. Divers touched the substrate more often while diving on soft sediment habitats than on coral reefs, but this did not result in greater environmental damage on soft sediment sites. Divers had a higher impact on the substrate and touch animals more frequently when observing or photographing cryptobenthic fauna. When using dSLR-cameras, divers spent up to five times longer interacting with fauna. With the unknown, long-term impacts on cryptobenthic fauna or soft sediment habitats, and the increasing popularity of underwater photography, we argue for the introduction of a muck diving code of conduct.

Biofluorescence as a survey tool for cryptic marine species.

As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty-one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data-deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of cryptic species. Adopting this technique will enhance researchers' ability to survey cryptic species and facilitate management and conservation of cryptic marine species.

Species richness accelerates marine ecosystem restoration in the Coral Triangle.

Ecosystem restoration aims to restore biodiversity and valuable functions that have been degraded or lost. The Coral Triangle is a hotspot for marine biodiversity held in its coral reefs, seagrass meadows, and mangrove forests, all of which are in global decline. These coastal ecosystems support valuable fisheries and endangered species, protect shorelines, and are significant carbon stores, functions that have been degraded by coastal development, destructive fishing practices, and climate change. Ecosystem restoration is required to mitigate these damages and losses, but its practice is in its infancy in the region. Here we demonstrate that species diversity can set the trajectory of restoration. In a seagrass restoration experiment in the heart of the Coral Triangle (Sulawesi, Indonesia), plant survival and coverage increased with the number of species transplanted. Our results highlight the positive role biodiversity can play in ecosystem restoration and call for revision of the common restoration practice of establishing a single target species, particularly in regions having high biodiversity. Coastal ecosystems affect human well-being in many important ways, and restoration will become ever more important as conservation efforts cannot keep up with their loss.

Developing a methodology of bioindication of human-induced effects using seagrass morphological variation in Spermonde Archipelago, South Sulawesi, Indonesia.

Seagrass is particularly susceptible to environmental degradation. The objective of the study is to develop an effective bioindicator to assess human-induced effects using morphological variation and fluctuating asymmetry (FA) of seagrass. Samples were collected from eight islands situated at different distance from mainland with different human population density and therefore expected to experience different level of anthropogenic pressure. Cd, Pb, Cu, Zn, nitrate, and phosphate were measured. Metals were also measured in tissues of seagrass. Metal concentrations in sediment, water, and seagrass did not exceed the quality standards required for marine life. Heterogeneity of FA was found among sites suggesting that there are some factors changing developmental instability of seagrass which is not associated to particular toxicants. This baseline study indicates that the water condition is still natural and shows no signs of metal contamination, therefore it does not cause a detectable stress on morphological variation and FA of seagrass.