LC/MS-based metabolite profiles of closely related sponge samples collected from Italy and Japan were analysed. Characteristic ion peaks observed in the MS data were used to guide the search for new metabolites, leading to the isolation of two new compounds, ficiformylenes A (1) and B (2). Their structures were elucidated by spectroscopic analyses, including 1D and 2D NMR and ESIMS/MS experiments, as well as ESIMS analysis of the products obtained by ozonolysis. These results demonstrate the utility of LC/MS-based comparative analysis of marine sponge secondary metabolites as an effective strategy for the discovery of novel natural products.

Worldwide, coral reefs are threatened by global and local stressors. One of the key local stressors is land-based nutrient pollution that enters coastal waters. However, detecting nutrient pollution remains challenging in oligotrophic, highly dynamic coastal waters. We integrated physicochemical water-quality measurements, macroalgae stable nitrogen-isotope analysis, and high-resolution molecular profiling of benthic cyanobacterial mat (BCM) communities in the Lease Islands, Indonesia. Across twelve sites categorized as Populated, Non-Populated, and River Mouth, we tested three hypotheses: (1) nutrients decline along a 1–75 m land-sea gradient; (2) Populated and River Mouth sites have higher nutrients, distinct δ¹⁵N and BCM communities; and (3) nutrient levels influence BCM community composition. Our results showed that while salinity and turbidity followed predictable land-sea gradients, only nitrate showed a significant, albeit weak, gradient. Phosphate, ammonium, and nitrite showed high variability in the nearshore zone (1–25 m), whereas the 50–75 m zone showed greater consistency, particularly for phosphate. When taking site levels as a whole, Populated sites had higher nutrient concentrations than Non-Populated sites. Macroalgal δ¹⁵N weakly indicated anthropogenic nitrogen influences due to limited species occurrence. BCM community composition differed significantly among site types, with River Mouth harboring the most divergent communities. Copiotroph (e.g., Pseudoalteromonas) and pathogenic taxa (e.g., Vibrio) were prevalent across all sites. Environmental factors explained 47% of the variation in BCM microbial community composition. Our study highlights that BCM microbial communities show potential promise as indicators of nutrient pollution, complementing water sampling and isotope analysis. We recommend further evaluation of possibly integrating BCM assessments into reef monitoring.

Current population genetics studies of sea turtles primarily rely on invasive tissue sampling or blood draws, which involve the capture and handling of the animals that require specific permits and resources. Moreover, this approach is limited by the sporadic visibility of turtles. In this study, we assessed the applicability of eDNA-based sampling to obtain mitochondrial haplotype data for leatherback turtle (Dermochelys coriacea) populations at three beaches in Sumatra, Indonesia (Northeast Indian Ocean). We collected seawater samples at two time points: immediately after a female left the beach (night samples) and 12 h later (morning samples) to reflect the common practice of conducting beach monitoring surveys at dawn. Our findings revealed that the eDNA samples captured identical haplotypes to those obtained from tissue samples. The haplotypes persisted in the eDNA from seawater samples up to 12 h after the females left the beach. We identified five haplotypes that correspond to those previously recorded in the Pacific, Atlantic, and Indian Oceans, showing the broad phylogeographic links between the Sumatra population and other global populations. Our results provide further evidence that noninvasive eDNA techniques could supplement traditional tissue sampling for studying sea turtle population genetics. This applies particularly to understudied populations or remote rookeries where traditional methods are difficult to implement and opens the possibility of using eDNA for population structure studies that could complement traditional monitoring programs.

Leatherback turtles (Dermochelys coriacea) are highly migratory and globally distributed, yet exhibit low overall genetic diversity. Currently, the species is divided into seven Regional Management Units (RMUs), and significant gaps remain in understanding genetic connectivity within the Indo-Pacific, particularly the Northeast Indian Ocean. Here, we investigate the genetic diversity and population structure of leatherback turtles sampled from five nesting sites in Sumatra, Indonesia. Using mitochondrial DNA (mtDNA) control region sequences from 57 individuals, we identified eight haplotypes, including one novel variant, with Sumatra exhibiting the highest haplotype (h = 0.786) and nucleotide diversity (π = 0.0040) among regional rookeries. There was a lack of significant stock structure based on our haplotype frequency data among rookeries in Sumatra (p>0.05). Phylogenetic and haplotype network analyses revealed that Sumatra contains lineages from both Indian and West Pacific Ocean clades, suggesting its role as a genetic bridge between these populations. Our results on population genetic structure support the recognition of Sumatra as a distinct Management Unit (MU), separate from other Northeast Indian Ocean populations. Our findings highlight the need to refine existing RMU boundaries and prioritize conservation actions in Sumatra to preserve its unique genetic composition and enhance connectivity across the Indo-Pacific.

Indonesia is recognized as a biodiversity hotspot within the Coral Triangle and is rapidly expanding its network of Marine Protected Areas (MPAs). MPAs are critical tools for conserving coral reefs, and MPA management plans serve as the foundational guidelines for conservation. Their effectiveness depends partly on how adequately coral reefs' stressors are addressed and integrated into actionable mitigation strategies. This study assessed the inclusion of stressors in current government-issued Indonesian MPA management plans. We analyzed the inclusion of stressor words within the comprehensive management plans and reviewed the action plan. By 2022, only 20 % of Indonesian MPAs had comprehensive management plans, comprising an introduction, zoning plan, and action plan. We found that most plans address stressors related to fishing. In contrast, less than one-third of the plans address land-based stressors, with nutrient pollution and plastic waste largely overlooked. While climate change was identified in about half of the plans, specific climate change impacts, such as rising sea surface temperature, were identified in only very few plans. Most management plans were broad, non-specific, and highly similar across locations, with stressors identified in the introduction rarely integrated into zoning and action plan sections, which may limit site-specific conservation efforts. Nevertheless, some plans showed a more targeted approach by addressing local stressors and proposing actionable responses. This study highlights the need for more site-specific and adaptive MPA plans. It offers a checklist to assess stressors in future Indonesian MPA management plan development, guiding increased responsiveness to evolving environmental challenges.

Tropical coastal ecosystems are increasingly threatened by rising seawater temperatures and terrestrial nutrient input, yet the combined impact of these stressors on food web complexity remains poorly understood. Using marine lakes in Raja Ampat, Indonesia, as natural analogs for varying environmental conditions, we investigated how temperature and terrestrial influence shape food web structure and carbon source utilization. We applied an approach at 2 scales, combining whole food web stable isotope analysis in 2 contrasting lakes-one with elevated temperature and high terrestrial input, the other with ocean-like conditions-with a broader survey of 16 additional lakes using the filter-feeding mussel Brachidontes as a proxy for baseline carbon sources. Biodiversity, food web complexity, and functional redundancy were reduced in the marine lake with higher temperatures and greater terrestrial input. Bulk stable carbon and nitrogen isotope values from Brachidontes from 16 different marine lakes revealed a shift in the main food source underlying the food web from marine to terrestrial organic matter, with a shift from particulate organic matter to the use of sponge-derived material (reworked/recycled organic material) in environments with high temperatures and high terrestrial inputs. The use of Brachidontes as an integrative indicator of basal carbon sources offers a valuable tool for monitoring and managing the ecological impacts of environmental change in tropical coastal systems. Extrapolating our findings to coastal marine systems, our results suggest a potential shift toward simplified, less resilient trophic structures in ecosystems with combined thermal and terrestrial stressors.

Sea turtles have been a conservation priority in Indonesia since 1978. Despite numerous regulations at national, regional, and local levels, sea turtle populations and habitats continue to decline. This study assessed current national and provincial (Aceh) regulations for sea turtles using text mining and an extensive review to identify strengths, weaknesses, gaps, and overlap. Local customary law (Hukum Adat Laot) from Aceh was included as a case study to compare constitutional and customary approaches to sea turtle conservation. The analysis of 47 terms across four categories—species, habitat, management, and protection—revealed six institutions involved in conservation, with the Ministry of Marine Affairs and Fisheries (MMAF) having the highest regulatory presence. However, substantial regulatory and institutional overlap was found, with no single institution clearly mandated to lead sea turtle protection. National and provincial regulations primarily emphasised management-related terms (50.19% in Aceh; 43.03% nationally), while species-specific and life-stage-related terms were rarely recognised. In contrast, the customary law Hukum Adat Laot demonstrated stronger provisions in the ‘species’ and ‘habitat’ categories, including explicit bans on adult turtle capture, regulated egg harvesting, and protections for nesting and foraging habitats. Effective management is often hindered by gaps and overlap in regulatory frameworks, which can lead to unclear jurisdiction, conflicting policies, and inefficiencies in enforcement. These challenges can create barriers to coordinated conservation efforts, making it difficult to implement consistent and effective protection measures for sea turtles. Although institutional and regulatory overlap pose challenges, integrating customary law into national conservation frameworks presents an opportunity to enhance species-specific protections, strengthen local engagement, and improve coordination. Recognising Hukum Adat Laot as an Other Effective Area-Based Conservation Measure (OECM) could improve enforcement and ecological outcomes for sea turtle conservation in Indonesia.

Tropical marine lakes are small land-locked marine waterbodies occurring in karstic coastal areas. During biodiversity surveys in 12 marine lakes in Raja Ampat, Southwest Papua province, Indonesia, we recorded at least 37 species belonging to 29 genera of hard corals. Their observed associated symbiont fauna consisted of bivalve molluscs and polychaete worms. Marine lake temperature ranged from 30.0 to 32.5 °C, acidity from pH 7.6 to 8.1, and salinity from 26.4 to 33.2 ppt. This study provides the first inventory of the marginal coral communities in the extreme habitat of marine lakes, under chronic extreme environmental conditions of higher temperatures, land-based nutrient loads, and sedimentation.

A new tetramic acid glycoside, aurantoside L (1), was isolated from the sponge Siliquariaspongia japonica collected at Tsushima Is., Nagasaki Prefecture, Japan. The structure of aurantoside L (1) composed of a tetramic acid bearing a chlorinated polyene system and a trisaccharide part was elucidated using spectral analysis. Aurantoside L (1) showed anti-parasitic activity against L. amazonensis with an IC50 value of 0.74 µM.

Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (<31 °C, 31–32 °C, and >32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes <31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4–18.8% hard coral, 3.5–26.3% CCA, and 15–15.5% turf algae, respectively), while the higher temperature marine lakes (31–32 °C and >32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (>31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant.

Marine lakes are bodies of seawater that are land-locked and maintain a subterranean connection to the surrounding sea. Here, we document the species diversity of benthic molluscs in 11 marine lakes in Raja Ampat, West Papua, Indonesia, using the roving diving survey method. We specifically tested for relationships between species richness and lake size and the degree of connection to the surrounding sea, and tested potential environmental drivers of community structure. We recorded 73 species, belonging to the classes Gastropoda (48 species, comprising 36 genera and 25 families), Bivalvia (24 species, consisting of 17 genera and 12 families), and Polyplacophora (one species). Molluscs from marine lakes are a subset of species also occurring in coral, seagrass, mangrove, and rocky shore habitats in the open sea. We found lake communities to mostly consist of grazers and filter feeders. The number of mollusc species significantly increased with increasing connection to the surrounding sea, but not with increasing surface area, indicating that dispersal potential may be the main driving force. Furthermore, we observed no significant influence of the environment on the variation in mollusc species composition among marine lakes. Still, we observed certain species to be exclusively present in either high or low-connected lakes, indicating a potential effect of environmental filtering. Marine lakes provide a unique ecosystem for diverse mollusc assemblages and as such should be protected.

The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F-ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.

In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30-60 m (upper mesophotic), and 60-90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.

Large grazers (megaherbivores) have a profound impact on ecosystem functioning. However, how ecosystem multifunctionality is affected by changes in megaherbivore populations remains poorly understood. Understanding the total impact on ecosystem multifunctionality requires an integrative ecosystem approach, which is especially challenging to obtain in marine systems. We assessed the effects of experimentally simulated grazing intensity scenarios on ecosystem functions and multifunctionality in a tropical Caribbean seagrass ecosystem. As a model, we selected a key marine megaherbivore, the green turtle, whose ecological role is rapidly unfolding in numerous foraging areas where populations are recovering through conservation after centuries of decline, with an increase in recorded overgrazing episodes. To quantify the effects, we employed a novel integrated index of seagrass ecosystem multifunctionality based upon multiple, well-recognized measures of seagrass ecosystem functions that reflect ecosystem services. Experiments revealed that intermediate turtle grazing resulted in the highest rates of nutrient cycling and carbon storage, while sediment stabilization, decomposition rates, epifauna richness, and fish biomass are highest in the absence of turtle grazing. In contrast, intense grazing resulted in disproportionally large effects on ecosystem functions and a collapse of multifunctionality. These results imply that (i) the return of a megaherbivore can exert strong effects on coastal ecosystem functions and multifunctionality, (ii) conservation efforts that are skewed toward megaherbivores, but ignore their key drivers like predators or habitat, will likely result in overgrazing-induced loss of multifunctionality, and (iii) the multifunctionality index shows great potential as a quantitative tool to assess ecosystem performance. Considerable and rapid alterations in megaherbivore abundance (both through extinction and conservation) cause an imbalance in ecosystem functioning and substantially alter or even compromise ecosystem services that help to negate global change effects. An integrative ecosystem approach in environmental management is urgently required to protect and enhance ecosystem multifunctionality.

Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti , Stryphnus fortis , and Weberella bursa . Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.

Marine lake in a karst landscape is one of the macro karst forms known as doline and is only found in some locations in the world. Moreover, the theory of marine doline formation is always associated with global sea-level rise which differs from one place to another due to several factors. This research was conducted to understand the formation process of marine lakes in Misool and how the water fills the basins formed especially at Holocene time. This was achieved by obtaining information on the longest underwater terrace which is also the longest standing water position recorded on the sea wall. The marine terraces were measured by sounding profiles to the sea bordering the seven marine lakes including Lenmakana, Balbullol, Lenkafal, Keramat, Karawapop, Keramat-2, and Keramat-3 as well as Harapan Jaya Sea. A total of 24 profiles were measured and stable isotopes δ18O and δD of water samples were used to determine the origin of water in the lakes. The results showed the longest terrace was at the depth of ˗33 and ˗3 m while the references from the area closest to Misool showed the same water level positions at 10,500 BP and 6,985 BP. Furthermore, the composition of δ18O and δD from lake water indicated the water samples were a mixture of groundwater and seawater with the seawater having the more dominant concentration and this allows it to fill the lake first through a previously formed cavity system.

The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to determine the parallels between the evolutionary histories of the host spiders and their associated microbial communities, together forming the “holobiont”. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawaiʻi, and outgroup taxa on older islands, we tested whether each component of the holobiont (the spider hosts, the intracellular endosymbionts, and the gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. In order to investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. Results showed that the host A. waikula is indeed structured by geographic isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different between Ariamnes species on different islands, but more homogeneous among A. waikula populations on the island of Hawaiʻi. Conversely, the gut microbiota was largely conserved across all populations and species, which we suspect are generally environmentally derived. Our results highlight that the different components of the holobiont have responded in distinct ways to the dynamic environment of the volcanic archipelago, showing the necessity of understanding the interplay between components to better characterize holobiont evolution.

Pleistocene environmental changes are generally assumed to have dramatically affected species' demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120-14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome-wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to -1/4th of present-day levels during the Last Glacial Maximum (LGM; 26-19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species' demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species' demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated.