The Coral Triangle is the region in the Indo-Pacific with the highest diversity of reef organisms. Coral reefs here have experienced increased anthropogenic stressors since the late 1970s due to destructive fishing, land reclamation, industrialization, and agriculture. Biological observations in the Spermonde Archipelago (SW Sulawesi, Indonesia) started only after large-scale disturbances had begun limiting insights into long-...

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 d...

Environmental DNA (eDNA) methods are increasingly viewed as alternate or complementary approaches to conventional capture-based surveys for marine conservation and fisheries management purposes, especially at large spatial scales in mega-biodiversity regions such as Indonesia. Decapod crustacean distribution and diversity across Indonesia are still poorly known, even for economically important fisheries commodities. This study...

Traditional morphological methods for species identification are highly time consuming, especially for small organisms, such as Foraminifera, a group of shell-building microbial eukaryotes. To analyze large amounts of samples more efficiently, species identification methods have extended to molecular tools in the last few decades. Although a wide range of phyla have good markers available, for Foraminifera only one hypervariab...

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 resto...

Due to difficulties with surveying, cryptobenthic fishes are understudied, which limits assessments of their extinction risk. Using a novel survey method (a combination of underwater visual census and underwater biofluorescence census), we surveyed the densities of two gorgonian seafan-associated pygmy seahorses ( Hippocampus bargibanti and H. denise ) in 63 sites across Indonesia. Densities were low for both seahorses (≤ 0.4...

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 thei...

Summary The study of complex microbial communities poses unique conceptual and analytical challenges, with microbial species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a ‘core’ microbiota approach, focusing only on the stable and permanent members of the community, is becoming increasingly popular. Given the various ways of defining a core microbiota,...

Localized impacts, such as eutrophication and overfishing, have been identified as major threats to reefs worldwide, resulting in changes in coral reef community composition, from coral‐dominance to algal‐dominance. Herbivory by fishes is frequently cited as a key process structuring benthic community response to stressors. Here, we experimentally tested the capacity of herbivorous fishes to remove macroalgae along an onshore–...

Coral reef degradation often involves a phase shift from coral‐ to macroalgal‐dominated reefs. Declining levels of herbivory or increasing supply of nutrients have both been suggested as a cause of increased algal abundance and consequent competitive overgrowth of corals. However, explicit demonstration of the processes involved and their relative strengths requires simultaneous tests of all three factors: competition, herbivo...