Jamaluddin Jompa's research while affiliated with Universitas Hasanuddin and other places

Publications (99)

Article
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Historically, ecological monitoring of marine habitats has primarily relied on labour-intensive, non-automated survey methods. The field of passive acoustic monitoring (PAM) has demonstrated the potential of this practice to automate surveying in marine habitats. This has primarily been through the use of ‘ecoacoustic indices’ to quantify attribute...
Article
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Mass coral bleaching events may have disproportionate effects on branching corals, leading to coral community restructuring, reduced biodiversity, and decreased structural complexity. This affects overall reef health and resilience. Functionally important, fast-growing branching Acropora corals were a historically dominant and vital component of In...
Article
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Marginal coral reefs are located in a limited aquatic environment, causing coral organisms to live under threat and only certain species of coral are able to survive. Porites lutea is one species of coral that is able to live in normal and marginal coral reef conditions. The purpose of this study is to determine the ecology of Porites lutea, the ph...
Article
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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 r...
Article
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Passive acoustic monitoring (PAM) involves recording the sounds of animals and environments for research and conservation. PAM is used in a range of contexts across terrestrial, marine and freshwater environments. However, financial constraints limit applications within aquatic environments; these costs include the high cost of submersible acoustic...
Chapter
Indonesian seagrass communities are among the most diverse compared with those of other tropical or temperate regions. In this chapter, we describe some of the results of our research on seagrass beds in Sulawesi during the German–Indonesian Research Project “Science for the Protection of Indonesian Coastal Ecosystems” (SPICE) from 2004 to 2016. We...
Chapter
Ecological and social processes of the Spermonde Archipelago, South Sulawesi, Indonesia, have been intensively studied during the Science for the Protection of Indonesian Coastal Ecosystems (SPICE) program. The archipelago is of specific interest to better understand how intensive exploitation of marine resources results in the degradation of reef...
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Pantropical degradation of coral reefs is prompting considerable investment in their active restoration. However, current measures of restoration success are based largely on coral cover, which does not fully reflect ecosystem function or reef health. Soundscapes are an important aspect of reef health; loud and diverse soundscapes guide the recruit...
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Water quality parameters can be indicators of pollution driving riverine, estuarine and coastal resource degradation. This study evaluated water quality in the downstream, estuarine and surrounding coastal waters of 8 major rivers around the western, southern and eastern coasts of South Sulawesi Province, Indonesia. Data on physical and chemical pa...
Article
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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...
Article
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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, sim...
Article
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Polapa FS, Werorilangi S, Ali SM, Jompa J. 2021. Physiological responses of scleractinian corals in marginal habitat. Biodiversitas 22: 4011-4018. This study aims to analyze physiological differences in corals in marginal habitats. Under different conditions, the production/respiration (P/R) ratio and photobiology of various coral genera were compa...
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Phytoplankton are primary producers that can be used as seawater condition indicators. Certain phytoplankton can proliferate, causing harmful algal blooms (HABs). The coastal waters of South Sulawesi, Indonesia are under pressure from land-based processes and activities resulting in inputs of organic and inorganic materials. This study analysed phy...
Article
Early‐diagenetic cementation of tropical carbonates results from the combination of numerous physico‐chemical and biological processes. In the marine phreatic environment it represents an essential mechanism for the development and stabilization of carbonate platforms. However, diagenetic cements that developed early in the marine phreatic environm...
Article
The availability of colonizable substrate is an important driver of the temporal dynamics of sessile invertebrates on coral reefs. Increased dominance of algae and, in some cases, sponges has been documented on many coral reefs around the world, but how these organisms benefit from non-colonized substrate on the reef is unclear. In this study, we d...
Article
Conservation area management includes all systematic efforts, deliberate or not, undertaken by stakeholders in the management of coastal areas in a conservation area. The most useful way to assess management effectiveness is evaluation based on the achievement of objectives set by policies at the national, regional and site levels. The research obj...
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he Banggai Archipelago is one of six major island groups around Sulawesi Island in Indonesia, within the Wallacea region. Initiated after two district level marine protected areas (MPAs) in the Banggai Archipelago became obsolete under the revised regional autonomy Act (UU 23/2014) before they had become operational, the more extensive provincial l...
Chapter
This study aimed to identify species of isolated bacterial with the nitrogen base sequence analysis method on nucleotide constituents 16S rDNA genes of bacterial disease-causing Black band disease. Identification was done by isolatied the bacteria, based on the appearance of the morphology of the colony, five isolates bacterias isolated from health...
Article
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The Banggai Archipelago is one of six major island groups around Sulawesi Island in Indonesia, within the Wallacea region. Initiated after two district level marine protected areas (MPAs) in the Banggai Archipelago became obsolete under the revised regional autonomy Act (UU 23/2014) before they had become operational, the more extensive provincial...
Article
Broad-scale studies and regional comparisons of Indonesia’s coral reefs are critical given the relative lack of information about these large, diverse, and threatened ecosystems. Most studies on reef benthic composition and distribution have largely focused on rather short transects spanning relatively small areas. Here, we quantify the shallow lar...
Article
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Yusuf S, Beger M, Tassakka ACMAR, Brauwer MD, Pricella A, Rahmi, Umar W, Limmon GV, Moore AM, Jompa J. 2021. Cross shelf gradients of scleractinian corals in the Spermonde Islands, South Sulawesi, Indonesia. Biodiversitas 22: 1415-1423. Coral reef ecosystems around the world have suffered extensive degradation, including the reefs of the Wallacea r...
Article
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We present one year of buying and selling data of the yellow coral goby (Gobiodon okinawae) in Banggai Laut District, Banggai Archipelago, Central Sulawesi, Indonesia. This data is the first to demonstrate that this species is being captured and exported from the region to be sold in the global saltwater aquarium trade. We present frequency, volume...
Article
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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 pro...
Article
Djunaidi A, Jompa J, Nadiarti N, Bahar A, Tilahunga SD, Lilienfeld D, Hani MS. 2020. Analysis of two whale shark watching destinations in Indonesia: status and ecotourism potential. Biodiversitas 21: 4511-4523. Botubarani in Gorontalo, on the northern coast of Tomini Bay and Labuhan Jambu in Teluk Saleh, Sumbawa recently became whale shark tourism...
Article
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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. denis...
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The Spermonde Archipelago, off the coast of southwest Sulawesi, consists of more than 100 small islands and hundreds of shallow-water reef areas. Most of the islands are bordered by coral reefs that grew in the past in response to paleo relative sea-level changes. Remnants of these reefs are preserved today in the form of fossil microatolls. In thi...
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Corals create complex reef structures that provide both habitat and food for many fish species. Due to 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...
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Scleractinian corals can reproduce in several ways, with two main sexual reproduction modes known as brooding and broadcast spawning. In this study, we described patterns of genetic variation within and connectivity between coral populations in western Indonesia (Seribu Archipelago), central Indonesia (Spermonde Archipelago), and eastern Indonesia...
Article
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Scleractinian corals can reproduce in several ways, with two main sexual reproduction modes known as brooding and broadcast spawning. In this study, we described patterns of genetic variation within and connectivity between coral populations in western Indonesia (Seribu Archipelago), central Indonesia (Spermonde Archipelago), and eastern Indonesia...
Article
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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 responsibl...
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Manta ray watching tourism worldwide has been reported to bring a significant economic impact that contributes to the effective management of sustainable wildlife tourism. This study was conducted to analyse the role of small-scale tourism businesses in Marine Protected Areas (MPAs) of Nusa Penida, Komodo, and Raja Ampat, both in Indonesia, that of...
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Coastal and small islands communities generally have limited access to fresh vegetables. The tropical seagrass Enhalus acoroides fruits during the rainy season, when sea conditions often prevent fishing. Coastal communities in several countries, including Indonesia, traditionally collect seagrass fruit for food and traditional remedies. This study...
Chapter
Marine management areas provide a key tool for efforts towards sustainable development, reconciling socio-economic goals with those for biodiversity conservation. Decisions about where and when to establish spatial management areas in the oceans are currently hampered by the uncertainties of incomplete, or overly general, information about biodiver...
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The aim of this study was to isolate black band disease (BBD) samples from hard coral (Pachyseris speciosa) and to identify the main pathogenic bacteria stimulating BBD. The research was conducted from October 2015 to March 2016. Samples (fragments of diseased corals) were collected from Pulau Barrang Lompo, Pulau Badi, Pulau Bonetambung, Pulau Sar...
Preprint
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Currently, the red alga Kappaphycus alvarezii is the species most commonly cultivated by seaweed farmers in the tropical Indo-Pacific. Seaweed farming over coral reefs is thought to have a negative impact on scleractinian corals. This study aims to determine the effect of K. alvarezii aquaculture over coral reefs on the recruitment of scleractinian...
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Umar W, Tassakka ACMAR, Jompa J. 2019. High genetic connectivity in a scleractinian coral (Lobophyllia corymbosa) around Sulawesi, Indonesia. Biodiversitas 20: 3484-3492. The life cycle of scleractinian corals begins with a pelagic larval phase subject to the influence of currents, with the potential to disperse propagules over vast geographical di...
Article
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Indonesia is one of the largest exporters of groupers, both live and dead, as part of the reef fish food trade. These fisheries sub-sector plays an important role in the livelihoods of fishing communities, especially for those living on small islands. The aim of this article is to provide a baseline profile of the trade as currently practiced and d...
Article
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Umar W, Tassakka ACMAR, Barber PH, Jompa J. 2019. Unexpected patterns of genetic connectivity in Lobophyllia corymbosa (Forskål, 1775) around Sulawesi, Indonesia. Biodiversitas 20: 2744-2749. Sulawesi is a strategic area for the biological networks of marine organisms, especially for Scleractinian corals. Sulawesi is located centrally in Indonesia...
Article
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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...
Article
Sea urchins of the genus Diadema, key herbivores in coral reef ecosystems, also provide habitat for other organisms. Our research extended Diadema biogeography in seaways east and west of Sulawesi and identified Diadema species associated with the endemic Banggai cardinalfish (Pterapogon kauderni) using field surveys and molecular DNA barcoding met...
Article
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Indonesia is a country composed of several thousand islands, many of them small, low-lying and densely inhabited. These are, in particular, subject to high risk of inundation due to future relative sea level changes. The Spermonde Archipelago, off the coast of Southwest Sulawesi, consists of more than 100 small islands. This study presents a datase...
Article
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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...
Article
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This study aimed to determine which bacteria trigger brown band disease (BrB) through assessing the level of pathogenicity of bacteria present and microscopic histological analysis of coral tissue cells. The study was conducted from October 2014 to March 2015. The bacterial culture stage was conducted at the Faculty of Medicine Microbiology Laborat...
Article
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The severely degraded condition of many coral reefs worldwide calls for active interventions to rehabilitate their physical and biological structure and function, in addition to effective management of fisheries and no‐take reserves. Rehabilitation efforts to stabilize reef substratum sufficiently to support coral growth have been limited in size....
Data
Composition and dissimilarity of bacterial communities at the inhabited and uninhabited island. (A) Cluster diagram based on Bray-Curtis dissimilarity coefficients constructed using average linkage. (B) Class-level taxonomic composition of the bacterial communities. FL, Free-living bacterial communities of the water column (>0.2 μm); PA, Particle-a...
Data
Rarefaction analysis of alpha diversity indices of bacterial communities at the inhabited and uninhabited island. Rarefaction analysis of alpha diversity indices of bacterial communities at the inhabited and uninhabited island for sequencing depths of 0 to 20,000 sequences using the R packageiNEXT. (A+B) Bacterial diversity of the free-living fract...
Article
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Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these...
Data
List of eigenvectors of the individual water quality parameters contributing to the principal components (PC) of Fig. 3. NOx−, nitrite/nitrate; PO43−, phosphate; Si, silicate; Chl a, Chlorophyll a; DOC, dissolved organic carbon; TEP, transparent exopolymer particles.
Data
Raw R-code for the submitted analyses. This is the provided raw code for the conducted bioinformatics analyses in R.
Data
Heatmap of centered log ratio (clr)-transformed sequence counts of potentially pathogenic OTUs identified in the inhabited and uninhabited island based on random forest analysis. Red colors indicate an enrichment of an OTU compared to the average sequence contribution of all OTUs in a sample, whereas blue colors indicate depletion. For each OTU, it...
Data
Heatmap of centered log ratio (clr)-transformed sequence counts of OTUs best suited to differentiate bacterial communities between the inhabited and uninhabited island based on random forest analysis. Red colors indicate an enrichment of an OTU compared to the average sequence contribution of all OTUs in a sample, whereas blue colors indicate deple...
Data
Number of generated (raw) and quality-checked (final) sequences produced from bacterial communities of the free-living and particle-attached fraction of the water column and reef sediment at the inhabited (BL: Barrang Lompo) and the uninhabited island (KK). OTU number (nOTU) and Inverse Simpson diversity index (invS) were calculated based on the co...
Data
Summary of the water quality parameters at the inhabited (BL: Barrang Lompo) and the uninhabited island (KK: Kodinggareng Keke). NOx−, nitrite/nitrate; PO43−, phosphate; Si, silicate; Chl a, Chlorophyll a; DOC, dissolved organic carbon; TEP, transparent exopolymer particles; N, number of replicates; SD, standard deviation; SEM, standard error of th...
Data
Bacterial diversity based on the inverse Simpson index at the inhabited and uninhabited island and its correlation with water quality parameters. (A+B) Bacterial diversity of the free-living fraction of the water column (>0.2 μm; FL). (C+D) Bacterial diversity of the particle-attached fraction of the water column (>3 μm; PA). (E+F) Bacterial divers...
Data
Performance of the random forest analysis to predict the inhabitation status of the islands based on their microbial communities. Each model was run with 10001 trees. Performance of the random forest analysis to predict the inhabitation status of the islands based on their microbial communities. Each model was run with 10001 trees.