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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,269 Documents
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Comparative evaluation of chloroplast DNA barcoding markers for authenticating ethnomedicinal plants from Surigao del Sur, Philippines FREDDIE A. BLASCO; RUBY RATERTA; GRECEBIO JONATHAN D. ALEJANDRO
Biodiversitas Journal of Biological Diversity Vol. 26 No. 10 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261033

Abstract

Abstract. Blasco FA, Raterta R, Alejandro GJD. 2025. Comparative evaluation of chloroplast DNA barcoding markers for authenticating ethnomedicinal plants from Surigao del Sur, Philippines. Biodiversitas 26: 5195-5203. Traditional medicine utilizing ethnomedicinal plants remains crucial for healthcare in developing countries, with authentication being critical for safety and efficacy. DNA barcoding offers a molecular solution for accurate species identification, particularly important for poorly documented flora in biodiversity hotspots. This study evaluated the performance of four chloroplast DNA barcoding regions (rbcL, matK, trnL-F, and trnH-psbA) for authenticating ethnomedicinal plants from the biodiverse Surigao del Sur mountain range, Philippines. This represents the first comprehensive molecular reference dataset for Surigao del Sur ethnomedicinal flora. Fresh leaf samples from 50 ethnomedicinal plant species representing 43 genera and 31 families were collected from three municipalities (Lanuza, Tago, and Tandag). Barcode performance of the four markers was assessed based on PCR success, sequencing quality, BLAST identification accuracy, genetic distance analysis, and phylogenetic reconstruction. The trnH-psbA region achieved the highest PCR amplification success (100%), while trnL-F exhibited optimal balanced performance with 94% PCR success rate. BLAST analysis revealed trnL-F had the highest identification rate (80%), followed by trnH-psbA (66%). The matK showed optimal species-level discrimination with 0.7% intra-generic divergence and achieved strong bootstrap support in phylogenetic analysis. The multi-locus approach combining trnL-F, trnH-psbA, and matK achieved 86% identification success rate. This study contributes 107 novel sequences and provides essential molecular tools for reliable species authentication, supports conservation of ethnomedicinal plant diversity in the Philippines, and establishes a foundation for quality control in traditional medicine practice and international trade.
Biodiversity and stratification of dye plants in urban green spaces at Universitas Syiah Kuala, Banda Aceh, Indonesia IQBAR IQBAR; NOVITA NOVITA
Biodiversitas Journal of Biological Diversity Vol. 27 No. 1 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270115

Abstract

Abstract. Iqbar, Novita. 2026. Biodiversity and stratification of dye plants in urban green spaces at Universitas Syiah Kuala, Banda Aceh, Indonesia. Biodiversitas 27 (1): d270115.  https://doi.org/10.13057/biodiv/d270115. Urban green spaces are increasingly recognized for their role in conserving biodiversity and supporting cultural ecosystem services. This study presents the first systematic assessment of dye-producing plant diversity and ecological stratification within a university-based green open space, positioning the campus as a living laboratory for biocultural conservation and sustainable natural dye innovation. Floristic surveys recorded 32 dye-producing plant species from 18 families in the Green Open Space (GOS) of Universitas Syiah Kuala (USK), Indonesia, with Fabaceae and Asteraceae as the dominant families. Species richness, growth forms, pigment classes, and plant parts used for dye extraction were analyzed across canopy, understory, and groundcover strata. Statistical analyses revealed significant differences in species richness and species composition among vegetation strata (ANOVA, p<0.05), indicating pronounced vertical structuring of dye-producing plants. Trees dominated the canopy layer, providing long-term sources of pigments and associated ecosystem services. In contrast, understory and groundcover shrubs and herbaceous plants contributed rapidly renewable pigments suitable for small-scale extraction and educational applications. Flavonoids, tannins, and anthocyanins were the most prevalent pigment classes, generating a wide spectrum of natural colors. Compared with other urban ethnobotanical studies in Southeast Asia, dye-plant richness at USK was relatively high, reflecting spatial heterogeneity and the combined presence of native and ornamental species. Overall, this study demonstrates that urban academic landscapes can serve as living laboratories that integrate biodiversity conservation, ethnobotanical knowledge, and sustainable eco-textile education into multifunctional urban green-space management.
Balinese Usada as a biocultural knowledge system revealed through the chemodiversity of two Ocimum species I NYOMAN ARSANA; PUTU LAKUSTINI CAHYANINGRUM; ANAK AGUNG AYU SAUCA SUNIA WIDYANTARI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 3 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270337

Abstract

Abstract. Arsana IN, Cahyaningrum PL, Widyantari AAASS. 2026. Balinese Usada as a biocultural knowledge system revealed through the chemodiversity of two Ocimum species. Biodiversitas 27 (3): d270337. https://doi.org/10.13057/biodiv/d270337. Ocimum tenuiflorum and Ocimum gratissimum are widely used in the Balinese Usada, a biocultural knowledge system that integrates plant diversity and culturally transmitted medical practices. However, systematic documentation linking comparative phytochemical diversity with functional differentiation between Ocimum species within this context remains limited. This study aims to compare the phytochemical profiles, antioxidant activity, and antibacterial activity of O. tenuiflorum and O. gratissimum to elucidate species-level differentiation as a character of biocultural biodiversity. The research procedure began with the process of extracting separately the leaves of O. tenuiflorum and O. gratissimum using ethanol, methanol, and hexane solvents. The active compounds were analyzed with Gas Chromatography-Mass Spectrometry (GC-MS). Total phenols and tannins were analyzed using the Folin-Ciocalteu reagent. Total flavonoids using quercetin. Antioxidant activity was analyzed using 2,2-Diphenyl-1-Picrylhydrazyl (DPPH). The antibacterial activity was tested using the diffusion method on Mueller-Hinton agar media, with four types of bacteria: Streptococcus mutans ATCC 25175, Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 27853. The results revealed that clear interspecific phytochemical differentiation of O. gratissimum was characterized by a predominance of phenylpropanoids, particularly eugenol, whereas O. tenuiflorum was dominated by methyleugenol and sesquiterpenes such as caryophyllene. These chemical differences were accompanied by distinct functional responses, with O. gratissimum exhibiting better antioxidant capacity (IC₅₀ 43.92±0.03 μg/mL) compared to O. tenuiflorum (IC₅₀ 79.45±0.01 μg/mL). Both species exhibited differently antibacterial inhibition patterns against the tested bacteria, indicating species-specific functional traits rather than bioactivity. Overall, this study demonstrates that interspecific chemodiversity in Ocimum reflects species-level differentiation within the Balinese Usada system. Integrating comparative phytochemical and functional analyses within a biocultural framework, the findings contribute to biodiversity science by highlighting chemical variation as a functional character of biocultural biodiversity.
Spatial variation in coral reef condition and reef fish assemblages along a proximity to Jakarta Bay, Indonesia RIKOH MANOGAR SIRINGORINGO; DIETRIECH GEOFFREY BENGEN; I WAYAN NURJAYA; BEGINER SUBHAN; GIYANTO GIYANTO; RISANDI DWIRAMA PUTRA; MUHAMMAD ABRAR; NI WAYAN PURNAMA SARI; LUDI PARWADANI AJI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261147

Abstract

Abstract. Siringoringo RM, Bengen DG, Nurjaya IW, Subhan B, Giyanto, Putra RD, Abrar M, Sari NWP, Aji LP. 2025. Spatial variation in coral reef condition and reef fish assemblages along a proximity to Jakarta Bay, Indonesia. Biodiversitas 26: 5919-5930. The coral reef ecosystems of the Seribu Islands, Indonesia, exhibit complex ecological interactions between benthic assemblages and reef fish communities under the combined influence of local anthropogenic pressures and regional environmental stressors. This study examined benthic composition and reef fish functional structure across 14 sites along a spatial gradient from Jakarta Bay, Seribu Islands, to the outer islands. Benthic cover was assessed using the Underwater Photo Transect (UPT) method, and reef fish assemblages were quantified through Underwater Visual Census (UVC). Analyses revealed that distance from Jakarta Bay had a weak and inconsistent influence on benthic composition, with a low explanatory power for variations in hard coral cover (R²: 0.023, p: 0.6). In contrast, corallivorous fish abundance increased significantly with distance from the bay (R²: 0.30, p: 0.043), indicating a more pronounced spatial response among higher trophic groups. Cluster analyses identified three distinct ecological assemblages aligned with the nearshore-offshore gradient, reflecting subtle yet detectable shifts in community structure. These findings suggest that while benthic recovery remains constrained by persistent sedimentation and nutrient enrichment, reef fish assemblages particularly corallivores retain spatial sensitivity to urban influence. The emerging ecological differentiation across the archipelago underscores that the Seribu Islands function as a transitional system shaped by both urban proximity and broader ecological processes. Effective management should therefore integrate local mitigation of land-based stressors with broader seascape-scale strategies to enhance reef resilience in urban-influenced marine ecosystems.
Diversity and composition of flowering plants in lahar-affected soils of La Salle Botanical Garden, Philippines ALYANNA MARIE I. PARAS; ISABELLE BIANCA M. CASA; JAIME ZURI S. SAN LUIS; LUIS IÑIGO B. BRAVO; ALISSA JOLIE M. CO; DONN RODRIGO ISIDORE B. INCIONG; JUAN CARLO T. GUMANGAN
Biodiversitas Journal of Biological Diversity Vol. 26 No. 12 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261211

Abstract

Abstract. Paras AMI, Casa IBM, Luis JZSS, Bravo LIB, Co AJM, Inciong DRIB, Gumangan JCT. 2025. Diversity and composition of flowering plants in lahar-affected soils of La Salle Botanical Garden, Philippines. Biodiversitas 26: 6089-6098. The 1991 Mt. Pinatubo eruption and subsequent lahar flows created extensive sterile volcanic substrates that eliminated pre-existing vegetation, initiating primary succession across the landscape in Philippines. Despite extensive research on agricultural recovery efforts, natural vegetation recolonization patterns in these extreme environments remain poorly documented. This study conducted a rapid biodiversity assessment of flowering plants in lahar-affected soils at the La Salle Botanical Garden (LSBG) in Porac, Pampanga, Philippines, to characterize early successional dynamics and identify functional traits enabling establishment in volcanic substrates. Using the Line Intercept Technique across two temporal surveys (August-September 2024), eight angiosperm species from eight families were recorded, comprising three native and five naturalized taxa. The community exhibited low diversity (H' = 0.58) and strong dominance by two invasive species: Passiflora foetida and Asystasia gangetica, which collectively accounted for > 54.56% of relative density. While these pioneer species possess stress-tolerant traits—including drought tolerance, rapid growth, and efficient dispersal—that enable persistence in nutrient-poor, physically unstable lahar substrates, their dominance raises concerns about invasion-mediated alternative stable states that may prevent progression toward native-dominated communities. The overwhelming presence of invasive species suggests that natural succession alone is unlikely to restore native vegetation without active management intervention. Our findings provide critical baseline data for long-term monitoring and emphasize the urgent need for early invasive species control coupled with targeted enrichment planting of stress-tolerant native species to shift succession trajectories toward restoration goals. This study highlights LSBG's role as a living laboratory for understanding tropical volcanic succession and demonstrates how functional trait approaches can inform restoration practice in extreme disturbance environments.
Phytochemical composition and antibacterial potential of Melastoma malabathricum against Staphylococcus aureus with in silico insights into MRSA target proteins FEBRIA ELVY SUSANTI; MAI EFDI; SYAFRIZAYANTI SYAFRIZAYANTI; ABDI WIRA SEPTAMA; NURYANI TURABBY
Biodiversitas Journal of Biological Diversity Vol. 26 No. 12 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261204

Abstract

Abstract. Susanti FE, Efdi M, Syafrizayanti, Septama AW, Turabby N. 2025. Phytochemical composition and antibacterial potential of Melastoma malabathricum against Staphylococcus aureus with in silico insights into MRSA target proteins. Biodiversitas 26: 6000-6013. The global rise in antimicrobial resistance highlights the need to explore new antibacterial agents derived from natural sources. Melastoma malabathricum, a medicinal plant rich in phenolic compounds, was investigated for its antioxidant and antibacterial properties, with additional in silico analysis of potential interactions with MRSA-related target proteins. Methanol extracts from different plant parts (leaves, stems, fruits, roots, and flowers) were evaluated for their Total Phenolic Content (TPC), antioxidant activity, and antibacterial effects against methicillin-sensitive Staphylococcus aureus (MSSA, ATCC 29213) and Escherichia coli (ATCC 25922). The flower extract showed the widest inhibition zone of 14.17 mm against S. aureus ATCC 29213 (MSSA), and the highest IC50 value (89.22 mg/L) was obtained from the root extract, indicating the lowest antioxidant activity. The TPC of the extracts reached 140.84 mg GAE/g. Molecular docking revealed that afzelin, quercetin, and trifolin may bind to MRSA-associated proteins, including PBP2a, DdlB, and FabH, suggesting possible mechanisms underlying the observed antibacterial effects. These findings imply that phenolic compounds in M. malabathricum could act through multiple molecular targets, contributing to its biological activities. However, since the antibacterial assays were conducted using a methicillin-sensitive strain, further validation using MRSA isolates is required to confirm the predicted inhibitory potential. Overall, this study provides a preliminary understanding of the phenolic composition and antibacterial potential of M. malabathricum, supporting its continued investigation as a natural source of bioactive compounds.
Mitochondrial COI gene-based phylogenetic and haplotype analysis of Manouria emys from Sumatra, Indonesia ASHRIFURRAHMAN ASHRIFURRAHMAN; SYAIFULLAH SYAIFULLAH; DEWI IMELDA ROESMA; DJONG HON TJONG; INDRI LESTARI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 12 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261224

Abstract

Abstract. Ashrifurrahman, Syaifullah, Roesma DI, Tjong DH, Lestari I. 2025. Mitochondrial COI gene-based phylogenetic and haplotype analysis of Manouria emys from Sumatra, Indonesia. Biodiversitas 26: 6224-6231. Genetic and phylogenetic analyses are essential for understanding the evolutionary relationships and genetic variation of the critically endangered Manouria emys, particularly in Indonesia, where molecular data remain limited. This study aimed to determine the phylogenetic placement and haplotype diversity of M. emys from Sumatra, Indonesia representing the first COI record from this region. A single sample collected from West Sumatra was analyzed through DNA extraction, PCR amplification of the COI (Cytochrome Oxidase Subunit I) gene, and sequencing. An 886 bp COI gene fragment was confirmed as M. emys through sequence similarity analysis and subsequently aligned with 29 global reference sequences for phylogenetic and haplotype analyses. Phylogenetic analysis using the Maximum Likelihood method showed that the Sumatran sample clustered within the M. emys emys clade, together with sequences from Borneo and the Taipei Zoo. Three subclades were observed within M. emys, corresponding to M. emys emys, M. emys phayrei, and one distinct genetic lineage of unconfirmed subspecies status. The analysis showed low genetic divergence within each subspecies but relatively high differentiation between M. emys and the outgroup. Haplotype analysis identified three main haplogroups, with the Sumatran sample showing close genetic affinity to M. emys emys from Borneo. The presence of multiple M. emys emys haplotypes reported from India may reflect population movement or human mediated translocation, highlighting the need for broader regional studies. This study provides the first molecular evidence of M. emys from Sumatra, offering a valuable genetic reference for future research, conservation management, and monitoring of wildlife trade involving this critically endangered tortoise.
Community knowledge and attitudes toward bird conservation in Bagek Kembar, West Lombok, Indonesia MUHAMMAD SYAZALI; GITO HADIPRAYITNO; MOHAMMAD LIWA ILHAMDI; I WAYAN SUANA; GDE CAHYADI WIRAJAGAT; SAFARIYANTI MANISA; SRI APRILIA NUR LARASATI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 2 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270202

Abstract

Abstract. Syazali M, Hadiprayitno G, Ilhamdi ML, Suana IW, Wirajagat GC, Manisa S, Larasati SAN. 2026. Community knowledge and attitudes toward bird conservation in Bagek Kembar, West Lombok, Indonesia. Biodiversitas 27 (2): d270202. https://doi.org/10.13057/biodiv/d270202. Birds in Bagek Kembar, West Lombok, Indonesia, play an important ecological role and support emerging birdwatching ecotourism. However, habitat changes and human activities continue to threaten their sustainability. This study aims to (i) assess community knowledge, perceptions, and attitudes toward bird conservation, (ii) examine the influence of family and teacher roles, and (iii) analyze the structural relationships among knowledge, perception, and attitude using the knowledge attitude behavior framework. Data were collected from 140 respondents selected by stratified random sampling across four education levels using a 20 item Likert-scale questionnaire. Data were analyzed using ANOVA, Chi-square tests, Pearson correlation, and structural equation modeling. The results showed that community knowledge (2.29 ± 0.40), perceptions (2.04 ± 0.73), and attitudes (2.96 ± 0.55) were generally in the moderate category, with significant differences among education levels (p < 0.01). Teachers exerted stronger influence (67.29%) than families (51.47%), especially at higher education levels. Knowledge directly influenced attitudes (β = 0.41, p < 0.001) and indirectly through perception (β = 0.36, p < 0.01), with a good model fit (CFI = 0.93; RMSEA = 0.05). These findings demonstrate that improving ecological knowledge alone is insufficient without strengthening positive perceptions. Integrating conservation education into local schools and community based ecotourism is essential for sustaining bird conservation in Lombok.
Coral resilience in marginal reefs of South Sulawesi, Indonesia FUNTY SEPTIYAWATI POLAPA; CHAIR RANI; JAMALUDDIN JOMPA; SUHARTO SUHARTO
Biodiversitas Journal of Biological Diversity Vol. 27 No. 3 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270333

Abstract

Abstract. Polapa FS, Rani C, Jompa J, Suharto. 2026. Coral resilience in marginal reefs of South Sulawesi, Indonesia. Biodiversitas 27 (3): d270333. https://doi.org/10.13057/biodiv/d270333. Coral reefs face escalating global and local threats, yet data on coral resilience to inform rehabilitation strategies remain limited, especially in marginal environments. We compared coral community structure and water quality between marginal and reference reefs in South Sulawesi, Indonesia, to identify stress-adapted genera with restoration potential. Generic diversity was comparable between marginal (16.3±7.5 genera) and reference sites (17.5±3.5 genera), but reference reefs exhibited 2.6× higher coral abundance. Coral abundance showed a strong negative correlation with water quality (r = -0.82). Non-metric multidimensional scaling revealed clear community segregation between reef types, with reef type explaining 37.6% of the variation in composition. Using performance ratios (marginal/reference abundance), we identified Turbinaria (exclusive to marginal sites), Platygyra (ratio = 4.60), Dipsastraea (4.00), and Galaxea (3.13) as genera with exceptional adaptive potential under marginal conditions. Despite a lower performance ratio (0.26), Porites maintained the highest absolute abundance across all sites, highlighting its ecological importance. Our findings provide science-based criteria for coral species selection in restoration programs. We recommend a combined strategy, prioritizing high-performance-ratio genera (Turbinaria, Platygyra, Dipsastraea, Galaxea) for their adaptive advantages while including ecologically dominant, stress-tolerant taxa like Porites to enhance restoration success. This recommendation is specifically targeted for reefs experiencing moderate water quality degradation (STORET scores 12-18) and elevated sedimentation as documented at our nearshore marginal sites in South Sulawesi. This targeted approach leverages marginal reefs as reservoirs of stress-adapted genotypes, offering a practical strategy for enhancing reef recovery in rapidly changing tropical seascapes. Our study underscores the conservation value of marginal reefs and provides actionable insights for reef restoration in Indonesia and similar regions facing cumulative environmental pressures.
Molecular and morphological identification of Argyrops and Acanthopagrus (Sparidae) in the Java Sea, Indonesia AGUS NURYANTO; FABIAN RIZKY FATHURAHMAN; DIAN BHAGAWATI; ERWIN RIYANTO ARDLI; DWI NUGROHO WIBOWO; ATANG ATANG
Biodiversitas Journal of Biological Diversity Vol. 27 No. 5 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270508

Abstract

Abstract. Nuryanto A, Fathurahman FR, Bhagawati D, Ardli ER, Wibowo DN, Atang. 2026. Molecular and morphological identification of Argyrops and Acanthopagrus (Sparidae) in the Java Sea, Indonesia. Biodiversitas 27 (5): d270508. https://doi.org/10.13057/biodiv/d270508. Accurate species identification is fundamental to effective fisheries management and understanding of marine biodiversity. Previous morphological records have reported Argyrops spinifer from Indonesian waters, including the Java Sea, Indonesia, while recent molecular evidence from southern Java identified Argyrops bleekeri. These inconsistencies highlight the need for integrative taxonomic approaches. This study aimed to evaluate sparid diversity along the northern coast of Java Island using morphological examination and DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Fish specimens were collected from four landing sites (Pekalongan, Cirebon, Indramayu, Karawang) along the Java Sea. A total of 31 specimens were examined, comprising 15 Acanthopagrus and 16 Argyrops. High-quality COI sequences were obtained from 30 specimens (96.8% success rate). Molecular identification assigned all Acanthopagrus specimens to Acanthopagrus pacificus (n:15). Among Argyrops, 14 specimens were identified as A. bleekeri, while only one specimen was identified as A. spinifer, representing just 6.7% of Argyrops samples. Genetic similarity values (99.04-100%) and low intraspecific K2P distances (0.0027-0.0036) confirmed species-level assignments, while phylogenetic analysis supported clear separation between taxa. The coexistence of A. bleekeri and A. spinifer at the Indramayu landing site provides the first molecular confirmation of A. spinifer in the Java Sea and demonstrates the limitations of morphology alone, as both species were indistinguishable based on external traits. These findings highlight the risk of species misidentification in fisheries data when relying solely on traditional taxonomy. Integrating molecular tools with morphological examination is therefore critical to avoid compromising stock assessments and biodiversity monitoring in Indonesian marine ecosystems.

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