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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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Waterborne parasite contamination and risk factors in natural water sources of Karen communities, Omkoi District, Thailand KULCHANA WONGTHONGLUA; JINTANA YANOLA; SANGOB SANIT; NATTHARINEE KONGTA; WOOTTICHAI NACHAIWIENG
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/d261150

Abstract

Abstract. Wongthonglua K, Yanola J, Sanit S, Kongta N, Nachaiwieng W. 2025. Waterborne parasite contamination and risk factors in natural water sources of Karen communities, Omkoi District, Thailand. Biodiversitas 26: 5955-5963. The Karen hill tribes in Omkoi District, Chiang Mai Province, Thailand, continue to experience a high burden of intestinal parasitic infections, likely linked to the use of untreated mountain water for daily consumption. This study investigated protozoan contamination in natural water sources and identified physicochemical factors associated with contamination risk. Water samples were collected from 30 natural sources during the dry (30 samples) and wet seasons (28 samples), totaling 58 samples. Each 20 L sample was filtered, concentrated, and examined using flotation, microscopy, nested PCR to detect Entamoeba histolytica and Entamoeba coli, and the addition of DNA sequencing to detect Giardia duodenalis and Cryptosporidium spp.. Physicochemical parameters, including pH, turbidity, total dissolved solids (TDS), dissolved oxygen, ammonia, chlorine, nitrate, and nitrite, were also measured. Fisher’s exact tests and logistic regression were applied to evaluate associations with contamination. To our knowledge, this study represents the first molecular assessment of protozoan parasites in Omkoi community water sources. E. histolytica was detected in two sources per season (6.67% dry; 7.14% wet), and E. coli in one source per season (3.33% dry; 3.57% wet). G. duodenalis and Cryptosporidium spp. were not detected. Significant associations were observed between contamination and elevated TDS (?200 mg/L; OR = 29.33; 95% CI = 2.08-423.66), ammonia (?0.5 mg/L; OR = 25.50; 95% CI = 1.88-345.83), and nitrite (>0.1 mg/L; OR = 51.00; 95% CI = 4.00-649.10) (P<0.05). Although these parameters are not visually detectable, green algal blooms may indicate nutrient-rich conditions conducive to contamination. In conclusion, routine water treatment, such as boiling or filtration, is recommended before consumption. Residents should avoid water sources with visible algal growth to reduce the risk of protozoan infection in these rural communities.
DNA extraction bias influences resistome profiles in seahorse skin microbiomes ROSE CHINLY MAE ORTEGA-KINDICA; JOSE LUIS BALCAZAR; SHARON ROSE M. TABUGO
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/d261020

Abstract

Abstract. Ortega-Kindica RCMH, Balcazar JL, Tabugo SRM. 2025. DNA extraction bias shapes resistome profiles in seahorse skin microbiomes. Biodiversitas 26: 5049-5056. Antimicrobial Resistance Genes (ARGs) are emerging environmental risks, particularly in coastal environments impacted by anthropogenic activities. Seahorses (Hippocampus spp.), as benthic and ecologically sensitive species, are in constant contact with biofilm-enriched sediments and can act as bioindicators of environmental ARGs. Their unique ecological niche and sensitivity to environmental changes make them ideal candidates for monitoring ARGs in marine ecosystems. In this study, the skin microbiome of Hippocampus barbouri was analyzed using shotgun metagenomics to assess the impact of two commercial DNA extraction kits, the HiMedia Water DNA Purification Kit (HMS) and the Qiagen DNeasy PowerSoil Pro Kit (QKS), on the detection of ARGs. DNA was extracted from the skin microbiome of 30 adult H. barbouri (Barbour's seahorse) collected from Cantiasay Island, Surigao del Norte, Philippines, and subsequently subjected to shotgun metagenomic sequencing. Across the samples, 17 ARG families were found with recovery varying between the extraction kits. The QKS kit yielded higher DNA concentrations and revealed a broader range of ARGs, including multidrug, macrolide, and ?-lactam. In contrast, the HMS kit recovered fewer ARG categories, possibly due to reduced cell lysis efficiency or the presence of inhibitors. Statistical analyses (p<0.05) confirmed significant kit-dependent differences in resistome profiles. These findings highlight that DNA extraction protocols can influence ARG detection and emphasize the need for rigorous methodological standardization in metagenomic studies. Furthermore, the detection of diverse ARGs in the skin microbiota of H. barbouri supports its potential as a sentinel species for environmental resistome monitoring in marine ecosystems.
Chloroplast genome variation and phylogeny of mutant Typhonium flagelliforme (Araceae) from Indonesia NESTI FRONIKA SIANIPAR; ZIDNI MUFLIKHATI; ENDANG RAHMAT; REFLINUR REFLINUR; KHOIRUNNISA ASSIDQI; DWIYANTARI WIDYANINGRUM
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/d261129

Abstract

Abstract. Sianipar NF, Muflikhati Z, Rahmat E, Reflinur, Assidqi K, Widyaningrum D. 2025. Chloroplast genome variation and phylogeny of mutant Typhonium flagelliforme (Araceae) from Indonesia. Biodiversitas 26: 5703-5713. Typhonium flagelliforme (rodent tuber) is an indigenous Indonesian medicinal plant valued for its anticancer properties. Mutation induced by gamma irradiation have produced mutant accessions with enhanced bioactivity, yet the underlying genetic basis remains poorly understood. To address this gap, we conducted a comparative analysis of complete chloroplast genomes from wild-type and mutant T. flagelliforme. Both genomes displayed a typical quadripartite structure, with lengths of 167,195 bp (wild-type) and 167,204 bp (mutant). Gene annotation revealed 118 genes in the wild-type, but only 116 in the mutant, with the absence of psaL and petN, genes related to photosystem I and the cytochrome b6f complex. In addition to both accessions preferring A/U-ending codons, simple sequence repeat (SSR) profiling identified 131 motifs in the wild type and 132 in the mutant. Divergent hotspot analysis detected high nucleotide diversity in loci, such as ndhE and ccsA. Phylogenetic reconstruction confirmed that both accessions form a monophyletic clade closely related to T. blumei, reinforcing their genetic proximity within the genus. These findings demonstrate that induced mutation results in localized plastome alterations without disrupting overall structural stability, thereby providing valuable genomic resources for phylogenetic inference, biodiversity conservation, and marker-assisted breeding in Typhonium and related Araceae taxa.
Fermented tofu dregs as a waste-derived biological feed resource for Pekin ducks (Anas platyrhynchos domesticus) ASNAWI ASNAWI; DWI KUSUMA PURNAMASARI; VIDIA JUNIA AYU NINGGRUM; ADE YOGA PRATAMA; MUHAMMAD RIZQI
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/d270314

Abstract

Abstract. Asnawi, Purnamasari DK, Ninggrum VJA, Pratama AY, Rizqi M. 2026. Fermented tofu dregs as a waste-derived biological feed resource for Pekin ducks (Anas platyrhynchos domesticus). Biodiversitas 27 (3): d270314. https://doi.org/10.13057/biodiv/d270314. Tofu dregs, a protein- and mineral-rich by-product of tofu production, remain underutilized in duck feed due to high fiber content, anti-nutritional factors, and variable moisture that limit their direct inclusion in practical diets. This study evaluated the effects of EM4-based solid-state fermentation on the nutritional quality of tofu dregs and assessed the performance of Pekin ducks fed diets in which commercial feed was partially replaced with fermented tofu dregs. Fermentation improved the nutritional profile of tofu dregs by increasing crude protein, total fat, selected essential and non-essential amino acids, and several macro- and micro-minerals, while reducing crude fiber, moisture, and ash contents. Feeding trials were conducted using 100 Pekin ducks allocated to four dietary treatments containing 0%, 10%, 20%, and 30% fermented tofu dregs in isoenergetic and isonitrogenous rations. Increasing inclusion of fermented tofu dregs up to 30% did not significantly affect final body weight, body weight gain, or feed conversion ratio, although feed intake increased at higher inclusion levels. These findings demonstrate that EM4-fermented tofu dregs can be utilized as a sustainable waste-derived feed resource to partially replace commercial feed in Pekin duck diets without compromising growth performance. Integrating fermented tofu dregs into duck feeding strategies offers a practical approach to valorize tofu processing waste, reduce reliance on conventional feed ingredients, and support more circular and environmentally friendly duck production systems in regions where tofu dregs are abundantly available.
Flowering response of torch ginger (Etlingera elatior) to PK fertilization RAMDAN HIDAYAT; PANGESTI NUGRAHANI; RAHMATUN NISFUL MAGHFIROH
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/d261230

Abstract

Abstract. Hidayat R, Nugrahani P, Maghfiroh RN. 2025. Flowering response of torch ginger (Etlingera elatior) to PK fertilization. Biodiversitas 26: 6305-6315. Demand for the flowers of Etlingera elatior has increased, but predictable and timely flowering is constrained by its naturally long vegetative phase. This research aimed to determine the combined effect of dosage and frequency of PK compound fertilizer in inducing flowering in torch ginger. The field trial was carried out at Dapoer Ketjombrang Garden, Giripurno Village, Bumiaji District, Batu City, East Java, Indonesia, from December 2023 to April 2024. A factorial experiment was conducted using a randomized complete block design (two factors: dosage (D): 50, 100, 150, 200 g/clump; frequency (F): 1, 2, 3 applications at 30, 30+45, and 30+45+60 DAT, respectively) with three replicates (36 plots, 3 plants/plot, total 108 plants) was used. Data were analyzed using a two-way ANOVA (dosage, frequency, dosage×frequency), and means were compared using Tukey’s HSD (α: 0.05). The combination D4F2 (200 g, 2x at 30 and 45 DAT) produced the earliest flowering (mean 21.89 DAT). The dosage D3 (150 g) produced the best vegetative growth and, when combined with F2, gave the highest number of flowers (23.78 flowers/clump). Dosage effects were significant (p<0.05) for several traits; frequency had limited main effects, but dosage×frequency interactions were observed. The highest C:N ratio, antioxidant level, and vitamin C were observed at D4; regression between C:N and flowering age showed R²: 0.92 (p: 0.041). Overall, applying 150-200 g PK fertilizer per clump in two applications (30 and 45 DAT) provides an effective strategy to induce earlier flowering and increase flower productivity under the conditions tested. Multi-season and multi-site validation is recommended before making broad recommendations.
Contrasting bleaching severity between marine protected and coral restoration areas on Pramuka Island, Indonesia ZULFANDRA BACHRUL KALAM; ALFAIZ ARSELAN; DENNY KHAERUDI; DONDY ARAFAT; NEVIATY P. ZAMANI; NYOMAN METTA N. NATIH; RADIXA RADYA RAMADHAN HARYANTO; INNA PUSPA; SYAMSUL BAHRI AGUS; BEGINER SUBHAN
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/d270531

Abstract

Abstract. Kalam ZB, Arselan A, Khaerudi D, Arafat D, Zamani NP, Natih NMN, Haryanto RRR, Puspa I, Agus SB, Subhan B. 2026. Contrasting bleaching severity between marine protected and coral restoration areas on Pramuka Island, Indonesia. Biodiversitas 27 (5): d270531. https://doi.org/10.13057/biodiv/d270531. The 2023-2024 global coral bleaching event provided an urgent context for assessing reef responses under contrasting management regimes. This study compared bleaching prevalence, hard coral cover, genus composition, and life-history strategy distributions between a Marine Protected Area (MPA) and an active coral restoration site (RPTRA Smiling Coral) on Pramuka Island, Thousand Islands, Indonesia. Surveys were conducted in January 2024 using a rapid photo-quadrat method across three depth strata (5, 10, and 15 m) at both sites. The MPA exhibited severely degraded coral cover (below 25% at all depths) and extremely high bleaching prevalence (83.75-91.81%), with near-total bleaching in dominant genera including Pachyseris spp. and Pleuractis spp. In contrast, the RPTRA restoration site showed bleaching rates below 33% across all depths, with Porites spp. displaying more stable responses. Despite uniform water temperatures of 30°C across all depths, bleaching was most severe at 5 m, suggesting that light intensity amplifies thermal stress in shallow habitats. Critically, all four life-history strategies were represented among bleached genera, indicating that even stress-tolerant corals are approaching their thermal tolerance limits. These findings indicate that sites under active restoration were associated with substantially lower bleaching prevalence and better ecological condition than the passively protected MPA, consistent with the hypothesis that active restoration enhances post-bleaching recovery capacity. This association has implications for the long-term biodiversity resilience of coral communities under escalating climate stress, though the observational design precludes direct causal attribution.
Ethnobotanical role of sago in wetland biodiversity and resilience in the Riau Archipelago, Indonesia TISRIN MAULINA DEWI; WORO SUMARNI; SAIFUL RIDLO; ADITYA MARIANTI
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/d261225

Abstract

Abstract. Dewi TM, Sumarni W, Ridlo S, Maryanti A. 2025. Ethnobotanical role of sago in wetland biodiversity and resilience in the Riau Archipelago, Indonesia. Biodiversitas 26: 6232-6239. Sago (Metroxylon sagu) is a tropical plant that plays an important role in wetland ecosystems and socio-economic resilience in Indonesia, particularly in the Riau Islands. This study aims to explore the role of sago ethnobotany in supporting biodiversity and ecosystem resilience in two locations, Musai (Lingga) and Alai (Karimun), and to identify how local wisdom-based sago management contributes to the conservation of the wetland ecosystem. The research approach employed was qualitative, semi-structured interviews (n = 40) with informants from various categories, including community leaders, traditional processors, farmers, and traditional leaders. Participatory observation was also conducted to explore local knowledge about sago management. The results showed that sago plays a dual role, serving as both a food source and economic commodity, and contributes to ecosystem management through management practices based on traditional ecological knowledge, such as crop rotation and selective pruning. Ethnobotanical index analysis shows that sago has the highest use value in the food category (UV = 1.00) and household economy/trade (UV = 0.63). This sago management also supports the achievement of Sustainable Development Goals (SDGs), particularly SDG 13 (Climate Action) and SDG 15 (Life on Land), by increasing carbon sequestration capacity and preserving wetland ecosystems. Strengthening local sago-based management and integrating traditional practices into wetland policy frameworks are essential for achieving both livelihood security and biodiversity conservation in the Riau Archipelago.
Species composition and size distribution of the tropical estuarine fishes in Matang Mangrove Forest Reserve (MMFR), Malaysia MUHAMAD IKRAM ZURAINI; SITI TAFZILMERIAM SHEIKH ABDUL KADIR; MUHAMMAD FADHLI MAT SOBRI; AZMI MARZUKI MUDA; SITI WAZNAH ABDURAHMAN; NURZUHRAH HASSAN; SAIFULLAH ARIFIN JAAMAN; MAIZAH M. ABDULLAH
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/d270137

Abstract

Abstract. Zuraini MI, Kadir STSA, Sobri MFM, Muda AM, Abdurahman SW, Hassan N, Jaaman SA, Abdullah MM. 2026. Species composition and size distribution of the tropical estuarine fishes in Matang Mangrove Forest Reserve (MMFR), Malaysia. Biodiversitas 27 (1): d270137. https://doi.org/10.13057/biodiv/d270137. The Matang Mangrove Forest Reserve (MMFR) in Perak, Malaysia, represents one of the most well-managed and ecologically significant mangrove ecosystems in the world. Spanning over 40,000 ha and protected since 1906, MMFR provides critical nursery and feeding habitats for a wide range of marine fauna, including commercially important fish, crustaceans, shellfish, and endangered marine cetaceans. This study was conducted to determine the diversity, composition and size distribution of estuarine fishes in three estuaries connected to the MMFR namely Kuala Larut (KL), Kuala Sangga (KS) and Kuala Gula (KG). Samplings were conducted in October, November and December 2021 using gill nets that were deployed along the estuarine gradients at the upper (near riverine areas), the middle, and the mouth (near the coastal interface) estuary. A total of 2,756 fish individuals, representing 42 species across 21 families, were collected. The most abundant family was Engraulidae (N: 1,400), dominated by Thryssa kammalensis by 49.96%, followed by the family Mugilidae (N: 504), primarily composed of Paramugil parmatus by 14.77%, and Ariidae (N: 457), dominated by Arius maculatus by 10.19%. The Shannon diversity index (H′) was highest at KL (2.12), followed by KS (1.63) and KG (1.35), with Pielou’s evenness index (J′) mirrored this trend. Meanwhile, species richness is highest at KS, followed by KL and KG, indicating heterogeneity in community composition among estuaries. The presence of three Near Threatened (NT) species listed by the IUCN, namely Protonibea diacanthus, Brevitrygon walga and Arius gagora, underscores the ecological significance of the estuarine habitats within the MMFR. This study provides an updated baseline data on fish diversity in MMFR, offering critical insights to guide future conservation planning and sustainable resource management.
Functional profiling of Syzygium aromaticum-associated bacteria reveals PGPR traits for tropical biofertilizer development HENRY KESAULYA; WAHYU HIDAYAT; RUMELLA SIMARMATA; JOGENEIS PATTY
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/d261215

Abstract

Abstract. Kesaulya H, Hidayat W, Simarmata R, Patty J. 2025. Functional profiling of Syzygium aromaticum-associated bacteria reveals PGPR traits for tropical biofertilizer development. Biodiversitas 26: 6130-6139. Syzygium aromaticum (clove) is a tropical spice of major economic and ecological importance in Indonesia, yet the microbial communities associated with its cultivation remain poorly characterized. Harnessing native Plant Growth-Promoting Rhizobacteria (PGPR) offers a sustainable alternative to chemical inputs and supports resilient agroecosystems. This study explored the biofertilizer potential of bacterial strains isolated from S. aromaticum-growing regions in Central Maluku, Indonesia. Rhizospheric and endophytic isolates were characterized using physiological assays and 16S rRNA sequencing to assess key PGPR traits, including auxin production, phosphate solubilization, nitrogen fixation, and enzymatic activities relevant to nutrient cycling and stress tolerance. Eleven isolates were obtained, with greater diversity from the rhizosphere (9 isolates) than from leaves (2 isolates). Screening demonstrated multiple plant-beneficial traits, including indole-3-acetic acid production, phosphate solubilization, and growth in nitrogen-free medium, complemented by hydrolytic enzyme activities and catalase-based stress tolerance. Three isolates showed particularly strong multifunctional profiles: T5RCHM21 (high IAA, phosphate solubilization, nitrogen-fixation trait, broad pH tolerance), T6RCHM3 (highest phosphate solubilization and cellulolytic activity), and T4RCHM3 (very strong catalase with additional enzymatic indices). 16S rRNA analysis grouped isolates mainly within Bacillus, with Brevibacterium, and  Klebsiella, supporting phenotype-driven selection and future field validation for practical application.
Nepenthesin activity of three Nepenthes species from Lore Lindu National Park, Central Sulawesi, Indonesia RAHMADINA RAHMADINA; MHD. RAFI’I MA’ARIF TARIGAN; NURUL HUDA PANGGABEAN; AMRU DAULAY; MUHAMMAD AIZRI FADILLAH; MUHAMMMAD FAISAL; MUHAMMAD IQBAL HIDAYAT; SUSILO SUDARMAN
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/d270225

Abstract

Abstract. Rahmadina, Tarigan MRM, Panggabean NH, Daulay A, Fadillah MA, Faisal M, Hidayat, MI, Sudarman S. 2026. Nepenthesin activity of three Nepenthes species from Lore Lindu National Park, Central Sulawesi, Indonesia. Biodiversitas 27 (2): d270225. https://doi.org/10.13057/biodiv/d270225. Carnivorous pitcher plants of the genus Nepenthes rely on proteolytic enzymes to supplement nutrient uptake in nutrient-poor habitats. Among these enzymes, nepenthesins are acid-stable aspartic proteases found in the digestive fluid. This study compared the morphology and enzymatic activity of three Nepenthes species (Nepenthes maxima, Nepenthes nigra, and Nepenthes tentaculata) from Lore Lindu National Park, Central Sulawesi, Indonesia. Morphological traits were measured in four 10×10 m plots, while nepenthesin activity was tested at four concentrations (50-200 µg/mL) using casein as substrate. Lower pitchers were generally larger and more robust, whereas upper pitchers were slender and showed interspecific variation. Enzymatic activity increased with concentration and ranged from 0.20 to 0.58 U, with N. tentaculata exhibiting the highest proteolytic activity. These results indicate species-specific digestive strategies shaped by habitat conditions and prey availability. Morphological traits showed weak correlations with enzymatic activity, suggesting that biochemical mechanisms play a more decisive role than pitcher structure. Overall, the findings enhance understanding of the adaptive ecology of Nepenthes and suggest the potential relevance of nepenthesins as acid-stable proteases for future biotechnological exploration.

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