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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 6,315 Documents
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Short Communication: Chromosome number and karyotype of five native Phalaenopsis spp. orchid from Indonesia SRI HARTATI; KRISTINA AYU ISNAENI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 7 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270703

Abstract

Abstract. Hartati S, Isnaeni KA. 2026. Short Communication: Chromosome number and karyotype of five native Phalaenopsis spp. orchid from Indonesia. Biodiversitas 27 (7): d270703. https://doi.org/10.13057/biodiv/d270703. Cytogenetic information on native Phalaenopsis species from Indonesia remains limited despite their importance in orchid breeding, taxonomy, and genetic conservation. Chromosome number and karyotype analyses provide essential information for understanding genome organization, evolutionary relationships, and species differentiation within the genus. This study aimed to characterize chromosome number and karyotype structure of five native species of Phalaenopsis (P. amabilis, P. amboinensis, P. deliciosa, P. gigantea, and P. violacea) from Indonesia using the aceto-orcein squashing method. Chromosome observations were performed on actively dividing root tip cells at the metaphase stage. The results showed that all examined species possessed the same chromosome number of 2n = 38, indicating a diploid condition with a basic chromosome number of x = 19. Chromosome morphology in all species was metacentric, resulting in a symmetrical karyotype formula of 2n = 2x = 38m. The average total chromosome arm lengths varied among species, ranging from 1.53±0.37 µm in P. gigantea to 2.53±0.61 µm in P. violacea. The Intrachromosomal Asymmetry Index (A1) indicated metacentric chromosome morphology, while the Interchromosomal Asymmetry Index (A2) showed low size variation among chromosomes. These findings provide cytogenetic information useful for taxonomy, breeding programs, and genetic conservation of Phalaenopsis.
Temporal dynamics and molecular characterization of acetic acid bacteria during palm vinegar (Arenga pinnata) fermentation RASTINA RASTINA; SAFIKA SAFIKA; ZINATUL HAYATI; WINDA YULIA; DARMAWI DARMAWI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 7 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270708

Abstract

Abstract. Rastina, Safika, Hayati Z, Yulia W, Darmawi. 2026. Temporal dynamics and molecular characterization of acetic acid bacteria during palm vinegar (Arenga pinnata) fermentation. Biodiversitas 27 (7): d270708. https://doi.org/10.13057/biodiv/d270708. Palm vinegar is a traditional fermented product whose quality depends on the ecological succession and metabolic activity of Acetic Acid Bacteria (AAB). This study evaluated the temporal dynamics of AAB populations and titratable acidity during spontaneous fermentation of Arenga pinnata palm sap from Aceh Besar, Indonesia, and identified a dominant isolate using phenotypic and molecular approaches. Fermentation samples were analyzed on days 3, 6, 9, 12, and 15 using culture-based enumeration, titratable acidity measurement, phenotypic characterization, PCR amplification of the 16S rRNA gene, sequencing, and phylogenetic analysis. AAB counts increased from 6.08 ± 0.04 log CFU/mL on day 3 to a maximum of 8.94 ± 0.03 log CFU/mL on day 12, followed by a slight decline on day 15. Titratable acidity showed a similar temporal pattern, increasing from 1.33 ± 0.40% on day 3 to a maximum value on day 12 before decreasing on day 15. One-way ANOVA indicated that fermentation time significantly influenced both AAB counts and titratable acidity (P < 0.05). The selected isolate, B2, showed phenotypic characteristics consistent with AAB, including Gram-negative staining, catalase activity, and halo formation on calcium carbonate-containing medium. Sequence-based identification placed isolate B2 within the Acetobacter group with 99.85% sequence identity. These findings suggest that day 12 represents a critical stage of active acetification under the conditions examined. The study provides preliminary culture-based and molecular information on AAB dynamics in traditional palm vinegar fermentation, while highlighting the need for broader community-level analysis and replicate sampling to better characterize microbial biodiversity.
Homegarden agroforestry for food, energy, and medicinal resources in the buffer zones of Wan Abdul Rachman Forest Park, Lampung, Indonesia ARIEF DARMAWAN; TRIO SANTOSO
Biodiversitas Journal of Biological Diversity Vol. 27 No. 8 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270802

Abstract

Abstract. Darmawan A, Santoso T. 2026. Homegarden agroforestry for food, energy, and medicinal resources in the buffer zones of Wan Abdul Rachman Forest Park, Lampung, Indonesia. Biodiversitas 27 (8): d270802. https://doi.org/10.13057/biodiv/d270802. Homegarden agroforestry systems are an important resource for local communities. This is particularly for those living in protected forest buffer zones, where human activities can put pressure on protected forests. This study aimed to examine plant diversity in homegarden agroforestry systems and their utilization by farmers’ households around the Wan Abdul Rachman Forest Park (Tahura WAR) in Lampung Province, Indonesia. This study employed a quantitative-descriptive approach to collect data on plant diversity and utilization through interviews and field visits to 30 purposively selected farming households in Talang Mulya Village, Teluk Pandan Sub-district, Pesawaran District. Homegardens’ plant species diversity was evaluated using the Shannon-Wiener index (H'), Margalef index (DMg), and Pielou index (E). Plant utilization was categorized as a source of food, energy, and medicinal resources for households. A total of 81 species belonging to 43 families were recorded. The plant community exhibited high diversity (H' = 3.32) and high species richness (DMg = 12.97). Species evenness (E) was recorded at 0.76, indicating a relatively balanced distribution. Functional classification showed that food-producing plants comprised 65.43% of total species, followed by medicinal (24.69%), fuelwood (17.28%), and ornamental species (44.44%). These homegardens are an important strategy for household resilience, supporting the availability of food, energy, and supplementary traditional medicinal resources, and emphasizing home gardens as sustainable land-use systems that provide essential ecosystem services.
DNA barcoding-based identification of Praxelis clematidea collected from Phu Tho Province, Vietnam PHAN THI THU HIEN; TRAN THI KIM THOA; HA MINH TAM
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270616

Abstract

Abstract. Hien PTT, Thoa TTK, Tam HM. 2026. DNA barcoding-based identification of Praxelis clematidea collected from Phu Tho Province, Vietnam. Biodiversitas 27 (6): d270616. https://doi.org/10.13057/biodiv/d270616. Praxelis clematidea, commonly known as praxelis, is a member of the family Asteraceae and is widely distributed in Vietnam. Morphological similarities with related taxa in Asteraceae often complicate accurate species identification. In this study, specimens of P. clematidea collected from Tu Vu Commune, Phu Tho Province, Vietnam (designated as P. clematidea TV) were identified using molecular markers. Four DNA barcode regions, including the nuclear ITS (Internal Transcribed Spacer) and three chloroplast markers (matK, rpoC1, and trnL), were amplified, sequenced, and analyzed phylogenetically. The resulting sequences were deposited in GenBank under accession numbers PX622467.1 (ITS), PX614615.1 (matK), PX614617.1 (rpoC1), and PX614618.1 (trnL). Phylogenetic analyses were performed using the Maximum Likelihood method implemented in Molecular Evolutionary Genetics Analysis version 12 (MEGA12). The ITS analysis placed P. clematidea TV together with P. clematidea (MN889429.1) with a bootstrap value of 96%. Similarly, matK grouped the sample with P. clematidea (accession numbers KX526581.1) with 96% bootstrap support, whereas trnL clustered it with P. clematidea (accession numbers KT002019.1 and KT002021.1) with a bootstrap value of 76%. The rpoC1 marker showed lower phylogenetic resolution, with the clade containing P. clematidea and Ageratum conyzoides (accession numbers MK905238.1) receiving a bootstrap value of 42%. These results demonstrate that the combined use of nuclear and chloroplast DNA barcodes provides reliable evidence for the identification and taxonomic placement of P. clematidea collected from Phu Tho Province, Vietnam.
Diversity of medicinal plants from local traditions in Rokan Hulu District, Riau Province, Indonesia DAHLIA DAHLIA; EVI SURYAWATI; ZULFARINA ZULFARINA; SRI WULANDARI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270624

Abstract

Abstract. Dahlia, Suryawati E, Zulfarina, Wulandari S. 2026. Diversity of medicinal plants from local traditions in Rokan Hulu District, Riau Province, Indonesia. Biodiversitas 27 (6): d270624. https://doi.org/10.13057/biodiv/d270624. Plant diversity in Rokan Hulu has given rise to a rich body of local wisdom. This indigenous knowledge includes the use of plants as traditional medicines, a practice that has persisted into the present century. Local knowledge plays a crucial role in plant conservation; however, it remains poorly documented, leading to the gradual erosion of these cultural practices. This study aims to identify the diversity of medicinal plant species and their uses, as well as to calculate key ethnobotanical indices, including use value (UV), plant part value (PPV), and fidelity level (FL). A qualitative approach was employed to describe medicinal plant species, methods of preparation and use, plant parts utilized, and types of ailments treated. Quantitative methods were applied to assess the relative importance of medicinal plants. Semi-structured interviews were conducted with 210 respondents selected through snowball sampling. A total of 178 medicinal plant species belonging to 63 families were recorded, with Zingiberaceae contributing the highest number of species (14 species). Herbaceous plants dominated the recorded species (32.58%). The highest UV was recorded for Curcuma longa (0.786), while the highest FL was observed for Hibiscus × rosa-sinensis (91.7%). Leaves were the most frequently used plant part (49.95%), as they are generally more abundant than other organs. Decoction was the most common method of preparation (50.6%), as local communities believe that boiling facilitates faster extraction of bioactive compounds and provides a safer preparation by eliminating pathogens. Oral administration (drinking) was the most prevalent mode of use (61.3%), as it is considered to enhance the absorption of active compounds by the body and is easier to apply.
Incidence, alternative hosts, and molecular diversity of rice tungro viruses in Bali, Indonesia LISTIHANI LISTIHANI; GUSTI NGURAH ALIT SUSANTA WIRYA; TRISNA AGUNG PHABIOLA; I MADE SUDARMA; I WAYAN SUANDA; DEWA GEDE WIRYANGGA SELANGGA; I GEDE RAI MAYA TEMAJA; WAFA’ NUR HANIFAH; RESTIANA MAULINDA; NI NYOMAN SISTA JAYASANTI; HERU ANGGARA
Biodiversitas Journal of Biological Diversity Vol. 27 No. 7 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270723

Abstract

Abstract. Listihani L, Wirya GNAS, Phabiola TA, Sudarma IM, Suanda IW, Selangga DGW, Temaja IGRM, Hanifah WN, Maulinda R, Jayasanti NNS, Anggara H. 2026. Incidence, alternative hosts, and molecular diversity of rice tungro viruses in Bali, Indonesia. Biodiversitas 27 (7): d270723. https://doi.org/10.13057/biodiv/d270723. Tungro disease is a significant threat to rice cultivation in Indonesia. The investigation of the presence of tungro viruses has never been reported in 9 districts and cities in Bali Province, Indonesia. This study aimed to analyze the incidence and severity of tungro disease, vector population density, the presence of weeds as alternative hosts, and the molecular character of Bali isolates. Research methods included sampling, observing the incidence and severity, analyzing population density of green leafhoppers, detecting RTBV and RTSV, DNA cloning, and sequencing analysis. The incidence and severity of tungro disease in Bali ranged from 80% to 100% and 28.49% to 64.73%, respectively. Population densities of Nephotettix virescens and N. nigropictus ranged from 5 to 20 and from 0 to 4 individuals per 10 double swings at each location. Eight weed species (Echinochloa crus-pavonis, Fimbristylis miliacea, Cyperus iria, Pontederia vaginalis, Ludwigia adscendens, L. octovalvis, Sphenoclea zeylanica, and Digitaria sanguinalis) were positive for tungro virus infection. The highest homology of RTBV and RTSV Bali isolates with Lombok isolates ranged from 98.0% to 98.7% and from 97.5% to 98.1%. RTBV and RTSV have disseminated across Bali. Based on coat-protein gene analysis derived from a small selection of clones, it indicates that these Bali isolates exhibit minimal genetic variation compared to other isolates from Indonesia.
Protein banding pattern and RAPD marker analysis of local Lampung cassava (Manihot esculenta) under PEG-induced drought stress ENDANG NURCAHYANI; HARDOKO INSAN QUDUS; AMIRAH AFIFAH MELTA; NUR AISYAH AMINI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 7 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270715

Abstract

Abstract. Nurcahyani E, Qudus HI, Melta AA, Amini NA. 2026. Protein banding pattern and RAPD marker analysis of local Lampung cassava (Manihot esculenta) under PEG-induced drought stress. Biodiversitas 27 (7): d270715. https://doi.org/10.13057/biodiv/d270715. Drought stress is one of the major environmental constraints limiting cassava (Manihot esculenta) productivity in Indonesia. Under controlled greenhouse conditions, Poly-Ethylene Glycol (PEG 6000) is widely used to simulate water-deficit stress by reducing water availability without causing direct toxicity to plant tissues. This study evaluated the physiological and molecular responses of local Lampung cassava to different levels of PEG-induced drought stress by integrating physiological measurements with protein banding patterns and Random Amplified Polymorphic DNA (RAPD) analyses. The experiment was arranged in a completely randomized design with five PEG 6000 concentrations (0%, 10%, 20%, 30%, and 40%). Physiological responses were assessed through total soluble carbohydrate, chlorophyll, and reducing sugar contents, whereas molecular responses were evaluated using SDS-PAGE protein banding pattern analysis and RAPD markers. Increasing PEG concentration significantly increased total soluble carbohydrate and reducing sugar contents, but reduced chlorophyll content. SDS-PAGE analysis revealed the appearance of a distinct protein band at approximately 34 kDa with 40% PEG treatment, accompanied by increased intensity of a ~50 kDa protein band at higher PEG concentrations. RAPD amplification using primer OPB-20 consistently detected a distinct DNA fragment of approximately 1,100 bp in PEG-treated plants but not in the control. These coordinated physiological and molecular responses indicate that PEG-induced drought stress triggers stress-associated biochemical and genomic changes in cassava. The identified protein and RAPD banding patterns represent preliminary candidate molecular indicators of drought responsiveness and provide a useful basis for future validation and early screening of drought-tolerant cassava genotypes.
Genomic characterization of Escherichia coli Cn5 and IrN exhibiting copper resistance and malachite green decolorization IMMANUELLA GRACE KRISTINA; WAHYU IRAWATI; DIKSON DIKSON; REINHARD PINONTOAN
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270623

Abstract

Abstract. Kristina IG, Irawati W, Dikson, Pinontoan R. 2026. Genomic characterization of Escherichia coli Cn5 and IrN exhibiting copper resistance and malachite green decolorization. Biodiversitas 27 (6): d270623. https://doi.org/10.13057/biodiv/d270623. Copper and textile dye pollution pose significant environmental threats because of their adverse effects on aquatic ecosystems and human health. Bioremediation using indigenous bacteria has emerged as an effective, eco-friendly, and cost-efficient alternative to conventional treatments. However, genomic studies on bacteria exhibiting both heavy-metal resistance and dye decolorization remain limited. This study served as a preliminary evaluation of indigenous bacterial isolates from Indonesia for their copper (Cu) resistance and Malachite Green (MG) decolorization phenotypes and genotypes. Phenotype assessment involved their growth and activity on liquid and solid Luria-Bertani media supplemented with increasing concentrations of CuSO4 or MG. Genotype assessment involved Nanopore whole-genome sequencing and annotation to determine taxonomic identity and putative functional genes. Two isolates, Cn5 and IrN, tolerated up to 12 mM CuSO₄ and 20 ppm MG dye. The MG decolorization assays revealed efficiencies of 90.8% for isolate Cn5 and 93.4% for isolate IrN after 4 days of incubation, indicating bioremediation potential. Whole-genome comparison, multilocus sequence typing, and phylogenetic analysis confirmed that both isolates belong to Escherichia coli. Comparative genomics identified gene clusters putatively associated with Cu resistance, including cop, cue, and cus genes. Functional annotation revealed four reductase genes, one peroxidase gene, and one laccase-encoding gene potentially involved in MG dye decolorization. This study provides a preliminary genomic characterization of E. coli strains combining Cu resistance and MG decolorization as a baseline for further investigation of their bioremediation-related potential.
Pteridophyte diversity at set-aside conservation areas in the natural gas industrial area in Bontang, East Kalimantan, Indonesia LINDA OKTAVIANINGSIH; DWI SUSANTO; MINTORO DWI PUTRA; MUKHLIS MUKHLIS; RIZKY RAHMAN; RETA YUDISTYANA; YOSVALDO GERRY SETIONO PUTRA
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/d270535

Abstract

Abstract. Oktavianingsih L, Susanto D, Putra MD, Mukhlis, Rahman R, Yudistyana R, Putra YGS. 2026. Pteridophyte diversity at set-aside conservation areas in the natural gas industrial area in Bontang, East Kalimantan, Indonesia. Biodiversitas 27 (5): d270535. https://doi.org/10.13057/biodiv/d270535. Pteridophytes (ferns) are ecologically important plants that contribute to oxygen production, moisture retention, erosion control, and environmental monitoring. Their conservation is therefore relevant not only in natural habitats but also within production and industrial landscapes. This study assessed fern species diversity, habitat preferences, distribution, and conservation status within a natural gas industrial area in Bontang, East Kalimantan, Indonesia. Field surveys were conducted annually in July from 2022 to 2025 at 11 locations using cruise and purposive sampling. Species were identified based on morphological characteristics and supported by taxonomic references and online databases. A total of 69 species representing 38 genera and 19 families were recorded, with Pteridaceae (16 species), Polypodiaceae (11), and Thelypteridaceae (11) being the most species-rich families. Most species were terrestrial (45 species; 65%), followed by epiphytic (16; 23%), climbing (6; 9%), and terrestrial-epiphytic species (2; 3%). Lygodium circinatum and Pyrrosia piloselloides were frequently recorded across the study area, whereas Helminthostachys zeylanica and Platycerium coronarium had restricted distributions. Most species were categorized as Not Evaluated by the IUCN Red List and Not Listed by CITES, indicating limited formal conservation assessment rather than confirmed population security. P. coronarium warrants particular attention because of its recognized conservation concern in parts of Southeast Asia. Overall, this study provides a baseline inventory of fern diversity in an industrial landscape and supports future ecological monitoring, conservation planning, and population-level studies in East Kalimantan, Indonesia.
Primates in reclaimed mining landscapes of South Kalimantan, Indonesia DEDE AULIA RAHMAN; IKSAN GUSTIAWAN; MEKKA RIADHAH; RIZA NOVIAN; RANDY SAPUTRA; YUNESTO YUNESTO; JOSHUA GILBERT; HANIFULLAH HABIBIE
Biodiversitas Journal of Biological Diversity Vol. 27 No. 7 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270724

Abstract

Abstract. Rahman DA, Gustiawan I, Riadhah M, Novian R, Saputra R, Yunesto, Gilbert J, Habibie H. 2026. Primates in reclaimed mining landscapes of South Kalimantan, Indonesia. Biodiversitas 27 (7): d270724. https://doi.org/10.13057/biodiv/d270724. Post-mining landscapes can provide secondary habitats for wildlife when ecological restoration is properly implemented. In South Kalimantan, reclamation areas within the mining concession of Perseroan Terbatas (PT) Adaro Energy Indonesia Tbk have developed into habitats utilized by several primate species, including the protected proboscis monkey and silvered langur. This study aimed to estimate the number of individuals and population density of proboscis monkeys and silvered langurs, as well as to identify strategic areas with potential for artificial canopy bridge development in the post-mining landscape of PT Adaro Indonesia. Field surveys were conducted using line transect and repeated concentration count methods during morning and afternoon observation periods across reclaimed and riparian habitats. Silvered langur abundance was estimated using distance sampling analysis, while proboscis monkey abundance was estimated through repeated concentration counts. The results recorded 10 groups of silvered langurs with an estimated abundance of 88.76 individuals and a population density of 58.16 individuals/km² distributed across five locations. Proboscis monkeys were detected primarily in riparian habitats within the Catchment of Nungkaran River area, totaling 28 individuals. The observed distribution patterns were consistent with the ecological characteristics of both species, with proboscis monkeys concentrated in riverine areas, while silvered langurs utilized a broader range of reclaimed vegetation habitats. Several strategic locations with potential for artificial canopy bridge development were also identified to improve canopy connectivity within fragmented reclaimed landscapes. These findings indicate that reclaimed vegetation and riparian corridors are utilized by protected primates in post-mining ecosystems and highlight the importance of maintaining vegetation structure and habitat connectivity in post-mining landscape management.

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