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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 6,259 Documents
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Short Communication: Morphological variation of Coffea liberica from Batangas, Philippines with implications for sustainable coffee production and breeding programs ABIGAIL MANGUIAT BALAN; PHEBE P. MENDOZA; ALAN RODELLE M. SALCEDO; GRECEBIO JONATHAN D. ALEJANDRO
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/d270149

Abstract

Abstract. Balan AM, Mendoza PP, Salcedo ARM, Alejandro GJD. 2026. Short Communication: Morphological variation of Coffea liberica from Batangas, Philippines with implications for sustainable coffee production and breeding programs. Biodiversitas 26 (1): d270149. https://doi.org/10.13057/biodiv/d270149. Coffea liberica, locally known as "kapeng barako" in the Philippines, represents an understudied yet economically significant coffee species with unique morphological characteristics and climate resilience. Despite its commercial presence across Southeast Asia and potential for specialty markets, comprehensive morphological assessments of Philippine C. liberica population remain limited. This single-site baseline study provides morphometric analysis of plants grown in Batangas, Philippines, investigating correlations between leaf architecture, fruit morphology, and bean characteristics to inform breeding and sustainable cultivation. Twelve coffee plants from a farm in Barangay Ludlod, Lipa, Batangas, were analyzed using standardized morphometric protocols. Statistical analyses included correlation analysis and ANOVA to examine relationships among leaf area, cherry volume, bean dimensions, and pulp thickness. Strong positive correlations were observed between leaf area and both cherry volume (r = 0.84, p<0.05) and bean volume (r = 0.92, p<0.05), indicating coordinated morphological development. Cherry and bean volumes showed moderate correlation, while pulp thickness correlated positively with both cherry and bean volumes and accounted for over half of variation in both traits. ANOVA revealed statistically significant differences in cherry size among individual plants, though the overall range of variation was relatively narrow compared to reported diversity in other coffee species. These findings establish baseline morphometric data for C. liberica from this site, demonstrating coordinated leaf-fruit development that may guide selection criteria for breeding. Results highlight the need for expanded multi-site studies to validate these relationships for improved productivity and climate adaptation strategies.
A multi-dimensional sustainability assessment of marine protected area management in Jemur Island on the Malacca Strait, Indonesia TRISLA WARNINGSIH; TOMI RAMADONA; ZULKARNAIN ZULKARNAIN; NURAINI NURAINI; RINETA KHAIRUNISSA; DEVIASARI DEVIASARI; ANDINI MUTHMAINNAH; ASWANDI ASWANDI
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/d270140

Abstract

Abstract. Warningsih T, Ramadona T, Zulkarnain, Nuraini, Khairunissa R, Deviasari, Muthmainnah A, Aswandi A. 2026. A multi-dimensional sustainability assessment of marine protected area management in Jemur Island on the Malacca Strait, Indonesia. Biodiversitas 27 (1): d270140. https://doi.org/10.13057/biodiv/d270140. Jemur Island in the Aruah Islands archipelago in the Malacca Strait, Riau Province, Indonesia, is a marine protected area (MPAs) with significant ecological value as a nesting habitat for green turtles and various economically valuable fish species. However, pressure from human activities and institutional limitations pose challenges to its sustainable management. This study aims to assess the sustainability of marine protected area management on Jemur Island using the Rapfish (Rapid Appraisal for Fisheries) method through a Multi-dimensional Scaling (MDS) approach across four dimensions: ecological, economic, social, and institutional. Data were obtained from in-depth interviews with stakeholders and field observations in mid-2024. The ecological dimension scored 61.44, indicating moderate sustainability, driven primarily by coral reef conditions and turtle nesting habitat quality, with fish abundance identified as the key leverage attribute. The economic dimension scored 64.08, also moderately sustainable, supported by fisheries-based livelihoods and emerging ecotourism, while resource dependency emerged as the critical leverage variable. In contrast, the social dimension scored 41.94, reflecting weak sustainability, with community awareness and participation identified as its main sensitivities. The institutional dimensions were categorized as less sustainable, scored 42.63, and similarly weak, largely influenced by coordination effectiveness and the adequacy of local management capacity. Pareto and leverage analysis further highlight that improvements in fish abundance, livelihood diversification, community engagement, and institutional strengthening offer the greatest potential to enhance overall sustainability. These findings emphasize the need for targeted, evidence-based management and interventions that prioritize ecological monitoring, community involvement, and institutional capacity building. The study provides a structured baseline for evaluating MPA performance in small-island settings and supports future efforts to design more adaptive and participatory conservation strategies.
Effects of lactic acid bacteria inoculants on fermentation characteristics and microbial community profiles of napier grass (Pennisetum purpureum) silage ROHMATUSSOLIHAT ROHMATUSSOLIHAT; RONI RIDWAN; AINISSYA FITRI; KI AGENG SARWONO; WULANSIH DWI ASTUTI; DUDI FIRMANSYAH; YANTYATI WIDYASTUTI; ARIO BETHA JUANSSILFERO; RUSLI FIDRIYANTO; MUHAMMAD RIDLA; NISA RACHMANIA MUBARIK; ANURAGA JAYANEGARA
Biodiversitas Journal of Biological Diversity Vol. 27 No. 4 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270438

Abstract

Abstract. Rohmatussolihat, Ridwan R, Fitri A, Sarwono KA, Astuti WD, Firmansyah D, Juanssilfero AB, Fidriyanto R, Ridla M, Mubarik NR, Jayanegara A. 2026. Effects of lactic acid bacteria inoculants on fermentation characteristics and microbial community profiles of napier grass (Pennisetum purpureum) silage. Biodiversitas 27 (4): d270438. https://doi.org/10.13057/biodiv/d270438. Napier grass (Pennisetum purpureum) is an important tropical forage; however, its high moisture content and low water-soluble carbohydrates (WSC) often impair silage fermentation. This study evaluated the effects of different lactic acid bacteria (LAB) inoculants on fermentation characteristics, nutrient preservation, and microbial community dynamics of napier grass silage. Four indigenous LAB strains, Companilactobacillus kimchii InaCC-B982, Lactiplantibacillus plantarum InaCC-B1028, Limosilactobacillus fermentum InaCC-B1024, and Levilactobacillus brevis InaCC-B1052, were applied individually and as a mixed inoculum and compared with an uninoculated control. Silage was sampled after 7, 14, and 28 days. LAB inoculation significantly improved fermentation quality compared with the control by accelerating acidification, lowering pH (3.69-3.86), increasing lactic acid concentration (2.38-4.90% DM), and suppressing yeasts and coliform bacteria. Among the inoculants, L. plantarum InaCC-B1028 showed the most consistent and superior performance, characterized by rapid and stable pH reduction (3.73-3.78), higher lactic acid production, minimal ammonia-N accumulation (≤0.08% DM), and improved crude protein retention (8.7-9.2% DM). In contrast, L. brevis and the mixed LAB treatment resulted in higher acetic acid concentrations, suggesting enhanced aerobic stability but less consistent nutrient preservation, whereas L. fermentum exhibited intermediate effects. Metagenomic analysis revealed that the bacterial community was dominated by Lactiplantibacillus and Companilactobacillus, with species such as L. plantarum, L. pentosus, L. paraplantarum, and C. kimchii contributing to fermentation dynamics. Genus-level dominance was consistent with species-level composition, indicating robust taxonomic structure across hierarchical levels. Overall, L. plantarum InaCC-B1028 is the most effective inoculant for improving fermentation efficiency, nutrient preservation, and microbial stability, highlighting its potential for enhancing silage quality in tropical forage systems.
Genetic diversity and connectivity of white shrimp (Penaeus merguiensis) in the North Coast of Central Java, Indonesia JASIEL JUNIOR KAROSEKALI; DIAH PERMATA WIJAYANTI; DWI HARYANTI; YEFTA OLIVIA
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/d270336

Abstract

Abstract. Karosekali JJ, Wijayanti DP, Haryanti D, Olivia Y. 2026. Genetic diversity and connectivity of white shrimp (Penaeus merguiensis) in the North Coast of Central Java, Indonesia. Biodiversitas 27 (3): d270336. https://doi.org/10.13057/biodiv/d270336. White shrimp (Penaeus merguiensis) is one of the major capture fisheries commodities in Central Java and has been classified as fully exploited under the Minister of Marine Affairs and Fisheries Decree No. 19/2022. Therefore, this study aims to investigate genetic diversity and population structure to provide a reference for capture fisheries management. A total of 48 specimens were collected from Tegal and Rembang, while 70 sequences from Demak waters were obtained from GenBank. DNA was extracted using Chelex, amplified by PCR, and sequenced with the Sanger method targeting the mtDNA Cytochrome C Oxidase subunit I (COI) gene. Results showed high haplotype diversity, low nucleotide diversity, and high-significant population structure. Harpending's Raggedness Index and neutrality tests indicated an expanding population with negative results. However, the Demak population showed a deviation with significant raggedness due to a steep mismatch and low nucleotide diversity. The haplotype network showed population-specific clustering patterns radiating from a central ancestral haplotype, suggesting restricted gene flow among locations. These patterns are consistent with the combined effects of monsoon-driven currents, differences in fishing grounds, and overfishing, although these factors were not directly tested in this study. These findings highlight the need for population-specific management strategies and strict monitoring of fishing efforts to ensure the sustainability of P. merguiensis in Central Java, Indonesia.
Revealing phylogenetic relationships of Cyprinidae based on DNA barcoding in Merangin Jambi Geopark, Indonesia TEDJO SUKMONO; TEJA KASWARI; PRADITA EKO PRASETYO UTOMO; TIA WULANDARI; SARWO EDY WIBOWO; FEBRINA ROLIN; NURJIRANA NURJIRANA
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/d270317

Abstract

Abstract. Sukmono T, Kaswari T, Utomo PEP, Wulandari T, Wibowo SE, Rolin F, Nurjirana. 2026. Revealing phylogenetic relationships of Cyprinidae based on DNA barcoding in Merangin Jambi Geopark, Indonesia. Biodiversitas 27 (3): d270317. https://doi.org/10.13057/biodiv/d270317. Cyprinidae, a dominant freshwater fish family, plays a crucial role in biodiversity and ecosystem functioning. The Merangin Jambi Geopark, under evaluation for the UNESCO Global Geopark Network, hosts a rich freshwater fish fauna, but morphological identification is challenging due to overlapping characters. This study employed DNA barcoding of the mitochondrial COI gene to identify species and investigate phylogenetic relationships of Cyprinidae. A total of 26 individuals representing 14 species across 10 genera were analyzed. The Cytochrome C Oxidase subunit I (COI) gene (~650 bp) was amplified and sequenced. Sequence analysis was performed using Basic Local Alignment Search Tool (BLAST), and a phylogenetic tree was constructed in MEGA 12. Sequence similarity ranged from 88.11% to 99.56%, with most species exceeding 96% identity, indicating strong intraspecific homogeneity and clear intergeneric divergence. Genetic distances ranged from 0.000 to 0.179, reflecting population stability in species such as Barbodes lateristriga and Rasbora spilotaenia, and high divergence in species like Luciosoma spilopleura and Epalzeorhynchos kalopterus. Phylogenetic reconstruction revealed two major clades, with samples clustering consistently with GenBank reference sequences, confirming accurate species identification and taxonomic placement. Based on IUCN status, most species were categorized as Least Concern, though several were Data Deficient or Not Evaluated, highlighting the need for local conservation attention. These findings demonstrate that DNA barcoding effectively complements morphological taxonomy and provides a robust framework for biodiversity monitoring. Furthermore, the study contributes to local conservation by informing habitat protection, species management, and sustainable freshwater resource utilization in the Merangin Jambi Geopark.
Seasonal impacts of microplastic contamination on benthic species using CMPI and PLI indices at Karangsong Estuary, West Java, Indonesia NOVERITA DIAN TAKARINA; RAHMADYFA MAULIDA AZZAHRAH; LUVIAN WASIS BUDIANTO; NATHAN JOSAFAT SOELIAS; MUHAMMAD ZULFIKAR ANWAR; YANDRA RIZKY SAMUDRA; ATHILA ZAHRA ARIESTA AKHMAD
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/d270125

Abstract

Abstract. Takarina ND, Azzahrah RM, Budianto LW, Soelias NJ, Anwar MZ, Samudra YR, Akhmad AAA. 2026. Seasonal impacts of microplastic contamination on benthic species using CMPI and PLI indices at Karangsong Estuary, West Java, Indonesia. Biodiversitas 27 (1): d270125. https://doi.org/10.13057/biodiv/d270125. Benthic species play a crucial role in estuarine environments. While there is ongoing research on microplastics, information regarding the seasonal variation of microplastics in benthic species remains limited. This study explores the impact of seasonal variation (wet and dry seasons) on microplastic contamination in two representative benthic species at the Karangsong Estuary in West Java, Indonesia. The samples were collected from nine sampling sites in the Karangsong Estuary, with a total of two benthic species and 27 individuals sampled. After a microplastic extraction procedure, Raman Spectroscopy was utilized to identify the microplastic polymers. During the wet season, the predominant types of microplastics found in both Telescopium telescopium and Metaplax longipes are fragments, pellets, and fibers, in that order. The results showed that total microplastic abundance was significantly higher during the wet season than the dry season (χ² = 9.108, p = 0.002), with M. longipes consistently accumulating more microplastics than T. telescopium. During the wet season, microplastic fragments dominated in both species, reaching 0.37 particles g⁻¹ wet mass in T. telescopium (95% CI: 0.06-0.74) and 107.18 particles g⁻¹ wet mass in M. longipes (95% CI: 0-256.00). In contrast, fibers were more prevalent in the dry season, particularly in M. longipes (18.78 particles g⁻¹ wet mass; 95% CI: 6.60-32.80). According to the Comprehensive Microplastics Pollution Index (CMPI), fragments were extremely dominant in M. longipes during the wet season (CMPI = 0.984), while fibers were dominant in T. telescopium during the dry season (CMPI = 0.638). Pollution Load Index (PLI) values for all shapes remained within the low contamination category. Polymer analysis indicated that polyethylene terephthalate (PET) and polyethersulfone (PES) were the dominant polymers in T. telescopium, whereas polypropylene (PP) was most frequently associated with M. longipes. Differences likely influence seasonal variation in microplastic contamination in rainfall, tidal dynamics, surface runoff, and fishing activity between seasons. Although this study is limited by sample size, estuarine coverage, and the use of Raman spectroscopy for polymer identification, the findings highlight clear seasonal patterns in microplastic contamination. These results underscore the importance of season-specific management strategies and support the potential use of M. longipes as a sensitive bioindicator for microplastic pollution in tropical estuaries.
Local wisdom of the Lingga Malay Community in harvesting and transporting sago in Lingga District, Riau Islands, Indonesia PRIMADHIKA AL MANAR; ERVIZAL A.M. ZUHUD; NURI ANDARWULAN; ANAS MIFTAH FAUZI; MOCHAMAD HASJIM BINTORO; AGUS HIKMAT; SYAWALNI HERMANIDA
Biodiversitas Journal of Biological Diversity Vol. 27 No. 4 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270415

Abstract

Abstract. Al Manar P, Zuhud EAM, Andarwulan N, Fauzi AM, Bintoro MH, Hikmat A, Hermanida S. 2026. Local wisdom of the Lingga Malay Community in harvesting and transporting sago in Lingga District, Riau Islands, Indonesia. Biodiversitas 27 (4): d270415. https://doi.org/10.13057/biodiv/d270415. Sago (Metroxylon sagu) plays an important role in the food system, culture, and ecological resilience of coastal communities in Indonesia, including the Lingga Malay Community in the Riau Islands, Indonesia. However, systematic documentation of traditional ecological knowledge (TEK) related to sago harvesting and transportation in this region remains limited. This study aimed to analyze local wisdom practices associated with sago harvesting and transportation among the Lingga Malay Community. A qualitative approach was applied through in-depth interviews with 100 informants across ten villages, participatory observation, and a literature review. Data were analyzed using thematic analysis supported by coding and triangulation techniques. The results reveal that the community possesses a well-developed TEK system for identifying harvestable sago palms based on morphological indicators and ecological conditions. Harvesting practices combine traditional techniques with selective semi-mechanized tools adapted to local environmental constraints. In addition, transportation systems are primarily water-based, using rakit and small motorized boats (pompong), reflecting adaptive strategies to the archipelagic and riverine landscape of Lingga. The utilization of sago residues further demonstrates resource-efficient practices embedded in local socio-ecological systems. These findings highlight the role of traditional knowledge in supporting adaptive resource management and sustaining local livelihoods in island ecosystems.
Fecal microbiome composition and lactic acid bacteria in Senduro goats revealed by 16S rRNA gene sequencing GUNTUR TRIMULYONO; SALAMUN SALAMUN; FATIMAH FATIMAH; ALMANDO GERALDI
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/d270522

Abstract

Abstract. Trimulyono G, Salamun, Fatimah, Geraldi A. 2026. Fecal microbiome composition and lactic acid bacteria in Senduro goats revealed by 16S rRNA gene sequencing. Biodiversitas 27 (5): d270522. https://doi.org/10.13057/biodiv/d270522. Senduro goat (Capra hircus) is an important breed widely cultivated in Senduro District, Lumajang Regency, East Java, Indonesia. This study aimed to describe the fecal microbiome composition and lactic acid bacteria (LAB) detected in Senduro goats from two age groups (1-2 months and 4-5 years) using 16S rRNA gene sequencing. The 16S rRNA gene amplicons from goat fecal samples were sequenced using next-generation sequencing (NGS), targeting the V3-V4 region. Based on descriptive analysis of two composite samples, variation in microbial diversity indices and taxonomic composition was observed between the two samples. Firmicutes and Bacteroidota were the dominant phyla in both samples, while several other taxa varied between the two samples. In the fecal samples of kid goats, the dominant phyla included Firmicutes, Bacteroidota, Actinobacteriota, Proteobacteria, Campylobacterota, and Fusobacteriota. In the fecal samples of adult goats (FKD), the dominant phyla were Firmicutes, Bacteroidota, Spirochaetota, Verrucomicrobiota, Fibrobacterota, and Desulfobacterota. LAB belonging to the genera Streptococcus, Lactobacillus, Ligilactobacillus, Limosilactobacillus, and HT002 were detected only in the kid goat sample (FKA), indicating variation in gut microbial composition between the two samples and providing preliminary insight into potential microbial candidates associated with early gut colonization in Senduro goats. Because each group was represented by a single composite sample, these findings should be interpreted as preliminary descriptive observations rather than evidence of age-related differences. This study provides baseline information on the fecal microbiome composition of Senduro goats and highlights the need for future studies with adequate biological replication and integrated functional analyses.
Development and validation of a tropical diatom-based index for bioassessment of the Yang River, Northern Thailand SUTTAYOT YIMPOOLSAP
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/d270206

Abstract

Abstract. Yimpoolsap S. 2026. Development and validation of a tropical diatom-based index for bioassessment of the Yang River, Northern Thailand. Biodiversitas 27 (2): d270206. https://doi.org/10.13057/biodiv/d270206. Freshwater ecosystems in tropical Asia are increasingly threatened by nutrient enrichment, organic pollution, and land-use intensification. Diatoms are widely recognised as sensitive biological indicators, yet most available diatom indices were developed for temperate regions and may not adequately reflect ecological conditions in tropical rivers. This study aimed to develop a regionally calibrated, river-specific Diatom Index using the Yang River, Northern Thailand, as a model tropical system for water quality assessment. Water sampling and benthic diatom collection were conducted across seven stations from November 2016 to April 2017. Physico-chemical parameters were analysed according to American Public Health Association (APHA 2017), and diatom assemblages were identified to the lowest possible taxonomic level. Indicator Values (IV) and Weighted Averages (WA) were computed for 29 dominant taxa, and the final Diatom Index (DI) was validated against the conventional Water Quality Index (WQI). The study addresses a key methodological limitation in tropical bioassessment by developing an index based on observed ecological responses of tropical diatom assemblages, rather than relying on tolerance values derived from temperate regions. Reproducibility was evaluated using three independent chemistry replicate datasets (R1-R3), which showed high consistency in WA/IV estimation and DI computation (ρ = 0.860-0.907, p < 0.001), indicating that the index-building process was robust and repeatable. The DI showed a significant positive relationship with WQI (ρ = 0.549, r² = 0.3102, p < 0.001), indicating that diatom assemblages effectively captured nutrient and organic pollution gradients. Spatial variation in diatom communities aligned with upstream-midstream-downstream differences in pH, DO, BOD, and nutrient levels. While developed from a single river system, the index provides a regionally appropriate and ecologically meaningful framework for diatom-based water quality assessment in tropical rivers, subject to further validation across additional catchments. The index offers a cost-effective and regionally calibrated approach for routine monitoring and supports improved management of tropical freshwater ecosystems.
The use of colchicine as an elicitor increases the accumulation of phenolics and flavonoids in Java cardamom (Amomum compactum) leaves WARAS NURCHOLIS; SYARIFAH IIS AISYAH; NURUL KOMALA; HEDER DJAMALUDIN; FACHRUR RIZAL MAHENDRA; RAIHAN PERMANA PUTRA
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/d270326

Abstract

Abstract. Nurcholis W, Aisyah SI, Komala N, Djamaludin H, Mahendra FR, Putra RP. 2026. The use of colchicine as an elicitor increases the accumulation of phenolics and flavonoids in Java cardamom (Amomum compactum) leaves. Biodiversitas 27 (3): d270326. https://doi.org/10.13057/biodiv/d270326. Java cardamom (Amomum compactum) is a medicinal plant valued for its secondary metabolites. This study examined the effects of colchicine treatment on plant morphology, physiology, and phytochemical content using vegetative buds collected from a wild population in West Java, Indonesia. A total of 80 buds were treated with colchicine at 0% (control), 0.1%, 0.2%, and 0.3% concentrations. Morphological parameters—including plant height, leaf number, and tiller count—were measured at 18 weeks after planting. Total Phenolic Content (TPC), Total Flavonoid Content (TFC), and antioxidant capacity were evaluated using ABTS, DPPH, FRAP, and CUPRAC assays. Colchicine treatment caused dose-dependent reductions in plant height and tiller number, with mild leaf shape alterations, but did not induce significant changes in chlorophyll content or stomatal density. TPC and TFC were significantly increased across all treated groups, with the highest TPC at 0.1% colchicine and the highest TFC and ABTS antioxidant activity at 0.3%. Flow cytometry confirmed that colchicine did not induce polyploidy in A. compactum. Bioinformatic analysis based on Arabidopsis thaliana orthologs revealed upregulation of genes involved in cytokinin signaling (RR17, RAP2.4, GIS2) and phenolic biosynthesis (LAP5, KMD3), supporting a possible hormonal mechanism underlying phytochemical enhancement. The results suggest that colchicine acts as a chemical elicitor, enhancing secondary metabolism without chromosomal duplication. These findings support the potential of colchicine for improving medicinal quality in Java cardamom. Further studies are recommended to optimize treatment parameters and validate gene-level responses directly in A. compactum for targeted phytochemical enhancement.

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