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Biodiversitas Journal of Biological Diversity
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
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.
Articles 6,259 Documents
Floristic composition and species diversity of Tra Vinh University campus, Vietnam NGHI KHAC NHU; TRINH NGOC AI; TRAN THI THAO DANG; TRAN XUAN LAM; QUAN NGOC GIAU; TRAN THI THUY DUONG; TRAN KIM NHU
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/d270230

Abstract

Abstract. Nhu NK, Ai TN, Dang TTT, Lam TX, Giau QN, Duong TTT, Nhu TTK. 2026. Floristic composition and species diversity of Tra Vinh University campus, Vietnam. Biodiversitas 27 (2): d270230. https://doi.org/10.13057/biodiv/d270230. The floristic composition and species diversity of the Tra Vinh University (TVU) campus, an understudied Urban Green Space (UGS) in Vietnam’s Mekong Delta, were comprehensively documented through field surveys conducted during 2023-2024. Six transects covering the campus were established, and all vascular plant species occurring within 50 m on both sides of each transect were recorded, photographed, and identified using standard taxonomic references and global databases. A total of 251 species, belonging to 195 genera, 74 families, 36 orders, and 2 phyla, were documented. Of these, 143 species (57%) were identified as native to Vietnam, including 3 endemic species. The flora was dominated by Fabaceae, Poaceae, and Asteraceae, which together accounted for more than 20% of total species richness. Herbaceous plants constituted the largest life-form group (41.4%), followed by trees (22.3%) and shrubs (20.7%). Of the whole recorded species in the flora, 248 possessed documented use-values, mainly medicinal (56.6%), ornamental (18.7%), and food (16.7%) plants. Seven species were listed as threatened under the IUCN Red List or the Vietnam Red Data Book, including Pterocarpus macrocarpus and Drynaria bonii. Despite being a managed urban area, the campus supports floristic diversity comparable to that of other tropical regions in southern Vietnam. The presence of rare and threatened species underscores the role of university campuses as important refugia for urban biodiversity. These findings highlight TVU’s potential for development into a botanical garden dedicated to the long-term ex situ conservation of native and rare plant species and the restoration of urban habitats.
Genomic and evolutionary perspectives on bacteriophage ΦAfa-NA1 targeting MDR Gram-negative bacteria in diabetic ulcer ERLIA NARULITA; DHIVA AULIA WINDA UTAMI; LAILI IZZATURROHMAH; HALIZA INAYAH ARRACHMI; RISKA AYU FEBRIANTI; RAYYAN ZHAFIR LUDFILLAH; AGUNG HARIS WIDIANTO; HARDIAN SUSILO ADDY; BINAR RAHMA UTAMI; KUSWATI KUSWATI; KAMALIA FIKRI
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/d261205

Abstract

Abstract. Narulita E, Utami DAW, Izzaturrohmah L, Arrachmi HI, Febrianti RA, Ludfillah RZ, Widianto AH, Addy HS, Utami BR, Kuswati, Fikri K. 2025. Genomic and evolutionary perspectives on bacteriophage ?Afa-NA1 targeting MDR Gram-negative bacteria in diabetic ulcer. Biodiversitas 26: 6014-6024. The rise of Multidrug-Resistant (MDR) bacterial infections poses a significant challenge in clinical settings, particularly for diabetic ulcer patients who are highly susceptible to persistent infections. This study reports the isolation, characterization, and genomic analysis of a novel lytic bacteriophage, ?Afa-NA1, specifically targeting MDR Gram-negative bacteria associated with diabetic ulcers in Indonesia. The bacteriophage was isolated from wound dressings and tested against four clinical isolates: Alcaligenes faecalis T17, Pseudomonas sp. FP1911, and the Gram-positive control Streptomyces violaceoruber S21. ?Afa-NA1 exhibited strong lytic activity against three Gram-negative isolates but none against the Gram-positive control, confirming host specificity. ?Afa-NA1 produced clear plaques with an average diameter of 3.0±0.5 mm on Alcaligenes faecalis T17, indicative of its potent lytic activity. Stability tests showed the phage retained >90% infective titer after 24 hours at -20°C and 4°C, and exhibited robust stability across a wide pH range (pH 6 to 11). One-step growth analysis revealed a short latent period of 21.7±8.1 minutes and a burst size of 27.7±1.5 PFU per infected cell. Genomic analysis showed ?Afa-NA1 possesses a 78,105 bp double-stranded DNA genome with 45.8% G+C content encoding 83 predicted open reading frames. Comparative genomics and phylogenetic reconstruction confirmed its placement among T7-like Podoviruses, consistent with its obligate lytic lifecycle and genomic architecture. However, the potential for therapeutic application remains preliminary, as host range testing was conducted on a limited panel of single clinical isolates, and all assays were performed in vitro.
Reproductive biology and pollination ecology of two edible Limnophila species in Thailand RUNGTIP MALAIPHIS; WITTAYA PAKUM; SIRIDUANGKAMOL KAPHANG; THOTSAPORN CHANOKKHUN; NOODUAN MUANGSAN; NATAPOT WARRIT; PRAPUN TRAIYASUT; CURT HRAD BARNES; SANTI WATTHANA
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/d270117

Abstract

Abstract. Malaiphis R, Pakum W, Kaphang S, Chanokkhun T, Muangsan N, Warrit N, Traiyasut P, Barnes CH, Watthana S. 2026. Reproductive biology and pollination ecology of two edible Limnophila species in Thailand. Biodiversitas 27 (1): d270117. https://doi.org/10.13057/biodiv/d270117. Culturally important native Thai herbs are declining due to habitat disturbance, overharvesting, and environmental stressors, including the use of herbicides. Limnophila geoffrayi, a native aquatic edible herb, has been especially affected by herbicide use and climate-driven rainfall anomalies. In contrast, the exotic Limnophila aromatica, introduced for edible herb usage, is widely vegetatively propagated. Both edible Limnophila species have poorly studied reproductive biology, which is important for native species conservation. The purpose of this study is to investigate the reproductive biology and pollination of the Thai native species L. geoffrayi to support conservation efforts, as well as to compare these traits to those of the introduced cultivated species, L. aromatica. Flowers of both species typically open for one day, with some L. geoffrayi flowers reopening on a second day. Diurnal opening and closing patterns corresponded with peak visitor activity. Solitary bees were the dominant pollinators, with 47.06% Sorensen’s similarity index of visitors between the two plant species. Although both species exhibit floral traits conducive to self-pollination, L. aromatica failed to produce fruit under both natural and insect-excluded conditions, indicating self-incompatibility. In contrast, L. geoffrayi consistently set fruit in bagged treatments, demonstrating self-compatibility and autonomous self-pollination, which resulted from polinator scant. High fruit set under natural conditions suggests strong reproductive assurance in the native species. Field observations also confirmed that both species provided pollen resources for solitary bees, which may contribute to cross-pollination within populations. Due to self-incompatibility and clonal propagation, introducing diverse genotypes is necessary for the long-term cultivation of L. aromatica. As an autonomously self-pollinating species that produces many seeds, L. geoffrayi may serve as a potential adaptation or resilience mechanism in the face of habitat disturbance and herbicide use. Being an annual herbaceous plant with different color forms, seed banking is required to support its conservation and sustainable use.
Ethnobotanical knowledge and its role in biodiversity conservation of Tatar Sunda, Indonesia LESY LUZYAWATI; IDAH HAMIDAH; LUTHFIYATI NURAFIFAH
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/d270218

Abstract

Abstract. Luzyawati L, Hamidah I, Nurafifah L. 2026. Ethnobotanical knowledge and its role in biodiversity conservation of Tatar Sunda, Indonesia. Biodiversitas 27 (2): d270218. https://doi.org/10.13057/biodiv/d270218. Tatar Sunda in Indonesia is an area distinguished by its exceptional biodiversity and enduring cultural heritage. However, this vital biocultural knowledge faces significant threats from modernization and the erosion of intergenerational transmission. To ensure effective biodiversity conservation, it is necessary to integrate biophysical, socio-economic, and cultural dimensions, specifically ethnobotanical knowledge. Therefore, this study aims to document the integration of biodiversity and indigenous ethnobotanical knowledge of Tatar Sunda community, focusing on medicinal and timber plant species and their conservation significance. This study was conducted in five representative communities across West Java and Banten Provinces in Indonesia selected to capture diverse ecological and cultural settings. A mixed-method ethnobiological approach combining qualitative ethnography and quantitative ethnobotanical indices (SUV, FUV, ICF, and FL) was employed. This approach was carried out through observation, semi-structured interviews with 120 local experts, and field documentation. A total of 83 medicinal plant species and 46 timber species were documented. Quantitative analysis revealed strong communal consensus for 23 disease categories and highlighted the high cultural importance of key families, notably Zingiberaceae (medicinal) and Fabaceae (timber). Species from Poaceae family were widely used by the community for both medicinal and timber purposes. Crucially, indigenous conservation practices, such as sacred forest protection (hutan larangan), restricted harvesting, and cultural taboos (pamali), were found to be crucial for maintaining ecological balance. This study provides a comprehensive baseline, confirming that TEK in Sundanese community is not a relic but a vital, sustainable strategy for biodiversity conservation.
Ethnobiology and symbolic roles of plants and animals in Javanese funeral rituals, Central Java, Indonesia LATIFAH RESTU PINASTI; MALFA AMORITA IFTITANI; MALIKASARI MALIKASARI; M. BAHRUL MUNA; SEVIANNA DANAH ZULFANI; MUHAMMAD INDRAWAN; TITI WAHYUNI; SURAPON SAENSOUK; AHMAD DWI SETYAWAN
Biodiversitas Journal of Biological Diversity Vol. 26 No. 9 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260949

Abstract

Abstract. Pinasti LR, Iftitani MA, Malikasari, Muna MB, Zulfani SD, Indrawan M, Wahyuni T, Saensouk S, Setyawan AD. 2025. Ethnobiology and symbolic roles of plants and animals in Javanese funeral rituals, Central Java, Indonesia. Biodiversitas 26: 4805-4820. This study explores the ethnobotanical and ethnozoological dimensions of funeral and post-funeral traditions among the Javanese Muslim community in Kalibawang, Wonosobo District, Central Java, Indonesia. The research aimed to document the species of plants and animals used in ritual practices, their symbolic meanings, and their integration with Islamic and local cultural values. A descriptive–exploratory approach was employed, combining qualitative interviews with 90 respondents, field observations, and quantitative analysis using the Relative Frequency of Citation (RFC) index. The findings revealed 19 plant species and 4 animal species involved in various stages of the ritual process. Flowers and leaves were the most frequently used plant parts, particularly Jasminum polyanthum, Magnolia × alba, Cananga odorata, and Oryza sativa, which held the highest RFC values (0.67-0.87). Among animals, Gallus domesticus ranked highest (RFC 0.67), followed by Bos indicus and Oreochromis spp.. These species function as ritual mediators expressing purity, devotion, fertility, and gratitude. The integration of Islamic principles with Javanese cosmology forms a harmonious synthesis that sustains both spiritual and ecological values. Moreover, the continuous use and cultivation of ritual species in homegardens contribute to biodiversity conservation through cultural continuity. The study concludes that the Kalibawang funeral tradition represents a living model of biocultural sustainability, where religious belief, cultural identity, and environmental stewardship coexist in a dynamic equilibrium that strengthens community resilience and moral ecology.
Ethnobiology of plant and animal-based foods among the Bajo People in Gorontalo, Indonesia MARGARETHA SOLANG; MUHAMMAD ISRA; JUSNA AHMAD; SYAM S. KUMAJI; MUHAMMAD NUR AKBAR; MARGARETA RAHAYUNINGSIH; ENNI SUWARSI RAHAYU; ADITYA MARIANTI; SUJATHA RAMASAMY
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/d270226

Abstract

Abstract. Solang M, Isra M, Ahmad J, Kumaji SS, Akbar MN, Rahayuningsih M, Rahayu ES, Marianti A, Ramasamy S. 2026. Ethnobiology of plant and animal-based foods among the Bajo People in Gorontalo, Indonesia. Biodiversitas 27 (2): d270226. https://doi.org/10.13057/biodiv/d270226. Indigenous communities maintain complex food systems that are closely linked to local biodiversity and traditional ecological knowledge (TEK). This study documents the ethnobiological knowledge of the Bajo people in Gorontalo, Indonesia, focusing on the diversity and culturally perceived functions of plant and animal-based foods. Fieldwork was conducted from April to June 2025 using semi-structured interviews, direct observation, and participatory approaches in three coastal villages. A total of 54 informants (37 men and 17 women, aged 35-76 years) reported the use of 25 species, comprising 11 plant species and 14 animal species, utilized for food, medicinal, and ritual purposes. Frequently cited species included Tacca leontopetaloides (ubi teo), Tridacna sp. (kima), Sesuvium portulacastrum (gaganga), Holothuria scabra (tripang putih), and Caulerpa lentillifera (lato). Quantitative ethnobiological indices indicated high cultural salience of T. leontopetaloides, which recorded the highest Relative Frequency of Citation (RFC = 0.78) and Use Value (UV = 0.82), followed by Tridacna sp. (RFC = 0.62; UV = 0.70). Traditional preparation techniques, including fermentation, boiling, and raw consumption, reflect adaptive strategies developed to optimize food use and culturally perceived health-related benefits. Although only a limited number of informants explicitly used the term “functional food,” local practices demonstrate an implicit understanding of the relationship between food and health. This study highlights how biodiversity, traditional ecological knowledge, and subsistence practices intersect within the Bajo food system, underscoring the relevance of ethnobiological knowledge for sustaining community-based food systems and supporting biodiversity conservation.
Weed diversity and microbial responses to glyphosate dissipation in amended coffee soils AI YANTI RISMAYANTI; YAYAN SUMEKAR; DEDI WIDAYAT; YUYUN YUWARIAH; ADITYA MURTILAKSONO
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/d270144

Abstract

Abstract. Rismayanti AY, Sumekar Y, Widayat D, Yuwariah Y, Murtilaksono A. 2026. Weed diversity and microbial responses to glyphosate dissipation in amended coffee soils. Biodiversitas 27 (1): d270144. https://doi.org/10.13057/biodiv/d270144. Glyphosate dissipation in tropical coffee soils is an important ecological concern because residue dynamics may influence weed communities and soil microbial activity. Understanding how soil amendments modify these responses is essential for strengthening sustainable weed management in perennial crops. This study evaluated the effects of biochar and manure on glyphosate dissipation, weed dynamics, and microbial respiration in Arabica coffee soils. A split-plot field experiment with three replications was conducted, combining two organic amendments and six glyphosate doses; weed biomass was analyzed using ANOVA, while glyphosate residues and soil microbial respiration were evaluated descriptively using composite samples. Before herbicide application, 19 weed species were recorded, dominated by Panicum repens, Cynodon dactylon, and Amaranthus spinosus. Following glyphosate application, weed diversity temporarily declined from H′ = 2.27 to 2.12 at 14 days after application (DAA) and subsequently recovered to 2.29-2.33 by 28-42 DAA, while community similarity remained high (>97%). Weed biomass was significantly affected by glyphosate dose at all observation times, with a significant interaction between glyphosate dose and soil amendment detected only at 28 DAA. Organic amendments, particularly biochar and manure, were associated with lower weed biomass and a less pronounced decline in weed diversity during the early phase of glyphosate application. Amended soils showed higher measured microbial respiration compared with unamended soils during the observation period. Glyphosate residue concentrations showed a faster apparent decline in amended soils, with lower measured values observed by 42 days after application. These findings indicate that organic materials are associated with differences in glyphosate dissipation and soil microbial respiration patterns. However, glyphosate residue and microbial respiration data were derived from non-replicated composite samples; therefore, observed trends should be interpreted cautiously. The use of organic amendments, particularly biochar, was associated with changes in weed biomass, microbial respiration patterns, and glyphosate dissipation in coffee soils, indicating their potential relevance for integrated and environmentally conscious weed management.
Combining ability analysis of rice genotypes for grain yield and related traits under direct-seeded conditions ZEESHAN ALI; MUHAMMAD NAEEM; IQRA RAFIQ; MUHAMMAD AJMAL; ABD HARIS BAHRUN; ACHMAD KAUTSAR BAHARUDDIN; ANNASTYA NUR FADHILAH; MUHAMMAD FUAD ANSHORI
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/d270138

Abstract

Abstract. Ali Z, Naeem M, Rafiq I, Ajmal M, Bahrun AH, Baharuddin AK, Fadhilah AN, Anshori MF. 2026. Combining ability analysis of rice genotypes for grain yield and related traits under direct-seeded conditions. Biodiversitas 27 (1): d270138. https://doi.org/10.13057/biodiv/d270138. Development of rice toward water scarcity and high input costs encourages a shift toward Direct-Seeded Rice (DSR) systems. Hybrid rice development is one solution to this system's challenge. Therefore, systematic analysis through combining ability is needed to develop hybrid rice on direct-seeded systems. This study aimed to evaluate the combining ability of rice genotypes for grain yield and related traits under DSR conditions. Twenty-seven genotypes from nine parents and 18 F1 crosses were evaluated using Line × Tester design under a Randomized Complete Block Design (RCBD) with three replications during 2023-2024. The results showed that genotype-by-genotype variance for all traits was significant in the analysis of variance. Line 23765 and tester 37768 were good general combiners, while crosses 6723 × 32274, 6728 × 32274, 6880 × 37768, and 7968 × 37667 showed high Specific Combining Ability (SCA) effects. Line 6728 exhibited a significant positive General Combining Ability (GCA) effect for grain yield per plant, while 6723 for grain weight per panicle and number of grains per panicle, indicating yield improvement potential. Both additive and non-additive genetic effects influence trait expression, with non-additive effects being more prominent. This hybrid rice selection process could help develop high-yielding rice varieties under direct-seeded conditions.
Phylogenetic diversity of culturable bacterial endophytes associated with Avicennia marina from coastal mangroves of the Eastern Province, Saudi Arabia ASMA A. ALANAZI; INÈS HAMMAMI; AISHA ALSHAMMARI; HANAN ALMAHASHEER
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/d270201

Abstract

Abstract. Alanazi AA, Hammami I, Alshammari A, Almahasheer H. 2026. Phylogenetic diversity of culturable bacterial endophytes associated with Avicennia marina from coastal mangroves of the Eastern Province, Saudi Arabia. Biodiversitas 27 (2): d270201. https://doi.org/10.13057/biodiv/d270201. Mangrove ecosystems host diverse endophytic bacterial communities that contribute to plant survival under saline and tidally fluctuating environments. This study investigates the phylogenetic diversity and in vitro functional traits of culturable bacterial endophytes associated with Avicennia marina collected from coastal mangroves of the Eastern Province, Saudi Arabia. A total of sixteen bacterial isolates were recovered from leaf tissues and identified based on 16S rRNA gene sequencing, revealing dominance of the genus Bacillus (B. safensis, B. subtilis, B. amyloliquefaciens, B. megaterium, and B. inaquosorum), along with Brevibacterium halotolerans, expanding current knowledge of region- and host-associated mangrove endophytes functional screening demonstrated variable hydrolytic enzyme activities, including protease, amylase, cellulase, and chitinase production. Qualitative dye-decolorization assays showed that several isolates were capable of transforming lignin-mimicking dyes under laboratory conditions. In vitro antibacterial activity against selected human pathogens was observed in a subset of isolates, with minimum inhibitory concentrations ranging from 0.312 to 5 mg/mL. Scanning electron microscopy revealed morphological alterations in treated bacterial cells, supporting the inhibitory effects observed in the antimicrobial assay. Overall, this study provides baseline data on the culturable endophytic bacterial diversity associated with A. marina in the Arabian Gulf region and highlights preliminary functional traits that warrant further genomic and in planta validation.
Gut bacterial communities in black soldier fly larvae Hermetia illucens from different rearing locations using metagenomic and culture-dependent approaches PONGPAN PHUENGMUN; KAMONRAT SUWANCHAISRI; JARIYA RODDEE; JUREEMART WANGKEEREE
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/d270123

Abstract

Abstract. Phuengmun P, Suwanchaisri K, Roddee J, Wangkeeree J. 2026. Gut bacterial communities in black soldier fly larvae Hermetia illucens from different rearing locations using metagenomic and culture-dependent approaches. Biodiversitas 27 (1): d270123. https://doi.org/10.13057/biodiv/d270123. The black soldier fly larva (BSFL; Hermetia illucens) has gained increasing attention as an alternative protein source for animal feed. Knowledge of its gut bacterial communities is critical for ensuring microbial safety and utilization in rearing systems. In this study, BSFL samples were collected from six different rearing locations, and their gut microbiota were characterized using both 16S rRNA amplicon sequencing (V3-V4 region) and culture-dependent techniques. Twelve amplicon libraries were constructed from pooled samples corresponding to different rearing sites. After quality filtering, the number of clean reads ranged from 73,108 to 75,871 sequences, and clustering of these reads yielded between 98 and 717 operational taxonomic units (OTUs). Alpha diversity indices, including Shannon (3.51-6.07), Simpson (0.82-0.97), and Chao1 (98.04-717.00), indicated that the BSFL gut harbored a diverse and dynamic bacterial community, with variation in microbial richness and evenness. The most abundant phyla were Proteobacteria, Firmicutes, and Bacteroidota. At the genus level, dominant taxa commonly detected included Dysgonomonas, Proteus, Enterococcus, Klebsiella, and Providencia. Among the detected taxa were potentially pathogenic bacteria, such as Campylobacter. Through culture-dependent analysis, 57 bacterial isolates belonging to Proteobacteria and Firmicutes were identified by 16S rRNA gene sequencing. The most frequently cultured genera included the foodborne pathogen Bacillus cereus, along with other species such as Bacillus amyloliquefaciens and Priestia megaterium. This study represents the first investigation of BSFL gut bacterial communities from multiple locations in Thailand integrating metagenomic and culture-dependent approaches. The findings expand current knowledge of BSFL gut bacterial communities and highlight important biosafety considerations. In addition, identifying gut-derived bacterial isolates represent promising candidates for further evaluation of their beneficial roles in improving BSFL rearing efficiency.

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