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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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Soil macrofauna abundance and soil characteristics of limestone post-mining land in Bogor, West Java, Indonesia BASUKI WASIS; FERNANDA REZA PUTRA; BAYU WINATA; ERIANTO INDRA PUTRA; GRAHAME APPLEGATE
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/d261044

Abstract

Abstract. Wasis B, Putra FR, Winata B, Putra EI, Applegate G. 2025. Soil macrofauna abundance and soil characteristics of limestone post-mining land in Bogor, West Java, Indonesia. Biodiversitas 26: 314-5323. Limestone mining can lead to the loss of soil fauna and a decline in soil quality on post-mining land. Soil, as a key component of forest ecosystems, exhibits distinct characteristics across site types. Revegetation is an important strategy to restore ecosystems and biodiversity through tree planting. This study, which aimed to assess the abundance of soil macrofauna, characterize site conditions, and evaluate the influence of soil properties on macrofauna abundance in the limestone post-mining area of PT Solusi Bangun Indonesia, Narogong, Bogor District, West Java, Indonesia, has yielded significant findings. Soil macrofauna were collected using hand sorting and hand capture methods, while biodiversity indices were calculated. Undisturbed soil samples (ring samples) were used for physical property analysis, and disturbed samples (0-20 cm depth) were used for chemical and biological analyses. Data were analyzed using Least Significant Difference (LSD) and negative binomial regression analysis. Macrofauna abundance in Old Revegetation 2010 (OR) sites (54±18.4 individuals) was significantly higher than in Open post-mining land (O) (0.5±0.7) and Young Revegetation 2018 (YR) sites (3.5±2.1) researched in 2023. Porosity, organic carbon, soil pH, soil respiration, and dry litter weight showed significant positive correlations with macrofauna abundance, while soil temperature had a significant negative correlation. These findings, which underscore the importance of revegetation and the role of soil macrofauna as an indicator of post-mining soil quality recovery, are of significant interest to the scientific community and conservation practitioners.
Spring water quality, discharge, and vegetation diversity across land management regimes in UB Forest, Malang, East Java, Indonesia YULIA AMIRUL FATA; RIFQI RAHMAT HIDAYATULLAH; MASHLAHATUL UMAMI; EREKSO HADIWIJOYO; MOCHAMMAD ROVIQ; CALVIN ILHAM ARVIANO; ROHMAH PUJI LESTARI; MUHAMMAD IKHSANUDIN; MUSLIM BINTANG SAMUDRA; TASYA WULANDARI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 7 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260747

Abstract

Abstract. Fata YA, Hidayatullah RR, Umami M, Hadiwijoyo E, Roviq M, Arviano CI, Lestari RP, Ikhsanudin M, Samudra MB, Wulandari T. 2025. Spring water quality, discharge, and vegetation diversity across land management regimes in UB Forest, Malang, East Java, Indonesia. Biodiversitas 26: 3610-3622. Springs in forested landscapes play a vital role in ensuring the availability of clean water and maintaining essential ecosystem services. This study explored the characteristics of springs in UB Forest, Malang, East Java, Indonesia, focusing on buffer zone conditions in secondary forest and pine plantation forest, water quality, discharge, and vegetation diversity under different land management regimes. The research was conducted across five tributary systems, where water quality was assessed through physical, chemical, and biological parameters, and vegetation diversity was evaluated using the Shannon-Wiener (H') and evenness (E) index. Spring discharge was measured using the volumetric method, with the highest discharge recorded at 0.5 m³/second. Springs in secondary natural forests showed better water quality, more stable discharge, and greater vegetation diversity compared to those in plantation or agroforestry systems. All springs are in riparian zones, within 1 to 30 meters from the nearest river, and the water quality meets drinking, raw water, and irrigation standards. The highest discharge occurred at Dampul 4 (0.5 m³/s), while other springs were below 0.2 m³/s. The buffer zones support 19 plant species, dominated by native vegetation (Ficus gul), with H' values ranging from 0.451 to 1.685 and E from 0.65 to 0.988. All chemical parameters comply with water quality standards (WQS-1 to WQS-4), except for chromium (Cr) and iron (Fe) levels in Petung 21-2 and Codo, which do not meet WQS-1. Positive correlations were found between vegetation diversity and NO2, Fe (moderate), and TDS (strong). These correlations indicate the potential for using vegetation diversity as an indicator of water quality. While the correlation between vegetation diversity and discharge was relatively low (R²: 20%), the findings emphasize the importance of maintaining natural vegetation and establishing protected buffer zones. The natural vegetation-based spring buffer zone protection strategy and long-term monitoring are needed for sustainable forest management efforts and water resource conservation in the tropical forest landscape.
Mangrove species distribution across soil texture gradients in Benoa Bay and Nusa Lembongan, Bali Province, Indonesia I GUSTI NGURAH PUTU DHARMAYASA; I PUTU SUGIANA; PONGPIPAT ANANTANASAKUL
Biodiversitas Journal of Biological Diversity Vol. 26 No. 6 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260633

Abstract

Abstract. Dharmayasa IGNP, Sugiana IP, Anantanasakul P. 2025. Mangrove species distribution across soil texture gradients in Benoa Bay and Nusa Lembongan, Bali Province, Indonesia. Biodiversitas 26: 2908-2915. This study unveils the crucial role of mangrove ecosystems in enhancing coastal resilience and mitigating climate change through carbon sequestration and shoreline stabilization. This study identifies strong relationships between soil particle composition (sand, silt, clay, and gravel) and the distribution of mangrove species across five genera-dominated zones (Rhizophora, Sonneratia, Avicennia, Bruguiera, and Ceriops) in Bali, Indonesia. By establishing 20 plots at two sites, Benoa Bay and Nusa Lembongan, and quantitatively measuring stand structure (tree and sapling density, diameter, canopy cover, and Mangrove Health Index (MHI) and soil parameters (texture, pH, water content, bulk density, and total organic matter), this study revealed that Ceriops tagal dominates soils with 35-45% silt and clay content; Bruguiera gymnorrhiza thrives in sandy soils exceeding 60% sand; and Sonneratia alba is associated with substrates containing over 20% gravel. Principal component analysis and Pearson correlation reveal significant negative effects of gravel on canopy cover (r: -0.73, p<0.01) and MHI (r: -0.74, p<0.01), and a positive correlation between sand content and sapling density (r: 0.56, p<0.01). These findings not only underscore the critical role of soil texture in mangrove distribution and forest health but also emphasize the need to consider edaphic conditions in restoration and conservation strategies. This knowledge is vital for enhancing ecosystem sustainability and biodiversity.
Assessment of biodiversity and conservation status of flora and fauna in Madiun City, East Java, Indonesia OKID PARAMA ASTIRIN; FETRIA WIDIYANTI; SURATMAN SURATMAN; NUGROHO ANDI PURNOMO; M. ARIF ROMADLON; HADI WIWIT HENDRO CAHYONO; DIAGAL WISNU PAMUNGKAS; WIDYA MEGA RAHMAWATI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 8 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260826

Abstract

Abstract. Astirin OP, Widiyanti F, Suratman, Purnomo NA, Romadlon MA, Cahyono HWH, Pamungkas DW, Rahmawati WM. 2025. Assessment of biodiversity and conservation status of flora and fauna in Madiun City, East Java, Indonesia. Biodiversitas 26: 3965-3972. Madiun City in East Java, Indonesia is a small municipality that has evolved into an urban center due to its strategic position as the hub of socio-economic activities, including trade, industry, and healthcare. Urbanization in the town poses a threat to biodiversity. This is due to changes in land use and cover, natural exploitation, introduction of exotic species, air and water pollution, and climate change. This study aims to explore biodiversity in Madiun City to inform the development of strategies and policies for natural resource management. The observations revealed that Madiun City is home to 122 tree species, 76 species of ornamental plants, and 143 species of animals, including mammals, birds, reptiles, amphibians, fish, and insects. Eight plant species and five animal species are listed in the IUCN Red List. Additionally, there are eight plants and five animals listed under CITES, as well as six animals listed as protected under the Indonesian Ministry of Environment and Forests' P106/2018. Leucopsar rothschildi, Padda oryzivora, and Pavo muticus are birds listed under all the three protection instruments, suggesting their conservation importance. Green open spaces with aviaries are crucial for conserving biodiversity, as they offer a range of ecological, aesthetic, social, and economic benefits. Community participation with the local government is vital to conservation programs in urban areas. Active community involvement in conservation programs and socialization can significantly support the success of biodiversity conservation.
Novel primers for mini-barcoding of seahorses for wildlife trade and seafood forensics ELAH MARIE M. SALAMIDA; SHARON ROSE M. TABUGO
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/d270335

Abstract

Abstract. Salamida EMM, Tabugo SRM. 2026. Novel primers for mini-barcoding of seahorses for wildlife trade and seafood forensics. Biodiversitas 27 (3): d270335. https://doi.org/10.13057/biodiv/d270335. Seahorses are charismatic fish facing increasing threats from habitat loss and the illegal wildlife trade. They are targeted and trafficked in the global market, further threatening their status. The high levels of both interspecific and intraspecific variability are also affecting the accuracy of species definition. Thus, this study developed a systematic pipeline for designing DNA mini-barcode primers using accessible software and integrated bioinformatics tools to enhance the detection of vulnerable seahorse species in wildlife trade and seafood forensics. The overarching goal is to support conservation efforts and promote the sustainable use of marine resources. DNA mini-barcodes, short sequences under 200 bp, show promise and can be useful for identifying species from degraded or processed samples. In this study, cytochrome b gene sequences—known for combining conserved and variable regions—were the basis for designing species-specific mini-barcode primers. These primers were tailored to improve molecular identification from low-quality seahorse samples, such as dried or frozen specimens commonly encountered in trade. Novel primers were initially evaluated using in silico Polymerase Chain Reaction (PCR), yielding four top-performing primer sets, which were subsequently validated by actual PCR. A total of nine Hippocampus spp. samples (four dried, five frozen) were used to test primer efficacy. PCR amplification and gel electrophoresis results confirmed that all primer sets successfully amplified DNA and produced good-quality PCR products. Sequencing data revealed accurate base-calling, with high percentage identity matches to reference sequences. These novel primers show potential for species identification in seahorse monitoring and enforcement contexts.
Molecular and virulence profiling of Aeromonas veronii from diseased Nile tilapia in Central Java, Indonesia DINI SISWANI MULIA; ZAHROTUN NISA; SUWARSITO SUWARSITO; CAHYONO PURBOMARTONO; OLGA OLGA; BOBY MUSLIMIN; AGUS SETYAWAN
Biodiversitas Journal of Biological Diversity Vol. 26 No. 7 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260750

Abstract

Abstract. Mulia DS, Nisa Z, Suwarsito, Purbomartono C, Olga, Muslimin B, Setyawan A. 2025. Molecular and virulence profiling of Aeromonas veronii from diseased Nile tilapia in Central Java, Indonesia. Biodiversitas 26: 3647-3657. Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) is a widely cultivated species with promising economic potential; however, bacterial infections pose a significant barrier to successful production. Molecular characterization is essential for accurately identifying pathogenic bacteria involved in disease outbreaks. This study aimed to determine the molecular and virulence of Aeromonas veronii isolated from diseased Nile tilapia in Central Java, Indonesia. Diseased fish were collected using a purposive sampling technique. Molecular identification was conducted using markers for 16S rRNA, gyrB, and ten virulence-associated genes, including aerA/haem, alt, ast, act, flaA, lafA, fstA, ahp, ela, and lip. Antibiotic susceptibility testing was performed using eight antibiotics: bacitracin (10 µg), penicillin (10 µg), amoxicillin (25 µg), ciprofloxacin (5 µg), vancomycin (30 µg), clindamycin (2 µg), tetracycline (30 µg), and chloramphenicol (30 µg). Results revealed that seven isolates were identified as A. veronii. All isolates (100%) harbored two significant virulence genes, aerA/haem and ela, while none of the isolates (0%) tested positive for the other eight virulence genes. The consistent presence of these two virulence factors suggests a high pathogenic potential of the isolates. Antibiotic susceptibility assays indicated that all isolates (100%) were resistant to bacitracin, penicillin, amoxicillin, vancomycin, and clindamycin, but remained sensitive to ciprofloxacin, tetracycline, and chloramphenicol. In conclusion, the present findings support the implementation of targeted diagnostic approaches for A. veronii infections. Detecting key virulence factors and multidrug resistance in A. veronii highlights its potential as a significant threat to aquatic animal health. Consequently, there is an urgent need to strengthen biosecurity measures, including routine microbial monitoring, judicious and responsible use of antibiotics, and improved environmental management practices. Furthermore, developing alternative strategies, such as vaccination, represents a proactive and sustainable long-term solution to enhance the resilience of aquaculture systems.
Influence of forest configuration and bird exclusion on insect herbivory in Indonesian oil palm smallholdings DIMAS HARYO PRADANA; NURUL LAKSMI WINARNI; MUFTI PETALA PATRIA; YASMAN YASMAN
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/d260934

Abstract

Abstract. Pradana DH, Winarni NL, Patria MP, Yasman. 2025. Influence of forest configuration and bird exclusion on insect herbivory in Indonesian oil palm smallholdings. Biodiversitas 26: 4640-4646. The insect pest control services provided by birds may help address one biological challenge in oil palm plantations. Previous studies suggest that understory birds contribute to this ecosystem service and that forest configuration may influence their effectiveness. We investigated whether understory birds reduce insect pests and whether forest configuration affects their pest control services in six oil palm smallholdings in Indonesia. Understory birds were surveyed using the point count method at 0-200 m from adjacent forests. Herbivory rates, used as a proxy for insect pest activity, were assessed through a bird enclosure experiment. The indirect bird effect on herbivory rate was also evaluated using this experiment. We used binomial Generalized Linear Mixed Model (GLMM) to analyze the effects of understory bird abundance and forest configuration on herbivory rates. Results showed the herbivory rate ranged from 0.01 to 0.84 mm². A weak negative relationship between understory bird abundance and herbivory in control treatments (z: -1.65, n: 12, p-value<0.1) was found, suggesting a limited pest control effect. However, no significant influence of forest distance or remnant size on herbivory rates was observed. Functional trait analysis revealed that the bird community was dominated by gleaners, omnivores, and large-bodied species, which are typically associated with insectivores. The absence of strong effects may be linked to small forest remnant sizes, low pest abundance, and the structural limitations of smallholder oil palm understory that limit the use of this habitat by forest understory birds. While understory birds show some potential for insect pest control, their effectiveness appears constrained under current conditions. It is clear that urgent action is needed. Habitat enhancement through reforestation and vegetation management to increase habitat connectivity, and may be necessary to support more robust pest control by bird communities in oil palm landscapes.
Ethnomedicinal survey and scientific validation of inflammation-healing plants used by the Tengger community in East Java, Indonesia WEKA SIDHA BHAGAWAN; WIWIED EKASARI; MANGESTUTI AGIL
Biodiversitas Journal of Biological Diversity Vol. 26 No. 7 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260707

Abstract

Abstract. Bhagawan WS, Ekasari W, Agil M. 2025. Ethnomedicinal survey and scientific validation of inflammation-healing plants used by the Tengger community in East Java, Indonesia. Biodiversitas 26: 3160-3173. This study investigates the profound ethnomedicinal knowledge of the Tengger community in East Java, Indonesia, with a specific focus on plant species traditionally used to manage inflammation and pain-related conditions. The primary objective was to meticulously document the medicinal plants utilized by the community and assess their pharmacological relevance through literature-based validation. Data were obtained through semi-structured interviews and in-depth observations with selected informants, using a snowball sampling technique. Quantitative indices (species use value, family use value, fidelity level, and informant consensus factor) were applied to evaluate each species' cultural and therapeutic significance. A total of 82 plant species belonging to 42 families were identified and utilized in various preparations to treat 15 inflammation and pain-related disorders. Notably, 4 of the 6 plant species with the highest species use value have been scientifically validated for their anti-inflammatory and analgesic activities, providing a solid foundation for the community's traditional knowledge. However, the pharmacological properties of Borreria laevis and Elaeocarpus longifolius remain unexplored. The enduring use of these medicinal plants is a testament to the community's rich ethnomedical tradition, and further pharmacological investigations may lead to the discovery of new therapeutic agents for treating inflammation and pain.
Total hemocyte and hemoglobin changes in nypa palm worm (Namalycastis rhodochorde) to Aeromonas sp. NrBF9 infection ARI HEPI YANTI; HERALDUS I. ARINENDO; TRI RIMA SETYAWATI; RIKHSAN KURNIATUHADI
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/d260903

Abstract

Abstract. Yanti AH, Arinendo HI, Setyawati TR, Kurniatuhadi R. 2025. Total hemocyte and hemoglobin changes in nypa palm worm (Namalycastis rhodochorde) to Aeromonas sp. NrBF9 infection. Biodiversitas 26: 4274-4283. Nypa palm worms (Namalycastis rhodochorde) are polychaetes essential to mangrove ecosystems as detritivores and decomposers. They also hold economic value for coastal communities through cultivation. However, pathogenic infections threaten their survival and aquaculture. Aeromonas sp. NrBF9, isolated from the worms’ fecal pellets, is an indigenous pathogen with hemolytic and DNase activities that likely cause hematological damage. Previous studies observed blanching symptoms in cultured worms exposed to Aeromonas from their feces, hypothesized to result from blood and hemocyte damage, though this remains unconfirmed. This study examined the hematological profile of nypa palm worms after dorsal injection with Aeromonas sp. NrBF9 at 10³, 10?, and 10? cells/mL. Parameters assessed included total hemocyte counts, hemoglobin levels, and hemocyte diameters. Hemolytic activity was tested using a smear method on worm blood agar. Results showed infected worms developed anemia, with significant reductions in total hemocyte counts (32.9%, 39.2%, and 39.9% decreases at 10³, 10?, and 10? cells/mL, respectively; p = 0.007, p<0.05), and hemocyte diameters (8.8%, 12.5%, and 15.0% decreases at 10³, 10?, and 10? cells/mL, respectively; p = 0.00, p<0.05). Infected worms also exhibited paler hemocytes and hemocyte aggregation, while hemoglobin levels remained unchanged (p = 0.679, p>0.05). Aeromonas sp. NrBF9 displayed ?-hemolytic activity on worm blood agar. These findings show changes in hemocyte counts and colonization caused by Aeromonas infection, emphasizing the need for early detection and management to minimize losses and boost nypa palm worm aquaculture productivity.
Molecular screenings of drought tolerance QTLs and agronomic performance in selected rice (Oryza sativa) cultivars SELVIA DEWI POHAN; HEPPY SETYA PRIMA; JAMSARI JAMSARI; TIKA RUNIFAH
Biodiversitas Journal of Biological Diversity Vol. 26 No. 8 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260807

Abstract

Abstract. Pohan SD, Prima HS, Jamsari, Runifah T. 2025. Molecular screenings of drought tolerance QTLs and agronomic performance in selected rice (Oryza sativa) cultivars. Biodiversitas 26: 3731-3744. This study aimed to identify Quantitative Trait Loci (QTL) associated with drought tolerance (qDTY) and evaluate their agronomic performance under both non-stress and stress conditions. Molecular analysis using eight SSR markers (RM236, RM276, RM511, RM520, RM28099, RM28130, RM28166, and RM1261) was conducted to detect the presence of targeted qDTY loci. A Completely Randomized Design (CRD) with three replications was applied to assess the effects of drought stress on rice plants. Two treatments were implemented: a non-stress control (C1, 100% of field capacity) and a drought stress condition (C2, 50% of field capacity). Agronomic traits such as PH, PTN, PL, NFG, NUFG, DTF, and DTM were measured to evaluate plant performance under both conditions. The SSR markers used for detecting qDTY loci exhibited polymorphism. The number of alleles per marker averaged 8.625, ranging from 1 (RM511) to 12 (RM236). RM236 and RM28099 showed the highest polymorphism with eight alleles each. Phenotypic evaluation found significant differences in trait performance between non-stress and drought-stress conditions. While all traits generally decreased under drought stress (C2), the extent of reduction varied among genotypes. Most genotypes appeared to exhibit a drought escape mechanism by shortening their DTF and DTM under drought stress.

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