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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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Biodiversity and conservation status of flora and fauna in Magetan, East Java, Indonesia: A focus on rare and protected species of mammals, birds and plants OKID PARAMA ASTIRIN; ARI PITOYO; AGUNG HIDAYAT; AMRITA YULI ASTUTI; WIDYA MEGA RAHMAWATI; RADEN WISNU NURCAHYO
Biodiversitas Journal of Biological Diversity Vol. 26 No. 4 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260412

Abstract

Abstract. Astirin OP, Pitoyo A, Hidayat A, Astuti AY, Rahmawati WM, Nurcahyo RW. 2025. Biodiversity and conservation status of flora and fauna in Magetan, East Java, Indonesia: A focus on rare and protected species of mammals, birds and plants. Biodiversitas 26: 1606-1617. Indonesia is recognized for its high level of species endemicity across its islands, but this biodiversity is under significant threat due to high loss rates. Magetan District, East Java Province, Indonesia comprises 8% of protected areas, located adjacent to Mount Lawu, which harbor substantial biodiversity. This study aims to assess the diversity, distribution and protection status of wildlife in Magetan, based on the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and the Minister of Environment and Forestry Regulation of the Republic of Indonesia, especially for mammals, birds and plants. The research utilized a combination of methods, including the collection of biodiversity data from 2013 to 2022, interviews with relevant stakeholders, and field observations. The findings identified three mammalian species and one plant listed under CITES Appendix I. Additionally, 19 wild animal species and one plant species were found to be rare and protected under the government regulation. Among these, five species belong to the mammal group, while 14 species are avifauna group. The highest concentrations of these protected species were observed in the Panekan and Plaosan Sub-districts, highlighting the importance of these two areas for conservation. Conservation strategies are required to protect these animals and plants by avoiding deforestation and habitat restoration. Other conservation strategies are by enforcing laws, addressing human-wildlife conflicts, raising awareness, and conducting regular monitoring. The study provides critical insights for conservation policy development and biodiversity documentation, specifically for Magetan District.
16S rRNA metagenomic analysis of the Asiatic worker honeybee (Apis cerana) gut microbiome from an apiary in Bandung, Indonesia ROSELINA DWIYANTI PUTRI; DIKSON DIKSON; HANS VICTOR; ASTIA SANJAYA; REINHARD PINONTOAN
Biodiversitas Journal of Biological Diversity Vol. 26 No. 4 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260417

Abstract

Abstract. Putri RD, Dikson, Victor H, Sanjaya A, Pinontoan R. 2025. 16S rRNA metagenomic analysis of the Asiatic worker honeybee (Apis cerana) gut microbiome from an apiary in Bandung, Indonesia. Biodiversitas 26: 1666-1674. Honeybees play a crucial role in crop pollination, and consequently, in maintaining global food security. Therefore, understanding their survivability and resilience to natural and human-induced factors is crucial. One critical aspect is the gut microbiome of the honeybees, which is comprised of diverse endosymbiotic bacteria that enhance nutrient uptake and pathogen resistance. Asiatic honeybees (Apis cerana) are commonly managed in Indonesian apiaries for honey production. Therefore, this study aimed to investigate the gut microbiome of A. cerana from a Bandung apiary using 16S rRNA metagenomic sequencing and analytical tools, such as Kraken2, Bracken, SILVA 16S database, and Vegan R library for genus-level identification and Alpha Diversity analysis. The analysis identified 81 genera, including the dominant genera (97.9%) Gilliamella, Lactobacillus, Snodgrassella, Apibacter, and Bifidobacterium. Given that Gilliamella constituted more than 50% of the microbiome, the gut microbiome had high genus richness, but potentially low genus diversity, as indicated by the five Alpha Diversity indices Chao1, ACE, Simpson, Inverse Simpson and Shannon indices. The core genera revealed in this study are consistent with A. cerana samples from Korea and Japan, with Apibacter uniquely present in A. cerana but absent in Western A. mellifera. This study provides insights into the diversity of A. cerana gut microbiome from an apiary in Bandung, Indonesia.
Spatial analysis of fish species composition in relation to fishing gear in the upper stream of Brantas River, Malang, East Java, Indonesia ARIEF SETYANTO; DADUK SETYOHADI; VIGA BALLACKA IRAWAN; SRI SUDARYANTI; NICO CAESAR; WAHYU ENDRA KUSUMA; AKHMAD TAUFIQ MUKTI; ANDIK ISDIANTO; WIRASTIKA ADIHAPSARI; EVELLINE DEWI LUSIANA; ANDRIA ANSRI UTAMA; ANDHIKA PRIMA PRASETYO; RANI EKAWATY; WINDRA NEKA; NORA AKBARSYAH
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/d260846

Abstract

Abstract. Setyanto A, Setyohadi D, Irawan VB, Sudaryanti S, Caesar N, Kusuma WE, Mukti AT, Isdianto A, Adihapsari W, Lusiana ED, Utama AA, Prasetyo AP, Ekawaty R, Neka W, Akbarsyah N. 2025. Spatial analysis of fish species composition in relation to fishing gear in the upper stream of Brantas River, Malang, East Java, Indonesia. Biodiversitas 26: 4193-4200. Inland water ecosystems in Indonesia, particularly in East Java with the Brantas River, hold significant potential for capture fisheries and aquaculture. Covering an area of 13.85 million hectares, this ecosystem includes rivers, natural lakes, and man-made reservoirs. The potential fish resources are projected to be substantial, with the capacity to enhance employment opportunities and boost regional income. However, the management and utilization of fisheries resources in inland waters remain underdeveloped, requiring optimization through appropriate policies and supportive infrastructure. The upper stream of the Brantas River not only provides water for industries and local water utilities but also functions as a critical habitat for various fish species, despite being predominantly managed by small-scale fishers. This study aims to evaluate the composition of fish catches based on fishing area and gear type in the Malang Raya Region of the Brantas River. A descriptive approach was employed for data collection, using random sampling from fishers at seven designated sampling stations. Data were collected within the rainy season through direct observation, interviews, and documentation. Statistical analysis was performed using ANOVA and Chi-Square methods, utilizing Microsoft Excel and SPSS version 27. The results indicate that variations in species composition of the catch were significantly influenced by the sampling stations and the types of fishing gear used.
Molecular identification and antimicrobial activities of Bacillus subtilis MS-01 isolated from Indonesian ethnic food lemea MARDHATILLAH SARIYANTI; PEGI MELANTI ADRI; RISKY HADI WIBOWO; AHMAD AZMI NASUTION; THORIQUL HIDAYAH; SIPRIYADI SIPRIYADI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260305

Abstract

Abstract. Sariyanti M, Adri PM, Wibowo RH, Nasution AA, Hidayah T, Sipriyadi. 2025. Molecular identification and antimicrobial activities of Bacillus subtilis MS-01 isolated from Indonesian ethnic food lemea. Biodiversitas 26: 1069-1074. The community in Bengkulu Province has a variety of traditional foods produced through fermentation, one of which is a bamboo shoot-based dish known locally as lemea. Bacillus subtilis, found in fermented foods, shows great potential as a probiotic due to its ability to inhibit harmful bacteria. Given its genetic diversity, molecular identification is crucial to differentiate between strains. This study represents the first isolation and identification of Bacillus strains from lemea, an ethnically fermented bamboo shoot from the Rejang tribe community in Bengkulu, Indonesia. This study aimed to evaluate the antibacterial activity and perform molecular identification analysis using the 16S ribosomal RNA gene region. The Bacillus isolate was identified using observations of macroscopic and microscopic morphological Lactic Acid Bacteria (LAB). Inhibition tests of Bacillus isolate were conducted using pathogenic bacteria, namely Escherichia coli, Salmonella typhimurium, and Enterococcus faecalis. The isolate demonstrated an exceptionally strong inhibitory effect, particularly against E. faecalis. Molecular identification involved polymerase chain reaction amplifying the 16S rRNA gene, producing an amplicon of approximately 1,300 base pairs. Sequence analysis via BLAST showed 99.84% similarity to B. subtilis strain X2, SSR17, NIBSM OsG1, BaBc-1, and strain LMV in GenBank. Phylogenetic analysis confirmed the isolate’s classification within the order Bacillales and family Bacillaceae. In conclusion, B. subtilis MS-01 was successfully isolated and identified, exhibiting antibacterial potential against both Gram-negative and Gram-positive pathogenic bacteria, with a particularly noteworthy effect against E. faecalis, thereby suggesting its potential as a probiotic with potent antimicrobial properties.
Behavioral response of plaintive cuckoos (Cacomantis merulinus) to playback of conspecific vocalizations YAUMUD RAIYARDHI; YENI ARYATI MULYANI; MIRZA DIKARI KUSRINI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 5 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260501

Abstract

Abstract. Raiyardhi Y, Mulyani YA, Kusrini MD. 2025. Behavioral response of plaintive cuckoos (Cacomantis merulinus) to playback of conspecific vocalizations. Biodiversitas 26: 2021-2027. The parasitic plaintive cuckoo (Cacomantis merulinus (Scopoli, 1786)) is difficult to study due to its elusive behavior. This research applied bioacoustic playback methods to explore the function of its vocalizations. The study, conducted at IPB University's Dramaga campus (267 ha) from March to August 2024, tested four different cuckoo sound patterns with varying amplitude (3-6 kU), frequency (2-4 kHz), and power (20-40 dB). Playback took place between 06:00 and 10:00 in known cuckoo territories, with each session followed by a 4-minute response observation. Spectrogram analysis and MANOVA were used to evaluate bird responses based on duration, amplitude, and frequency. Pattern A elicited communicative behavior and attracted the cuckoo to the sound source. Pattern B signaled territorial claims and competition, while pattern D functioned to repel other individuals. Pattern C had no effect, confirming that it was not a cuckoo call. MANOVA results demonstrated significant multivariate effects of playback type on the acoustic responses of the plaintive cuckoo, as shown by all four test statistics (e.g., Wilks’ Lambda: p = 0.017; Pillai’s Trace: p = 0.040). These results provide insight into conspecific communication within the family Cuculidae and demonstrate how vocalization types relate to behaviors such as attraction, territoriality, and defense.
Isolation and characterization of plant growth-promoting rhizobacteria from wild rice (Oryza rufipogon) in the Mekong Delta, Vietnam NGUYEN TRI YEN CHI; NGUYEN LU KHOI MINH; QUACH VAN CAO THI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260321

Abstract

Abstract. Chi NTY, Minh NLK, Thi QVC. 2025. Isolation and characterization of plant growth-promoting rhizobacteria from wild rice (Oryza rufipogon) in the Mekong Delta, Vietnam. Biodiversitas 26: 1221-1228. Rhizospheric bacteria play a very crucial role in crops, especially rice. In contrast to cultivated varieties, wild rice (Oryza rufipogon), which is abundantly found in Mekong Delta canals, may have distinct rhizobacterial populations. Therefore, the objective of this work was to isolate and characterize Plant Growth-Promoting Rhizobacteria (PGPR) from wild rice with the characteristics of nitrogen fixation, phosphate solubilization, and IAA synthesis. A total of 12 bacterial strains, including seven bacterial strains of nitrogen-fixation and five strains of phosphate-solubilizing microbes, from four rhizospheric soil samples of wild rice in Tien Giang and Vinh Long provinces of the Mekong Delta, Vietnam. The results showed that strain B?1.2 had the highest nitrogen fixation activity with NH4+ content of 0.281±0.007 mg/L. In contrast, strain B?1.3, had the highest phosphorus solubilizing ability with a halo diameter of 1.123 ± 0.025 mm. Also, the finding showed that six out of twelve bacterial strains were capable of synthesizing IAA (Indole-3-Acetic Acid), of which strain B?2.3.1 produced the highest IAA with a concentration of 0.053 ± 0.001 mg/L after 8 days of bacterial inoculation. In particular, B?2.3.2, B?1.3, and B?2.4 simultaneously exhibited the ability of nitrogen fixation, phosphate solubilization, and IAA synthesis. The strain B?1.3 was identified as Stenotrophomonas sp. based on colony morphology, biochemical characteristics, and 16S rRNA gene sequencing with 91.74% similarity. To our knowledge, this is the first report of isolation of rhizospheric bacteria from O. rufipogon with the characteristics of nitrogen fixation, phosphorus solubilization, and IAA production in the Mekong Delta, Vietnam.
Diversity, carbon stock and economic value of the mangrove ecosystem in Wakatobi Biosphere Reserve, Indonesia ABDUL MANAN; LA BACO SUDIA; UMAR ODE HASANI; SURYA CIPTA RAMADHAN KETE; LA GANDRI; ASRAMID YASIN; AGUSRINAL AGUSRINAL; ISABELA ISABELA
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260308

Abstract

Abstract. Manan A, Sudia LB, Hasani UO, Kete SCR, Gandri L, Yasin A, Agusrinal, Isabela. 2025. Diversity, carbon stock and economic value of the mangrove ecosystem in Wakatobi Biosphere Reserve, Indonesia. Biodiversitas 26: 1095-1104. Mangrove ecosystems significantly contribute to climate change mitigation through the absorption and storage of carbon. This research evaluates the diversity, carbon stock, and economic valuation of mangrove ecosystems within the Wakatobi Biosphere Reserve. Data collection occurred at 11 stations distributed among four primary islands: Kaledupa, Wangi-Wangi, Tomia, and Binongko. Diameter at Breast Height (DBH) measurements were utilized to estimate biomass and carbon storage, employing species-specific allometric equations. Economic valuation utilized carbon trading data from the Indonesia Stock Exchange (IDX Carbon) as of 3 January 2025, alongside the Social Cost of Carbon (SCC) and Voluntary Market (VM) prices. The mangrove ecosystem of the Wakatobi Biosphere Reserve covers an area of 10,994 hectares and is in excellent ecological condition. The Shannon-Wiener Diversity Index values for tree and pole strata demonstrate moderate diversity (1-3), with Kaledupa and Binongko classified as moderate, whereas Wangi-Wangi and Tomia are categorized as low (<1). The evenness score indicates a high classification for tree strata (>0,6), with the exception of Wangi-Wangi, which is classified as medium (0,4-0,6). Wangi-Wangi Island is classified as low for splinter strata (<0,4), whereas Tomia, Kaledupa, and Binongko Islands are classified as medium. The composition of mangrove species differed across islands, with Sonneratia alba, Rhizophora mucronata, Bruguiera gymnorrhiza, and Ceriops tagal identified as the most prevalent species and significant contributors to carbon sequestration. The total carbon stock was estimated at 329,82.06 tons, with Kaledupa Island exhibiting the highest stock at 317,226.51 tons, while Binongko Island recorded the lowest at 2,053.8 tons. The economic valuation of carbon storage indicates significant potential: IDR 18,763,377,420 or USD 1,159,307 (IDX Carbon), IDR 266,390,582,055 or USD 16,459,103 (SCC), and IDR 43,155,274,293 or USD 2,666,375 (VM), underscoring the financial importance of mangrove conservation. This signifies a potential for revenue generation in the Wakatobi region, offering a hopeful prospect for the future. This study highlights the ecological and economic significance of mangroves and establishes a basis for sustainable conservation and management strategies aimed at improving the resilience of the Wakatobi Biosphere Reserve.
Ensemble modelling to assess the dynamics of invasive plant species under changing climate in Bagmati Province, Nepal MANISH SHRESTHA; SONY BARAL; UTTAM BABU SHRESTHA; RIPU MARDHAN KUNWAR
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/d260604

Abstract

Abstract. Shrestha M, Baral S, Shrestha UB, Kunwar RM. 2025. Ensemble modelling to assess the dynamics of invasive plant species under changing climate in Bagmati Province, Nepal. Biodiversitas 26: 2589-2600. Invasive Alien Plant species (IAPs) present a significant threat to biodiversity, particularly under changing climatic conditions. This study investigates the distribution patterns of three IAPs, viz. Ageratina adenophora, Chromolaena odorata, and Lantana camara, within Bagmati Province, Nepal, under both current and projected climate scenarios (SSP245 and SSP585). Using species occurrence data from field surveys, available secondary data, and eight bioclimatic variables, we applied an ensemble modelling approach across twelve Global Circulation Models (GCMs). The findings reveal that, under present conditions, A. adenophora occupies the most extensive suitable area (4,121.6 km²), whereas C. odorata occupies the least (1,964.07 km²). Future projections indicate an increase in habitat suitability for all three IAPs in future climates. Specifically, under SSP245, L. camara shows a 12.4% rise in suitable habitat area during the period 2021-2040, with C. odorata showing a 15.6% increase during 2041-2060. Under SSP585, the suitability of L. camara is projected to increase substantially by 37.2% and 40.7% in the periods 2021-2040 and 2041-2060, respectively. This highlights the more conducive environment created by climate change for IAPs in the future. The models demonstrate higher suitability in the middle mountain regions and a decline in suitability with increasing elevation. Specifically, C. odorata favors tropical zones, and A. adenophora and L. camara thrive in subtropical regions. These IAPs pose the greatest risks to cropland and forest ecosystems, adversely affecting local economies and biodiversity. The high-performance metrics of the models (AUC: 0.85-0.92, TSS: 0.51-0.67) confirm their reliability, with Precipitation of Driest Month (BIO14) being the most significant variable under current climate conditions and Mean Diurnal Range (BIO2) emerging as critical for future climate scenarios. These results emphasize the need for proactive site-specific management strategies to mitigate the impacts of IAPs under climate change.
Norovirus contamination in the restrooms of markets in Bangkok, Thailand KITWADEE RUPPROM; URAPORN PHUMISANTIPHONG; THANWA WONGSUK; KANCHANA HIRUNWONG
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260341

Abstract

Abstract. Rupprom K, Phumisantiphong U, Wongsuk T, Hirunwong K. 2025. Norovirus contamination in the restrooms of markets in Bangkok, Thailand. Biodiversitas 26: 1406-1413. Norovirus is among the most important causative agents of acute nonbacterial gastroenteritis. The transmission of norovirus can occur through the fecal-oral route, including person-to-person contact and contaminated food, water, and environmental surfaces. This study first investigated norovirus contamination in the restrooms of local markets in Bangkok, Thailand, using Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) and subsequent semi-nested RT-PCR. An RT-qPCR tested on 211 samples found norovirus GII in 9.5%, GI in 4.3%, and a mix of GI and GII in 1.4% of samples. The urinal flush valves had a higher contamination rate for norovirus than the doorknobs (18.7% vs. 12.5%). Meanwhile, doorknobs had a greater quantity of noroviruses than urinal flush valves (1.68 × 103 ± 3.83 × 103 RNA copies vs. 6.07 × 102 ± 8.71 × 102 RNA copies). Further, the female restrooms and doorknobs were more significantly contaminated with GII than GI (p = 0.048). Using semi-nested RT-PCR, only GII was detected in 31.4% of RT-qPCR-positive samples, and GII.4 was identified as the dominant genotype. Our results revealed a high prevalence of norovirus contamination on frequently touched surfaces in non-outbreak situations. This is significantly beneficial for norovirus outbreak prevention, health risk assessment, and molecular epidemiological investigation of norovirus infection.
Composting domestic sewage using Trichoderma isolates were from agricultural soils NGUYEN PHUONG THUY; NGUYEN NGOC TRAI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 4 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260424

Abstract

Abstract. Thuy NP, Trai NN. 2025. Composting domestic sewage using Trichoderma isolates were from agricultural soils. Biodiversitas 26: 1743-1753. This study aimed to evaluate the efficacy of Trichoderma spp. in enhancing the composting process of sewage sludge from domestic treatment plants. The research focused on improving organic matter decomposition and compost quality while addressing microbial safety. Thirteen Trichoderma isolates were screened from agricultural soils, with Trichoderma afroharzianum (isolate BCS3) identified as having the highest cellulase activity. Composting trials involved six treatments: one control, five sewage sludge combinations, and a T. afroharzianum BCS3 bioproduct. Parameters such as temperature, moisture content, pH, and the physicochemical and microbiological properties of the final compost were monitored throughout the 30-day process. All treatments completed the composting process with characteristic thermophilic phases. Treatment 3, featuring an optimal mix of sludge and T. afroharzianum BCS3 bioproduct, exhibited the most significant thermophilic activity, indicating enhanced microbial activity and rapid organic matter decomposition. Trichoderma-treated compost showed increased organic matter, improved nitrogen and phosphorus availability, and higher concentrations of humic substances. All composts met microbial safety standards, testing negative for E. coli and Salmonella. Trichoderma spp., particularly T. afroharzianum BCS3, significantly enhanced the composting of sewage sludge by accelerating organic matter breakdown and improving nutrient profiles. This sustainable approach offers an efficient solution for sludge management, producing high-quality organic fertilizer for agricultural use.

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