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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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Antimicrobial activity of Bacillus paramycoides from Xiem duck against poultry pathogens NGUYEN PHUONG THUY; NGUYEN THANH TUU
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261118

Abstract

Abstract. Thuy NP, Tuu NT. 2025. Antimicrobial activity of Bacillus paramycoides from Xiem duck against poultry pathogens. Biodiversitas 26: 5567-5573. Antimicrobial Resistance (AMR) in poultry production poses a significant threat, demanding the development of effective antibiotic alternatives. This study aimed to isolate and identify native Bacillus strains from the gastrointestinal tract of Vietnamese Xiem ducks (Cairina moschata) and screen them for antagonistic activity against key poultry pathogens. Using heat-shock isolation and agar well diffusion assays, 30 different Bacillus species were obtained from 50 healthy ducks. In vitro screening via an agar well diffusion assay showed that over 93% of these isolates possessed broad-spectrum antagonistic activity against Escherichia coli, Salmonella enterica, and Staphylococcus aureus. Among 30, isolate B10 exhibited the highest efficacy, creating significant inhibition zones against E. coli (?10 mm), S. enterica (6-9 mm), and S. aureus (6-9 mm). Molecular analysis of the 16S rRNA gene identified isolate B10 as Bacillus paramycoides. This study reports the first identification of B. paramycoides from Xiem ducks, highlighting the importance of indigenous poultry as a reservoir for novel, host-derived probiotics. However, given its taxonomic affiliation with the B. cereus group, a rigorous safety evaluation, including genomic screening for virulence factors, is an essential prerequisite for its future development and application in sustainable poultry farming.
Ecological diagnosis of Lake Batur (Bali, Indonesia) post-disturbance using multimetric phytoplankton indices SANG AYU MADE PUTRI SURYANI; I GEDE SUDIARTA; NI MADE DARMADI; DEWA GEDE SEMARA EDI; I KETUT SUDIARTA; GEDE AGUS SURYA PRATAMA; I MADE ABDI JANAGUNA; I PUTU SUGIANA
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/d261014

Abstract

Abstract. Suryani SAMP, Sudiarta IG, Darmadi NM, Edi DGS, Sudiarta IK, Pratama GAS, Janaguna IMA, Sugiana IP. 2025. Ecological diagnosis of Lake Batur (Bali, Indonesia) post-disturbance using multimetric phytoplankton indices. Biodiversitas 26: 4982-4990. Plankton communities are rapid responders to environmental change and serve as sensitive indicators of ecological stress in tropical volcanic lakes. In July 2025, Lake Batur (Bali, Indonesia) experienced a major fish mortality linked to hypolimnetic upwelling and nutrient enrichment from aquaculture. To assess post-disturbance conditions, we sampled three sites with varying aquaculture intensity—Seked (low), Buahan (moderate), and Trunyan (high, mortality epicenter)—one week after the event. Field measurements included temperature, pH, dissolved oxygen, conductivity, redox potential, nutrients, and sulfide, while phytoplankton analysis covered diversity (Shannon–Wiener), evenness (Pielou), dominance (Simpson), and saprobity (Dahuri). Results revealed clear spatial contrasts. Trunyan showed the strongest stress signals, with oxygen depletion, negative redox potential, and elevated ammonia, while Seked and Buahan displayed milder alterations. In total, 23 phytoplankton genera were identified, dominated by diatoms such as Ulnaria and Actinotaenium. Trunyan exhibited reduced richness, lower diversity (H’ = 1.84), and higher dominance (D = 0.27), indicating a shift toward opportunistic taxa. Saprobity values showed a gradient of organic pollution, increasing from Seked (1.5) to Trunyan (2.0), consistent with aquaculture intensity. These findings highlight the value of integrating multimetric plankton indices with physicochemical data to distinguish natural upwelling effects from anthropogenic nutrient loading. While diatom persistence suggests some resilience, recovery of sensitive taxa depends on reducing nutrient inputs and regulating aquaculture. This integrative framework offers a practical diagnostic tool for adaptive lake management and contributes to achieving clean water, climate action, and aquatic biodiversity goals.
Mangrove restoration priorities across coastal landscape typologies ASWIN RAHADIAN; LILIK BUDI PRASETYO; YUDI SETIAWAN; CECEP KUSMANA
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/d270305

Abstract

Abstract. Rahadian A, Prasetyo LB, Setiawan Y, Kusmana C. 2026. Mangrove restoration priorities across coastal landscape typologies. Biodiversitas 27 (3): d270305. https://doi.org/10.13057/biodiv/d270305. Mangrove restoration in Indonesia is a new episode and a milestone paradigm in the management of natural resources and the coastal environment after the era of timber extraction. It is crucial for advancing biodiversity conservation, strengthening climate change mitigation, and refining future restoration practices from conceptual, technical, and methodological perspectives. This study aims to develop restoration approaches implemented in Indonesia and to propose an integrated framework based on landscape typology. Mangrove restoration approaches were identified through a comprehensive literature review and a priority assessment using the PROMETHEE method across landscape typologies, based on sustainability indicators derived from stakeholder interviews. We integrate our PROMETHEE results with a geospatial approach to produce a spatially explicit priority map. Various mangrove restoration approaches applied in Indonesia have demonstrated both strengths and limitations. Despite their partial nature, they are evidence-based and have been tested across diverse locations. The results of the study revealed that, in deltas and estuaries, protection approaches prioritize natural regeneration; on the open coast, ecological engineering is prioritized; in the backward zone, intensive planting is prioritized; and, in addition to intact mangroves, priority protection with species enrichment is prioritized. Compared to the partial approach, integrating mangrove restoration with landscape typologies will maximize ecological success and long-term socio-economic sustainability.
Genetic variation of the Mudskipper (Periophthalmus argentilineatus) in the mangrove ecosystem, North Coast of Aceh, Aceh Province, Indonesia IRMA DEWIYANTI; PUTRI KHAIRANI AMALIA SIREGAR; CHITRA OCTAVINA; NURFADILLAH NURFADILLAH; NURFADLI NURFADLI; KASI MARIMUTHU
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/d261237

Abstract

Abstract. Dewiyanti I, Siregar PKA, Octavina C, Nurfadillah, Nurfadli, Marimuthu K. 2025. Genetic variation of the Mudskipper (Periophthalmus argentilineatus) in the mangrove ecosystem, North Coast of Aceh, Aceh Province, Indonesia. Biodiversitas 26: 6399-6409. Mudskipper (Periophthalmus argentilineatus), a species belonging to the Gobiidae family of the Perciformes order, is an important ecological indicator of mangrove health, yet information on its genetic diversity in Aceh remains limited. This study analyzes genetic variation in mudskipper populations from the northern coast of Aceh using mitochondrial Cytochrome Oxidase Subunit I (COI) gene sequencing. Although the species has been widely studied in other regions of Indonesia, no molecular genetic baseline has ever been reported for Aceh populations, creating a critical gap in understanding their genetic structure and conservation status. Twenty samples were collected in Aceh Besar and Banda Aceh populations and combined with 19 additional COI sequences obtained from GenBank. The results showed that the mudskipper species in the research locations were P. argentilineatus. In addition, P. argentilineatus populations from Aceh Besar and Banda Aceh showed no detectable genetic variation, as reflected by low genetic distance values indicating close genetic relatedness. This pattern suggests that similar environmental pressure may be contributing to genetic homogeneity between the two populations. However, genetic variation of P. argentilineatus was moderate in the Bali population, and there was a high genetic distance between the Aceh Besar and Bali populations, as well as Banda Aceh and Bali (0.393). These findings highlight the need for conservation strategies that maintain mangrove habitat integrity and promote connectivity among regional mudskipper populations. Maintaining mangrove habitat connectivity and implementing periodic genomic monitoring are critical future steps to preserve gene flow in P. argentilineatus populations along the North Coast of Aceh.
Revealing genetic markers and evolutionary insights within Piperaceae in chloroplast genome architecture of Indonesian Piper betle ENDANG RAHMAT; LAURA ANINDITA; NESTI FRONIKA SIANIPAR; KHOIRUNISSA ASSIDQI; YOUNGMIN KANG; KENNETH HAPPY; ADHITYO WICAKSONO
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261146

Abstract

Abstract. Rahmat E, Anindita L, Sianipar NF, Assidqi K, Kang Y, Happy K, Wicaksono A. 2025. Revealing genetic markers and evolutionary insights within Piperaceae in chloroplast genome architecture of Indonesian Piper betle. Biodiversitas 26: 5906-5919. Piper betle is one of the most significant medicinal plants in Southeast Asian tradition, yet its genomic resources remain limited compared to other members of the genus. In this study, we report the first complete chloroplast genome of an Indonesian isolate of P. betle, providing a much-needed reference for future molecular work. The genome was assembled into 161,313 bp with a typical quadripartite structure consisting of an LSC (88,995 bp), an SSC (18,201 bp), and two nearly identical IRs (27,057 and 27,060 bp). A total of 113 genes were annotated, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. Repeat analysis revealed 70 cpSSRs, markedly fewer than those described in other Piper species, along with 104 long repeats dominated by palindromic types. Sliding-window analysis detected variable regions in ndhG and ndhI in addition to the well-known hotspots ycf1 and rpl32-ndhF, two novel loci that may serve as species-specific markers. Phylogenetic reconstruction clustered the Indonesian isolate with P. hancei, P. nigrum, and P. kadsura, yet comparison with a Chinese isolate indicated paraphyletic placement across two clades which may indicate a role of geographic divergence in shaping plastome evolution. The results of these genomic resources reveal reduced SSR content, novel divergence hotspots in ndhG and ndhI, and the paraphyletic relationship with the Chinese isolate: creating potential in marker development and evolutionary studies, while also laying the groundwork for future applications in conservation and biotechnology.
Population dynamics modelling of Scirpophaga incertulas based on climatic factors in Mardingding, Karo, North Sumatra, Indonesia TRI YANINTA GINTING; HERMANU TRIWIDODO; I WAYAN WINASA; NINA MARYANA
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/d261016

Abstract

Abstract. Ginting TY, Triwidodo H, Winasa IW, Maryana N. 2025. Population dynamics modelling of Scirpophaga incertulas based on climatic factors in Mardingding, Karo, North Sumatra, Indonesia. Biodiversitas 26: 5003-5011. The yellow stem borer (Scirpophaga incertulas) is a major rice pest in Southeast Asia whose outbreaks are strongly influenced by climatic conditions. This study developed and evaluated dynamic models of S. incertulas populations in Mardingding Sub-district, Karo District, North Sumatra, Indonesia, during a single cropping season (January-April 2025). Field monitoring was conducted weekly at three sites using light traps, accompanied by assessments of infestation intensity and incidence. Climate data, including temperature, relative humidity, and rainfall, were obtained from NASA POWER (Prediction of Worldwide Energy Resources). To assess whether population differences among sites were statistically significant, an Analysis of Variance (ANOVA) was performed. The results revealed a significant difference in S. incertulas populations across locations (F = 8.10, F-critical = 3.28, p < 0.05), underscoring the influence of site-specific agroecosystem conditions. The relationships between climate variables and pest dynamics were further analyzed using multiple linear regression and a discrete logistic growth model. Results indicated that the logistic model provided more accurate estimates of S. incertulas population dynamics compared to linear regression, with the lowest prediction error (18.45%) observed at Tanjung Pamah. At this site, populations remained low (1.5-4.5 individuals) under average conditions of 22.89°C, 89.44% relative humidity, and 5.90 mm rainfall. Peak infestation intensity and incidence across sites occurred approximately six weeks after planting, under mean conditions of 23°C, 89% relative humidity, and 5-6 mm rainfall. These findings demonstrate that integrating climatic drivers with logistic models improves forecasting of S. incertulas outbreaks, particularly in relatively homogeneous rice systems. Such approaches support early-warning systems, reduce reliance on chemical control, and strengthen biodiversity-friendly rice pest management.
Cytotoxicity of Acanthus ilicifolius root endophytes based on acid-induced enhancement and metabolites of Penicillium javanicum ERNY QUROTUL AINY; KHOLIS A. AUDAH; MARSELINA I. TAN; I NYOMAN P. ARYANTHA
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/d270322

Abstract

Abstract. Ainy EQ, Audah KA, Tan MI, Aryantha INP. 2026. Cytotoxicity of Acanthus ilicifolius root endophytes based on acid-induced enhancement and metabolites of Penicillium javanicum. Biodiversitas 27 (3): d270322. https://doi.org/10.13057/biodiv/d270322. Mangrove ecosystems are characterized by extreme environmental fluctuations, driving associated endophytic fungi to evolve adaptive metabolic strategies. These microbial communities represent an untapped reservoir of chemical diversity, yet their metabolic response to abiotic stressors, such as acidity, remains underexplored. This study investigates the ecological and chemical plasticity of endophytic fungi isolated from Acanthus ilicifolius roots. Using a stress-driven culture approach, we evaluated the effect of acidic fermentation on the metabolic profiles and cytotoxic potential of bioactive isolates. Among the screened strains, Penicillium javanicum 2RA6 exhibited a distinct physiological response to acidic stress. While neutral conditions favored vegetative growth, acidic fermentation triggered a fundamental metabolic reprogramming, shifting the biosynthetic output from constitutive polyketides to a specialized stress ‘portfolio’. Comparative metabolomics revealed the enrichment of diverse fatty acid amides (including putative 9-oxo-(10E, 12E)-Octadecadienoic Acid (9-oxo-ODA), α-Eleostearic Acid (α-EA), and Palmitoyl Ethanolamide (PEA)) and diketopiperazines. This chemical reorganization correlated with a marked increase in specific cytotoxicity against MCF-7 breast cancer cells, mediated primarily through apoptosis-like pathways. These findings suggest that mimicking environmental stressors is a viable strategy to unlock cryptic biosynthetic gene clusters. This study highlights the importance of mangrove habitats as reservoirs of metabolic diversity and demonstrates that acid-enhanced cultivation can access bioactive fungal metabolites typically overlooked in standard fermentations.
Diversity of onion nematode fauna in agrocenoses of different altitudinal zones in Fergana Valley, Uzbekistan SARDORBEK KAMBAROV; KHOLISA ESHOVA; SARDORBEK NARZULLAYEV; FARKHOD TO‘XTASINOV; ODILJON ZOKIROV; ZAFARBEK TURDIEV; BEKZOD OTAKULOV; SHAHLO TURSUNOVA; SHAHBOZ KHUJAMOV
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/d260920

Abstract

Abstract. Kambarov S, Eshova K, Narzullayev S, To’xtasinov F, Zokirov O, Turdiev Z, Otakulov B, Tursunova S, Khujamov S. 2025. Diversity of onion nematode fauna in agrocenoses of different altitudinal zones in Fergana Valley, Uzbekistan. Biodiversitas 26: 4479-4489. During research conducted from 2020 to 2024, the biodiversity of nematode fauna associated with onion plants (Allium cepa) cultivated in agrocenoses across different altitudinal zones of the eastern part of the Fergana Valley was thoroughly investigated. As part of the study objectives, a total of 276 samples were collected from the onion root system and its surrounding rhizosphere soils during the spring, summer, and autumn seasons using the route survey method, of which nematodes were detected in 245 samples. The samples were processed following Berman's funnel technique. Based on the obtained results, 39 nematode species belonging to 7 orders and classified within the classes Adenophorea and Secernentea were identified in the onion root system and rhizosphere soils, representing 22 genera. An uneven distribution of the identified species across the altitudinal zones was observed. Within the faunal composition, species of the order Rhabditida were the most diverse in terms of species richness. The study demonstrated that nematode species composition and ecological structure vary significantly depending on the altitudinal zones. In the lower hill zone, 34 species were recorded, whereas 30 species were documented in the upper hill zone and 12 species in the lower mountain zone. This indicated a link between these patterns and the region's ecological characteristics. According to Bongers' classification, nematodes identified in onion fields were assigned as follows: 7 species to the Cp-1 group, 26 species to Cp-2, 2 species to Cp-3, 3 species to Cp-4, and 1 species to Cp-5. Aporcelaimellus obtusicaudatus (C-p 5), which occurred across all three zones, is considered a highly specialized and adaptable species. The results of the study provide a scientific basis for a deeper understanding of the region's biodiversity and for managing the dynamics of nematode fauna in agrocenoses.
Otolith morphometrics for growth and conservation assessment of endangered Napoleon wrasse (Cheilinus undulatus) in Sabah, Malaysia EKO HENDRI GUNAWAN; CHING FUI FUI; AUDREY DANING TUZAN; NAZIA ABDUL KADAR; FITTRIE MEYLLIANAWATY PRATIWY; IBNU DWI BUWONO; SHIGEHARU SENOO
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261135

Abstract

Abstract. Gunawan EH, Fui CF, Tuzan AD, Kadar NA, Pratiwy FM, Buwono ID,  Senoo S. 2025. Otolith morphometrics for growth and conservation assessment of endangered Napoleon wrasse (Cheilinus undulatus) in Sabah, Malaysia. Biodiversitas 26: 5770-5779. The endangered Napoleon wrasse (Cheilinus undulatus) plays a vital role as a carnivorous fish in coral reef ecosystems. However, it faces severe threats from overfishing and habitat degradation, necessitating evidence-based conservation strategies. This study assessed growth pattern, biological condition, and size structure by integrating fish morphometric and otolith metrics from 41 specimens collected in Eastern Sabah, Malaysia. Fish total length from 27.51 to 103.88 cm (mean SD = 35.28±11.72 cm) and body weight from 330.24 to 19400.85 g (mean SD = 757.32±2934.41 g). Linear regression revealed a near-isometric length-weight relationship (b = 3.062, 95% CI [2.904, 3.219], r² = 0.975, p<0.001), indicating proportional growth with robust model fit. Fulton's condition factor (K) was stable across size classes (range: 1.319-2.089, mean ± SD: 1.695±0.189), showing no significant differences (ANOVA, p>0.05) and suggesting consistent physiological health amid environmental pressures. Size distribution was skewed toward juveniles and intermediates (<40 cm, 78% of samples), highlighting potential recruitment overexploitation. Otolith metrics demonstrated strong predictive power, with otolith weight correlating highly with fish length (r² = 0.784, p<0.001) and weight (r² = 0.766, p<0.001), validated through cross-validation (CV-MSE comparable to in-sample MSE) and residual diagnostics confirming normality, homoscedasticity, and independence. These findings highlight the vulnerability of C. undulatus populations in Eastern Sabah, which juvenile exploitation may undermine recovery potential. Otolith-based metrics provide cost-effective, essential baseline data for stock assessments, enabling precise monitoring of growth and demographics. For future conservation management, this supports implementation of minimum size limits, enhanced marine protected areas, and community-led surveillance, fostering sustainable recovery of this iconic species and reef biodiversity.
Species diversity, canonical correspondence, and phenetic analysis of microalgae in the Tancak Maesan River, Bondowoso, Indonesia SULIFAH APRILYA HARIANI; ANGGUN RESTU KURNIAWATI; ABDU ROHMAN; YUNANTA CHANDRA BUANA
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261121

Abstract

Abstract. Hariani SA, Kurniawati AR, Rohman A, Buana YC. 2025. Species diversity, canonical correspondence, and phenetic analysis of microalgae in the Tancak Maesan River, Bondowoso, Indonesia. Biodiversitas 26: 5612-5625. Microalgae are microscopic autotrophic organisms that inhabit various aquatic environments, including the Tancak Maesan River, Bondowoso, Indonesia. They play an essential role as primary producers in aquatic ecosystems and serve as bioindicators of water quality. Anthropogenic activities within the area may influence the microalgal community. The high diversity of microalgae also reflects considerable morphological variation among species. Due to their morphological plasticity and the limited availability of identification keys, morphological and anatomical characterization is crucial for phenetic analysis. This study aimed to analyze the diversity and phenetic characteristics of microalgae found in the Tancak Maesan River. Eleven species were identified, belonging to three divisions (Ochrophyta, Charophyta, and Chlorophyta). Navicula sp. had the highest density across all sampling sites. The diversity index indicated a moderate category (H? = 2.0906). The evenness index shows a high value (E = 0.8386), while the dominance index falls into a low category (D = 0.1436). Canonical Correspondence Analysis revealed that two microalgal species (Cymbella sp. and Pinnularia sp.) were strongly correlated with three abiotic parameters (pH, salinity, and Total Dissolved Solids). According to phenetic analysis, Achnanthes inflata and Navicula sp. cluster together with the highest similarity (Jaccard coefficient = 0.833). This study concludes that community activities and abiotic and anthropogenic conditions influence the presence of microalgae. The findings affirm the role of microalgae as sensitive bioindicators of water quality, responding to both natural and human-induced environmental changes. Consequently, this research establishes a crucial baseline for the river's microalgal diversity and underscores the importance of phenetic characterization for future ecological and monitoring studies.

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