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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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Molecular identification of a novel endophytic fungus Botryotrichum murorum associated with tomato in Iraq ALAA A. AL-RIFAIE; MARWAN Y. AL-MAQTOOFI
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/d260639

Abstract

Abstract. Al-Rifaie AA, Al-Maqtoofi MY. 2025. Molecular identification of a novel endophytic fungus Botryotrichum murorum associated with tomato in Iraq. Biodiversitas 26: 2970-2977. Due to the economic importance of tomato crops in Iraq, this study was designed to investigate new endophytic fungal species related to Sordariomycetes (Ascomycota), a class known for its diverse ecological roles. From Al-Zubair region, which includes well-known farms of tomato and located in the South of Basrah Province in Iraq, a total of 35 cultivated vegetable tomato (Solanum lycopersicum) samples were collected. These samples were processed by cutting them into small pieces sized (5-6 mm) using sterile blades. Two isolation protocols, including the Solid Culture Method (SCM) and the Moist Culture Method (MCM), were employed for endophytic fungal isolation. The recovered endophytic fungi were purified, and axenic cultures of each isolated fungal species were then identified initially based on macro and micro-morphological features. For accurate taxonomy, molecular technique was utilized by genomic DNA extraction and PCR amplification of multigene sequences such as ITS (Internal Transcribed Spacers 1 and 2 including the 5.8S nrDNA), LSU (D1/D2 domains of the 28S nrDNA), RPB2 (partial RNA polymerase II second largest subunit gene), TEF-1? (translation elongation factor 1-alpha gene) and ?-tubulin (TUB2) gene were used for identification. Phylogenetic analysis showed the isolation of Botryotrichum murorum as a dominant endophytic fungal species. This species was reported for the first time as a novel isolation in the Iraqi mycobiota.
Botanical, phytochemical, and bioactivity characterization of Coleus scutellarioides KARTINI KARTINI; RIZKYA AJENG SHEVIRA SHEVIRA; FINNA SETIAWAN; ADITYA TRIAS PRADANA; AZMINAH AZMINAH; JOHAN SUKWEENADHI; A’LIYATUR ROSYIDAH; RETNO WIDYOWATI
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/d260748

Abstract

Abstract. Kartini K, Shevira RA, Setiawan F, Pradana AT, Azminah A, Sukweenadhi J, Rosyidah A, Widyowati R. 2025. Botanical, phytochemical, and bioactivity characterization of Coleus scutellarioides. Biodiversitas 26: 3623-3633. Coleus scutellarioides, commonly known as miana in Indonesia, is a versatile ornamental plant with a longstanding history of traditional medicinal use, particularly for treating inflammation and metabolic disorders. This study focuses on the purple variety due to its prevalence in traditional medicine and its distinctive features, including deep purple foliage with serrated margins. A comprehensive characterization was conducted, including botanical identification, physicochemical tests, and spectroscopic analysis (TLC, ATR-FTIR) to support its standardization as a medicinal crude drug. Biological activities were assessed for in vitro antioxidant (DPPH, NO) and enzyme inhibition (?-glucosidase, ?-amylase, xanthine oxidase) assays. Botanical analysis confirmed distinct morphological and microscopic traits, aiding in varietal identification. The physical evaluation yielded acceptable standardization values: loss on drying (8.86% w/w), total ash (9.35% w/w), and acid-insoluble ash (2.57% w/w). The thick extract exhibited a moisture content of 20.04% w/w, with total and acid-insoluble ash contents of 5.44% w/w and 3.72% w/w, respectively. Thin layer chromatography and spectral analysis confirmed the presence of flavonoids and phenolic acids, with total flavonoid contents of 0.59 mg QE/g (crude drug, i.e., dried plant material prior to extraction) and 1.64 mg QE/g (concentrated extract). Extractive values indicated that water-soluble constituents dominate. Biological assays demonstrated significant antioxidant activity (IC?? = 70.06 µg/mL), moderate ?-glucosidase (IC?? = 630 µg/mL), weak xanthine oxidase (IC?? = 900 µg/mL) and nitric oxide (IC?? = 2.52×10³ µg/mL) inhibition, but no ?-amylase inhibition activity. These findings support the traditional use of C. scutellarioides and provide scientific evidence for its potential as a natural remedy for oxidative stress and metabolic disorders.
Mapping above-ground carbon of mangroves using Sentinel-2 satellite imagery in the east coast of North Sumatra Province, Indonesia ACHMAD SIDDIK THOHA; PURWANTO PURWANTO; PIPIT WIJAYANTI; RITA NOVIANI; RAVINESH ROHIT PRASAD; SHOFIA PUTRI NASIBAH
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/d260822

Abstract

Abstract. Thoha AS, Purwanto, Wijayanti PW, Noviani R, Prasad RR, Nasibah SP. 2025. Mapping above-ground carbon of mangroves using Sentinel-2 satellite imagery in the east coast of North Sumatra Province, Indonesia. Biodiversitas 26: 3916-3925. Accurate estimation of carbon stocks in mangrove ecosystems is essential for assessing blue carbon potential. Conventional methods using field surveys to estimate Above-Ground Carbon (AGC) require significant amount of time and costs. Mangrove carbon stock can be calculated quickly and cost-effectively by utilizing satellite technology and publicly available data. The purpose of this study is to determine the best model for estimating AGC in mangrove forests managed by community in east coast of North Sumatra, Indonesia, using Sentinel-2 Imagery. The study was conducted on two different mangrove conditions following community-led restoration efforts, i.e. mangrove forest planted with a single species of Rhizophora mucronata, and restored mangrove forest consisted of 6 tree species. Field-measured AGC was estimated using the allometric equation of tree Diameter at Breast Height (DBH) and used as dependent variable. Sentinel-2 satellite imagery was used to derive several vegetation indices using reflectance values, which were used as independent variables. Several carbon estimation models were developed and validated with the best model was those with the lowest error and the highest coefficient of determination (R²). It was discovered that the model that employed Normalized Difference Vegetation Index (NDVI) and Total Ratio Vegetation Index (TRVI) was the best for estimating AGC in monospecies mangroves, while the model that employed NDVI and Inverted Red Edge Chlorophyll Index (IRECI) was the most accurate when estimating AGC in multispecies mangroves. In monospecies mangrove forest, AGC estimate ranged 0-200 Mg/Ha, while in multispecies mangrove forest, the estimate ranged 0-400 Mg/Ha. The higher AGC estimates in multispecies forests indicate that a more diverse mangrove species has a higher carbon sequestration capacity than homogeneous forests. The findings of this study indicate that AGC mapping using Sentinel-2 Imagery also supports blue carbon initiatives, mangrove ecosystem service assessments, and conservation-based policy-making.
Screening and characterization of lactic acid bacteria from the gastrointestinal tract of a native chicken (Gallus gallus f. domesticus) as probiotics KHAIRIL ANWAR; RYAN ARYADIN PUTRA; INE KARNI; ALI KURNIAWAN; REZKI AMALYADI; LALU UNSUNNIDHAL; DJOKO KISWORO; MUHAMAD ALI
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/d260610

Abstract

Abstract. Anwar K, Putra RA, Karni I, Kurniawan A, Amalyadi R, Unsunnidhal L, Kisworo D, Ali M. 2025. Screening and characterization of lactic acid bacteria from the gastrointestinal tract of a native chicken (Gallus gallus f. domesticus) as probiotics. Biodiversitas 26: 2653-2661. Probiotic bacteria have been reported to confer beneficial effects on poultry health and performance. Nevertheless, probiotic strains derived from Indonesian native chickens are not widely available, restricting the application of appropriate probiotic strains as an alternative substitution for antibiotic growth promoters in the poultry industry. In the present study, we aimed to screen, identify, and characterize Lactic Acid Bacteria (LAB) strains from the gastrointestinal tract of a native chicken (Gallus gallus f. domesticus). A native chicken was purchased from an officially approved slaughterhouse. The gastrointestinal tracts, including the small intestine and cecum, were gathered aseptically and used for bacterial isolation. A total of three LAB isolates were obtained and subjected to initial screening according to the morphological, biochemical, and molecular analyses. Two selected isolates (LC12 and LC16) demonstrating Gram-positive, rod-shaped, catalase-negative, and non-motile characteristics were tested under simulated gastrointestinal conditions to reveal potential probiotic characteristics, followed by amplifying and sequencing the 16S rRNA gene. The results demonstrated that two selected isolates had high survival rates, greater than 90% at pH 7.2 and 55% at pH 2.0 after 2-hour and 4-hour incubation, respectively, suggesting adaptability over a wide range of pH conditions. Both isolates indicated tolerance to 0.3% bile salt with a survival rate of more than 70%. Molecular identification using partial-length 16S rRNA sequences showed that the isolates LC12 and LC16 were genetically identified as Lactobacillus johnsonii strain 6-3 with a similarity of 100% for both isolates. The selected LAB isolates are promising probiotic candidates for favorable applications in the poultry industry.
Diversity and composition of invasive understory plants in Kapalo Banda Taram Ecotourism Area, West Sumatra, Indonesia DEWI NURHASANAH; SOLFIYENI SOLFIYENI; HAFIZUL MAULANA MUFTI; TESRI MAIDELIZA
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/d260922

Abstract

Abstract. Nurhasanah D, Solfiyeni, Mufti HM, Maideliza T. 2025. Diversity and composition of invasive understory plants in Kapalo Banda Taram Ecotourism Area, West Sumatra, Indonesia. Biodiversitas 26: 4500-4510. Invasive plants are species that establish and spread rapidly outside their natural habitats, often dominating new environments. This study aims to analyze the composition, structure, and diversity of invasive understory plants (seedlings and ground vegetation) in the Kapalo Banda Taram Ecotourism Area, Lima Puluh Kota District, West Sumatra Province, Indonesia. This study used a survey method using two transects with purposive sampling. Location 1 (transect 1) in the eastern part and Location 2 (transect 2) in the southern part of the area. The length of each transect was 50 meters, and along the transect, 25 plots measuring 2×2 meters were systematically placed on each transect. In each plot, observations were made regarding the presence of species, the number of individuals, and environmental factors. Results showed that in Location 1, there were 18 families, 26 genera, 26 species, and 1,213 individuals of understory plants, including 9 invasive families, 14 genera, 14 species, and 1,168 individuals. In Location 2, there were 9 families, 16 genera, 17 species, and 734 individuals, with 5 invasive families, 10 genera, 10 species, and 614 individuals. The dominant families in Location 1 were Melastomataceae (31.16%), Cyperaceae (28.85%), and Poaceae (28.28%), with Cyperus rotundus as the most dominant species (IVI: 43.92%). In Location 2, Asteraceae dominated (50.14%), with Chromolaena odorata as the most dominant species (IVI: 57.52%). The Shannon-Wiener diversity index (H') indicated moderate diversity, with values of 2.34 and 2.26. Canonical Correspondence Analysis (CCA) revealed that environmental factors such as light intensity, humidity, temperature, and soil pH significantly influence the distribution and dominance of invasive understory species. This study provides valuable insights into the management of invasive plants in the Kapalo Banda Taram Ecotourism Area, aiding conservation and sustainable tourism efforts.
Ecological characterization and conservation strategy of binjai (Mangifera caesia) in South Kalimantan, Indonesia MUHAMMAD ADAM MALIK; AMIN SETYO LEKSONO; GUNAWAN GUNAWAN; SAIFUL ARIF ABDULLAH
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/d260815

Abstract

Abstract. Malik MA, Leksono AS, Gunawan, Abdullah SA. 2025. Ecological characterization and conservation strategy of binjai (Mangifera caesia) in South Kalimantan, Indonesia. Biodiversitas 26: 3827-3842. Binjai (Mangifera caesia), a member of the Anacardiaceae family native to Southeast Asia, faces severe threats from timber extraction and habitat loss in South Kalimantan, Indonesia, while limited ecological data have hindered targeted conservation. This study assessed the distribution, ecological characteristics, and conservation strategies of binjai through field observations, purposive and snowball sampling, and ecological surveys in 21 plots (20×20 m each). Environmental factors measured included elevation, air temperature, humidity, light intensity, soil temperature, soil moisture, and soil pH, while vegetation data were collected using nested subplots across understory to tree levels and analyzed using Principal Component Analysis (PCA), vegetation analysis, and SWOT analysis. A total of 21 binjai trees were recorded in home yards, rice fields, and mixed gardens, with PCA revealing that air humidity (70.00-82.33%) and soil moisture (52.78-63.89%) were the most influential habitat factors. Vegetation surveys identified 74 associated species from 38 families, with dominant taxa including Cynodon dactylon and Oryza sativa in the understory, Caryota mitis and M. caesia at seedling level, Musa paradisiaca and Bambusa spinosa at sapling and pole levels, and Cocos nucifera and Durio zibethinus at the tree level. Diversity indices (H?=1.53-2.81) indicated moderate diversity across vegetation layers, reflecting ecological stability. The SWOT analysis highlighted weaknesses such as low community awareness and reliance on aged trees, as well as threats from land conversion and limited legal protection. Accordingly, recommended strategies include in situ protection through sustainable management and agroforestry integration, ex situ germplasm preservation in botanical gardens, environmental education to raise awareness, and cross-sector collaboration to enhance the conservation and economic value of binjai
Molecular characterization and antimicrobial potential of lactic acid bacteria isolated from the Muscovy duck gut NGUYEN PHUONG THUY; NGUYEN THANH TUU
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/d260745

Abstract

Abstract. Thuy NP, Tuu NT. 2025. Molecular characterization and antimicrobial potential of lactic acid bacteria isolated from the Muscovy duck gut. Biodiversitas 26: 3590-3599. The rise of antibiotic resistance in poultry necessitates sustainable alternatives like probiotics. The Muscovy duck (Cairina moschata (Linnaeus, 1758)), a vital Vietnamese agricultural breed with an uncharacterized gut microbiota, is a promising source of such beneficial bacteria. This study aimed to isolate and identify Lactic Acid Bacteria (LAB) from the gastrointestinal tract of Muscovy ducks and evaluate their in vitro antimicrobial activity against key poultry pathogens. A total of thirty LAB isolates were obtained from the crop, gizzard, small intestine, and cecum using selective media. These isolates were screened for antimicrobial activity against Escherichia coli, Salmonella sp., and Staphylococcus aureus using the agar well diffusion method. The most effective isolation was identified through 16S rRNA gene sequencing. Among the isolates, D11 demonstrated the most potent and broad-spectrum inhibition, producing inhibition zones of 1.90±0.35 cm against E. coli, 1.97±0.42 cm against Salmonella sp., and 2.30±0.35 cm against S. aureus. Molecular analysis identified isolate D11 as Companilactobacillus farciminis, with a 99.64% sequence identity to the reference strain. This is the first report of C. farciminis isolation from Muscovy ducks, expanding the known microbial biodiversity of this species. The isolate's potent antimicrobial activity positions it as a strong probiotic candidate to support sustainable and healthy duck production.
Filtration rate and remediation effectiveness of blood cockle (Tegillarca granosa) as a bioremediator of vannamei shrimp pond effluent IHWAN IHWAN; RAJUDDIN SYAMSUDDIN; KHUSNUL YAQIN; DODY DHARMAWAN TRIJUNO; ANDI NIARTININGSIH; ABDUL HARIS; MUHAMMAD FARID SAMAWI; SRI WAHYUNI RAHIM; HASNI HASNI; YUNUS ANUGERAH SANI; SALWAN GHULAM; SITI MARIAM; HUSNUL KHATIMA; ALMUNAWAR ALMUNAWAR; MUTMAINNA ZALSABILA
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/d260828

Abstract

Abstract. Ihwan, Syamsuddin R, Yaqin K, Trijuno DD, Niartiningsih A, Haris A, Samawi MF, Rahim SW, Hasni, Sani YA, Ghulam S, Mariam S, Khatima H, Almunawar, Zalsabila M. 2025. Filtration rate and remediation effectiveness of blood cockle (Tegillarca granosa) as a bioremediator of vannamei shrimp pond effluent. Biodiversitas 26: 3985-3993. The intensive culture of whiteleg shrimp (Litopenaeus vannamei) generates organic waste that can disrupt the balance of aquatic ecosystems. The blood cockle (Tegillarca granosa), a filter-feeding organism or bivalve remediation, has potential as a natural biofilter for remediating such waste. This study aimed to evaluate the filtration and bioremediation effectiveness of T. granosa on aquaculture waste from L. vannamei ponds, considering variations in size and density. Laboratory-scale experiments were conducted using a two-factor factorial design, with two levels of cockle size (2-3 cm and 4-5 cm) and two levels of density (15 and 30 individuals per 10 L, replicated three times for each level of density. Observed water quality parameters included Total Organic Matter (TOM), nitrite (NO?), nitrate (NO?), phosphate (PO?), and other physicochemical parameters. The results showed that T. granosa effectively remediated waste, with the highest TOM remediation rate of 24.49%, nitrate removal of 18.32%, phosphate removal of 21.67%, and COD removal of 26.75%, achieved at a size of 4-5 cm and density of 30 individuals per 10 L. The highest nitrite remediation effectiveness was achieved at a treatment size of 4-5 cm and a density of 15 individuals per 10 L. The filtration rate of T. granosa reached 4.71 mL/h in the treatment with a size of 4-5 cm and a density of 30 individuals/10 L. The optimal treatment was Treatment D. Therefore, utilizing T. granosa as a natural biofilter can be a sustainable strategy for managing intensive whiteleg shrimp pond waste, contributing to aquaculture sustainability and promoting water improvement, especially when size and density factors are carefully considered in its application. These findings highlight the potential of T. granosa as an effective biofilter species for integration into IMTA systems to enhance water quality and sustainability.
Morphological and biological characteristics of black-headed caterpillar, Opisina arenosella (Lepidoptera: Xyloryctidae) HONG-UNG NGUYEN; THI-THANH-NGA SON; THI-XUAN TRINH; NGUYEN-QUOC-KHANH CHAU
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/d260644

Abstract

Abstract. Nguyen H-U, Son T-T-N, Trinh T-X, Chau N-Q-K. 2025. Morphological and biological characteristics of black-headed caterpillar, Opisina arenosella (Lepidoptera: Xyloryctidae). Biodiversitas 26: 3021-3029. The black-headed caterpillar, Opisina arenosella, has recently emerged as a significant pest affecting coconut production in the Mekong Delta, Vietnam. Research on the morphological and biological characteristics of this species was conducted at the laboratory of Tra Vinh University, Vietnam, to serve as a basis for the development of its effective management strategies. The results revealed that O. arenosella eggs were oval, creamy yellow in color, turning reddish brown just before hatching. The average size of the eggs was 0.72±0.13 mm x 0.42±0.10 mm. The larval color was remarkably diverse, varying from white to reddish-brown with multiple stripes on the body. They have a black or dark brown head and range in length from 1.35±0.12 mm to 15.10±2.97 mm, with widths from 0.2±0.02 mm to 1.65±0.07 mm. Opisina arenosella pupae were initially grayish-white and later transform into blackish-brown. The average size was 11.33±1.25 mm x 2.63±0.38 mm for female pupae and 9.30±0.99 mm x 2.07±0.30 mm for male pupae. Female adults had an average body length of 10.7±1.47 mm, light gray, while male adults were darker, averaging 8.62±0.72 mm in body length. The average life cycle of O. arenosella was 75.6±26.9 days, which includes 5.62±1.70 days for the egg stage, 38.7±1.89 days for larval stage, amd 8.02±1.18 days for male pupae and 8.05±0.85 days for female pupae.
Colchicine mutagenesis effects on the characteristics and correlation of the M2 variant population of rice varieties SUNTAREE SURSON; SUPHASIT SITTHAPHANIT; JAKKAPAT PRACHACHIT; THARADOL JITJAK; KHUMPANAT WONGKERSON; TANAKORN RACHAPILA
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/d260532

Abstract

Abstract. Surson S, Sitthaphanit S, Prachachit J, Jitjak T, Wongkerson K, Rachapila T. 2025. Colchicine mutagenesis effects on the characteristics and correlation of the M2 variant population of rice varieties. Biodiversitas 26: 2355-2367. Rice is a self-pollinating plant. In conventional rice breeding, variability is created in rice by crossbreeding. The method of crossbreeding rice is complicated because it requires much expertise to breed. The method of creating genetic variability in rice using chemicals, such as colchicine, is simple. This study used colchicine-induced variability in rice seeds, after which M1 generation variant plants with awn seeds were selected to create an M2 population for selection and to study the variation in the characteristics and correlation of rice. The results of the present study revealed that the M2 population of each M1 variant differed from the parental plants that did not receive colchicine in many morphologies and yield components. In addition, the M2 variant populations of each rice variety also differed. The study of the correlation values revealed interesting results for many traits, such as when rice seeds with awns appeared, the percentage of pollination was low. High tillering resulted in a high number of panicles, full grains, full grain weight, and number of leaves, but it also reduced the stomatal width, plant height, leaf width, leaf length, first shoot diameter, and SPAD value. This study selected mutant rice lines that had potent agronomic characteristics to improve Thai rice varieties.

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