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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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Systematics molecular investigation of Palo fish (Betta sp.) in the Harau Valley, West Sumatra using the COI gene UMMI KURNIA PUTRI; DEWI IMELDA ROESMA; DJONG HON TJONG
Biodiversitas Journal of Biological Diversity Vol. 26 No. 2 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260217

Abstract

Abstract. Putri UK, Roesma DI, Tjong DH. 2025. Systematics molecular investigation of Palo fish (Betta sp.) in the Harau Valley, West Sumatra using the COI gene. Biodiversitas 26: 698-705. Palo fish (Betta sp.) is a local ornamental fish in the Harau Valley, Lima Puluh Kota, West Sumatra, Indonesia, which was suspected to be a new species from the Betta of the Pugnax group based on the Cytochrome b gene. Molecular investigations using more reliable genes were needed to validate the taxonomic status of Palo fish and determine the phylogenetic relationship with other Betta species. The cytochrome oxidase I (COI) gene has been recognized for identification at the species level. Liver tissue samples were taken from eight Palo fish individuals from four Rangkak Hill tributaries in Harau Valley. Eight Palo fish and 44 comparison sequences were analyzed using the Aliview, IQ Tree, and MEGA VII programs. The 641 bp COI gene sequences analysis showed that Palo fish from four tributaries in Harau Valley had 100% nucleotide base similarity (identical), which shared the same haplotype. Palo fish have a close relationship with Betta stigmosa and have the least genetic distance to Betta cf. apollon (2.6%), followed by Betta ferox (3.1%) and Betta apollon (3.7%). The genetic distance values show the differences at the subspecies level within the same species. Palo fish from Harau Valley confirmed as Betta cf. stigmosa. Comprehensive studies on Betta species need to be carried out to complete the systematics of the Betta group.
Culturable marine fungal biodiversity from the south coast of Jember, East Java, Indonesia ENDAH PUSPITASARI; KARTIKA SENJARINI; I DEWA AYU RATNA DEWANTI; VIRLIANA FEBRIANTI; FITRIANTI MILHATUL HASANAH; ANTJE LABES
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/d260642

Abstract

Abstract. Puspitasari E, Senjarini K, Dewanti IDAR, Febrianti V, Hasanah FM, Labes A. 2025. Culturable marine fungal biodiversity from the south coast of Jember, East Java, Indonesia. Biodiversitas 26: 3000-3010. Marine fungi with their unique environment are a promising source for drug discovery. Their distinct natural products, different from those of terrestrial fungi, give them potential bioactivity. However, not all marine fungi are culturable. This research aimed to determine the biodiversity of culturable marine fungi from Jember south coast, East Java, Indonesia. The sampling was conducted on samples available on the Jember south coast, East Java, Indonesia, including seawater, sand, wood remains, green algae, and red algae. The isolation of marine fungi using fungal basal media. Once a single colony with different morphotypes was obtained, it was characterized based on its morphology (macroscopically and microscopically using bright field and scanning electron microscope) and molecularly. The fungal morphological features were described based on the colony’s and cell’s appearance. The molecular characteristics were carried out using DNA barcoding based on the internal transcribed spacer. The results revealed 17 isolates of culturable marine fungi from Jember south coast. They were dominated by the genus Penicillium (47.059%), followed by Scopulariopsis and Curvularia (17.647%), Aspergillus (11.765%), and Cladosporium (5.882%); members of phylum Ascomycota. The results showcase the rich diversity of species that have potential as drug candidates. Further studies are needed to reveal their bioactivity.
Environmental determinants of reef fish community structure in Sempu Strait, East Java, Indonesia ANDIK ISDIANTO; KHALIL GIBRAN; ADE YAMINDAGO; SYARIFAH HIKMAH JULINDA SARI; ADI TIYA YANUAR; DESY SETYONINGRUM; ARIEF SETYANTO; LISA NUR HIDAYAH; KRISTINA MARSELA; MUCHAMAD FAIRUZ HAYKAL; AULIA LANUDIA FATHAH; BERLANIA MAHARDIKA PUTRI; SUPRIYADI SUPRIYADI; OKTIYAS MUZAKY LUTHFI; DWI CANDRA PRATIWI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 12 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251214

Abstract

Abstract. Isdianto A, Gibran K, Yamindago A, Sari SHJ, Yanuar AT, Setyoningrum D, Setyanto A, Hidayah LN, Marsela K, Haykal MF, Fathah AL, Putri BM, Supriyadi, Luthfi OM, Pratiwi DC. 2024. Environmental determinants of reef fish community structure in Sempu Strait, East Java, Indonesia. Biodiversitas 25: 4781-4789. The Rumah Apung located in Sempu Strait, Malang District, East Java, Indonesia, is home to diverse coral reef ecosystems that provide vital ecological services and support local livelihoods. However, these ecosystems face significant threats from both natural environmental changes and anthropogenic activities. Understanding how environmental factors influence reef fish communities is critical to inform effective conservation strategies. This study investigated the influence of environmental factors on the community structure of coral reef fish in the Sempu Strait waters, East Java, using Underwater Visual Census (UVC) and Principal Component Analysis (PCA). Conducted from August 2023 to May 2024 at the Sempu Strait Floating House Station, this study aimed to assess the impact of water quality, substrate type, and food availability on the diversity and abundance of coral reef fish. The main results revealed a significant correlation between the community structure of coral reef fish and environmental variables such as water clarity, salinity (r = 0.65, p<0.01), pH (r = 0.55, p<0.05), dissolved oxygen (r = 0.70, p<0.01), and sediment type. Seasonal variations significantly affected water quality, with cold nutrient-rich water during the east monsoon increasing fish biomass by about 30%. Human activities, especially recreational diving and fishing activities, were correlated with a 20% decline in coral reef fish populations, highlighting the anthropogenic pressure on this ecosystem. PCA provides insight into the complex interdependencies within coral reef ecosystems, illustrating how multiple environmental factors combine to influence reef fish dynamics. The study concludes that effective management and conservation strategies, such as establishing marine protected areas, implementing community-based monitoring programs, and promoting sustainable tourism practices, are essential, supported by regular environmental monitoring, are essential to maintain the biodiversity and ecological integrity of coral reefs in the Sempu Strait. These strategies should address both natural environmental changes and anthropogenic impacts to mitigate their adverse effects on coral reef ecosystem conditions.
Ethnopharmacological study of medicinal plants used on usadha rare remedies in Bali Province, Indonesia I GEDE WIDHIANTARA; I MADE WISNU ADHI PUTRA; NI KADEK DWIPAYANI LESTARI; PUTU ANGGA WIRADANA; ANAK AGUNG AYU PUTRI PERMATASARI; NI KADEK YUNITA SARI; NI PUTU LIDYA WINDARISTA; GLADYS ELIZABETH; TEGUH HARI SUCIPTO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 12 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251208

Abstract

Abstract. Widhiantara IG, Putra IMWA, Lestari NKD, Wiradana PA, Permatasari AAAP, Sari NKY, Windarista NPL, Elizabeth G, Sucipto TH. 2024. Ethnopharmacological study of medicinal plants used on usadha rare remedies in Bali Province, Indonesia. Biodiversitas 25: 4723-4736. Lontar usadha rare is an inventory of ancient manuscripts on traditional Balinese medicine, with a focus on the system of treating disorders in children. This manuscript presents various information about various types of medicinal plants, formulation methods, and application by the Balinese people for hundreds of years. However, most of the knowledge contained in the lontar is only known to traditional medical practitioners and includes behaviors that are typical of the usage of medicinal plants. This study aimed to examine and document the diversity of medicinal plants used in usadha rare in Bali Province, Indonesia. Data were collected through direct interviews conducted with traditional medical practitioners selected using a purposive sampling method. This study was conducted from May to September 2024, and data that was successfully collected included the type of plant, regional name, Latin name, parts used, method of application, and diseases treated. Data collected were analyzed subjectively and quantitatively using diagrams, graphs, and tables, and then the Use Value (UV) was used to assess the results. The results showed that there were 65 types of medicinal plants from 34 families successfully identified in usadha rare treatment. Plant families most frequently used by traditional medical practitioners include Zingiberaceae (12.31%), Asteraceae (7.69%), as well as Apiaceae, Apocynaceae, Euphorbiaceae, Menispermaceae, Piperaceae, and Rubiaceae, each with 4.62%. In most cases, leaves were more widely used, followed by fruits, bark, rhizomes, and flowers. Boiling and pounding were the basic methods in making preparations from medicinal plants, while topical external use was the most common way of administering medicine to infants and children. Medicinal plants were often used to treat fever, diarrhea, bloating, and body warming, relieve coughs and toothaches, and heal wounds in children.
Diversity of bioactive compounds from Parmotrema xanthinum as antimicrobial potential through in-vitro and in-silico assessment OKY KUSUMA ATNI; ERMAN MUNIR; NURSAHARA PASARIBU
Biodiversitas Journal of Biological Diversity Vol. 25 No. 11 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251143

Abstract

Abstract. Atni OK, Munir E, Pasaribu N. 2024. Diversity of bioactive compounds from Parmotrema xanthinum as antimicrobial potential through in-vitro and in-silico assessment. Biodiversitas 25: 4438-4449. Lichens, integral to ecosystem diversity, are known for producing bioactive secondary metabolites with significant pharmacological applications, particularly in antimicrobial therapies. This study evaluates the antimicrobial potential of Parmotrema xanthinum through in vitro and in silico approaches, emphasizing its role in biodiversity and drug discovery. Methanol extracts of P. xanthinum were tested against Gram-negative and Gram-positive bacteria, as well as pathogenic yeast, using the disc diffusion method. The extracts exhibited notable antimicrobial activity, particularly against Escherichia coli (18.6 ± 0.44 mm) and Salmonella enterica serovar Typhi (15.8 ± 0.25 mm). Gas chromatography-mass spectrometry (GC-MS) analysis identified 29 bioactive compounds, evaluated for drug-likeness using Lipinski's rule of five and biological activity predictions. Molecular docking studies with penicillin-binding protein 3 (PBP3) of Pseudomonas aeruginosa (PDB ID: 6I1E) revealed strong binding affinities. Notably, benzenepropanoic acid, ?-(2,5-dioxopyrrolo)-, exhibited a binding energy of -5.9 kcal/mol, while 2,2,3,3-tetramethylcyclopropanoic acid, phenyl ester, showed -5.2 kcal/mol. These findings highlight P. xanthinum as a valuable source of bioactive compounds with potential for combating bacterial resistance. Further investigations into its bioactive mechanisms, pharmacodynamics, and safety profiles are recommended to advance its development as a viable candidate for antimicrobial drug discovery.
Implication of microplastic presence in sediment and blood clams Anadara granosa (Mollusca: Bivalvia) in the Musi Estuary, Indonesia M. AKBAR RAHMAN; ROZIRWAN ROZIRWAN; WIKE EKA AYU PUTRI; GUSTI DIANSYAH; MELKI MELKI; ICA DELYA; REDHO YOGA NUGROHO
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/d260422

Abstract

Abstract. Rahman MA, Rozirwan, Putri WEA, Diansyah G, Melki, Delya I, Nugroho RY. 2025. Implication of microplastic presence in sediment and blood clams Anadara granosa (Mollusca: Bivalvia) in the Musi Estuary, Indonesia. Biodiversitas 26: 1720-1733. Microplastic pollution poses a serious risk to estuarine ecosystems, affecting sediments and benthic species. Blood clams Anadara granosa represent a significant commercial seafood product in Indonesia, including those from the Musi Estuary. This study investigated the risks associated with microplastic contamination in sediments and A. granosa in the Musi Estuary, located in South Sumatra, Indonesia. Sediment samples were extracted using sodium chloride (NaCl, 1.2 g cm-3) and hydrogen peroxide (30% H2O2). In contrast, A. granosa samples were digested with 10% KOH for microplastic extraction. The abundance and shape of microplastics were analyzed from both samples. Pollution risk assessment was conducted through the calculation of the Pollution Load Index (PLI), Nemerow Pollution Index (NPI), and Bioconcentration Factor (BCF). The results revealed the presence of microplastics in sediments, with a mean abundance of 1.31±0.41 particles/g dw, while in A. granosa, it was 21.05±10.31 particles/ind. Both samples exhibited high microplastic bioaccumulation (NPI>2), although the pollution load remained relatively low (minor category, PLI<10). The bioconcentration factor between A. granosa and sediment was determined to be 23.28, indicating that the A. granosa absorbed microplastics present in the sediment. These findings highlight the significant bioaccumulation potential of microplastics in A. granosa within the Musi Estuary. The local community and government need to establish mitigations for future microplastic management efforts.
Construction of a CRISPR/Cas9-mediated genome editing system in manipulating OsART1 from Oryza sativa cv. Inpago 5 MIFTAHUL HUDA FENDIYANTO; EKO SETIAWAN; MENTARI PUTRI PRATAMI; IFAN RIZKY KURNIYANTO; FANDRI SOFIANA FASTANTI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 2 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260241

Abstract

Abstract. Fendiyanto MH, Setiawan E, Pratami MP, Kurniyanto IR, Fastanti FS. 2025. Construction of a CRISPR/Cas9-mediated genome editing system in manipulating OsART1 from Oryza sativa cv. Inpago 5. Biodiversitas 26: 920-927. Understanding the mechanism of aluminum (Al) tolerance in rice (Oryza sativa) cv. Inpago 5 can be done by mutating the ART1 gene to see which Al tolerance genes have decreased expression globally. This study aimed to construct a pRGEB32 vector containing sgRNA-ART1 derived from rice cv. Inpago 5. The construction of the pRGEB32-sgART1 vector was carried out by designing sgRNA, restriction-ligation, transformation, plasmid isolation, verification of target inserts, and sequencing of sgRNA-ART1. The results indicate that the construction of the recombinant vector pRGEB32-sgRNAART1 was carried out by combining digestion and ligase reactions. The construction of the recombinant pRGEB32 construction showed a high level of success in this study. The success of the ART1 sgRNA amplicon in recombinant Escherichia coli indicated this. Annotation studies showed that the pRGEB32 cassette plasmid sequence showed more than 99% homology with the recombinant pRGEB32-sgART1 sequence, especially only 1% was different, namely 20 bp of sgRNA that appeared different. After checking with alignment on the plasmid annotation using the MAAFT alignment method, it was found that 20 bp of ART1 sgRNA was successfully inserted into the pRGEB32-sgART1 recombinant vector. In conclusion, the construction of pRGEB32-sgART1 in this study was successful and showed the presence of a 425 bp band amplicon for the insertion from the region between M13 reverse and sgRNA-ART1.
Diversity of traditional vegetables and spices as local food security for the Gayo Tribe, Aceh, Indonesia CUT NELLY; LIA FITRIYANA; TARAHA DILLA SANTI; SAUDAH SAUDAH
Biodiversitas Journal of Biological Diversity Vol. 25 No. 12 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251206

Abstract

Abstract. Nelly C, Fitriyana L, Santi TD, Saudah. 2024. Diversity of traditional vegetables and spices as local food security for the Gayo Tribe, Aceh, Indonesia. Biodiversitas 25: 4699-4711. Food is a fundamental necessity that is essential for human sustenance. The variety of traditional vegetables and spices, harvested from forests, fields, or home gardens, is critical to local food security. This study aimed to investigate the variety and utilization of local vegetables and spices by the Gayo community in Pining Sub-district, Gayo Lues District, Aceh, Indonesia and their contribution to sustainable food security. A field survey and semi-structured interviews five villages identified 75 taxa of vegetables and spices from 36 families with Zingiberaceae being the most dominant. The findings show women, who made up 68.0% of respondents, are key knowledge holders, passing down traditional plant knowledge through daily practices. Species such as Cocos nucifera L. and Etlingera elatior (Jack) R.M.Sm. showed the highest use value and frequency, underscoring their cultural and nutritional significance. However, the Gayo community faces threats, including land-use changes and the loss of traditional knowledge among the younger generation, jeopardizing plant conservation and sustainable food systems. Strategies such as sustainable agroforestry, local seed banks, and restoring traditional knowledge are essential to preserve biodiversity and ensure local food security. This research highlights the importance of preserving the diversity of traditional vegetables and spices as key elements of food security and cultural heritage.
Antibacterial activity of phyllospheric bacteria isolated from Rhizophora mucronata against Escherichia coli and Bacillus subtilis DEBIE RIZQOH; SILVA DWI YOLANDA; ENNY NUGRAHENI; SIPRIYADI SIPRIYADI; MELLYTA ULYANDARI; RIZKY HADI WIBOWO; OKTOVIANI OKTOVIANI; ELLEN MAIDIA DJATMIKO; ANNISA AMELIA PUTRI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 1 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260121

Abstract

Abstract. Rizqoh D, Yolanda SD, Nuhraheni E, Sipriyadi, Ulyandari M, Wibowo RH, Oktoviani, Djatmiko EM, Putri AA. 2025. Antibacterial activity of phyllospheric bacteria isolated from Rhizophora mucronata against Escherichia coli and Bacillus subtilis. Biodiversitas 26: 199-210. The treatment of bacterial infection often involves the administration of antibiotics. However, the increasing use of antibiotics has led to bacterial resistance. The black mangrove Rhizophora mucronata is a vital biological resource containing bioactive compounds with potential antibacterial properties. The objective of this study was to investigate the antibacterial potential of phyllospheric bacteria from R. mucronata leaves against Escherichia coli and Bacillus subtilis. The study was carried out using descriptive experimental research. In the initial stage, phylospheric bacteria were isolated from the leaves of R. mucronata using serial dilution method. The results showed that a total of 641 colonies were isolated from R. mucronata. Out of them, 53 dominant phyllospheric bacterial isolates were identified, which exhibit regular round shape with smooth edges colonies, flat elevation, moist texture and produce yellow color pigment. Gram staining revealed 42 Gram-positive and 11 Gram-negative bacterial isolates. The antibacterial activity test showed that 10 isolates had the ability to inhibit the growth of E. coli, 6 isolates inhibited the growth of B. subtilis and 3 isolates inhibited both bactera. Among 19 isolates, three isolates, namely BF1, BF4, and BF17 showed the best antimicrobial activity. The result of phytochemical tests revealed that all the crude extracts contained alkaloid, tannins, and saponins. Gas chromatography-mass spectrometry analysis showed potential metabolites, such as: [3,4-D]pyrimidine-5,7-dione, cyclo (L-Pro-L-Val), maculosin, 2,3,4-Trihydroxybenzaldehyde (TBA), phenethyl alcohol (PEA) tryptophol, benzene ethanol and benzeneacetic acid. The present study concluded that phyllospheric bacteria produce several active compounds that can inhibit bacterial growth.
Traditional treatments for treating lengkauk disease employed by the community in the Segedong Sub-district, Mempawah District, West Kalimantan Province, Indonesia RUQIAH GANDA PUTRI PANJAITAN; DESTI RAHMADANI; HAYATUL FAJRI; DIAN AKBARINI; ZHU CAIPING
Biodiversitas Journal of Biological Diversity Vol. 26 No. 1 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260110

Abstract

Abstract. Panjaitan RGP, Rahmadani D, Fajri H, Akbarini D, Caiping Z. 2025. Traditional treatments for treating lengkauk disease employed by the community in the Segedong Sub-district, Mempawah District, West Kalimantan Province, Indonesia. Biodiversitas 26: 94-101. Lengkauk is an illness that affects children, resulting in symptoms such as weight loss, abdominal bloating, frequent fever, irritability, lethargy and weakness. Other characteristics include pale palms, soles and face, stunted growth and decreased appetite. The use of plants as traditional medicine for treating lengkauk in children in the Segedong Sub-district, Mempawah, West Kalimantan, Indonesia is still practiced by the local community, although this knowledge is primarily held by certain elderly individuals, such as local shamans and midwives. This study aimed to identify the types of plants used, the parts of the plants employed, the preparation methods and the treatment practices for managing lengkauk. A qualitative research methodology was utilized with data collection conducted through triangulation techniques including interviews, observations and documentation. The research identified six types of plants used to treat lengkauk (i) bawang merah (Allium cepa); (ii) jengkol (Archidendron jiringa); (iii) kelapa hijau (Cocos nucifera); (iv) lempuyang (Zingiber zerumbet); (v) moje (Barleria cristata); and (vi) sirih hijau). The parts of the plants used include leaves, bulbs, fruits and rhizomes. These six plants belong to different families: Acanthaceae (B. cristata), Amaryllidaceae (A. cepa), Arecaceae (C. nucifera), Fabaceae (A. jiringa), Piperaceae (P. betle) and Zingiberaceae (Z. zerumbet).

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