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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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Isolation and evaluation of the antimicrobial activity of endophytic fungi from Orthosiphon aristatus HERLAND SATRIAWAN; NIKY AFRILIA ZAIMI; ARIED ERIADI; MAI EFDI; TRINA EKAWATI TALLEI; REGINA ANDAYANI; DIAN HANDAYANI
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/d260245

Abstract

Abstract. Satriawan H, Zaimi NA, Eriadi A, Efdi M, Tallei TE, Andayani R, Handayani D. 2025. Isolation and evaluation of the antimicrobial activity of endophytic fungi from Orthosiphon aristatus. Biodiversitas 26: 963-970. Orthosiphon aristatus, known as cat's whiskers or Javanese tea in Indonesia, has been used in traditional medicine to enhance urination, treat kidney inflammation, mitigate kidney stones, regulate diabetes, address albuminuria and syphilis, alleviate rheumatism, reduce blood glucose levels, and function as an antibacterial agent. The purpose of this study was to investigate the endophytic fungal resources of Orthosiphon aristatus and evaluate its potential as a source of bioactive compounds, particularly against antibiotic-resistant pathogens like Methicillin-resistant Staphylococcus aureus (MRSA). Eleven fungal isolates were obtained from the plant’s leaves, stems, and roots. The ethyl acetate extract of isolates was subjected to comprehensive antimicrobial screening at a concentration of 5%. Three isolates-OAA1, OAA3, and OAD1-exhibited considerable antibacterial activity, with OAD1 displaying the most significant efficacy, as evidenced by a 12.57 ± 1.09 mm inhibition zone against MRSA. Nevertheless, none of the extracts could suppress the proliferation of Candida albicans. Subsequent molecular identification verified that OAD1 was Aspergillus niger. The phytochemical analysis revealed that the triterpenoid and flavonoid groups exhibited a positive reaction, whereas the alkaloid and phenol compound groups exhibited a negative response. The findings highlight the potential of endophytic fungi from O. aristatus as promising sources of novel bioactive compounds, especially for addressing antibiotic-resistant pathogens like MRSA. The identification of A. niger as a powerful antibacterial-producing organism presents promising prospects for the creation of novel pharmaceuticals, particularly regarding multidrug-resistant infections. This study emphasizes the pressing necessity for additional research to identify and characterize the specific compounds that confer antibacterial activity and to investigate their extensive therapeutic applications.
Discovery of potential alleles for iron (Fe) toxicity tolerance in rice: Phenotypic and genotypes analysis of doubled haploid lines LILI CHRISNAWATI; MIFTAHUDIN MIFTAHUDIN; DWINITA WIKAN UTAMI
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/d260233

Abstract

Abstract. Chrisnawati L, Miftahudin, Utami DW. 2025. Discovery of potential alleles for iron (Fe) toxicity tolerance in rice: Phenotypic and genotypes analysis of doubled haploid lines. Biodiversitas 26: 851-858. Tidal swamplands present a promising opportunity for expanding rice cultivation. However, iron (Fe) toxicity poses major obstacles to development. To overcome these challenges, it is crucial to develop Fe-tolerant rice genotypes and identify molecular markers, such as single nucleotide polymorphisms (SNPs). This study aimed to identify Fe-tolerant doubled haploid rice genotypes and SNP markers related to Fe toxicity tolerance. The experiment was carried out by cultivating 45 doubled haploid rice lines (BMIP 1-BMIP 33 and BMIP 39-BMIP 50), derived from reciprocal crosses between IR54/Parekaligora and Bio 110/Markuti, under Fe-toxic conditions. Phenotypic evaluations were based on the leaf bronzing symptom (LBS) score and genotype analysis was performed using high-throughput sequencing of 384 SNPs. SNPs correlated with phenotypic data were analyzed using the Tassel 2.0 software, with significance set at a p-value <0.05. The results showed that there were 12 highly Fe-tolerant and 33 lines with moderate tolerance and seven SNPs were identified in proximity to QTLs/genes associated with iron (Fe) toxicity and abiotic stress responses, namely qFETOX-2, OsIRT, OsFRO2, OsNRAMP5, and Cyclin-like F-box. Phylogenetic analysis grouped Fe-tolerant lines, including BMIP 25, BMIP 26, BMIP 46, BMIP 47, BMIP 48, BMIP 49, and BMIP 50, with Mahsuri as the positive control, showing shared genetic traits. These results provided valuable markers for breeding programs to obtain Fe-tolerant rice.
Elucidating hard coral community in tropical coral reefs of Pulau Bidong and nearby islands, South China Sea MOHMAD FUAD NUR QAMARINA; WEE HIN BOO; YU HAI PING; ZAINUDIN BACHOK; CHE DIN MOHD SAFUAN
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/d260144

Abstract

Abstract. Qamarina MFN, Boo WH, Ping YH, Bachok Z, Safuan CDM. 2025. Elucidating hard coral community in tropical coral reefs of Pulau Bidong and nearby islands, South China Sea. Biodiversitas 26: 444-457. This study investigates the intricate dynamics of hard coral communities within the tropical coral reefs of the South China Sea, a region renowned for its high marine biodiversity. Data were collected through video sampling to assess the hard coral composition around Pulau Bidong and nearby islands, analyzing variations of hard coral communities across different variables such as island, depth, habitat, and exposure. In total, 40 hard coral genera from 15 families were identified in the study area. Overall, Acropora (22.41% ± 22.17) emerged as the most prominent genus, followed by Porites (5.8% ± 10.27). Acropora dominated in leeward reefs (28.70% ± 22.84) and sandy habitats (29.11% ± 23.89), both sheltered from intense winds and currents. Porites were abundant in exposed reefs (13.69% ± 16.4) with submerged habitats (35.64% ± 8.42) and windward reefs (9.33% ± 10.47) with rocky habitats (8.17% ± 9.46), both of which are subject to higher physical disturbances. Varying local conditions significantly influence the composition of hard coral communities in these tropical reefs. These findings underscore the urgent need for conservation in disturbed reefs, as they should be protected from intense human activities to preserve hard coral diversity. The recommendation that sheltered areas, such as leeward reefs, may be more suitable for water activities and controlled human development supports the responsible utilization of Pulau Bidong and nearby islands while ensuring the long-term sustainability of the marine ecosystem. Overall, this study provides a foundational understanding of how local environmental variables affect hard coral communities in the South China Sea, a crucial insight for developing effective coral reef management strategies amid increasing pressures from climate change.
Morphology and molecular identification of the trematode Echinostoma revolutum metacercariae, as a new parasite of amphibians in Uzbekistan ELMUROD E. IKROMOV; ERKIN F. IKROMOV; HIKMET SAMI YILDIRIMHAN; NURHAN SÜMER; LAYLO AKMURADOVA; ABDURAHMON YUSUPOV; OYBEK O. AMIROV; ILHOMJON RUSTAMOV; BEKZOD USMONOV
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/d260914

Abstract

Abstract. Ikromov EE, Ikromov EF, Yildirimhan HS, Sümer N, Akmuradova L, Yusupov A, Amirov OO, Rustamov I, Usmonov B. 2025. Morphology and molecular identification of the trematode Echinostoma revolutum metacercariae, as a new parasite of amphibians in Uzbekistan. Biodiversitas 26: 4412-4423. This study examined the helminth fauna of two frog species, Pelophylax terentievi, Pelophylax sp., in eastern (Ferghana Valley: Andijan, Namangan and Ferghana) and central Uzbekistan (Bukhara, Navoi and Samarkand regions). We identified the metacercarium trematode Echinostoma revolutum, for the first time in this context, which is an intestinal parasite commonly found in various waterfowl. At the same time, we studied amphibians for the first time as new intermediate hosts of the parasite. This article discusses the morphology and molecular characteristics of E. revolutum found in the eye cavities, kidneys and body cavities of P. terentievi and Pelophylax sp. in the central and eastern geographical regions of Uzbekistan. Our analyses showed that the trematode, E. revolutum, differs morphologically from other ecomorphs in terms of body size, cyst diameter and localization. This study also provided molecular data for the genus Echinostoma in the ITS1+5.8S+ITS2 regions of ribosomal DNA, forming a well-supported clade in the phylogenetic tree. The sample we examined, E. revolutum (UZ), was in the monophyletic group together with a sample extracted from the NCBI database (E. revolutum MZ409811) and had a common ancestor. These results provide molecular evidence to support the identification of E. revolutum species in our study. In addition, our analysis showed that Echinostoma sp. MZ409812 is a sister group to E. revolutum (clade J). E. miyagavai (clade I), E. nasincovae (clade L), E. paraensei and E. maldonadoi (clade M) are the closest groups to E. revolutum. Our results contribute to the understanding of the species and genetic diversity of the genus Echinostoma and the species E. revolutum. The high infection rate (up to 14%) of the amphibians P. terentievi and Pelophylax sp. with these parasites indicates a significant biological threat, which requires enhanced monitoring and development of measures to protect waterfowl in the region, underscoring the importance of this study in preserving the ecological balance.
Isolation of lactic acid bacteria as potential probiotic candidates from the digestive tract of Gobiopterus sp. MIKKA HAKKINEN; ABDUL RAHEM FAQIH; ASEP AWALUDIN PRIHANTO; SEPTI ANITASARI
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/d260249

Abstract

Abstract. Hakkinen M, Faqih AR, Prihanto AA, Anitasari S. 2025. Isolation of lactic acid bacteria as potential probiotic candidates from the digestive tract of Gobiopterus sp. Biodiversitas 26: 1008-1017. The distinctive ecological niche presented by the volcanic Lake Ranu Grati offers a fascinating setting for the exploration of microbial diversity, with a particular focus on lactic acid bacteria (LAB), which are renowned for their advantageous characteristics and hold significant promise as potential probiotics. The fish species Gobiopterus sp., which resides within this lake, presents a compelling opportunity for the isolation of novel strains of lactic acid bacteria (LAB). The objective of this study was to isolate and characterize probiotic bacteria from the digestive system of Gobiopterus sp. and to find bacterial strains that can improve aquaculture cultivation, health, and disease resistance. This study obtained 30 bacterial isolates originating from the digestive tract of Gobiopterus sp., of which 8 isolates were Gram-positive and catalase-negative. These isolates showed the ability to tolerate acid and bile salts which were one of the properties for probiotic candidates. Antibacterial activity varied among the isolates, with some showing significant inhibition against Aeromonas hydrophila, Vibrio alginolyticus, and Vibrio harveyi. Enzyme activity test found that the selected isolates can produce protease and cellulase enzymes. The selected isolates had sufficient hydrophobicity properties ranging from 23-41% and the DNA sequencing results identified the 3 isolates as the member of genus Enterococcus. The results of this study yielded isolates that have the potential as probiotics in the field of aquaculture. Therefore, further research should be conducted for the comprehensive characterization and safety assessment required for the use of probiotic bacteria.
Chemical fingerprint of robusta coffee beans from various local clones in Tanggamus, Lampung Province, Indonesia ALVI YANI; MURHADI MURHADI; SUBEKI SUBEKI; TANTO. P. UTOMO
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/d260520

Abstract

Abstract. Yani A, Murhadi, Subeki, Utomo TP. 2025. Chemical fingerprint of robusta coffee beans from various local clones in Tanggamus, Lampung Province, Indonesia. Biodiversitas 26: 2222-2234. This research was conducted to analyze the chemical composition of dry-processed green coffee beans from several local?robusta clones, namely Randu Alas, Kasio, Komari, Kopi Hijau, and Kopi Kuning. The study was held from May to August 2024 in Way Harong Village, Lampung Province, Indonesia, with analysis done in two laboratories. The analysis included defect values, coffee quality, moisture content, yield, and density based on the Indonesian National Standard (SNI). The study was designed using a Completely Randomized Design with five treatments and three replications. Chemical fingerprints were identified using UPLC-MS/MS and MassLynx software. The results showed defect values of 14.15-29.15 (grades 2-3), yields of 19.30-21.16% (highest in Kopi Hijau and Komari), moisture content of 7.79-11.34% (lowest in Kopi Kuning), and density of 601.66-605.66 g/cm³. The chemical compositions were consistent up to Rt 7.38 minutes but varied beyond this point, with 18 compounds in Randu Alas, 20 in Kasio, 19 in Komari, 15 in Kopi Hijau, and 18 in Kopi Kuning. Overall, 10 major compounds were identified, including caffeine, chlorogenic acid, 4-aminobenzoic acid, trans-zeatin, umbelliferone, hymecromone, cynarine, (3aR,4R,5R,7aR)-4-(4-Hydroxy-3-methoxyphenyl)-1-oxo-7-[(2R,3R)-3,5,7-trihydroxy-4-oxo-3,4-dihydro-2H-chromen-2-yl]-1,3,3a,4,5,7a-hexahydro-2-benzofuran-5-carboxylic acid, benzyl 2-methyl-4-(4-nitrophenyl)-6-oxo-1,4,5,6-tetrahydro-3-pyridine carboxylate and Methyl (1R,3R)-1-(1,3-benzodioxol-5-yl)-2,3,4,9-tetrahydro-1H-?-carboline-3-carboxylate.
Investigation of endophytic bacteria associated with Paederia foetida: Population, characterization, antibacterial, and pathogenicity analysis MELDA YUNITA; MORGAN OHIWAL; JUEN CARLA WARELLA; ELPIRA ASMIN; SITI NUR AZIZAH; PRESLI GLOVRIG SIAHAYA
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/d260247

Abstract

Abstract. Yunita M, Ohiwal M, Warella JC, Azizah SN, Asmin E, Siahaya PG. 2025. Investigation of endophytic bacteria associated with Paederia foetida: Population, characterization, antibacterial, and pathogenicity analysis 26: 981-991. The aim of this study was to obtain non-pathogenic endophytic bacterial isolates that can be developed as antibacterials for further applications. Endophyte isolation was carried out in 4 different media to obtain diverse endophytes and characterized macroscopically and microscopically. Endophyte screening was done through antibacterial tests against 10 different pathogenic bacteria. Pathogenicity analysis was performed on Blood Agar Plate (BAP) to differentiate pathogenic and non-pathogenic group of endophytic bacteria. The results showed that Starch Casein Agar was the best media for isolation in terms of total population and morphological characteristics compared to the other three media. A total of 27 isolates were collected according to the different morphology. Screening through antibacterial tests revealed that 19 endophytic isolates were significantly able to inhibit various species of pathogenic bacteria (p-value of 0.001). Pathogenicity analysis showed that 8 of 19 isolates (HR1, HR2, HR3, K2, NL3, S2, A2, and A9) were categorized as ? hemolysis, while the other 11 isolates were categorized as ? hemolysis and ? hemolysis. The study concluded that 8 endophytic bacterial isolates associated with P. foetida leaves had the strong potential to be developed and can be applied in advanced antibacterial applications.
Phytochemical composition and bioactivity of Parkia timoriana leaf extract from Kediri, Indonesia in various solvent polarities ATMIRA SARIWATI; FITA SARI; VENTY SURYANTI; DESI SUCI HANDAYANI; HILDA ALFIYANI SETYONO; NINIS YULIATI
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/d251227

Abstract

Abstract. Sariwati A, Sari F, Suryanti V, Handayani DS, Setyono HA, Yuliati N. 2024. Phytochemical composition and bioactivity of Parkia timoriana leaf extract from Kediri, Indonesia in various solvent polarities. Biodiversitas 25: 4900-4908. The potential therapeutic uses of bioactive chemicals found in natural sources have led to a significant increase in focus on their investigation in recent years. Parkia timoriana (DC.) Merr. has secondary metabolites, which have been used as a traditional medicine. This work studies the phytochemical composition and bioactivities evaluation of the P. timoriana leaf extract of varying solvent polarities, such as methanol, water, ethyl acetate, and hexane. The methanol extract has the highest secondary metabolite contents, excluding terpenoids contents. The Follin-Ciocalteu method showed that the total phenolic content of methanol extract was 302.02 mg GAE/g. The aluminum chloride colorimetric method revealed that the total flavonoid content of the methanol extract was 256.85 mg QE/g. The tannin acid, alkaloids, saponins, and terpenoids contents of methanol extracts were determined by Spectrophotometer UV-Vis, which were found to be 32.07 mg TAE/g, 23.86 mg CoE/g, 18.35 mg DE/g, 5.23 mg Linalool Eq./g, and respectively. The highest terpenoid contents were found in hexane extract, which was 11.34 mg of Linalool Eq./g. Antioxidant activities of the extracts were assessed by measuring the free-radical of 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and scavenge of 2,2'-azinobis (3-ethylbenzene-thiazoline-6-sulfonic-acid (ABTS)). The methanol extract was shown to have the strongest antioxidant activity, where the DPPH and ABTS IC50 values were 47.78 and 39.54 µg/mL, respectively. The methanol extract exhibited the greatest antimicrobial activities, where the inhibition zone for Candida albicans and Escherichia coli fungus were 21 and 22 mm, respectively. Antidiabetic effects were assessed in vitro by blocking ?-amylase and ?-glucoside. The methanol extract shows an inhibition of 50.19 µg/mL for ?-glucoside and 42.50 µg/mL for ?-amylase. The secondary metabolites of P. timoriana leaf are great building blocks for making potent medications.
Diversity of diurnal birds and their ecological role in Papua’s oil palm plantation landscape, Indonesia RASYID AFFANDI; YANTO SANTOSA; ROZZA TRI KWATRINA
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/d260228

Abstract

Abstract. Affandi R, Santosa Y, Kwatrina RT. 2025. Diversity of diurnal birds and their ecological role in Papua’s oil palm plantation landscape, Indonesia. Biodiversitas 26: 799-809. Oil palm plantations significantly impact biodiversity, particularly in Indonesia, where they play a crucial economic role. However, the ecological consequences remain underexplored in Papua, especially for avian communities. This study examines bird diversity and ecological roles within Papua's oil palm agroecosystem. Observations were conducted in various land cover types in Kaureh Sub-district, Jayapura District, Papua, Indonesia, including oil palm blocks, High Conservation Value (HCV) areas, secondary forests, and shrubs. Using transect surveys, we recorded 46 bird species from 23 families, with the highest species richness in HCV areas. Bird communities contribute vital ecosystem services such as seed dispersal, pollination, and pest control. Granivorous and frugivorous species facilitate habitat regeneration, while insectivorous birds mitigate pest outbreaks, reducing the need for chemical pesticides. Raptors and carnivorous species regulate small mammal populations, enhancing ecological stability. Statistical analysis revealed significant correlations between bird abundance and environmental factors, including vegetation diversity and proximity to HCV areas. Despite their ecological importance, oil palm plantations exhibited lower species richness and evenness than natural habitats. Conservation strategies should integrate bird-friendly management practices, such as maintaining native vegetation, establishing ecological corridors, and minimizing chemical inputs. Enhancing biodiversity in oil palm landscapes can support agricultural productivity and environmental sustainability. This study underscores the need for further research and conservation efforts to balance economic gains with biodiversity preservation in Papua's oil palm agroecosystems.
Fishing area mapping and gear competition in Paiton Waters, East Java, Indonesia WAHIDA KARTIKA SARI; WAHYU PUTRI FAJAR RAHMALINDA; LEDHYANE IKA HARLYAN; ABU BAKAR SAMBAH; TAKASHI FRITZ MATSUISHI; STEVEN RUST
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/d260211

Abstract

Abstract. Sari WK, Rahmalinda WPF, Harlyan LI, Sambah AB, Matsuishi TF, Rust S. 2025. Fishing area mapping and gear competition in Paiton Waters, East Java, Indonesia. Biodiversitas 26: 636-650. Fisheries in the northern waters of Java Island, Indonesia, particularly in East Java, exhibit high complexity, requiring comprehensive management to effectively address multiple challenges. However, this complexity requires simplification of contributing variables to facilitate sustainable management. One potential solution is spatial clustering. This study aims to analyze species diversity, identify the distribution of fishing gear, cluster areas and fishing gear, and assess indications of competition between fishing gear operating at the Paiton Fish Landing Base (PPI). This study used the Hierarchical Cluster Analysis (HCA) method. The results showed that species diversity in Paiton waters was categorized as moderate (0.00-1.52), with species richness categorized as low (0.00-0.72). Spatial clustering identified two clusters of fishing areas and one cluster of different fishing gears. Fishing areas near the harbor and close to Madura Island are dominated by Indian scad Decapterus russelli, while the central part of the Madura Strait is dominated by Bullet tuna Auxis rochei. Gear groupings showed competition between gillnets and driftnets, both of which target Savalai hairtail Lepturacanthus savala. This research contributes to fisheries management by providing insights into the spatial distribution and competition of fishing activities, supporting better resource allocation and sustainable practices in the region.

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