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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 detection of Dorylaimus stagnalis (Durjan, 1845), in the rhizosphere of soybean plants in Jember District, Indonesia ANKARDIANSYAH PANDU PRADANA; ZIDNA NURUL IZZATIKA; HARDIAN SUSILO ADDY
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/d260440

Abstract

Abstract. Pradana AP, Izzatika ZN, Addy HS. 2025. Molecular detection of Dorylaimus stagnalis (Durjan, 1845), in the rhizosphere of soybean plants in Jember District, Indonesia. Biodiversitas 26: 1913-1919. Nematodes, members of the phylum Nematoda, are ubiquitous soil organisms whose community composition provides critical insights into soil health and ecosystem function. The genus Dorylaimus is of particular ecological interest due to its adaptability and role in nutrient cycling within diverse terrestrial environments. This study documents the first molecular and morphometric confirmation of Dorylaimus stagnalis (Dujardin, 1845), in the rhizosphere of soybean (Glycine max) in Jember District, Indonesia. Soil samples were systematically collected from 15 distinct sites within soybean fields using a standardized protocol, and nematodes were extracted via the Whitehead tray method. Detailed morphological observations were made using an Olympus BX50 light microscope, and morphometric measurements were obtained following De Man’s ratios, which collectively confirmed diagnostic features consistent with D. stagnalis as reported in previous studies. Molecular characterization was performed by PCR amplification of the 28S-D2D3 region followed by Sanger sequencing. Subsequent phylogenetic analysis revealed 94% sequence similarity to established reference sequences (AY592994.1 and AY592995.1) and a low genetic distance of 0.1058, thereby substantiating the taxonomic identity of the specimens. This study’s integrative approach not only verifies the presence of D. stagnalis in Indonesia but also indicates subtle morphometric variations potentially attributable to local environmental pressures. Its findings expand the current understanding of nematode biodiversity in Indonesian agroecosystems and provide a framework for future research on sustainable soil management practices.
Influence of extraction techniques on the phytochemical contents and antioxidant properties of Pometia pinnata seed extracts POPI PATILAYA; IMAM BAGUS SUMANTRI
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/d260744

Abstract

Abstract. Patilaya P, Sumantri IB. 2025. Influence of extraction techniques on the phytochemical contents and antioxidant properties of Pometia pinnata seed extracts. Biodiversitas 26: 3582-3589. Matoa (Pometia pinnata) seeds contain phytochemicals with vigorous antioxidant activity. However, their antioxidant activity may be affected by extraction techniques. Here, we report the impacts of extraction techniques on the chemical constituents and antioxidant properties of P. pinnata seed extracts. The plant seeds were collected in Medan (Indonesia) in January 2020. The seed extracts, obtained by maceration and Soxhlation, were evaluated for their phytochemicals and antioxidant properties. GraphPad Prism 10 was used to analyze the data, with one-way ANOVA and Tukey’s tests at a 5% significance level. The results demonstrated that the extraction yields of P. pinnata seeds obtained by maceration (10.41-38.63%) were slightly lower than those by soxhlation (15.95-49.78%). The total phenolic contents of extracts obtained by maceration (EM) and soxhlation (ES) were 25.29-46.88 mg g-1 and 46.46-93.26 mg g-1, respectively. The total flavonoid contents of EM and ES were 0.90-11.77 mg g-1 and 3.25-20.78 mg g-1, respectively. In the antioxidant assay, IC50 values of EM and ES were 63.95-1035.14 µg mL-1 and 37.25-102.02 µg mL-1, respectively. The results suggest that soxhlation was more effective than maceration, yielding higher phytochemical contents and antioxidant properties of P. pinnata seed extracts.
Adaptive leaf morphology and anatomy of Rhizophora apiculata under environmental gradients in Tulic, Argao, Cebu, Philippines with implications for conservation TRICIA JOY JARAPAN; MILLISCENT FLORES; DIANA ROSE CUIZON; CHRISTINE MAE ROBLE; AARON NIÑO LANANTE; DEXTER YBURAN; CHARIZ NIÑA ENAL; MEKHAILA EMNACEN; SYLVESTER T. CORTES; JOSEPH JOEL N. ALMAGRO; ZERRY AYN Z. RETUBADO; ANNE S. LORCA
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/d260640

Abstract

Abstract. Jarapan TJ, Flores M, Cuizon DR, Roble CM, Lanante AN, Yburan D, Enal CN, Emnacen M, Cortes ST, Almagro JJN, Retubado ZAZ, Lorca AS. 2025. Adaptive leaf morphology and anatomy of Rhizophora apiculata under environmental gradients in Tulic, Argao, Cebu, Philippines with implications for conservation. Biodiversitas 26: 2978-2991. Mangrove forests provide critical ecosystem services, including coastal protection, biodiversity conservation, and carbon sequestration. However, they are increasingly threatened by environmental stressors, such as salinity fluctuations, habitat degradation, and climate change. Understanding species-specific adaptive responses to these stressors is essential for developing effective conservation strategies. This study investigated how coastal gradients and canopy light zones influence the morphological and anatomical leaf traits of Rhizophora apiculata in Tulic, Argao, Cebu, Philippines. A total of five quadrats of 5x5 m were placed in each of the landward, midward, and seaward zones. In each zone, environmental parameters including soil salinity, pH, and light intensity were recorded. Leaf samples were collected and analyzed for length, width, and anatomical features using the nail polish and potato impression method. Results demonstrated pronounced leaf plasticity in seaward individuals, with significant variations in width-related traits, while landward individuals exhibited limited morphological flexibility. The middle canopy zone showed strong adaptation to variable light conditions, with spongy mesophyll development and petiole length contributing notably to physiological performance. These findings suggest the role of leaf trait plasticity in enhancing the resilience of R. apiculata to changing environmental conditions. Incorporating trait-based approaches into mangrove conservation and restoration planning can strengthen ecosystem stability and sustain the protective and ecological functions of mangrove forests under different stressors.
Selection of Ficus spp. species for rehabilitation of degraded land in Kuningan District, West Java, Indonesia YAYAN HENDRAYANA; ILHAM ADHYA; DEDE KOSASIH; IMAM WIDHIONO; FAWAZ FAUZI ALFAHRI; INDRI SIGI APRIANTIKA; SURYA VAINES
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/d260711

Abstract

Abstract. Hendrayana Y, Adhya I, Kosasih D, Widhiono I, Alfahri FF, Apriantika IS, Vaines S. 2025. Selection of Ficus spp. species for rehabilitation of degraded land in Kuningan District, West Java, Indonesia. Biodiversitas 26: 3199-3208. Land degradation is an environmental problem caused by various factors, including unsustainable land use, deforestation, and harmful agricultural practices. An effective method to overcome this problem is through land rehabilitation by replanting trees in the degraded areas. Therefore, this study aimed to select Ficus tree species for the rehabilitation of critical lands in Kuningan District, West Java, Indonesia. Data was collected using a field survey by making observation plots to document the presence of Ficus tree species in three land use types in the district, namely sand excavation area (Cidahu, Ciawigebang, and Japara Sub-districts), community gardens (Ciniru, and Hantara Sub-districts), and secondary forests (Selajambe, Subang, Cilebak Sub-districts). Vegetation analysis was conducted to calculate the importance value index and species similarity index. The results showed that there were 16 Ficus tree species across the surveyed locations with six species were found simultaneously in all three land uses, including F. benjamina, F. fistulosa, F. septic, F. variegata, F. ampelas, F. virens var. glabella. Other species included F. annulata, F. callosa, F. elastica, F. fulva, F. gibbosa, F. hispida, F. microcarpa, F. racemosa, F. sinuata, and F. subulata. Thus, the six species are recommended for the rehabilitation of degraded lands in Kuningan District.
Collembola diversity across three successional stages in a reclaimed tropical mining tailing site, Central Papua, Indonesia SRIHARTATI HARTO; MUSYAFA MUSYAFA; SUMARDI SUMARDI; SURYO HARDIWINOTO; RISANDIKA ASTANOVIA DEWI; PRAKTITA PURADYATMIKA; ROBERTH SARWOM
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/d260519

Abstract

Abstract. Harto S, Musyafa, Sumardi, Hardiwinoto S, Dewi RA, Puradyatmika P, Sarwom R. 2025. Collembola diversity across three successional stages in a reclaimed tropical mining tailing site, Central Papua, Indonesia. Biodiversitas 26: 2210-2220. Reclamation of tailing-impacted land by PT Freeport Indonesia aims to mitigate soil degradation and restore the underground microfauna ecosystem. Collembolas are utilized as bioindicators to evaluate reclamation success. This study investigated Collembola diversity across three reclamation stages (10, 14, and 21 years) and natural forest, along with their relationships to soil fertility and heavy metal contamination. Sampling was conducted across three soil types and three litter types, totaling 840 sample plots, using a modified Berlese funnel extraction. According to the Shannon-Wiener Diversity Index, Collembola diversity was classified as high in natural forests and 21-year-old reclaimed areas and moderate in 14- and 10-year-old areas. Canonical Correspondence Analysis (CCA) showed that organic matter, carbon, and phosphorus were key factors influencing Collembola's presence. Metal analysis indicated associations between Entomobryidae and Poduridae with lead (Pb) in the oldest reclaimed site, while Neanuridae correlated with mercury (Hg) in the 14-year site. Collembola's diversity and species richness increased with the reclamation age, highlighting the importance of reclamation duration in supporting ecosystem recovery. These findings emphasize the value of long-term reclamation in enhancing soil microfauna communities, improving soil fertility, and guiding sustainable land management in post-mining landscapes.
Genome mining, metabolite fractionation, and evaluation of antibiofilm activity of endophytic Priestia megaterium AJ5 against methicillin-resistant Staphylococcus aureus JEPRI AGUNG PRIYANTO; GENIA SOTYA SINARAWADI; MUHAMMAD EKA PRASTYA; ORHINTA MUTIARA JATI; NISA RACHMANIA; ZETRYANA PUTERI TACHRIM
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/d260634

Abstract

Abstract. Priyanto JA, Sinarawadi GS, Prastya ME, Jati OM, Rachmania N, Tachrim ZP. 2025. Genome mining, metabolite fractionation, and evaluation of antibiofilm activity of endophytic Priestia megaterium AJ5 against Methicillin-resistant Staphylococcus aureus. Biodiversitas 26: 2916-2925. Endophytic bacteria, particularly Priestia megaterium, are a source of secondary metabolites that are valuable for medicinal purposes. Therefore, this study aimed to mine the Secondary Metabolite Gene Clusters (SMGCs) within the complete genome of AJ5 strain, fractionate its secondary metabolites, and evaluate its antibiofilm activity against Methicillin-Resistant Staphylococcus aureus (MRSA). The bacterium had a complete genome length of 5,750,510 bp and was closely related to P. megaterium NCTC10342, with an Average Nucleotide Identity (ANI) of 98.37%. AntiSMASH analysis showed that the bacterium possessed 5 types of SMGCs, including Non-Ribosomal Peptide Synthetase (NRPS)-Independent (NI) siderophores, 3 types of terpenes, and type III Polyketide Synthase (PKS). In addition, 2 selected fractions obtained from thin-layer chromatography and column chromatography procedures exhibited strong anti-MRSA activity. F9 and F12 fractions had Minimum Inhibitory Concentrations (MIC) of 117.5 ?g/mL and 180 ?g/mL, respectively. Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) analysis indicated that these 2 fractions contained nigakilactone H, tetratriacontanamine, 2-(p-Anisyl)-5-methyl-1-hexene, and other unidentified compounds. The compounds were also capable of suppressing biofilm formation of MRSA by up to 81.54%±1.80 for the F9 and 77.01%±1.96 for F12 fraction after treatment with 1×MIC. All selected fractions also exhibited eradication activity against established MRSA biofilms up to 79.23±1.96%. In conclusion, this study showed the SMGCs profile and their metabolite products found within the genome of AJ5 strain, as well as its antibiofilm potential against MRSA. The thoroughness of our research process and the validity of our findings suggest that genome-based screening and in vitro assays could significantly accelerate the development of novel anti-MRSA agents.
Evaluation of the potential of starter culture from Indonesian kefir grains on the characteristics of fermented milk during storage PUTRI DIAN WULANSARI; NOVIA RAHAYU; ANDRI KUSMAYADI; RIO JATI KUSUMA
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/d260533

Abstract

Abstract. Wulansari PD, Rahayu N, Kusmayadi A, Kusuma RJ. 2025. Evaluation of the potential of starter culture from Indonesian kefir grains on the characteristics of fermented milk during storage. Biodiversitas 26: 2368-2374. This study aims to evaluate the physicochemical quality of fermented milk produced using starter cultures derived from Indonesian kefir grains that were subcultured in goat's milk. Cow's milk was used as the raw material. The starter cultures consisted of a single strain: Lactobacillus plantarum (Orla-Jensen, 1919) Bergey et al., 1923 strains BP and DI, and Lactiplantibacillus plantarum A strain ES. Fermentation was carried out by inoculating the pasteurized milk with the cultures, followed by storage at 4°C for up to 20 days. The parameters observed during storage included pH value, total Lactic Acid Bacteria (LAB), Free Fatty Acid (FFA), acidity, and moisture content. The results showed that both the type of starter culture and the storage duration significantly affected all measured parameters. Lactobacillus plantarum strain DI produced fermented milk with the lowest pH value, and this value decreased over time. The total LAB count increased in samples inoculated with strain BP and DI but slightly decreased in strain ES during storage. FFA levels increased for all strains over time; acidity rose in samples with strains BP and DI but decreased in samples with strain ES; moisture content declined across all samples during storage. This study confirms that starter cultures derived from Indonesian kefir grains, when combined with appropriate storage conditions, significantly influence the physicochemical quality of fermented milk.
Residual stand damage caused by logging operations in secondary forest in Berau District, East Kalimantan, Indonesia YOSEP RUSLIM; DIAH RAKHMAH SARI; ROCHADI KRISTININGRUM; EMI PURWANTI; WIDIA SRI UTAMI; SELAMET ASHARI; FENTY LEONIKA
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/d260513

Abstract

Abstract. Ruslim Y, Sari DR, Kristiningrum R, Purwanti E, Utami WS, Ashari S, Leonika F. 2025. Residual stand damage caused by logging operations in secondary forest in Berau District, East Kalimantan, Indonesia. Biodiversitas 26: 2148-2156. In Indonesia, selective logging now mainly occurs on logged-over forests following the second rotation. Yet, information is lacking on the impacts of logging operation in these secondary forests. This study aims to determine the impacts of logging operations, particularly tree felling and log skidding, on residual stands in secondary forest and to see the relationship between felling intensity and stand damage and forest opening. This study was conducted in a logging concession in Berau District, East Kalimantan Province, Indonesia. To determine changes in stand structure before and after harvesting, 6 plots of 100x100 m were established. After felling and skidding, an inventory was conducted to record the number of damaged trees and the type of damage. The result revealed that with harvesting intensity averaged 11 trees per hectare, it caused residual stand damage due to felling and skidding of 17.85% and 16.62%, respectively. The most common type of damage after tree felling was broken trees, with an average of 19 trees ha-1, and the main damage during the skidding process was collapsed/tilted trees, with an average of 28 trees ha-1. In addition, it was found that the average opening of skid roads after the harvesting process was 13.26%. We suggest mitigation strategies including planning the skid road before harvesting, opening the skid road before felling, limiting the number of trees felled per hectare, implementing directional felling, and extending the maximum winching.
Genetic characterization of butterfly pea (Clitoria ternatea) with different flower colors and petal types using SRAP markers SUSANTI INDRIYA WATI; SAMANHUDI SAMANHUDI; ENDANG YUNIASTUTI; EDI PURWANTO
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/d260806

Abstract

Abstract. Wati SI, Samanhudi S, Yuniastuti E, Purwanto E. 2025. Genetic characterization of butterfly pea (Clitoria ternatea) with different flower colors and petal types using SRAP markers. Biodiversitas 26: 3722-3730. The butterfly pea (Clitoria ternatea) is an essential medicinal and ornamental plant in Indonesia, known for its diverse petal colors and forms. This study aimed to assess genetic diversity among eight C. ternatea accessions with varying flower colors and petal types using 10 SRAP primer combinations. The 114 DNA bands were amplified, and the average degree of polymorphism across all primer combinations was 87.12%. Two primer combinations (Me3Em3 and Me4Em4) displayed 100% polymorphism. The markers showed an average Polymorphic Information Content (PIC) of 0.31, while the mean Resolving Power (RP) and Marker Index (MI) were 5.50 and 3.24, respectively. The genetic relationships using UPGMA and PCoA revealed two main groups: Cluster 1, which included 1U (purple flower, single petal), 1Pn (pink flower, single petal), 2U (purple flower, double petal), and 2Pn (pink flower, double petal), and Cluster 2, which included 1B (blue flower, single petal), 1Pt (white flower, single petal), 2B (blue flower, double petal), and 2Pt (white flower, double petal). STRUCTURE analysis revealed a more precise genetic separation, with accessions 1U, 1B, 1Pn, and 1Pt clustered in Cluster 1, and 2U, 2B, 2Pn, and 2Pt clustered in Cluster 2. These findings are not only important for breeding programs, but also for conservation strategies. They provide valuable insights that can guide efforts to preserve the genetic diversity of C. ternatea, highlighting the crucial role of this research in the broader context of plant conservation.
Comparative analysis reveals distinct floral scent patterns in three Durio species CHUAH YEAN MAE; NUR FARIZA M. SHAIPULAH; MOHAMED NOR ZALIPAH
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/d260705

Abstract

Abstract. Mae CY, Shaipulah NFM, Zalipah MN. 2025. Comparative analysis reveals distinct floral scent patterns in three Durio species. Biodiversitas 26: 3136-3143. The floral scents of three durian species were collected using the dynamic headspace method and analyzed by Gas Chromatography-Mass Spectrometry (GC-MS). A total of 52 volatile compounds from nine different chemical classes were detected from Durio zibethinus, D. lowianus, and D. graveolens flowers. The floral profiles of D. zibethinus were dominated by alkanes and sesquiterpenes, whereas those of D. lowianus and D. graveolens were dominated by triterpenes and sesquiterpenes, respectively. The hexane eluates extracted more sesquiterpenes than hexane:ethyl acetate eluates. In D. zibethinus flowers, squalene was identified as the predominant volatile compound in hexane extracts, while ?-caryophyllene dominated in hexane:ethyl acetate extracts. Squalene was the primary volatile component in hexane extracts of D. lowianus flowers, whereas (E,E)-?-farnesene predominated in the hexane:ethyl acetate fraction. (E,E)-?-farnesene was the dominant volatile compound emitted from D. graveolens flowers, prevailing in both hexane and hexane:ethyl acetate extracts. Sulfur-containing compounds were absent from all three species. The diverse terpene composition, bright red petals, and extended flowering period of D. lowianus suggest a generalist strategy targeting multiple pollinator groups across both day and night. This study revealed different pollination strategies among three durian species through their distinct floral volatile profiles, highlighting the intricate and multifaceted nature of plant-pollinator relationships in tropical ecosystems.

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