Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb <p dir="ltr"><em>Journal of Tropical Biodiversity and Biotechnology (JTBB)&nbsp;</em>is an open-access, peer-reviewed journal dedicated to the publication of novel research concerned with the advancement of tropical biology studies in the Southeast Asia Region.&nbsp; It publishes original research articles, short communication, and reviews on the following subjects: 1. Studies on Biodiversity; 2. Ecological Studies; and 3. Biotechnology.</p> en-US m.ilmi@ugm.ac.id (Miftahul Ilmi) jtbb.biologi@ugm.ac.id (Salwa Shabria Wafi) Thu, 09 Jan 2025 00:00:00 +0700 OJS 3.1.2.0 http://blogs.law.harvard.edu/tech/rss 60 Understanding The Current Knowledge and Potential Research of Indonesia's Only Protected Amphibian: The Bleeding Toad (Leptophryne cruentata) https://journal.ugm.ac.id/v3/jtbb/article/view/12477 <p>Globally, amphibian populations are facing a substantial decline attributed to environmental degradation and lack of public attention. Indonesia, which one of countries with the high number of amphibian species in the world, paradoxically holds the record for the highest number of data-deficient amphibians. Indonesia currently has only one protected species, the bleeding toad (<em>Leptophryne cruentata</em>) also categorized as Critically Endangered. Considering this, our study undertakes a comprehensive review of bleeding toad research, highlighting research gaps and identifying potential topics for future investigations. In this study, we used an electronic database to acquire relevant studies aligned with our research objectives. The literature collection process involved the utilisation of the Publish or Perish (PoP) and manual internet searches. Our documentation reveals limited literature on bleeding toads, comprising only 20 reviews, with a notable prevalence of grey literature. This underscores the critical endangerment of bleeding toads, coupled with their neglect in research endeavours. Furthermore, our examination presents limited information on crucial aspects, such as taxonomy, morphology, geographical distribution, habitat characteristics, encounter records, behaviour, protection status, threats, and bioprospecting. The research gap is exceptionally high, with only two out of the 11 research topics attaining sufficient research status. Our findings underscore the urgent need for further research in this area. We identified at least 18 potential research areas that were essential for completing the baseline data. These findings serve as a valuable resource for researchers and policymakers seeking to address the critical endangerment of bleeding toads and to formulate effective conservation strategies.</p> Rizki Kurnia Tohir, Mirza Dikari Kusrini, Ani Mardiastuti, Dede Aulia Rahman Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12477 Thu, 09 Jan 2025 00:00:00 +0700 Antifeedant Activity of Limonoids from the Seeds of Lansium domesticum Corr. Against Subterranean Termite Coptotermes curvignathus https://journal.ugm.ac.id/v3/jtbb/article/view/11823 <p><em>Lansium domesticum</em> is one of <em>Meliaceae</em> plants produces limonoids with various biological activities, except for anti termites. Seven limonoids, dukunolides A-D (DA-DD), F (DF), and langsatides A-B (LA and LB), each previously isolated from the seeds of <em>L</em>.<em> domesticum</em> and prepared at 5 %, together with methanol root extract (MRE) 5 % were evaluated for insecticidal activity against <em>Coptotermes curvignathus</em>. Fifty workers and five soldiers of <em>C</em>.<em> curvignathus</em> were tested in a No-Choice Test to determine which limonoid was the most active. Dukunolides A-D, F, langsatides A-B, and MRE showed weaker antifeedant activity than the regent 50sc (positive standart, 8.04 %), except for dukunolide B (DB) that was stronger antifeedant activity, with a 7.28 % paper weight loss and 33.3 % mortality against <em>C. curvignathus</em>. Conclusion, this study showed limonoid compounds that were isolated from the seeds of <em>L. domesticum</em> could be developed for antitermite drugs.</p> Rudiyansyah, Eka Pebri Malinda, Andi Hairil Alimuddin, Ajuk Sapar, Yuliati indrayani Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/11823 Fri, 10 Jan 2025 00:00:00 +0700 Enhanced Antibacterial Potential of Fractionated Bioactive Compounds Isolated from Endophytic Nigrospora oryzae UILRZ1 in Ocimum gratissimum https://journal.ugm.ac.id/v3/jtbb/article/view/12019 <p>The recurring global health challenges due to antimicrobial resistance require an impulsive response to search for alternative drugs with strong activities against multidrug-resistant pathogens. This study evaluated and screened endophytic fungi of strong antibacterial potential from <em>Moringa oleifera</em> and <em>Ocimum gratissimum</em>. Primer pairs of ribosomal DNA's internally transcribed spacer regions (ITS1 and ITS4) were used to determine their evolutionary relationships. A principal component analysis (PCA) biplot was used to identify the most effective endophyte at a 95% confidence level (P˂0.05).&nbsp; Improved culture conditions for the production of bioactive metabolites was done using the Taguchi design of experiment. Considering PCA biplot analysis, <em>Nigrospora oryzae</em> UILRZ1 from <em>Ocimum gratissimum</em> was most effective against selected pathogens. Production of metabolites was optimum at pH 5, 0.3 % (w/v) protein, 6-day inoculation time, and 4-plug inoculum, while variable of highest contribution was percentage of protein used. The column and thin layer chromatography were used to fractionate the extracts after optimization of production conditions while GCMS analysis was adopted to identify the chemical compounds. The crude extract's minimum inhibitory concentration (MIC) for chosen test microorganisms was 256 μg/mL prior optimization; while fractions of partially purified optimized extract of <em>Nigrospora oryzae</em> UILRZ1 showed enhanced antibacterial activity against <em>Staphylococcus aureus</em> with a MIC of 64 μg/mL. Efficient synthesis of bioactive metabolites was significant in the enhanced antibacterial activity against <em>S. aureus.</em></p> Rahmat Folashade Zakariyah, Risikat Nike Ahmed, Kamoldeen Abiodun Ajijolakewu, Abdulmumeen Amao Hamid Copyright (c) 2024 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12019 Fri, 10 Jan 2025 00:00:00 +0700 The Distribution and Behaviour of Lesser Whistling-Duck (Dendrocygna javanica) at Lang Sen Ramsar site in Mekong Delta Vietnam https://journal.ugm.ac.id/v3/jtbb/article/view/11957 <p>This study aimed to investigate the distribution, behaviour, potential food, competitor, and potential predator of Lesser Whistling-Duck (<em>Dendrocygna javanica</em>) by direct observations at six sub-zones in the Lang Sen Ramsar site in the south of Vietnam, from September 2021 to August 2022. Two hundred sixty nine (269) individuals of the <em>D. javanica</em> were seen on site mainly in pairs and small flocks. The survey showed that Lesser Whistling-Duck often appears in areas with water lettuce and duckweed at sub-zone 9, wild rice and lotus fields at sub-zone 12, and low water level fluctuation at sub-zone 5 in the early morning and late afternoon. The food source of Lesser Whistling-Duck in the reserve Lang Sen are mainly plants (duckweed, water lettuce, young shoots or seeds of lotus, water lily, water hyacinth, and wild rice) and small animals (snail, worm, shrimp, fish, and insect). This bird species is relatively sensitive to environmental influences and their ability to perceive, reflect, and make sound depends on the size of flocks<strong>.</strong> The carnivores often damage the Lesser Whistling-Duck including black kite, greater coucal, lesser coucal, and python. They are also affected by competition for food and habitat of other waterbirds, activities of tourists, and people around the reserve. The result of observation of Lesser Whistling-Duck is a concern from new area, so it added the information on the distribution of the species, including behaviour, the potential food, competitors, predators, and human threats, which are important in managing the species.</p> <p>&nbsp;</p> Le Diem Kieu, Nguyen Thanh Lam, Pham Quoc Nguyen, Nguyen Thanh Giao Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/11957 Mon, 13 Jan 2025 00:00:00 +0700 Biodegradable Sheets from Dried Mycelia of Edible Mushrooms https://journal.ugm.ac.id/v3/jtbb/article/view/14001 <p>Due to its quick growth and biodegradability, mushroom mycelium has been used to create alternative materials. This study aimed to produce mycelium sheets from market-purchased edible mushrooms (<em>Lentinus </em>sp. and <em>Pleurotus</em> sp.). They were isolated and cultured in various liquid media. The production of four mycelium sheets was successful. After drying, the sheets of <em>Pleurotus</em> sp. using potato dextrose broth had the largest water contact angle. With a tensile strength, the sheet of <em>Lentinus</em> sp. using malt extract broth obtained the highest value. The dried mycelium sheet from <em>Pleurotus</em> sp. cultured on yeast extract broth had the greatest hardness value in the microhardness testing. After 7 days, the residual dry weight of the sheets in different conditions—soil burying, soil surface exposure, and water immersion—was less than 50% of the initial weight.&nbsp; This work has demonstrated the biodegradability of mycelium sheets.</p> Chairat Pattarasiripol, Wuttiwat Jitjak, Jesper T. N. Knijnenburg Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/14001 Fri, 17 Jan 2025 00:00:00 +0700 Exploration the Potency of Copper and Dyes Multi-Resistant of Indigenous Bacteria Isolated from Cikijing River, West Java https://journal.ugm.ac.id/v3/jtbb/article/view/12527 <p>Various types of textile dye have been reported to contaminate the Cikijing River, West Java, Indonesia due to its location within the industrial region of Rancaekek District. It has been understood that certain bacterial species develop copper resistance and dye decolourisation as a mechanism of stress adaptation. The study aims at isolating and characterising copper and dye resistance as well as decolourisation ability of bacteria isolated from the Cikijing River. Copper-resistant bacteria were isolated using a series dilution method on Luria Bertani media supplemented with the addition of 1-10 mM CuSO<sub>4</sub>. Purified bacterial isolates were then tested for copper resistance onto LB agar medium supplemented with CuSO<sub>4</sub> concentrations ranging from 0 mM to 20 mM and decolourisation of various dyes. A total of 59 copper-resistant bacteria were successfully isolated, nine of them showed the highest copper resistance with a MIC value from 11 mM up to 16 mM CuSO<sub>4</sub> and resistance to&nbsp; &nbsp;4 types of dyes up to 700 ppm. The 16S rDNA analysis showed that the nine isolates were <em>Klebsiella</em> sp., <em>Klebsiella pneumoniae</em>, <em>Lysinibacillus boronitolerans</em>, <em>Lysinibacillus fusiformis</em>, <em>Bacillus proteoliticus</em>, <em>Pseudomonas stutzeri</em>, <em>Klebsiella variicola</em>, <em>Citrobacter freundii</em>, <em>and Klebsiella variicola</em>. Out of nine isolates, five were found resistant to 5 mM CuSO<sub>4</sub> and decolourise Methylene Blue, Congo Red, and Basic Fuchsine dyes at a maximum concentration of 700 ppm.</p> Wahyu Irawati, Reinhard Pinontoan, Triwibowo Yuwono, Indah Sofiana, Valentine Lindarto, Dwi Ningsih Susilowati Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12527 Mon, 20 Jan 2025 11:07:22 +0700 Present and Future Distribution Model using MaxEnt: A Risk Map for Dengue Haemorrhagic Fever based on Aedes aegypti Mosquitoes Distribution in Malang Region, East Java, Indonesia https://journal.ugm.ac.id/v3/jtbb/article/view/12678 <p>The prevalence of Dengue Haemorrhagic Fever (DHF), a disease prevalent in countries with tropical and sub-tropical climates, including Indonesia, has exhibited a notable increase over the past two decades. A study case of a region experiencing this surge is Malang Region, which situated in East Java. The transmission of DHF within individual human is facilitated by the existence of <em>Ae. aegypti</em>, which serves as one of the intermediate vector mosquitoes. MaxEnt modelling was employed to analyse the niche and distribution of <em>Ae. aegypti</em>. The results of this study demonstrated that the integration of environmental and anthropogenic variables in a combination model provided&nbsp; more comprehensive approach for comprehending the niche and distribution patterns of <em>Ae. aegypti</em> compared to relying only regarding a climatic model. Areas characterised by higher temperatures, high population density, and limited vegetation cover possess the inherent capacity to serve as suitable habitats for <em>Ae. aegypti</em>. According to the modelling results, the distribution of <em>Ae. aegypti </em>in Malang region currently encompasses approximately 14.5 % (545.5 km<sup>2</sup>) of the total area. It is projected that this distribution can potentially expand to 15.5 % (568.9 km<sup>2</sup>) by the year 2040. Several sub-districts, namely Klojen, Blimbing, Sukun, Lowokwaru, Kedungkandang, Pakisaji, and Kepanjen, have been classified as high-risk areas that require special concern. The combination model of environmental variables and anthropogenic variables provide more comprehensive approach to understand the niche and the distribution patterns of <em>Ae. aegypti</em> in Malang Region compared to relying solely on climate models.</p> Zulfaidah Penata Gama, Bagyo Yanuwiadi, Puji Rahayu, Rafi Jauhar Khalil, Miftah Farid Assiddiqy, Muhammad Asyraf Rijalullah, Nia Kurniawan Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12678 Fri, 24 Jan 2025 00:00:00 +0700 Stand Structure Characteristics of Fragmented and Primary Forests and Their Correlation to Carbon Stocks https://journal.ugm.ac.id/v3/jtbb/article/view/13362 <p>Stand structure contributes to forest biodiversity and productivity. The disparity of stand structure between fragmented and primary forests and how they affect carbon storage are poorly understood. This study determined differences among some stand parameters in fragmented and primary forests and the correlation between forest stand structure and carbon stock. Twenty-five replicate quadrats were established in Bukit Durang and Division 5, representing the fragmented forests, and Lambir Hills National Park and Kubah National constitute the primary forests. All trees with diameter at breast height of 10 cm and above were measured, and the tree species were recorded. Aboveground biomass was calculated and converted to carbon stock. Statistical analyses showed that tree density is comparable among the forests. However, species abundance, species dominance, basal area aboveground biomass, and carbon stocks are different . Large-diameter trees significantly contribute to carbon storage. Principal component analyses revealed basal area, tree diameter and carbon stock were positively intercorrelated and associated. Species dominance and tree density are intercorrelated and strongly associated. Conversely, the number of species is negatively correlated to species dominance and tree density. This study showed the significance of tree diameter in impacting carbon stock.</p> Afifi Nazeri, Ismail Jusoh, Mohamad Hasnul Bolhassan Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/13362 Mon, 03 Feb 2025 00:00:00 +0700 Utilising Plant Extracts as Lures to Capture Ambrosia Beetles (Coleoptera: Curculionidae) in Cocoa Plantation https://journal.ugm.ac.id/v3/jtbb/article/view/13392 <p>The ambrosia beetle (Coleoptera: Curculionidae) is a significant pest affecting cocoa plants in South Sulawesi. The high intensity of their attacks poses a serious threat to cocoa production, causing plants to wilt and die. This study developed traps baited with active ingredient compounds from various plant species, including coffee, carrot leaves, fermented cocoa wood, and eucalyptus oil, and compared their efficacy with ethanol. Beetles collected in these traps were identified based on morphological characteristics using a stereo microscope. The attraction test results indicated that all treatments successfully attracted ambrosia beetles, with ethanol capturing the highest number of individuals (1391). The results showed that ethanol and other extracts could capture ambrosia beetles of various kinds. The highest number of captures was found in ethanol and carrot leaf extract treatments. Additionally, eleven species were identified: <em>Coccotrypes</em> sp., <em>Diuncus quadrispinulosus</em>, <em>Eccoptopterus spinosus</em>, <em>Hypothenemus </em>sp. 1, <em>Hypothenemus</em> sp. 2, <em>Hypothenemus </em>sp. 3, <em>Xyleborus affinis</em>, <em>Xylosandru s mancus,</em> <em>Xylosandrus crassiusculus</em>, <em>Xylosandrus eupatorii</em>, and <em>Xylosandrus morigerus</em>.<em>&nbsp;</em>Traps baited with carrot leaf extract were most effective in capturing <em>Hypothenemus</em> sp. 3. These findings underscore the importance of developing various attractant traps utilising plant chemical compounds to detect and identify ambrosia beetle species and mitigate severe crop damage.</p> Sylvia Sjam, Vien Sartika Dewi, Ade Rosmana, Asman, M. Bayu Mario, Elkawakib Syam’un, A. Amrullah, Syahribulan, Nuriadi, Nur Azizah Fitriyanti, Alim Nur Syafitri Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/13392 Mon, 10 Feb 2025 00:00:00 +0700 Biodiversity and Ecosystem Services Analysis to Develop a University Botanical Garden: A Case Study in the University of Palangka Raya, Central Kalimantan https://journal.ugm.ac.id/v3/jtbb/article/view/12520 <p>Information on existing site characteristics both biotic and abiotic factors is mandatory to provide an initial picture for a baseline to develop a botanical garden. This study aimed to analyse the biodiversity and ecosystem services in the candidate botanical garden area as an existing site, a case study in the University of Palangka Raya (UPR) to prepare the university botanical garden development. The fieldwork was conducted in 5 transects consisting of 100 plots with a plot size of 20x20 m<sup>2</sup>. The results showed that the site is categorized as a Sundaland peat swamp forest ecoregion. The peatlands thickness varies from shallow to medium and deep, with the remaining area reaching 75 % of the total campus. The floristic condition is categorized as an early stage of succession after fires, consisting of 26 plant species belonging to 25 genera and 18 families, with various potential uses. Wildlife comprised 42 species including amphibians, reptiles, birds, fishes and prawns, also insects. Three high conservation value plants and two wildlife were documented. The stand carbon storage reached 14.33 tons/ha. A botanical garden consists of both natural and artificial ecosystems, thus it is important to strategically plan in setting the plant collections layout and species enrichment efforts. The UPR botanical garden will provide the conservation of native and endemic plants of Kalimantan, with high conservation value, potentials, and local wisdom value; and provide ecosystem services for storing carbon, improving hydrological services, habitat and protection for various existing and incoming wildlife.</p> <p>&nbsp;</p> Lia Hapsari, Muhammad Rizki, Maulidi Andri, Joko Ridho Witono, Inggit Puji Astuti , Dina Safarinanugraha, Wihermanto, Erna Shinta, Yohanes Edy Gunawan, Hendrik Segah, Sulmin Gumiri Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12520 Fri, 14 Feb 2025 12:57:55 +0700 The Effect of Thidiazuron and Naphtalene Acetic Acid on In Vitro Development of Eria hyacinthoides (Blume) Lindl Orchid https://journal.ugm.ac.id/v3/jtbb/article/view/11929 <p><em>Eria hyacinthoides </em>(Blume) Lindl. is an Indonesian orchid species found in Sumatra, Java, and Bali. This orchid is a sympodial orchid with flowers that has fragrant aroma, suspected containing phytochemicals for herbal medicines, so mass plant propagation is necessary. The aim of this research is to obtain the best <em>in vitro </em>conditions for this orchid through somatic embryos using growth regulators and analysing the structure of the <em>Dendrobium Orchid Homeobox 1 </em>(<em>DOH1</em>) homologous gene in <em>E. hyacinthoides </em>to <em>Dendrobium ‘</em>Madame Thong-In’ which is known to induce bud formation. The method used in this study: (1) the leaves of the plant spread about 20 - 30 days from shoots measuring about 6.3-6.7cm on the mother plant aged ± 8 years, stored in an incubation room with picture of 16 hours of light and 8 hours of darkness in the heat. 25 ± 1 ℃, (2) compared Murashige and Skoog, Vacin and Went, Knudson C and New Phalaenopsis growth to get the best medium, (3) added PGR to medium (Thidiazuron (TDZ) 1 - 3 mg L<sup>-1</sup> and Naphthalene-1-acetic acid (NAA) 1-3 mg L<sup>-1</sup>), (4) isolate &nbsp;&nbsp;partial gen <em>DOH1 </em>homologous by using primer of <em>DOH1</em>, (5) analyse sequence of PCR products. Optimal medium for callus embryogenesis production from leave was Knudson C + TDZ 1 mg L<sup>-1</sup> + NAA 1 mg L<sup>-1</sup>. Amplification of DNA fragments using degenerate primers of <em>DOH1 </em>resulted 175 bp, indicating similarity about 88.64 % with between the <em>DOH1 </em>gene structure in <em>E. hyacinthoides </em>and in <em>Dendrobium </em>‘Madame Thong-In’.</p> Rita Foorantika, Khoirun Nisa Pratiwi, Endang Semiarti Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/11929 Mon, 17 Feb 2025 00:00:00 +0700 Phenol and Tannin Contents of Fresh Phyllodes and Leaf Litter Materials from Three Acacia Species in Brunei Darussalam https://journal.ugm.ac.id/v3/jtbb/article/view/11810 <p>Invasive <em>Acacia</em> species are increasingly spreading into degraded forests in Brunei Darussalam since their initial planting in the 1990s. Information on the secondary metabolites of these invasive <em>Acacia</em> species is important in understanding their effects on leaf litter decomposition rates of invaded forests in Brunei. This study aimed to quantify the pH, total phenolic, and total tannin content of three invasive <em>Acacia</em> species (<em>Acacia auriculiformis</em> A. cunn ex Benth., <em>Acacia holosericea</em> A. Cunn. Ex G. Don and <em>Acacia mangium</em> Willd.) and one co-occurring native heath tree species (<em>Buchanania arborescens</em> (Blume) Blume) in Brunei Darussalam. pH, total phenolic and total tannin contents were measured and compared between leaves of the four species, as well as between leaf types (fresh phyllodes vs. leaf litter samples). All three invasive <em>Acacia</em> species recorded higher pH, total phenolic and total tannin contents than the native species. High pH and total phenolic content were observed in fresh phyllodes than leaf litter samples of all studied species but no differences were observed in total tannin contents for both fresh phyllodes and leaf litter samples. Higher pH, total phenolic and total tannin contents in all <em>Acacia</em> species may reduce leaf palatability to herbivores and detritivores, resulting in slower degradation processes compared to the native tree species, thus potentially affecting leaf litter decomposition rates in <em>Acacia</em>-invaded heath forests. Overall, the study on differences in secondary compounds between species and leaf types has provided insights into the decomposition rate of <em>Acacia</em> species compared to the native tree species.</p> Safira Jamil, Rahayu Sukmaria Sukri, Faizah Metali, Salwana Md. Jaafar Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/11810 Fri, 21 Feb 2025 09:33:24 +0700 The Complete Mitochondrial Genome of Critically Endangered Painted Terrapin, Batagur borneoensis (Testudines: Geoemydidae) https://journal.ugm.ac.id/v3/jtbb/article/view/13529 <p>Characterising mitochondrial genomes is a key to studying evolution in vertebrates including turtles. This study employed Next-Generation Sequencing (NGS) to characterise mitochondrial DNA sequences in <em>Batagur borneoensis</em> (Schlegel &amp; Muller, 1844)<em>.</em> We reported the nearly complete mitogenome to clearly characterise the gene sequence of <em>B. borneoensis</em> which has been deposited in GenBank under the accession number&nbsp;PP228865. Phylogenetic analyses using Maximum Likelihood (ML) on the 13 protein-coding genes were conducted with MEGA X Version 11 software. This study presents the second in-depth analysis of the <em>B. borneoensis</em> mitochondrial genome, spanning 16,397 base pairs and containing 13 protein-coding genes, 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a major non-coding region, two non-coding regions: L-strand origin replication (OL) and control region (OH). The sequence length and organisation of this species' mitochondrial genome fall within the typical range and gene arrangement found in vertebrate species. Most genes, except for seven tRNAs and <em>nad6,</em> were encoded on the primary DNA strand. All protein-coding genes (PCGs) began with an ATG initiation codon, except for <em>cox1</em> and <em>trnF</em> which started with GTG codon, and <em>nad3_0</em>, started with a TTA codon. These findings enhanced our understanding of nucleotide composition and molecular evolution in the genus <em>Batagur</em>. Phylogenetic analyses identified vulnerable and ecologically important species, aiding biodiversity and ecosystem protection. They also expanded the dataset for comparative studies within the Geoemydidae family. Additionally, this research may help develop primers and conservation strategies for future studies.</p> Nor Ainsyafikah Madiran, Han Ming Gan, Shahreza Md Sheriff, Aliyu Garba Khaleel, Muhammad Zaid Nasir, Chik Maslinda Omar, Mohamad Zulkarnain Mohd Dali, Muhammad Syafiq Aiman Mohd Nasir, Norshida Ismail, Ahmad Syazni Kamarudin Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/13529 Mon, 24 Feb 2025 08:50:05 +0700 From Bean to Biosphere: Vegetation Dynamics and Biodiversity in Arabica Coffee Agroforestry at Ijen Geopark https://journal.ugm.ac.id/v3/jtbb/article/view/12405 <p>This study evaluates vegetation biodiversity and ecological conditions at the Bondowoso Biosite of <em>Kebun Kopi</em>, Ijen Geopark, to support sustainable Arabica coffee production. Three agroforestry plots (KR1-3) and a plantation plot (PN) were analyzed for species composition. In KR1, <em>Acacia auriculiformis</em> (IVI=110) and <em>Trema orientalis</em> (IVI=190) are prominent. KR2 is dominated by <em>A. auriculiformis</em> (IVI=160) and <em>Ricinus communis</em> (IVI=80), while <em>Casuarina equisetifolia</em> is significant in KR3. The PN plot shows a more even IVI distribution between <em>Falcataria mollucana</em> and <em>Grevillea robusta</em>. Tukey's test reveals significant differences between KR1 and PN, and KR2 and PN plots (p-adj=0.001). The highest existence values are Anisoptera marginata (66.67%) in KR1, <em>T. orientalis</em> (53.33%) in KR2, <em>C. equisetifolia</em> (46.67%) in KR3, and <em>Toona sureni</em> (26.67%) in PN. Results indicate significant variations in species diversity, evenness, and dominance across plots, influenced by ecological, geographical, and anthropogenic factors. Higher Shannon-Wiener and Evenness indices in KR1 and KR2 suggest diverse species compositions are vital for ecosystem health, while KR3's dominance of few species highlights the need for biodiversity conservation. This research recommends regenerative Arabica coffee farming practices and sustainable conservation strategies at the Bondowoso Biosite of <em>Kebun Kopi.</em></p> Nilasari Dewi, Agung Sih Kurnianto Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12405 Fri, 28 Feb 2025 11:05:07 +0700 Phytosociology of Trees in Siranggas Wildlife Sanctuary Area, North Sumatra, Indonesia https://journal.ugm.ac.id/v3/jtbb/article/view/13679 <p>The lower mountainous region's Siranggas Wildlife Sanctuary is a conservation area with a variety of tree species, however it is susceptible to exploitation-related harm. Despite the area's ecological advantages, little is known about the diversity of tree species and their associations. Therefore, the purpose of this study was to ascertain the Siranggas Wildlife Sanctuary Area's tree species diversity and associations. Using the purposive sampling approach, the study was carried out from March to April 2022. Five plots, each measuring 30 by 60 meters, were set up at various heights. The Importance Value Index (IVI) and the Shannon-Wiener Diversity Index (H') were used to examine the vegetation data. Associations between tree species were identified by considering two species with the highest IVI in the observation plot. The results showed that there were 119 tree species, 38 families, and 79 genera in the Siranggas Wildlife Sanctuary Area. The diversity index across the plot was relatively high with an H' value &gt; 3. Trees with a height of 10 to 15 meters were the prevalent canopy height profile in the plot, while the dominant trunk diameter across the whole plot was 10 to 20 cm. The association that occurred in the study area was the <em>Schima wallichii – Syzygium cerasiforme</em> based on two of the greatest IVI and their distribution throughout all plots from varying altitudes. Future forest management and restoration initiatives in the Siranggas Wildlife Sanctuary area can benefit from the presence of both of these species.</p> <p>&nbsp;</p> Ahmad Fikry Tarigan, Etti Sartina Siregar Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/13679 Mon, 03 Mar 2025 00:00:00 +0700 Effect of Benzyl-Adenine and Thidiazuron on In Vitro Multiplication of Ginger (Zingiber officinale Rosc.) Shoots https://journal.ugm.ac.id/v3/jtbb/article/view/12172 <p>The wilt disease caused by <em>Ralstonia solanacearum</em> and the leaf spot disease caused by <em>Phyllosticta </em>sp. are significant co<em>ns</em>traints in ginger cultivation as they can lead to crop failure. One approach to eliminating these diseases is to use disease-free ginger plantlets obtained through tissue culture propagation. This study investigated the influence of plant growth regulators, i.e., Benzyl Adenine (BA) and Thidiazuron (TDZ), on the in vitro multiplication of large white ginger shoots. The tested treatments included combinations of BA (0, 1, 2, 3 mg L<sup>-1</sup>) and TDZ (0, 0.1, and 0.2 mg L<sup>-1</sup>), with ten replicates each. A complete randomised factorial experimental design was employed. The observed variables were shoot height, number of shoots, number of leaves, and number and length of roots at 2, 4, 6, and 8 weeks of age. The results indicated an interaction between TDZ and BA for shoot number and root length. The highest numbers of shoots were obtained after eight weeks using 0.1 mg L<sup>-1 </sup>TDZ alone without BA. Meanwhile, the longest roots were obtained after eight weeks using a specific combination of TDZ and BA concentratio<em>ns</em>. Based on this study, we proposed a strategy to implement this protocol to induce the formation of shoots, leaves, and roots in a multistep tissue culture propagation.</p> Endang Gati Lestari , Sitti Fatimah Syahid , Rossa Yunita, Tara Puri Ducha Rahmani, Imam Bagus Nugroho , Lee James Watson Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12172 Fri, 07 Mar 2025 08:06:47 +0700 Genotyping and Phytochemical Analysis of Kayu Pule Plant as Local Bali Medicinal Plant https://journal.ugm.ac.id/v3/jtbb/article/view/13086 <p>The bark of Kayu Pule plants in Bali is empirically known as a traditional medicinal ingredient and has been developed as a cosmetic and other health ingredient; however, scientific research has yet to be conducted on the profiles of the plant. This study aimed to determine the plant species, examine the scientific function of the compounds, and the antioxidant activity of the plant's ethanolic extract. This study performed a DNA analysis of the plant using matK primer, and the amplified DNA sequences were used to determine the phylogenetic tree. Based on the molecular analysis, the Kayu Pule plant bark from Bali, which was used as medicine, was <em>Alstonia scholaris</em>. The main compounds in Kayu Pule bark, such as ergost-5-en-3-ol and 12-oleanen-3-yl acetate, had anti-inflammatory, antioxidant, and antimicrobial properties. The antioxidant strength of the Kayu Pule plant was measured with IC50 of 3.7 μg mL<sup>-1</sup> with a very strong category. This research showed the potential of Kayu Pule for developing medicinal and cosmetic products.</p> I Ketut Suada, I Gede Putu Wirawan, I Nyoman Wijaya, Anak Agung Sagung Intan Gayatri, Gusti Ayu Putu Tiara Adi Hantari, Maria Malida Vernandes Sasadara, Putu Krisnawan Kalimutu, I Made Oka Parwata Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/13086 Wed, 12 Mar 2025 09:41:30 +0700 Exploring the Diversity of Arbuscular Mycorrhizal Fungi in Zingiberaceae Family Plants at the Tukung Gede Mountain Natural Reserve https://journal.ugm.ac.id/v3/jtbb/article/view/12567 <p>Arbuscular mycorrhizal fungi (AMF) are essential in improving soil quality and facilitating plant nutrient and water uptake through mutualistic associations. However, limited research exists on the diversity and distribution of AMF associated with plants in the Zingiberaceae family, especially in unique ecological habitats such as the Tukung Gede Mountain Natural Reserve. This study aims to assess and document the diversity of AMF linked to Zingiberaceae plants in this reserve. Sampling was performed at three locations with distinct plant compositions to explore the diversity of AMF genera. Soil samples were processed using a wet sieve technique, while root samples were chemically stained to evaluate AMF colonization. Key parameters studied included diversity indices, spore density, genus-level identification, and root colonization rates. The findings revealed the presence of eight AMF genera: <em>Sclerocystis</em>, <em>Septoglomus</em>, <em>Acaulospora</em>, <em>Gigaspora</em>, <em>Glomus</em>, <em>Scutellospora</em>, <em>Racocetra</em>, and <em>Rhizophagus</em>, identified based on spore morphology. Root staining revealed structural AMF infections, including vesicles, internal hyphae, and arbuscules. <em>Zingiber officinale </em>exhibited the highest AMF colonization rate (88%) among the Zingiberaceae plants studied, whereas <em>Zingiber zerumbet </em>had the lowest (56%). <em>Etlingera Solaris </em>and <em>Zingiber officinale </em>showed the highest spore densities at 172 and 254 spores per 100g of soil, respectively. AMF diversity indices varied across locations, with values of 0.78 (Station I), 0.95 (Station II), and 0.84 (Station III). This research emphasizes the extensive AMF diversity within Zingiberaceae plants and its potential importance for conservation and ecological sustainability.</p> Rida Khastini, Iing Dwi Lestari, Indah Juwita Sari, Nida Septiani Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/12567 Fri, 14 Mar 2025 10:31:51 +0700 New Report of Dysmicoccus brevipes Cockerell (1893) (Hemiptera: Pseudococcidae) on Heliconia sp., Lagenaria sp., and Zea mays L. Root in Bali Indonesia https://journal.ugm.ac.id/v3/jtbb/article/view/13563 <p>The pink pineapple mealybug, scientifically known as <em>Dysmicoccus brevipes</em> (Cockerell) (Hemiptera: Pseudococcidae), can associate with all part of the plant, including the roots. Additionally, it plays crucial role as a carrier of plant viruses, highlighting its importance in relation to host plants. Reports of <em>D. brevipes</em> infestations on above-ground plant parts in Indonesia have been documented since 1917. However, there is a lack of data on the infestation of subterranean plant parts or roots by this organism which highlights the significance of this research. This article presents the identification of mealybugs on the roots of <em>Heliconia</em> sp., <em>Lagenaria</em> sp., and <em>Zea mays</em> L. from Bali, Indonesia, using a morphological method based on determination keys by Williams (2004) and a molecular method based on the MtCOI gene. The findings of this study suggested that the species observed on all three host plants was <em>D. brevipes</em>, making it the most recent record of <em>D. brevipes</em> presence on <em>Heliconia </em>sp., <em>Lagenaria </em>sp., and <em>Z. mays</em> roots in Bali, Indonesia.</p> I Putu Sudiarta, Komang Saraswati Devi, Gusti Ngurah Alit Susanta Wirya, Putu Shinta Devi, Febri Eka Wijayanti, Made Getas Pudak Wangi Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/13563 Mon, 17 Mar 2025 00:00:00 +0700 Impact of Global Climate Shifts on the Biodiversity and Functionality of Marine Zooplankton Communities https://journal.ugm.ac.id/v3/jtbb/article/view/14575 <p>The impact of climate change is one of the biggest crises facing humanity today. Not only humans are affected, but also the conditions of the marine environment, including zooplankton communities, which are a key component in the marine food chain. This study reviews the analysis of the impact of global climate shifts on biodiversity and the function of marine zooplankton communities. Specifically, the study addresses how temperature changes, ocean acidification, and other stressors affect zooplankton communities. In addition, the study includes an analysis of case studies and regional variations on the impacts of climate change on zooplankton communities, as well as discusses methodologies that can be used in studying the effects of climate change. We also evaluate existing knowledge gaps and identify future research directions that are needed. Through this latest evaluation, the research highlights the importance of continuous monitoring and a multi-stressor research approach. The study also emphasizes the importance of designing effective adaptation strategies for marine zooplankton communities, which are highly relevant to future sustainable marine conservation policies. The results of this study show the urgency of further research to maintain the integrity of marine ecosystems in facing the challenge of global climate change.</p> Angkasa Putra, Sarifah Aini, Hamdani, Cici Maulida, Lalu Achmad Jani Qhadaffi, Monica Ryan, Harminto, Made Ariana, Raedy Anwar Subiantoro, Tashwir Copyright (c) 2025 Journal of Tropical Biodiversity and Biotechnology https://journal.ugm.ac.id/v3/jtbb/article/view/14575 Fri, 07 Feb 2025 15:58:23 +0700