HAYATI Journal of Biosciences (HAYATI J Biosci; p-ISSN: 1978-3019; e-ISSN: 2086-4094) is an international peer-reviewed and open access journal that publishes significant and important research from all area of biosciences fields such as biodiversity, biosystematics, ecology, physiology, behavior, genetics and biotechnology. All life forms, ranging from microbes, fungi, plants, animals, and human, including virus, are covered by HAYATI J Biosci. HAYATI J Biosci published by Department of Biology, Bogor Agricultural University, Indonesia and the Indonesian Society for Biology. We accept submission from all over the world. Our Editorial Board members are prominent and active international researchers in biosciences fields who ensure efficient, fair, and constructive peer-review process. All accepted articles will be published on payment of an article-processing charge, and will be freely available to all readers with worldwide visibility and coverage. HAYATI J Biosci has been also indexed/registered in SCOPUS, Asean Citation Index, DOAJ, SINTA, National Library of Medicine Catalog, Crossref, ROAD, CABI, EBSCO, Publons, Scilit, Agricola, ProQuest and others.
Bogor Agricultural University, Indonesia
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CRISPR/Cas9-Mediated Targeting of SD1 Gene in Indonesian Local Varieties: Transformation and Preliminary Phenotypic Assessment of Semi-Dwarf Traits
Indonesia boasts a wealth of local rice germplasm, with approximately 8,500 varieties recorded by IRRI, many of which feature adaptive traits and resistance to biotic and abiotic stresses. Nevertheless, it is likely limited by excessive plant height, which makes it sensitive to lodging. In contrast, the improved yields of modern semi-dwarf rice are twice those of older varieties, but are less resilient to local Indonesian stresses. This study focused on introducing semi-dwarf characteristics into two local varieties, Ketan Hitam and Pandan Wangi, via CRISPR/Cas9-mediated gene editing, which enables specific mutations and encodes the GA20-oxidase enzyme involved in gibberellin biosynthesis. A CRISPR/Cas9 construct (pRGEB32::SD1) carrying two sgRNAs targeting exon 1 and exon 2 was successfully designed and validated. Following Agrobacterium tumefaciens-mediated transformation and hygromycin selection. Ketan Hitam exhibited good survival, whereas Pandan Wangi depicted browning and poor regeneration. One regenerated Ketan Hitam T0 plantlet presented a preliminary semi-dwarf phenotype. PCR analysis verified the presence of the CRISPR/Cas9 construct. This study provides an initial demonstration of transformation probability and early phenotypic response in Ketan Hitam. Nevertheless, the phenotypic assay is based on a single T0 specimen, describing a key limitation of this study. The findings provide a basis for further multi-generational evaluation and agronomic improvement of Indonesian local rice.
Copyright (c) 2026 Mohammad Ubaidillah, Ihsan Habibi, Angger Aisyah Hadiahning Gusti, Rosalina Diva Aurela , Sri Hartatik, Kacung Hariyono, Rikno Harmoko https://creativecommons.org/licenses/by-nc/4.0
Exploration of the Natural Habitat of Apis dorsata Forest Bees in the Samota Biosphere Reserve, Sumbawa: An Ecological Study and Vegetation Diversity
The Samota Biosphere Reserve, located on Moyo Island in Sumbawa, Indonesia, is a key ecological area, especially for the forest honey bee, Apis dorsata. This study investigated the natural habitat of A. dorsata and the factors influencing its nesting preferences within this reserve. A multidisciplinary approach, integrating field surveys, laboratory analysis, and geospatial technology, including Geographic Information System (GIS) tools, was used to identify the optimal nesting sites for A. dorsata. The study found that A. dorsata favors tall trees (≥15 meters) with open branches (inclination of 5°-25°), particularly species such as Ceylon Oak, Kapong, and Milkwood. These trees, characterized by a trunk diameter ≥30 cm, provided the most suitable nesting sites. Additionally, the elevation range of 50-300 meters above sea level was found to be critical for nest location. Forests with minimal human disturbance (such as roads or agricultural expansion) were prioritized. A GIS-based spatial analysis identified a total core habitat area of 2,993.03 hectares (29.93 km2), which currently meets the ecological requirements of the bee. These findings are essential for establishing conservation strategies for A. dorsata. The research highlights the importance of protecting forested areas, particularly those with the preferred tree species and suitable elevation ranges, to support bee populations. By preserving the integrity of the core habitat zones and minimizing human disturbances, this study provides actionable insights to ensure the long-term sustainability of A. dorsata populations within the Samota Biosphere Reserve, Sumbawa.
Copyright (c) 2026 Erwan, Muhammad Muhsinin, Dwi Kusuma Purnamasari, Sukarne, Bambang Supeno, Agussalim https://creativecommons.org/licenses/by-nc/4.0
Vegetation Structure and Species Composition Along a Canal-Distance Gradient Across Different Peatland Land Use Types
Tropical peatlands are critical ecosystems that provide habitat for biodiversity and store large amounts of carbon, yet they are increasingly degraded due to land-use conversion, drainage, and recurrent fires. This study examined vegetation structure and species composition along a canal-distance gradient (10-350 m across three peatland land-use types: rubber plantation, secondary forest, and burned peatland. Vegetation surveys were conducted using 40 nested plots covering four growth strata (trees, poles, saplings/shrubs, and seedlings/herbs). Community structure was analyzed using the Importance Value Index (IVI), Shannon–Wiener diversity index (H′), Margalef’s richness index (DMg), Pielou’s evenness index (E), and Simpson’s dominance index (C). Differences in environmental parameters among land-use types were tested using one-way ANOVA (p<0.05). Secondary forests exhibited the highest species richness and diversity with balanced structural complexity, whereas rubber plantations showed simplified communities dominated by Hevea brasiliensis. Burned peatlands were characterized by pioneer tree species and dense fern understorey, indicating successional arrest. Secondary forests had higher biodiversity than rubber plantations, which in turn had higher biodiversity than burned peatlands. These findings highlight that land-use intensity, canal proximity, and fire history jointly regulate vegetation dynamics in tropical peatlands and highlight the importance of forest conservation, plantation diversification, and restoration through rewetting and enrichment planting.
Copyright (c) 2026 Sinta Haryati Silviana, Bambang H. Saharjo, Sigit Sutikno, Yenni Vetrita https://creativecommons.org/licenses/by-nc/4.0
Investigation of Galactinol Synthase Genes in Plant Defense Mechanisms against Adverse Environmental Conditions in Hot Pepper (Capsicum annuum)
The galactinol synthase (GolS) and raffinose synthase (RS) play crucial roles in the synthesis of raffinose family oligosaccharides, which are involved in stress protection, carbohydrate transport, and fruit development in plants. This study aimed to conduct a genome-wide identification and characterization of GolS and RS genes in hot pepper (Capsicum annuum) and to investigate their responses to environmental and hormonal factors. Six CaGolS and seven CaRS genes were identified in the pepper genome. Structural analysis showed that CaGolS genes have relatively compact exon-intron arrangements, while CaRS genes possess more complex structures. Phylogenetic comparison with related species revealed strong evolutionary conservation within the Solanaceae group. Transcriptome analysis showed that CaGolS1, CaGolS2, CaGolS3, CaRS2, and CaRS7 were highly responsive to abiotic stresses such as cold, heat, salinity, and osmotic stress, as well as to hormonal treatments involving abscisic acid, jasmonic acid, salicylic acid, and ethylene. Several genes also showed differential expression during fruit development and ripening, indicating their contribution to sugar metabolism and stress adaptation during maturation. The results provide new insights into the GolS and RS gene families in hot pepper and identify potential gene targets for developing stress-tolerant and high-quality pepper cultivars.
Copyright (c) 2026 Ngoc Thi Bich Chu, Ha Duc Chu, Phi Bang Cao, Cuong Ba Cao https://creativecommons.org/licenses/by-nc/4.0
Isolation, Screening, Characterization, and Identification of Potential Probiotic Lactic Acid Bacteria (LAB) from the Gut of Whiteleg Shrimp (Litopenaeus vannamei)
Bacterial diseases represent a major constraint on the sustainability of shrimp aquaculture. Increasing antibiotic resistance necessitates eco-friendly alternatives. This study isolate and characterizes bacteriocin-producing Lactic Acid Bacteria (LAB) from the gut of healthy farmed Litopenaeus vannamei to evaluate their probiotic potential. Thirty presumptive LAB isolates were obtained from 50 shrimp samples. In vitro assessment included tolerance to simulated gastrointestinal conditions (pH 1.5 and 3% bile salts), safety (hemolysis and antibiotic susceptibility), and antimicrobial activity against four pathogens: Vibrio parahaemolyticus, V. harveyi, V. alginolyticus, and V. vulnificus. Isolate LV4 maintained viable counts of 6.72±0.13 Log CFU/mL at pH 1.5 and 5.17±0.48 Log CFU/mL at 3% bile salts. The neutralized cell-free supernatant of LV4 exhibited proteinaceous, broad-spectrum antimicrobial activity against all tested Vibrio pathogens. Isolate LV4 was non-hemolytic and sensitive to most clinically relevant antibiotics. Molecular identification using 16S rRNA gene sequencing identified LV4 as Enterococcus faecalis. This study confirms that the gut of L. vannamei is a valuable reservoir for robust LAB. Isolate E. faecalis LV4 is a strong candidate for further development as a probiotic to enhance shrimp health and disease resistance in aquaculture.
Copyright (c) 2026 Thuy Nguyen Phuong, Tuu Nguyen Thanh https://creativecommons.org/licenses/by-nc/4.0
Combination Effect of Culture Media and Silver Nanoparticle on the Effectiveness of Tobacco Anther Regeneration
Anther culture is an effective biotechnological approach to accelerate the production of homozygous lines in tobacco breeding. This study evaluated the interaction between culture media (Murashige and Skoog/MS and Chu’s N6) and silver nanoparticle (AgNP) concentrations on in vitro anther regeneration of tobacco (Nicotiana tabacum L.). The experiment was arranged in a completely randomized design with ten treatment combinations consisting of two basal media and five AgNP concentrations (0, 2.5, 5, 7.5, and 10 ppm), each replicated three times. Quantitative parameters included callus formation, shoot regeneration, rooting response, regeneration percentage, and contamination rate. MS medium supplemented with 2.5 ppm AgNPs (K2) produced the optimal response, showing 100% callus formation and the highest shoot regeneration percentage (89%). Root formation was observed only in treatments K2 and K4. In contrast, higher AgNP concentrations (≥7.5 ppm), particularly in Chu’s N6 medium, significantly reduced regeneration percentages (ANOVA, p<0.05). The promotive effect of low AgNP concentration is associated with suppression of ethylene activity, antimicrobial action, and regulation of reactive oxygen species (ROS), which collectively enhance cell division and organogenesis. These findings indicate that MS medium supplemented with 2.5 ppm AgNPs is optimal for tobacco anther regeneration and suitable for doubled-haploid production.
Copyright (c) 2026 Mohammad Nur Khozin, Yusuf Dary Ahnaf, Parawita Dewanti, Didik Pudji Restanto, Iryono https://creativecommons.org/licenses/by-nc/4.0
Phenetic Study of Tabernaemontana divaricata (L.) R.Br. ex Roem. & Schult. in Thailand
Pinwheel Jasmine (Tabernaemontana divaricata L.; Apocynaceae) is widely distributed across South Asia, Thailand, and southern China and exhibits substantial morphological variation. This variability has resulted in persistent taxonomic confusion, particularly in Thailand, where distinguishing among phenotypic forms and related taxa remains challenging. Accurate taxonomic delimitation is essential for botanical classification, horticultural applications, conservation, and the reliable identification of plant resources. This study examined the taxonomic status of Pinwheel Jasmine in Thailand using numerical taxonomic approaches, including cluster and discriminant analyses. A total of 40 morphological characters (20 quantitative and 20 qualitative) were assessed across 210 operational taxonomic units (OTUs) representing seven phenotypes. Both analyses consistently resolved the OTUs into two distinct groups: (1) T. divaricata ‘Ceylon Jasmine’ (Phud Supachok) and (2) other Pinwheel Jasmine forms. Five quantitative characters were identified as the most diagnostic: lamina length (LML), lamina width (LMW), corolla lobe length (CLL), distance from the corolla tube base to stamen attachment (DCS), and style length (STL). These traits exhibited exceptionally high F-values in K-means cluster analysis (404.11, 432.90, 327.54, 530.04, and 181.02, respectively; p<0.01), indicating strong discriminatory power. The results demonstrate that Phud Supachok is consistently and clearly morphologically distinct from other Pinwheel Jasmine forms. However, because this study is based solely on phenetic data, additional molecular evidence is required before definitive taxonomic conclusions can be made. Integrative studies combining molecular and morphological data are recommended to refine species delimitation within Tabernaemontana.
Copyright (c) 2026 Wilaiwan Nuchthongmuang, Sahanat Petchsri, Thaweesakdi Boonkerd, Siriporn Sripinyowanich, Touchkanin Jongjitvimol https://creativecommons.org/licenses/by-nc/4.0
Unveiling the Taxonomy and Potency of Boletellus minimatenebris (Wild Edible Mushroom) in Indonesia
Boletellus is a small genus of Boletaceae which is mostly distributed in the tropical area worldwide. Recently, several new species of Boletellus were introduced, including B. minimatenebris from Mexico in 2023. In 2024, a wild edible Boletellus resembling B. minimatenebris were encountered in forests and sold in traditional markets in Kendari, Indonesia. The current study was aimed at examining the taxonomical identity of our specimens and unraveling nutritional properties of this mushroom. The basidiomata was described based on the macro- and micromorphological characters. The molecular analysis and phylogenetic tree construction were performed using ITS 1/2 sequence. The proximate analyses were determined in accordance with AOAC. The combination of morphological and molecular analyses confirmed the identity of our specimens as B. minimatenebris. The indigenous people in sampling site use this species for self-consumption and sell it to local market. B. minimatenebris BO24644 is distinguished by smaller basidiomata when compared to other species within Boletellus but is larger compared to specimens from type locality. The inferred phylogenetic tree nested our specimen in the clade of B. minimatenebris from type locality (Mexico) and was a sister clade to B. aurocontextus. The proximate analysis showed low moisture and fat content, moderate fiber, high mineral presence, and a notably high protein level. In addition, the GC-MS analysis of methanolic extracts from B. minimatenebris revealed a diverse chemical profile dominated by fatty acid esters, sulphurous acid derivatives, and terpenoid. These results show the potential of B. minimatenebris BO24644 as a promising functional food.
Copyright (c) 2026 Ivan Permana Putra, Oktan Dwi Nurhayat, Pande Ayu Nayakasih Permatananda, Agessty Ika Nurlita, Lilis Supratman, Kania Dewi Shiyam, Sitti Aida Adha Taridala https://creativecommons.org/licenses/by-nc/4.0
Comparison of Chemical Composition and Quality of Honey from Tetragonula clypearis and Apis cerana in North Lombok, Indonesia
The quality of honey is strongly influenced by bee species and the types of plants used as nectar sources. This study aimed to evaluate and compare the quality of honey produced by Tetragonula clypearis and Apis cerana in North Lombok, Indonesia. Honey samples from T. clypearis were collected in Salut Village, Kayangan District, while samples from A. cerana were collected in Sukadana Village, Bayan District. The results revealed that honey from T. clypearis had significantly higher moisture content, ash, protein, total phenolics, minerals, and amino acids compared to honey from A. cerana. In contrast, the reducing sugar content was significantly higher in A. cerana honey. However, fat and flavonoid contents showed no significant differences between the two types of honey. Seventeen amino acids were identified in T. clypearis honey, while fourteen amino acids were identified in A. cerana honey. Based on the overall chemical composition, T. clypearis honey exhibited better quality compared to A. cerana honey.
Copyright (c) 2026 Agussalim, Ali Agus, Nafiatul Umami, Wan Iryani Wan Ismail https://creativecommons.org/licenses/by-nc/4.0
Perceptual Advantages of People Living in Semeru Volcanic Areas, Indonesia: An MRCV (Multiple Response Categorical Variable) Analysis
Why populations persist in active volcanic zones poses a fundamental challenge to risk perception models. We propose that perceptual advantages wherein tangible and intangible benefits filtered through local worldviews underpin this resilience. Through a thematic analysis of an open-ended question/answer study of communities in Mount Semeru, Indonesia, we identify six core frameworks of perceptual advantages. Analysis of Multiple Response Categorical Variable (MRCV) reveals that residents of high-risk zones cognitively amplify bio-cultural and livelihood benefits, showing significantly higher odds of emphasizing BIRTH/FAMILY (lineage/kin ties, birthright, and deep social networks that create an intergenerational connection to the land) and ECONOMIC (livelihood opportunities, including agriculture and volcano-driven tourism) advantages, while safe-zone residents prioritize ambient CLIMATE-related benefits (a preferred quality of life attributed to the region’s cool, fresh air and superior air quality). Crucially, the influence of gender is context-dependent, as significant disparities in perception vanish within the high-risk zone. In this environment, the shared experience of chronic volcanic threat supersedes gender distinction to foster a "community of fate". Within this collective, a shared risk-benefit calculus and a unified identity override individual perspectives. These findings demonstrate that persistence in hazardous environments reflects an active cognitive recalibration of risk and benefit, necessitating disaster policies that integrate these perceptual realities.
Copyright (c) 2026 Yanti Ariyanti, Sarah Nila, Winati Nurhayu, Dimitri Dubois, Kanthi Arum Widayati, Tri Atmowidi, Clément Mettling, Michel Raymond, Marc Willinger, Bambang Suryobroto https://creativecommons.org/licenses/by-nc/4.0
Valuable Bioproducts Production of Haematococcus lacustris Integrated with Phycoremediation of Liquid Digestate of POME (LDP) Under a Continuous Three-Stage Cultivation System
Integrating astaxanthin production by using Haematococcus lacustris with the LDP phycoremediation provides multiple benefits. However, as a highly sensitive organism, the cultivation needs to be regulated, such as selecting the most favorable media, regulating light intensity, adjusting LDP conentration, and evaluating the effect of NaCl on astaxanthin biosynthesis. In this study, we developed a new cultivation method, three-stage continuous cultivation system, by regulating the light intensity at each stage of microalgae growth. Based on the evaluation, the ideal medium was MES-volvox. The favorable light intensity for the adaptation phase was 600 lux, with the best LDP concentration of 3.75% and NaCl 1 g/L. The desirable light intensity in the three-stage cultivation system was 600 lux (days 0-6), 1,200 lux (days 6-16), and 3,500 lux (days 16-30). This system produced density, biomass, and astaxanthin content up to 91.54 × 104 cells/mL, 1 g/L, 0.83 g/L, respectively. Remarkably, the enrichment of NaCl did not reduce the density, carbohydrate, protein, or pigment content. Therefore, it may serve as a safe astaxanthin-enhancing stressor in the cultivation of this microalgae.
Copyright (c) 2026 Angga Puja Asiandu, Arief Budiman, Andhika Puspito Nugroho, Eko Agus Suyono https://creativecommons.org/licenses/by-nc/4.0
Detection of the PR-1 Resistance Gene and SSR-Based Genetic Diversity Analysis of S2 Lines in Local South Sulawesi and Introduced Maize
Maize cultivation in Indonesia faces significant challenges, particularly the prevalence of downy mildew. Plants infected by Peronosclerospora spp., the causal agents of this disease, increase the expression of pathogenesis-related (PR-1) proteins as an induced defense mechanism. Developing superior varieties through breeding programs requires robust germplasm management to maintain broad genetic diversity. Therefore, utilizing biomolecular methods to detect resistance genes and analyze genetic diversity is a strategic approach for maize genetic improvement. This study aimed to evaluate the basal expression of the PR-1 gene associated with downy mildew resistance and analyze the genetic diversity of S2 lines derived from local South Sulawesi maize (Sinjai and Tana Toraja) and introduced maize (National Varieties and CIMMYT). Of the 30 lines used, consisting of 5 lines from local Sinjai maize, 15 lines from local Tana Toraja maize, and 10 lines of introduced maize, all were detected to have the PR-1 gene. Meanwhile, the genetic diversity analysis using 15 pairs of SSR primers from 10 chromosomal loci spread across corn obtained an average number of alleles of 10.27 alleles/locus and an average polymorphism information content (PIC) value of 0.76 (very informative). Cluster analysis shows a similarity coefficient value ranging from 0.68 to 0.96, with two main clusters at a similarity coefficient of 0.68. Cluster I consists of 27 lines, and Cluster II consists of 3 lines. The greatest genetic distance is possessed by the lines LK1 and BK5. The presence of the PR-1 gene and the high genetic diversity observed in the S2 lines represent promising genetic materials for developing maize varieties with durable resistance to downy mildew.
Copyright (c) 2026 Iin Kusmawati, Juhriah, Rosana Agus https://creativecommons.org/licenses/by-nc/4.0
Vital But Vulnerable: The Population Structure of Macaca maura in Bantimurung Bulusaraung National Park, South Sulawesi
Macaca maura is an endemic primate of South Sulawesi, currently listed as Endangered due to habitat fragmentation and increasing anthropogenic pressure. This study aims to analyze the population density, age structure, spatial distribution, and food types consumed by M. maura in the Karaenta Forest, TN Babul. This field study was conducted over four months (August–November 2024) using a grid-based home-range survey. The study area was divided into 1 × 1 km² grid plots; each encounter with M. maura was recorded with X–Y coordinates to visualize the movement patterns of each group. Data were collected through direct observation of eight groups (A–H) with a total of 193 individuals. Group sizes ranged from 13 individuals (Group F) to 39 individuals (Group A). Population density ranged from 52 to 134 individuals/km² with an average of 92 individuals/km². The age distribution, with an average IFR of 0.69, indicates that there is less than one infant per adult female in the M. maura population, suggesting a low reproductive rate. Most individuals were observed on the ground rather than in trees or on cliffs, indicating a preference for terrestrial habitats. Dietary records show considerable flexibility, with 27 plant species being utilized. These findings underscore the need for targeted habitat management strategies aligned with the species' ecological needs. This study provides baseline data to support future evidence-based conservation planning and environmental monitoring of M. maura.
Copyright (c) 2025 Warda Murti, Fatchur Rohman, Murni Saptasari, Ibrohim Ibrohim https://creativecommons.org/licenses/by-nc/4.0
Population Dynamics of Pests and Natural Enemies of Rice (Oryza sativa L.) Across a Karst Distance Gradient in the Bantimurung-Bulusaraung Exokarst Region, Bantimurung District, Maros Regency, South Sulawesi
Exokarst landscapes possess distinctive geomorphological and microclimatic characteristics that influence arthropod abundance and community structure in rice (Oryza sativa L.) ecosystems. Cooler and more humid microhabitats near karst formations can function as refuges that support resource stability, habitat connectivity, and trophic interactions. This study examined how distance from a karst cliff affects the abundance and composition of pest and natural enemy arthropods. Observations were conducted at three distances (0, 200, and 400 m), representing near-karst, transitional, and outer-karst microclimate zones in Kalabbirang, Bantimurung District, Maros Regency, South Sulawesi, Indonesia. A total of 1,483 individuals from 21 species were recorded. Arthropod abundance was highest at 400 m (549 individuals), followed by 0 m (477 individuals) and 200 m (457 individuals). Although total abundance was lower at 200 m, this site showed the highest species richness (S = 2.78), Shannon diversity (H′ = 2.15), and evenness (E = 0.76), indicating a more balanced community structure. Dominance was greatest at 400 m (D = 0.20), largely due to the high abundance of Coccinella sp. (205 individuals). Bactrocera dorsalis was most abundant at 0 m (125 individuals), Nephotettix virescens peaked at 200 m (106 individuals) but declined at 400 m (10 individuals), while Leptocorisa oratorius increased toward 400 m (70 individuals). Predator communities were dominated by Lycosa pseudoannulata (317 individuals). Correlation and PCA results indicate that karst-related microclimatic gradients structure arthropod communities and contribute to stronger natural pest suppression in outer-karst zones.
Copyright (c) 2026 Amiruddin Amin; Sylvia Sjam, Itji Diana Daud https://creativecommons.org/licenses/by-nc/4.0
Panicle Trait Diversity and Its Impact on the Productivity of Indonesian Foxtail Millet (Setaria italica L. Beauv.) Genotypes
Foxtail millet is a climate-resilient cereal crop that is growing in importance in food security and sustainable agriculture. This study aimed to identify panicle traits associated with yield, determine functional traits suitable for selecting high-productivity genotypes, and classify superior local Indonesian foxtail millet genotypes. Eight genotypes were evaluated using a randomized complete block design with three replications. Correlation analysis of 31 panicle traits revealed that grain filling rate, panicle weight, grain weight per panicle, grain weight per plant, and grain numbers on the middle and lower primary branches were positively associated with yield. Several of these traits also exhibited high broad-sense heritability and moderate GCV and PCV values, indicating their potential for selection. Principal component and two-way heatmap cluster analyses identified Buru, ICERI-7, Hambapraing, and Mauliru-2 as high-yielding genotypes. The findings provide critical insights for foxtail millet breeding programs in Indonesia focused on improving yield.
Copyright (c) 2025 Marisa Vidya Luthfiani, M Reza Pahlevi, Bambang Sapta Purwoko, Sintho Wahyuning Ardie https://creativecommons.org/licenses/by-nc/4.0
Seaweed Diversity and Bioactive Compounds in Panjang Islands, Central Java, Indonesia
The biodiversity of seaweed encompasses a wide array of potential bioactive compounds applicable to various industries, particularly pharmaceuticals. This study aimed to collect seaweed diversity data from Panjang Island, Jepara, Central Java, Indonesia, and to identify the bioactive compounds and biological activity of each seaweed species for preliminary screening. Random sampling was used to collect the sample. Qualitative identification of bioactive compounds was performed using the maceration method for extraction, phytochemical screening tests, and pigment identification based on Rf values on TLC. Antibacterial screening tests were performed against Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria, followed by testing against pathogenic fungi (C. albicans) using the disk diffusion method, and an antioxidant test using the DPPH method. The results showed that six species from three phyla (Chlorophyta, Phaeophyta, and Rhodophyta) exhibited distinct morphological characteristics, and the types of bioactive compounds produced by each species differed. The biological activity test results showed a low inhibitory activity. Antibacterial and antifungal biological activities were at the value of (<5 mm), and antioxidant biological activity was (>750 ppm). However, the active compounds and pigments with potential antibacterial, antifungal, and antioxidant properties can be optimized in various fields of bioindustry in the future.
Biodiversity Biotechnology Marine Ecology
Copyright (c) 2026 Wilis Ari Setyati, Rini Pramesti, Angela Salsalina Putri, Danendra Aquila Azfa Risandhi, Syifa Shafira Firdaus, Josua Gabriel Lumban Gaol https://creativecommons.org/licenses/by-nc/4.0
Shifting Root Strategies: Impacts of Forest Conversion on Fine Root Traits in Monoculture Systems
The intensification of land-use from natural forests to monoculture systems such as rubber and oil palm plantations alters soil structure and resource availability, thereby affecting fine root acquisition strategies. This study assessed the impact of land-use intensification on fine root morphology, water content, and acquisition strategies across different land-use types. Fine root samples were collected from four systems: natural forest, jungle rubber, rubber, and oil palm plantations (five plots per system). Fine roots were classified into absorptive (first–third order) and transportive (fourth–fifth order), and traits were analyzed using WinRHIZO Pro 2020a. The results showed a decline in absorptive root length along the intensification gradient, with oil palm significantly shorter than forest and jungle rubber. In contrast, root length per area (RLA) was higher in the forest than in rubber plantations. Absorptive root tip length was significantly greater in oil palm compared to rubber. Transportive root length also declined, with significant differences only between oil palm and jungle rubber. Fine root diameter (FRD) and root tissue density (RTD) tended to increase, while specific root length (SRL) and specific root area (SRA) tended to decrease in absorptive roots. In transportive roots, SRL was inconsistent, and SRA remained stable. Water content tended to decrease in absorptive roots but remained relatively stable in transportive roots.
Copyright (c) 2026 Susi Susilawati, Sulistijorini Sulistijorini, Sasya Samhita, Triadiati Triadiati https://creativecommons.org/licenses/by-nc/4.0
Introduction of the OsGERLP Gene into Potato cv. IPB CP3 to Develop Aluminum Stress-Tolerant Potato Lines
The OsGERLP gene is an aluminum (Al) stress tolerance gene. Potato cv. IPB CP3 is a horticultural crop that has not been proven to be tolerant to Al; therefore, enhancing its tolerance through genetic transformation is necessary. This research aims to obtain transgenic potatoes cv. IPB CP3 contains the OsGERLP gene and is tolerant to Al stress. Experimental methods include transforming potatoes with the OsGERLP gene via Agrobacterium tumefaciens, transgene integration testing, in vitro assays of transgenic plants under low pH and Al stress, and analysis of transgene expression. The results showed that the transformation efficiency achieved was relatively high at 47.03%, with a regeneration efficiency of 42.19%. The transgenic clones had longer roots and more roots than the non-transgenic ones under aluminum stress. The transgenic clones GERLP2, GERLP3, and GERLP4 exhibited the greatest root growth enhancement under stress conditions and the highest OsGERLP gene expression levels. These clones have the potential to be developed into Al-tolerant potato varieties. Future research is required to evaluate aluminum stress tolerance, tuber yield performance, and transgene stability across the three clones under greenhouse and field conditions of the three clones.
Copyright (c) 2026 Farah Mahfudhah, Aris Tjahjoleksono, M. Miftahudin https://creativecommons.org/licenses/by-nc/4.0
Ground-Dwelling Insects as Bioindicators for Post-Mining Restoration in Pangkep Regency, South Sulawesi, Indonesia
Ground-dwelling insects are key indicators of ecosystem health due to their roles in decomposition, nutrient cycling, and the dynamics of food webs. Post-mining lands often suffer from environmental degradation, requiring effective reclamation strategies. This study assessed the relationship between microclimate and ground-dwelling insect composition in reclaimed limestone and clay mining sites at PT Semen Tonasa, Pangkep Regency, South Sulawesi, Indonesia. Insects were sampled using pitfall traps across sites with different reclamation years. Diversity indices Shannon-Wiener (H'), richness (R), evenness (E), dominance (D), correlation analysis, and principal component analysis (PCA) were used to evaluate patterns. A total of 23,294 individuals representing 36 species, 26 families, and nine orders were recorded. Dominant species included Dolichoderus thoracicus and Carebara diversa, indicating high ecological adaptability. The highest diversity (H' = 2.09) and richness (R = 3.32) were found in the 2017 clay site, while the 2018 limestone site had the highest evenness (E = 0.85) and dominance (D = 0.36). Correlation analysis showed that soil temperature and humidity were significantly positively associated with insect diversity (r>0.60, p<0.05). PCA revealed air temperature, humidity, soil pH, and light intensity as key factors influencing insect communities, accounting for 52.08% (PC1) and 28.63% (PC2) of the variance. These findings highlight the importance of microclimate-informed management for successful post-mining land restoration.
Copyright (c) 2026 Sitti Nuraeni, Nurul Amelia Wulandari, Andi Prastiyo https://creativecommons.org/licenses/by-nc/4.0
Arrowroot (Maranta arundinacea L.) Tuber Extract Modulated Gut Microbiota and Improved Glycemic Control in Type 2 Diabetic Mice
Type 2 diabetes mellitus (T2DM) is a metabolic disorder characterized by hyperglycemia and has become a global health concern. Gut microbiota alterations significantly influence diabetes onset, which can be mitigated through prebiotic intake. Arrowroot tubers (Maranta arundinacea L.) possess prebiotic potential due to their oligosaccharide and dietary fiber content. This study evaluated the effects of arrowroot tuber extract on blood glucose, glucose tolerance, and gut microbiota composition in a T2DM mouse model. Tubers were macerated in ethanol, and BALB/c mice were fed a high-fat diet for five weeks, followed by streptozotocin injection (35 mg/kg) to induce T2DM. Mice received 150 mg of arrowroot tuber extract orally for 28 days. Blood glucose levels were measured on days 0, 14, and 28, and an oral glucose tolerance test (OGTT) was performed. Cecal samples collected after four weeks underwent 16S rRNA sequencing, and data were analyzed using One-Way ANOVA (p<0.05). Treatment with arrowroot tuber extract for 28 days reduced blood glucose levels by 40.5% and improved glucose tolerance. The extract modulated gut microbiota, decreasing harmful bacteria while increasing short-chain fatty acid (SCFA)-producing genera such as Lachnospiraceae NK4A136, Ligilactobacillus, and Alistipes. These results indicate that arrowroot tuber extract can beneficially alter gut microbiota composition and ameliorate hyperglycemia, suggesting its potential as a prebiotic-based therapeutic strategy for managing T2DM.
Copyright (c) 2025 Artini Pangastuti, Putri Regita Anggraini, Shanti Listyawati, Siti Lusi Arum Sari https://creativecommons.org/licenses/by-nc/4.0
Preclinical Evaluation of HPV Type 52 L1L2 Chimeric Protein as a Cervical Cancer Vaccine Candidate
High-risk human papillomaviruses (HPVs) are the primary etiological agents of cervical cancer, accounting for more than 300,000 deaths annually worldwide. Current prophylactic vaccines based on recombinant L1 major capsid virus-like particles (VLPs) have demonstrated strong efficacy but are restricted to a limited spectrum of HPV types. To address this limitation, the present study evaluated a recombinant L1L2 chimeric protein derived from HPV type 52 as a potential candidate for a broad-spectrum vaccine. The chimeric protein was expressed in Escherichia coli strain BL21 (DE3) and purified for immunization studies. Female BALB/c mice (Mus musculus, n = 5 groups) were immunized, and immune responses were analyzed by enzyme-linked immunosorbent assay (ELISA) and pseudovirion-based neutralization assays (PBNA). The recombinant L1L2 vaccine candidate induced detectable antibody responses against HPV antigens; however, neutralizing activity remained modest. Histopathological analysis of liver and kidney tissues showed no evidence of toxicity, supporting the safety profile of the candidate. In summary, these results suggest that the HPV type 52 L1L2 chimeric protein represents a promising platform for the development of cervical cancer vaccines, although further optimization is required to achieve robust cross-neutralizing efficacy.
Copyright (c) 2025 Isti Kartika Sari, Joko Pamungkas, Apon Zaenal Mustopa, I Wayan Teguh Wibawan, Jendri Mamangkey, Sheila Chairunnisa, Herman Irawan, Ai Hertati, Nurlaili Ekawati, Rifqiyah Nur Umami, Ela Novianti, Maritsa Nurfatwa, Huda Shalahudin Darusman https://creativecommons.org/licenses/by-nc/4.0
A Comparative Study of Penicillin G Acylase Expression in Two Escherichia coli Strains: BL21 (DE3) and Arctic Express
The growing demand for semisynthetic beta-lactams has directed attention towards enzymes, specifically Penicillin G Acylases (PGAs), for their potential in synthesizing these antibiotics. This study delves into the expression of Achromobacter xylosoxidans PGA (AxPGA) in Escherichia coli, with a focus on enhancing the yield of active PGA, often constrained by a complex maturation process. The optimization of PGA expression included variations in IPTG concentration and the addition of CaCl2. Furthermore, the study compared PGA expression in E. coli BL21 (DE3) with that in E. coli Arctic Express (DE3), capable of co-expressing chaperones (chaperonin Cpn60 and Cpn10). Induction with 0.5 mM IPTG resulted in the highest hydrolytic activity in both strains, with Arctic Express (AE) exhibiting significantly higher activity due to improved folding facilitated by cold-adapted chaperonins. Alongside optimal IPTG induction, the addition of 10 mM CaCl2 in the culture media significantly increased PGA activity in both strains, highlighting that Ca2+ supplementation is an effective strategy to enhance the yield of functional PGA. Subcellular fractionation demonstrates that the periplasmic fraction yielded higher volumetric and specific activities compared to the cytoplasmic fractions in both E. coli strains, highlighting the importance of periplasmic processing for PGA maturation. This suggests that extracting the periplasmic fraction is an effective strategy for recovering active PGA while avoiding or reducing contamination either from co-expressed cytoplasmic chaperones or other intracellular proteins. These findings emphasize that induction strategy, ionic stabilization, and host strain selection play synergistic roles in increasing active recombinant PGA expression.
Copyright (c) 2026 Kartika Sari Cendana, Sri Rezeki Wulandari, Gabriela Christy Sabbathini, Maria Ulfah, Dini Achnafani, Abinawanto, Sunni Sofiah Aniqah, Is Helianti, Niknik Nurhayati https://creativecommons.org/licenses/by-nc/4.0
Pathogenicity, Molecular Identification, and Integrated Disease Management of Nigrospora oryzae on Rice
The opportunistic fungal pathogen Nigrospora oryzae poses a growing threat to global rice production, especially given its enhanced virulence in co-infections with other pathogens. This study aimed to characterize the pathogen and identify effective integrated disease management strategies. Isolates from Indonesia were identified using morphological and molecular markers, including the ITS and ACT genes, which confirmed a strong genetic link to a rice-native strain from China, ruling out a recent host jump from oil palm. Pathogenicity assays demonstrated the fungus’s opportunistic nature, as its virulence and disease progression were significantly heightened when co-inoculated with Curvularia lunata. In vitro fungicide tests revealed a high sensitivity to methyl thiophanate (EC50 ~250 ppm ) but a lower sensitivity to azoxystrobin. Furthermore, silicon application effectively suppressed the disease, highlighting that some rice varieties responded better than others; the IPB 3S variety experienced a 30% reduction in disease incidence compared to 16% in Situ Bagendit. These findings establish a comprehensive framework for integrated disease management, combining varietal selection and silicon application with targeted chemical control to combat this emerging threat.
Copyright (c) 2026 Hagia Sophia Khairani, Nurbaiti Santika Prima, Daniella Elva Talita, Anggi Nindita, Efi Toding Tondok, Suryo Wiyono https://creativecommons.org/licenses/by-nc/4.0
Preparation and Characterization of P(3HB-co-HHX)/Silk Fibroin Nanofiber for Chondrogenic Differentiation on Human Adipose Mesenchymal Stem Cell
This study explored the proliferative and chondrogenic diﬀerentiation capacities of nanofiber containing silk fibroin hybrid Bombyx mori silkworm cocoons (Japan-China SP-01 variant from Indonesia) and PHA P(3HB-co-3HHx) on human adipose mesenchymal stem cells. First, the scaffolds were prepared for electrospinning by combining two distinct biomaterials, consisting of silk fibroin derived from hybrid Bombyx mori silkworm cocoons, with a combination of 3-hydroxybutyrate (3HB) and 3-hydroxyhexanoate (3HHx). The effects of various ratios of P(3HB-co-3HHx)/Silk Fibroin nanofiber mixture on proliferative and differentiation capacity were then investigated. Following that, the morphology, chemical compositions, contact angle, tensile strength, roughness, cell viability, and human adipose mesenchymal stem cell differentiation of the nanofiber were investigated by collagen type 2 gene expression. The results of scanning electron microscopy showed the mean diameter of the nanofiber ranged from 370-600 nm. Following that, 16,000 volts was prominent for nanofiber manufacture in all ratios. It was also demonstrated that the nanofiber has significant mechanical properties, acceptable hydrophilicity and smoothness, and appropriate cell viability (up to 99.1% compared to the control on silk fibroin nanofiber). Although PHA increased tensile strength, silk fibroin administration to the mixture predominantly enhanced chondrogenic differentiation, as evidenced by modulation of chondrogenic collagen type 2 (up to 8.718-fold) gene markers. Furthermore, the physicochemical characteristics of the nanofiber mixture significantly influenced the proliferation and differentiation of human adipose mesenchymal stem cells. The results of the tests showed that silk fibroin administration into a nanofiber mixture has improved chondrogenesis and showed great potential as a cartilage tissue scaffold.
Copyright (c) 2026 Andri Pramesyanti Pramono, Retno Yulianti, Muhamad Alif Razi, Karina, Shaik Ling Ang, Kumar Sudesh, Hanan, Yuni Cahya Endarwati, Muhammad Radian Ghoza https://creativecommons.org/licenses/by-nc/4.0
Characterization of Lignin Biosynthesis Encoding Gene, SiCOMT, from Nine Indonesian Foxtail Millet (Setaria italica (L.) P. Beauv.) Genotypes
Caffeic acid O-methyltransferase (COMT) is an essential enzyme that catalyzes the biosynthesis of lignin monomer units. Foxtail millet (Setaria italica) possesses three COMT-encoding genes. However, only SiCOMT1 and SiCOMT2 are considered expressed. This study investigates the characteristics of the two COMT-encoding genes across nine Indonesian foxtail millet genotypes. Phylogenetic analysis revealed that SiCOMT1 is closely related to N-methyltransferase genes, which are not involved in the lignin biosynthesis pathway. Meanwhile, SiCOMT2 is closely related to O-methyltransferase genes involved in lignin biosynthesis. SiCOMT2 from nine Indonesian foxtail millet genotypes exhibits 15 synonymous and three non-synonymous SNPs. SiCOMT2 amino acid showed Ala67Thr and Pro72Ala variations within the methyltransferase dimerization domain, and Glu146Asp within the O-methyltransferase domain. Among these, the Pro72Ala substitution is predicted to reduce the structural stability of the encoded protein. These findings suggest that SiCOMT2 may serve as a promising target for future genetic research and crop improvement strategies aimed at enhancing biomass quality by modifying lignin content and composition.
Copyright (c) 2026 Ramadaniarto Rizqullah, Nirwanti Saenal, M Reza Pahlevi, Willy Bayuardi Suwarno, Daisuke Tsugama, Sintho Wahyuning Ardie https://creativecommons.org/licenses/by-nc/4.0
Silicon Enhances Banana Resistance to Fusarium oxysporum f.sp. cubense through Ethylene Signaling Modulation and Root Tissue Protection
Fusarium oxysporum f.sp. cubense Tropical Race 4 (Foc TR4) is an agent of banana's vascular wilt that severely hampers production. It has been indicated that silicon (Si) might play a role in plant defense, but the banana–Foc pathosystem mechanism needs to be investigated. This study aimed to assess the impact of Si supplementation on banana plant responses to Foc infection, particularly using a completely randomized design arranged in four treatments: Control, Foc, Si, and Si*Foc. The transcript levels of the ethylene-receptor (EIN1, EIN3), ethylene-response factor (ERF1, ERF2), and the defense marker PR4 were quantified using qRT-PCR. Phenotypic observation, corm lesion severity, and root anatomy were also evaluated. Results indicated that early ethylene signaling (EIN1, EIN3) was down-regulated, and ERF2 was up-regulated in the presence of Si during Foc infection. Foc-infected plants treated with Si displayed smaller lesion areas, greater root structural stability, and less aerenchyma formation. Plant growth reduction caused by Foc was also relieved by Si, showing increased root-to-shoot biomass ratios and modified leaf shape. Multivariate analysis validated differences in physiological and transcriptional patterns in Si*Foc plants. These results indicate that Si improves banana resistance to Foc by regulating ethylene-mediated defense, tissue integrity, and stress resistance.
Copyright (c) 2025 Arief Pambudi, Yunus Effendi, Lisdar I Sudirman, Miftahudin https://creativecommons.org/licenses/by-nc/4.0
Evaluation of the MicroRNA184 Levels in Women with Miscarriage Association with Toxoplasmosis, Rubella, and CMV Infections
MiR-184 plays a significant regulatory role in immunity during pregnancy. Its dysregulation in toxoplasmosis and rubella infection is strongly associated with increased risk of abortion . Further clinical studies are needed to validate miR-184 as a diagnostic marker and therapeutic target in pregnancy complications. One hundred specimens of blood were taken from the miscarriage ladies, with age ranges between 15 and 50 years, who were complaining of TORCH infections. The findings showed that the age range group (<20-29 years) was the highest at (59.0%), followed by (30-39 years) at (36.0%), and then (40-46 years) 5 (5.0%). Distribution of infections according to residency showed the patients that living in rural areas were higher 59 (59.0%) than those who lived in urban areas (41.0%), while the number and percentage of acute infections with rubella were higher 29 (29%) than toxoplasmosis (4.0%) in aborted women with TORCH infections. However, 4 (4.0%) of Toxoplasmosis was recorded compared to 0 (0.0%) CMV infection. The evaluation of IgM antibodies showed that Rubella IgM levels were higher at 29 (29.0%) in comparison to CMV IgM levels of 0 (0.0%). The number and percentage of rubella IgM levels among the age group (<20-29) were higher (18.0%) than in other age groups, while it was (9.0%) among the age group (30-39) years and 4 (4.0%) among Toxoplasmosis. Out of 100 patients, gene expression of MicroRNA-184 was done on 33 patients, and the results revealed that 10 (27.2%) of the aborted women were carriers of Toxoplasmosis, CMV, and Rubella IgM, and they had positive MicroRNA-184.
Copyright (c) 2026 Sarah A. Mahmood, Salwa S. Muhsin, Rawah A. Faraj https://creativecommons.org/licenses/by-nc/4.0
Exploring the Genetic Landscape of Octopus cyanea: Connectivity and Population Structure in Northern Waters of Sumatra
Octopus cyanea is an ecologically and economically important cephalopod with wide larval dispersal influenced by ocean currents. However, geographic isolation among island clusters in northern Sumatra may restrict gene flow and shape population structure. This study investigated the genetic diversity and connectivity of O. cyanea from five populations (Aceh Island, Weh Island, Banyak Island, Simeulue Island, and Nias Island) using mitochondrial cytochrome c oxidase subunit I (COI) sequences. A total of 21 individuals were successfully amplified, yielding 651 bp fragments. Sequence analysis revealed 11 haplotypes across populations, with haplotype diversity (Hd) ranging from 0.285 in Banyak Island to 0.800 in Aceh Island, and nucleotide diversity (π) between 0.001 and 0.009. Pairwise genetic distances varied from 0.000 to 0.004, with the highest divergence observed between Simeulue Island and Nias Island (0.004), while Aceh Island and Weh Island showed no differentiation. AMOVA indicated that most genetic variation occurred within populations (68.74%), with an overall Fst of 0.315, suggesting low to moderate genetic structuring. The haplotype network demonstrated shared haplotypes among four populations, whereas Simeulue Island harbored unique haplotypes, indicating partial genetic isolation. These results highlight substantial genetic connectivity among O. cyanea populations in northern Sumatra, facilitated by larval dispersal via ocean currents, but also emphasize localized divergence in Simeulue Island. The findings provide critical baseline data for developing ecosystem-based fisheries management, supporting shared stock strategies while accounting for population-specific conservation needs.
Copyright (c) 2026 Mutia Ramadhaniaty, Adrian Damora, Intania Moula, Nur Fadli, Nanda Muhammad Razi, Zainal A Muchlisin https://creativecommons.org/licenses/by-nc/4.0
Application of Lactic Acid Bacteria to Produce Bioactive Compounds from Tofu Waste Using Pineapple Bromelain Enzyme
Tofu is one of the main human foodstuffs and has become an alternative substitute for animal protein. Tofu contains relatively high protein, and active compounds, but the waste produced during the tofu processing process is very abundant, namely 3.5 million tons per year in Indonesia. The production of active compounds from tofu waste can use bromelain enzymes. The bromelain enzyme in this study was produced from the fermentation of pineapple leaf waste using Pediococcus pentosaceus E7. The production of active compounds from tofu waste has not been widely reported, so this study aimed to produce active compounds from tofu waste. This study began with bromelain production, measurement of bromelain activity, bromelain precipitation, peptide production from tofu waste, Liquid Chromatography-Mass Spectrometry (LC-MS) analysis, and antibacterial testing of active compounds derived from tofu waste degradation. The results showed that the peptide content of tofu liquid waste degraded using the bromelain enzyme was 41.01±0.06 mg/mL. The LCMS results showed that 18 bioactive compounds were contained in the degradation products of tofu liquid waste. The active compounds derived from the degradation of tofu waste are capable of inhibiting the growth of Salmonella Typhimurium ATCC 14028, yielding a clear zone index of 2.53±0.12.
Copyright (c) 2026 Zulfiqar Lukman, Dimas Andrianto, Anja Meryandini https://creativecommons.org/licenses/by-nc/4.0
Transcriptomic Dissection of Long-Juvenility in Soybean: A Comparative Study of Grobogan Cultivar and Its Derivative Long Juvenile AP18 Line
The long juvenile (LJ) trait in soybean extends the vegetative phase, enabling cultivation in low-latitude regions. This study investigated transcriptomic differences between the Grobogan cultivar (control) and the AP18 (LJ) soybean line using RNA-seq. Young leaf tissues from plants at the vegetative stage were collected under field conditions and sequenced using the Illumina NovaSeq 6000 platform. After quality filtering and alignment to the soybean reference genome, 24,716 expressed transcripts were retained for analysis. Differential expression analysis identified 5,005 upregulated and 4,534 downregulated transcripts in AP18 relative to Grobogan. Functional enrichment analysis revealed the upregulation of genes involved in ribosome biogenesis and secondary metabolism, and the downregulation of genes related to photosynthesis and energy metabolism. While known LJ-related genes FT2A (E9) and ELF3B (J) showed differential expression, the magnitude was modest. These findings highlight widespread transcriptomic reprogramming associated with the LJ trait, providing insight into potential pathways that influence juvenile phase extension.
Copyright (c) 2025 Habib Rijzaani, I Made Tasma https://creativecommons.org/licenses/by-nc/4.0