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All Journal HAYATI Journal of Biosciences Jurnal Ilmu Pertanian Indonesia Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Biotechnology Biology, Medicine, & Natural Product Chemistry Jurnal Sumberdaya Hayati BIOLINK (Jurnal Biologi Lingkungan, Industri, Kesehatan) Menara Perkebunan Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Jurnal Natural Quagga: Jurnal Pendidikan dan Biologi Bioma : Jurnal Ilmiah Biologi Berita Biologi Biodiversitas Journal of Biological Diversity
Rika Indri Astuti
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus IPB Darmaga, Bogor 16680
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Education Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Physics Public Health

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Bacterial community profiles of leaves of wild and cultivated pohpohan (Pilea melastomoides (Poir.) Wedd.) plants based on a metagenomic analysis EVRICK YONANTIKO; RIKA INDRI ASTUTI; SRI BUDIARTI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 9 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250921

Abstract

Abstract. Yonantiko E, Astuti RI, Budiarti S. 2024. Bacterial community profiles of leaves of wild and cultivated pohpohan (Pilea melastomoides (Poir.) Wedd.) plants based on a metagenomic analysis. Biodiversitas 25: 2996-3004. Recent studies show that fresh vegetables serve as hosts for diverse endophytic bacterial communities. In Indonesia, certain tropical plants are consumed fresh without cooking, which may raise concerns regarding human health and food safety. Pilea melastomoides (Poir.) Wedd. is a traditional food plant consumed fresh as a vegetable by the Sundanese people in Indonesia. This plant grows in the wild and can be cultivated in a standard plantation, thereby raising the question of the endophytic bacterial communities in both planting systems. Thus, this study aimed to profile the bacterial communities in wild and cultivated P. melastomoides via a metagenomic approach targeting the 16S rRNA gene. Data analysis revealed that the leaf samples collected from the cultivated plants exhibited the highest diversity, as indicated by the diversity indices of species richness based on Chao1 (0.0244), Shannon (0.0291), and species evenness based on Pielou (0.0282). The most abundant bacterial phyla identified were Firmicutes and Proteobacteria. In cultivated plants, the predominant endophytic bacteria included: Limosilactobacillus (5.38%), Escherichia/Shigella (4.96%), Bacillus (4.76%), Salmonella (3.57%), and Staphylococcus (3.57%). In contrast, certain genera of pathogenic bacteria, such as Escherichia/Shigella (15.59%), Bacillus (10.48%), Limosilactobacillus (9.00%), Salmonella (7.78%), and Listeria (5.94%), were dominant among the wild plants. The findings of pathogenic bacteria are dominated by Gram-negative bacteria, which play a role in the nitrogen, carbon, and sulfur cycles. The stable and consistent presence of endophytic bacteria in plant tissues provides opportunities for long-term studies for food safety and sustainable agricultural practice strategies. Further analysis should be conducted to confirm the virulence of these pathogens in both wild and cultivated P. melastomoides plants.
Effect of probiotic yeast Pichia kudriavzevii 2P10 and mannan-oligosaccharide on the intestine health of rat infected with Salmonella Typhimurium RAHAYU WULAN; RIKA INDRI ASTUTI; YAYA RUKAYADI; SRI ESTUNINGSIH; ANJA MERYANDINI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 1 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260133

Abstract

Abstract. Wulan R, Astuti RI, Rukayadi Y, Estuningsih S, Meryandini A. 2025. Effect of probiotic yeast Pichia kudriavzevii 2P10 and mannan-oligosaccharide on the intestine health of rat infected with Salmonella Typhimurium. Biodiversitas 26: 335-344. Recent evidence suggests that probiotic yeast is efficacious against bacterial infections. This study evaluated the effects of dietary supplementation with the live yeast probiotic Pichia kudriavzevii 2P10, Mannan-Oligosaccharide (MOS), and their combination on the growth performance and intestinal health of male Sprague-Dawley (SD) rats infected with Salmonella Typhimurium ATCC 14028 (ST). Two groups were studied: one without ST infection, including P. kudriavzevii 2P10 (PRO), MOS, and their combination (PMOS), and one with ST infection, including CONTROL.ST, PRO.ST, MOS.ST, and PMOS.ST. A diet of 108 CFU/mL PRO and 5% MOS was administered orally for 15 days, followed by a challenge with 108 CFU/mL ST in the ST group. After three days of challenge, the parameters were observed. The findings of this research are that ST infection in rats can cause colonization of ST in the ileum, causing a decrease in white blood cells, necrosis of epithelial cells, and an increased villous-to-crypt ratio (VCR) as a response to inflammation. The administration of PRO, MOS, and their combinations prevents inflammation, as proven by the absence of necrosis and epithelial desquamation. PRO, MOS, and their combinations stimulate intestinal health by increasing villus height, width, and VCR. MOS was found to be the best for increasing lactic acid bacteria. During ST infection, P. kudriavzevii 2P10 can coagulate with ST in the ileum, with this yeast-bacteria binding mechanism allowing free Salmonella Typhimurium cells to bind more to P. kudriavzevii 2P10 cells than to intestinal epithelial cells so that bacterial infection can be prevented. In conclusion, P. kudriavzevii 2P10 administration was the best for stimulating growth performance and intestinal health and preventing severe ST infection in male SD rats, offering promising avenues for further research and potential practical applications in human and animal nutrition and health.
Pyocyanin derived from the marine sponge-associated bacterium, Pseudomonas aeruginosa P1.S9, has the potential as antibacterial DOVA KELVIN MESRIAN; RIKA INDRI ASTUTI; MUHAMMAD EKA PRASTYA; ARIS TRI WAHYUDI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 11 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251113

Abstract

Abstract. Mesrian DK, Astuti RI, Prastya ME, Wahyudi AT. 2024. Pyocyanin derived from the marine sponge-associated bacterium, Pseudomonas aeruginosa P1.S9, has the potential as antibacterial. Biodiversitas 25: 4139-4147. Sponge-associated bacteria are a prolific source of secondary metabolites. Among them, pyocyanin-producing Pseudomonas aeruginosa is a subject of great interest. Pyocyanin is a blue-green pigment known for its enormous biological activity, one of the most notable being antimicrobial. Therefore, this study was performed to optimize the production, to characterize the chemical structure, and to test the antimicrobial activity of pyocyanin. As the sole isolate used, Pseudomonas aeruginosa P1.S9 provided a fundamental premise for pyocyanin synthesis by revealing the presence of phzM and phzS genes. The proteins generated from these genes were highly compatible with two enzymes involved in the pyocyanin production pathway. During the optimization, the maximum level of pyocyanin produced was 29.057±0.691 µg mL-1. The concentration was obtained using a modified King's A medium incubated at 27°C within four days. To assess its purity, the chemical structure of pyocyanin was confirmed by several spectroscopic techniques including UV-Visible (UV-Vis), Fourier Transform Infrared (FT-IR), and Nuclear Magnetic Resonance (1HNMR). All test results closely resemble purified pyocyanin compared to several prior studies. In terms of antimicrobial activity, pyocyanin was effective against ATCC strains of Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Its strongest minimum inhibitory concentration (MIC) was 62.5 µg mL-1 against Bacillus subtilis. Subsequently, the accumulation of reactive oxygen species (ROS) as a major mechanism of pyocyanin antibacterial activity has also been verified. The bacterial pathogens cells treated with pyocyanin displayed a brighter luminescence compared to the control without pyocyanin after the addition of 2',7'-dichlorodihydrofluorescein diacetate (H2DCF-DA). Ultimately, the present work comprehensively characterized pyocyanin's promising producer and antibacterial properties.
Peat-derived Streptomyces spp. isolated from edamame rhizosphere with plant growth-promoting properties IRA ERDIANDINI; ARIS TJAHJOLEKSONO; RIKA INDRI ASTUTI; EDI HUSEN; ARIS TRI WAHYUDI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 1 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260132

Abstract

Abstract. Erdiandini I, Tjahjoleksono A, Astuti RI, Husen E, Wahyudi AT. 2025. Peat-derived Streptomyces spp. isolated from edamame rhizosphere with plant growth-promoting properties. Biodiversitas 26: 326-334. Peatlands, which are known for their high organic matter content, are common habitats for actinomycetes. These microorganisms have been recognized for their potential as plant growth promoters. However, there have been limited reports on peat-derived actinomycetes with plant growth-promoting properties, especially in edamame-cultivated peatlands. This study aimed to isolate and investigate plant growth-promoting actinomycetes in the rhizosphere of edamame-cultivated peatlands. The results showed that a total of 46 strains were isolated from the edamame rhizosphere during the anthesis and reproductive phase. Importantly, 36 of these strains were found to be biologically safe, as showed by the negative hemolysis and hypersensitivity test. All 36 strains produced indole-3-acetic acid in the range of 2.42 to 50.07 µg/mL. Based on the in vivo plant growth-promoting activity assay, strains RT34, AR26, AR39, and BT59 promoted the highest primary root growth of edamame sprouts. Interestingly, the acetylene reduction assay revealed that only RT34 and AR39 strains exhibited nitrogenase activity as high as that of Azotobacter sp. as a positive control. The nitrogenase activity of these strains was up to 27.42 nmol C2H4 h-1tube-1 and 28.10 nmol C2H4 h-1tube-1. Furthermore, quantitative phosphate solubilization assay showed phosphate solubilization up to 527.76 µg/mL in the range of 258.31 to 527.76 µg/mL. Based on 16S rRNA sequencing, these strains were closely related to the genus Streptomyces. The finding of present results strongly indicates that these Streptomyces strains have plant growth-promoting properties and can be proposed as biostimulants to enhance edamame growth in peatlands.
Implications of biodiesel production for enhancing thermostable T1.2RQ lipase secretion in Pichia pastoris via chaperone co-expression ESTI PUSPITASARI; YEPY HARDI RUSTAM; ANDREAS ADHI SATYA; ANTONIUS SUWANTO; ARIS TRI WAHYUDI; RIKA INDRI ASTUTI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 9 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260927

Abstract

Abstract. Puspitasari E, Rustam YH, Satya AA, Suwanto A, Wahyudi AT, Astuti RI. 2025. Implications of biodiesel production for enhancing thermostable T1.2RQ lipase secretion in Pichia pastoris via chaperone co-expression. Biodiversitas 26: 4557-4566. The thermostable T1.2RQ lipase from Geobacillus stearothermophilus (isolated from Indonesian hot springs) was expressed in Pichia pastoris GS115 via multicopy integration (6X). Co-expression of chaperones bmh2 (797 bp) and sso2 (875 bp) was achieved using Gibson Assembly and pPICZAwbe. Transformants GS115/T1.2RQ(6X)_bmh2#3 showed 71% higher activity (p = 0.017) versus controls, while sso2 reduced activity by 23% (p = 0.028). SDS-PAGE confirmed a 43 kDa band, and tributyrin assays verified extracellular secretion. In biodiesel trials, the lipase reduced Palm Fatty Acid Distillated Free Fatty Acid (PFAD FFA) to 4.9%, meeting SNI 7182:2015 standards. This study demonstrates bmh2’s role in alleviating Endoplasmic Reticulum (ER) stress and advancing bacterial lipase production in yeast, with applications in sustainable biodiesel.C) analysis showed methyl palmitate (C16:0) and methyl stearate (C18:0) as the dominant Fatty Acid Methyl Ester (FAME) species. This research demonstrates that bmh2 is the most effective chaperone for co-expression with a six-copy lipase, increasing extracellular activity. The enzyme produced by heterologous expression in Pichia can be used for lab-scale biodiesel production, comparable to that expressed in Escherichia coli. This is the first report of G. stearothermophilus T1.2RQ lipase, and these findings advance bacterial lipase gene expression research in the P. pastoris expression system. Future work should optimize tandem chaperone systems (bmh2 + PDI) and pilot-scale fermentation. This study underscores Indonesia’s microbial biodiversity as a resource for novel biocatalysts, aligning with Biodiversitas’s mission to bridge ecology and biotechnology.
COMPARATIVE ANTIBACTERIAL ACTIVITY OF HONEY FROM DIFFERENT BEE SPECIES AGAINST PATHOGENIC BACTERIA Andhika Rahesta Devi; Rika Raffiudin; Rika Indri Astuti
BIOLINK (Jurnal Biologi Lingkungan Industri Kesehatan) Vol. 13 No. 1 (2026): Biolink August
Publisher : Universitas Medan Area

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31289/biolink.v13i1.17325

Abstract

The increasing prevalence of antibiotic-resistant bacteria encourages the exploration of natural antibacterial agents with lower risk of promoting resistance. Honey is a promising candidate due to its acidity, high osmolarity, and bioactive compounds. However, comparative studies on the antibacterial activity of Indonesian honey from different bee species remain limited. This study compared the antibacterial activity of ten Indonesian honey samples produced by four bee species (Apis mellifera, Apis dorsata, Apis cerana, and Tetragonula laeviceps). The target bacteria used were Escherichia coli ATCC8739, Staphylococcus aureus ATCC6538, and Pseudomonas aeruginosa ATCC15442. Antibacterial activity was evaluated using the disc diffusion assay, followed by bacterial viability, LD50 determination and proximate analysis of the most active samples. All honey samples inhibited Escherichia coli, whereas only TG1_PND from T. laeviceps inhibited all three pathogens. Viability assay indicated the strongest inhibition at 100% honey concentration, with the lowest LD50 (81%) against Pseudomonas aeruginosa. Proximate analysis showed that TG1-PND possessed the lowest pH, suggesting that its antibacterial activity may be related to organic acid-induced osmotic stress. These findings demonstrate the potential antibacterial activity of T. laeviceps honey and its development as a natural antibacterial agent.
Co-Authors A M Sabbah, Sajida ADI YULANDI Agung Priyanto, Jepri Ai Hertati, Ai AKHMAD ENDANG ZAINAL HASAN Akmaliyah, Rizna Alfaridza, Annisa Nourma ALFIYAN, ACHMAD Amani, Febriyanti Nur Andhika Rahesta Devi ANDREAS ADHI SATYA Anja Meryandini Antonius Suwanto Apon Zaenal Mustopa Aris Tjahjoleksono Aris Tri Wahyudi Armanisa, Khafifah Chairunnisa, Sheila Chihombori, Tatenda Calvin DAROJATUL ULYA DELFIANI ANGGIAS PUTRI Dina Aribah DINI NURDIANI DOVA KELVIN MESRIAN DOVA KELVIN MESRIAN Dudi Hardianto, Dudi EDI HUSEN Efrida Martius Ekawati, Nurlaili ESTI PUSPITASARI EVRICK YONANTIKO Fathiah, Muhammad Fadhil Fatimah Firyal Noviatanti Nabilah Hartono, Faisal Diniamal HERMAWATY ABUBAKAR Ika Rahmatul Layly Iman Rusmana IRA ERDIANDINI Irawan, Herman Irmanida Batubara IS HELIANTI Jendri Mamangkey Jepri Agung Priyanto Jun Nomura Kartini Kramadibrata Lenka, Audria Bayu Lisdar Idwan Sudirman Mahsunah, Anis Herliyati Manguntungi, Baso Martha, Ina MUHAMMAD EKA PRASTYA Muhammad Eka Prastya Muhammad Hilman Aulia Muhammad Zulfiqri, Aldy Mutiara, Ilma Nabila Tsoerayya Gustia Pudjas Nadila Fany Ashafani Nadiyah Salsabilah Nadya Nabila Qurani Nampiah Sukarno Nasution, Uli Julia NISA RACHMANIA MUBARIK Nurfadhilla Rahmadhani Nurhakiki Prastya, Muhammad Eka Puspitasari, Dian Japany Puspitasari, Esti RAHAYU WULAN Rahayu Wulan Rahayu Wulan Rakhman, Ira Meylan Nafarah Refli, Redoyan Rifqiyah Nur Umami, Rifqiyah Nur RIKA RAFFIUDIN Ririn Herni Putri Rustam, Yepy Hardi Sarah Asih Faulina Sarah Asih Faulina, Sarah Asih Satya, Andreas Adhi Sidiq, Muhammad Raffel SRI BUDIARTI SRI ESTUNINGSIH SRI LISTYOWATI Sri Budiarti Sri Budiarti Poerwanto Sri Estuningsih Sri Listiyowati Theresia Yolanda Avelina Trinugroho, Joko P Uci Cahlia WENANG MAHARSIWI WIDYA ESTI PURWANINGTYAS Wulan Tri Wahyuni YAYA RUKAYADI Yaya Rukayadi YAYA RUKAYADI YEPY HARDI RUSTAM Yohanes Bernadino Putera Saju Zulhaerati Zulhaerati