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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Akuatika Jurnal Ilmu Dasar Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology BERKALA SAINSTEK Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Agricultural Science Indonesian Journal of Biotechnology Jurnal Perlindungan Tanaman Indonesia Journal of Tropical Biodiversity and Biotechnology UNEJ e-Proceeding JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA ANNALES BOGORIENSES Marine Research in Indonesia Biosaintifika: Journal of Biology & Biology Education Menara Perkebunan International Journal of Environment, Engineering, and Education International Journal of Environment, Engineering & Education International Journal of Oil Palm Annales Bogorienses Biodiversitas Journal of Biological Diversity
Antonius Suwanto
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Jl. Agathis 1, Darmaga-Bogor, Indonesia 16680
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Control & Systems Engineering Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Veterinary

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SOLATION AND CHARACTERIZATION OF A NOVEL BENZOATE- UTILIZING Serratia marcescens DWI SURYANTO; ANTONIUS SUWANTO
BIOTROPIA No. 21 (2003)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (424.953 KB) | DOI: 10.11598/btb.2003.0.21.184

Abstract

A new benzoate-utilizing strain, Serratia marcescens DS-8, isolated from the environment was characterized. The strain was enterobacilli, Gram negative, mesophilic, non halophilic, and aerobic bacterium that showed motile ovale-rod shaped cells. The isolate produced extracellular chitinase, protease, and prodigiosin (a red pigment produced by several Serratia strains yielding bright red or pink colonies). A physiological assay using Microbact* test showed that the strain was closely related to Klebsiella ozaenae  (49.85%) and Serratia liquefaciens  (24.42%), respectively. However, 16S rRNA sequence analysis indicated that the strain was closely related to  S. marcescens  DSM 30121 with similarity level of 98%. DS-8 strain was able to synthesize its own vitamins. Optimum growth in benzoate was obtained at pH between 7-8.5 and NaCl concentration of 1-1.5% (w/v). The isolate could grow in benzoate-containing medium up to 10 mM. Other carbon sources that could support the growth of DS-8 were casamino acid, glutamate, glucose, acetate, potato starch, and ethanol. Keywords: Serratia marcescens/aromatic degradation/168 rRNA sequence
ISOLATION AND CHARACTERIZATION OF MANNANOLYTIC THERMOPHILIC BACTERIA FROM PALM OIL SHELL AND THEIR MANNANASE ENZYME PRODUCTION PROPERTIES ANTONIUS SUWANTO; SUMARDI; MAGGY T HENAWIDJAJA; T RESNAWATI P URWADARIA
BIOTROPIA No. 25 (2005)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2005.0.25.211

Abstract

A mannanolytic thermophilic bacterium (L-07) was isolated from palm oil shell after 2 days ofenrichment in liquid medium supplemented with 1% palm kernel meal as mannan source. Sequenceanalysis of 16S-rRNA indicated that L-07 was similar (98%) to  Geobacillus stearothermophilus, aspecies of thermophilic aerobic bacteria. We found that  G. stearothermophilus L-07 producedextracellular β-1,4-mannanases, but no β-manosidase and α-galactosidase activities. The growth of L-07reached its maximum (3.0 x 106 cell/ml) at 12-20 hours, while the highest  β-mannanase activity (0.52U/ml) was observed in culture medium after 36 hours of cultivation at 60oC. The medium containinglocust bean gum was the best for producing extracellular β-1,4-mannanases compared with kolang kaling,konjak, and palm kernel meal. SDS-PAGE and zymogram analysis demonstrated that crude mannanasecomplex of L-07 from locust bean gum containing medium comprised three active bands with molecularweight of 85, 73 and 50 kDa.   Keywords :  Extracellular enzyme/mannanase/Geobacillus stearothermophilus
DYNAMICS OF MICROBIAL COMMUNITY DURING TEMPEH FERMENTATION Antonius Suwanto
BIOTROPIA Vol. 28 No. 1 (2021): BIOTROPIA Vol. 28 No. 1 April 2021
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (524.271 KB) | DOI: 10.11598/btb.0.0.0.820

Abstract

Tempeh is sliceable soybean-cake fermented by Rhizopus oligosporus. Various bacteria were detected in tempeh employing cultivation technique with limited information about their origin or sources. The present study aimed to examine the source/s of bacterial community in tempeh by combining metagenomics analysis and cultivation technique. Samples were obtained from a number of steps in tempeh production employing two-times boiling of soybean (WJB tempeh production). All samples were plated on Enterobacteriaceae and Lactic Acid Bacteria medium. Total DNA were extracted directly from tempeh for metagenomics analysis, employing High-Throughput Sequencing (HTS) and cloned 16S rRNA genes. Firmicutes and Proteobacteria were the predominant and second dominant bacteria existed in fresh tempeh (FT) obtained by metagenomics analysis. In contrast, cultivation technique showed that Proteobacteria was the predominant phylum, suggested that most of the Firmicutes were not culturable. FT was dominated by Lactobacillus and Acetobacter. Both FT and soaking water (SW) were dominated by same species of Lactobacillus, i.e. L. delbreuckii and L. mucosae, indicated that SW was probably the source of bacterial community established in the final product of fermentation. Predominant bacteria in starter culture (SC), Acinetobacter, was not detected in FT, indicating that bacteria in SC might not play significant role in bacterial community development in FT.
Bacterial communities associated with white shrimp (Litopenaeus vannamei) larvae at early developmental stages ARTINI PANGASTUTI; ANTONIUS SUWANTO; YULIN LESTARI; MAGGY TENNAWIJAYA SUHARTONO
Biodiversitas Journal of Biological Diversity Vol. 11 No. 2 (2010)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d110203

Abstract

Bacterial communities associated with white shrimp (Litopenaeus vannamei) larvae at early developmental stages. Biodiversitas 11 (2): 65-68.Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to monitor the dynamics of the bacterial communities associated with early developmental stages of white shrimp (Litopenaeus vannamei) larvae. Samples for analysis were egg, hatching nauplii, 24 hours old nauplii, and 48 hours old nauplii which were collected from one cycle of production at commercial hatchery. TRFLPresults indicated that the bacterial community associated with early stages of shrimp development might be transferred vertically from broodstock via egg. There was no significant difference between bacterial communities investigated, except the bacterial community of 48 hours old nauplii. Diversity analyses showed that the bacterial community of egg had the highest diversity and evenness, meanwhile the bacterial community of 48 hours old nauplii had the lowest diversity. Nine phylotypes were found at all stages with high abundance. Those TRFs were identified as γ- proteobacteria, α-proteobacteria, and bacteroidetes group.Key words: Litopenaeus vannamei, bacterial community, T-RFLP
Lipolytic bacteria and the dynamics of flavor production in Indonesian tempeh Naswandi Nur; Anja Meryandini; Maggy Thenawidjaja Suhartono; Antonius Suwanto
Biodiversitas Journal of Biological Diversity Vol. 21 No. 8 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210850

Abstract

Abstract. Nur N, Meryandini A, Suhartono MT, Suwanto A. 2020 Lipolytic bacteria and the dynamics of flavor production in Indonesian Tempeh. Biodiversitas 21: 3818-3825. During the process of tempeh maturation, lipolytic bacteria become an integral part of tempeh and even have important roles in determining the quality of resulting tempeh. This study was conducted to examine correlation between lipolytic bacteria which were present in three tempeh samples i.e. CMG, EMP, RTI, and their roles in liberation of free fatty acid. Lipolytic bacteria were found in each tempeh sample which were approximately 0.1 % of total bacterial population. CMG harbored the highest lipolytic bacterial population at 1.04 × 106 cfu g-1 followed by EMP at 2.88 × 105 cfu g-1, and RTI at 1.72 × 104 cfu g-1. Tempeh aroma and texture showed strong correlation between the numbers of bacterial population during the period or stages of tempeh maturation. Moreover, we also found a unique correlation between dynamic of lipolytic population and aroma changes. Free fatty acid profiling indicates that lipolysis activity was presence during fermentation of tempe where each tempeh samples showed some differences in liberation of dominant free fatty acid. 16S rRNA sequencing from a hundred of lipolytic isolates was identified and classified as member of the phylum Proteobacteria, Firmicutes, and Actinobacteria, other isolates were classified as uncultured clone.
Tempeh flour as an excellent source of paraprobiotics WILFADRI PUTRA JONESTI; CAHYA PRIHATNA; GRISELDA HERMAN NATADIPUTRI; ANTONIUS SUWANTO; ANJA MERYANDINI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 3 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240357

Abstract

Abstract. Jonesti WP, Prihatna C, Natadiputri GH, Suwanto A, Meryandini A. 2023. Tempeh flour as an excellent source of paraprobiotics. Biodiversitas 24: 1817-1823. Tempeh, a functional fermented food from Indonesia, has many benefits for human health. The presence of oligosaccharides, live and dead microbes in tempeh can function as prebiotics, probiotics, or paraprobiotics. This study aimed to determine the composition of live and dead lactic acid bacteria (LAB) and Enterobacteriaceae in tempeh flour using microbiological and molecular quantifications. Two samples of tempeh flour based on the drying process, i.e., sun-dried and oven-dried, were analyzed. Bacteria were quantified using standard plate count and qPCR, while bacterial cells damaged by the drying process were quantified using Propidium Monoazide-Quantitative Polymerase Chain Reaction (PMA-qPCR). Tempeh flours contained live bacteria as many as 4-5 log CFU/g and intact dead bacterial cells as many as 9 log CFU/g. The number of bacteria only differed slightly between the two drying processes. Based on qPCR analysis, the LAB number was higher than Enterobacteriaceae in tempeh flour. In addition, the bacterial population by qPCR was higher than by cultured analysis. These results indicated that sun-dried or oven-dried tempeh flour could be a functional food because it contained high amounts of live and dead bacteria as candidates for probiotics and paraprobiotics based on PMA-qPCR analysis.
Characterization of endophytic bacterial isolates from oil palm (Elaeis guineensis) seedlings and ramets for their plant growth promoting potential IDA AYU PUTU SURYANTI; MARIA INDAH PURNAMASARI; CAHYA PRIHATNA; IMAN RUSMANA; ARIS TRI WAHYUDI; ANTONIUS SUWANTO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251040

Abstract

Abstract. Suryanti IAP, Purnamasari MI, Prihatna C, Rusmana I, Wahyudi AT, Suwanto A. 2024. Characterization of endophytic bacterial isolates from oil palm (Elaeis guineensis) seedlings and ramets for their plant growth-promoting potential. Biodiversitas 25: 3775-3788. Using sterile tissue culture to cultivate oil palm (Elaeis guineensis Jacq.) seedlings results in the loss of beneficial endophytic bacteria, which can lead to various growth issues, including abnormal flower development and reduced palm oil production. The study aimed to investigate the potential endophytic bacteria in oil palm seedlings and ramets that serve as plant growth promoters. This research began with isolating and characterizing bacterial isolates with plant growth-promoting traits, then identification using 16S rRNA gene sequencing. In vitro and in vivo growth tests were carried out to assess the prospects of these bacterial isolates. Seventeen bacterial isolates were successfully cultured from oil palm seedlings and ramets (seedlings from tissue culture), with 12 and 5 isolates, respectively, which displayed characteristics of plant growth-promoting bacteria: 88% could produce aminocyclopropane-1-carboxylate (ACC) deaminase, 18% exhibited nitrogen-fixing abilities, 47% demonstrated phosphate solubilization, and 12% were producers of indole-3-acetic acid (IAA) hormone, which. One of the isolates, designated as 3AK, was indicated as the Aeromonas genus, which originates from the environment and has all the plant growth-promoting properties tested qualitatively in this study. In vitro growth testing showed that 3AK isolate had the most significant average lengths for both shoots (4.4±0.4 cm) and roots (8.2±0.5 cm). In the greenhouse experiment (in vivo), the oil palm seedlings treated with bacteria, such as 3AK, exhibited differences in shoot and root dry weight compared to the control group, and the difference was statistically significant. These findings collectively indicate that endophytic bacteria code 3AK is isolated from oil palm root, identified as Aeromonas taiwanensis through 16S rRNA gene sequencing, and has the potential as a plant growth promoter. Inoculation of Aeromonas taiwanensis strain 3AK and PsJN as Burkholderia phytofirmans strain PsJN (already known as a model for promoting plant growth) was carried out for the first time on the growth of oil palm seedlings.
Exploring the microbial diversity and functional potential of Domas Crater of Mount Tangkuban Perahu, Indonesia, through shotgun metagenomics HARYONO BUDI SANTOSO; ANTONIUS SUWANTO; RAHADIAN PRATAMA
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/d251160

Abstract

Abstract. Santoso HB, Suwanto A, Pratama R. 2024. Exploring the microbial diversity and functional potential of Domas Crater of Mount Tangkuban Perahu, Indonesia, through Shotgun Metagenomics. Biodiversitas 25: 4613-4626. Domas Crater, an extreme environment in Indonesia, is known for high temperatures and acidic conditions, providing a unique habitat for specialized microbial communities. These extreme conditions increase the possibility of discovering thermophilic enzymes with valuable biotechnological applications. Therefore, this study aimed to explore the microbial diversity in Domas Crater using shotgun metagenomics to analyze both previously reported microbes and novel microorganisms comprehensively. Shotgun metagenomics is particularly advantageous in identifying microbial species that cannot be cultured using conventional methods, enabling the exploration of microorganisms with considerable potential. The application of next-generation sequencing technologies and bioinformatics tools allowed the successful reconstruction of eight high-quality Metagenome-Assembled Genomes (MAGs), a testament to the technical proficiency of the study. The genomes were further characterized based on the functional genes, including the enzymes in carbohydrate metabolism or Carbohydrate-active enzymes (CAZyme), biosynthetic gene clusters for secondary metabolite (BGCs), and genes associated with micronutrient metabolism. The results showed that the microbial community was dominated by Hydrogenobaculum and Sulfurisphaera, both known for adaptation to extreme environments. Moreover, the first Hydrogenobaculum and Thermocladium were recorded in Indonesia as the novel discoveries of the study. These findings highlight the significance of Domas Crater as a reservoir for novel microbial species, particularly in terms of thermophilic microorganisms with unique enzymatic properties.
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.
Co-Authors . EFRIWATI . Melani . NURHAIMI-HARIS A A Hermosaningtyas A A Hermosaningtyas, A A ADI YULANDI Agus PURWANTARA Agus Purwito Agustin Wydia Gunawan Agustina, Delia Alfred Michael ALINA AKHDIYA RUSMANA AMARILA MALIK AMARILA MALIK Andi Khaeruni Andi Khaeruni ANDREAS ADHI SATYA Andreas Adhi Satya Andreas Adhi Satya Anja Meryandini ARI SUSILOWATI Arifudin Rafif , Muhammad Ghildan Arild Ranlym Arifin Arina Amalia Putri Aris Tjahjoleksono ARIS TRI WAHYUDI ARIS TRI WAHYUDI Aris Tri Wahyudi Artini Pangastuti ARTINI PANGASTUTI Asmini Budiani Basil J NIKOLAU BIBIANA W LAY Budi Tjahjono BUDI TJAHJONO Budinarta, Widyah C Hanny Wijaya CAHYA PRIHATNA CAHYA PRIHATNA CAHYA PRIHATNA Cahya Prihatna Cahya Prihatna CECILIA ANNA SEUMAHU CECILIA ANNA SEUMAHU DEBORA HADISUSANTO Delia Agustina Desniar - - DIAH ISKANDRIATI DIANA ELIZABETH WATURANGI Djoko Santoso Dondin Sajuthi DWI SURYANTO DWI SURYANTO DWI SURYANTO Dyah Kusuma Anggraini Edi Husen Edi Husen EDI HUSEN ERNIN HIDAYATI ESTI PUSPITASARI ESTI PUSPITASARI Esti Puspitasari ESTI PUSPITASARI Esti Utarti Eunice Limantara EVELINE AYU Felicia Felicia Felicia Kartawidjajaputra Ferymon Mahulette Ferymon Mahulette Ferymon Mahulette, Ferymon G. A. Wattimena Gayuh Rahayu Griselda Griselda GRISELDA HERMAN NATADIPUTRI Griselda Herman Natadiputri Griselda, Griselda Hajrial ASWIDINNOO HAJRIAL ASWIDINNOOR Hariyatun Hariyatun Hariyatun, Hariyatun Hariyatun, Hariyatun HARYONO BUDI SANTOSO Hermosaningtyas, Anastasia Aliesa IDA AYU PUTU SURYANTI IMAN RUSMANA Iman Rusmana Inez H.S. Loeddin Suharsono It Jamilah IVAN HANJAYA JOANITA SADELI KATHARINA JESSICA Kusharyoto, Wien Kusharyoto, Wien Lilis Nuraida Linda Wati LISTYA UTAMI KARMAWAN Ludovika Jessica Virginia MAGGY T HENAWIDJAJA Maggy T Suhartono Maggy T Suhartono MAGGY T. SUHARTONO MAGGY T. SUHARTONO Maggy T. Suhartono MAGGY TENNAWIJAYA SUHARTONO Maggy Thenawidjaja Suhartono MAGGY THENAWIJAYA SUHARTONO Maria Dita Febriani Lumban Gaol MARIA INDAH PURNAMASARI Maria Indah Purnamasari Maria Indah Purnamasari Maria Indah Purnamasari Maria Sugiharti Meity S. Sinaga MEITY SURADJI SINAGA Muhamad Azwar Syah Muhammad Agus Muljanto MUHAMMAD ZAIRIN Jr. Naswandi Nur Ni Nyoman Tri Puspaningsih NISA RACHMANIA MUBARIK NURITA TORUAN-MATHIUS NURUL AINI PRIHASTO SETYANTO Prihasto Setyanto Prihatna , Cahya Puspitasari, Esti QURROTA A’YUN R. Sapto Hendri Boedi Soesatyo Raden Ajie Syahbarie RAHADIAN PRATAMA RAHAYU WIDYASTUTI RASTI SARASWATI RASTI SARASWATI Rasti Saraswati Rasti Saraswati RATIH DEWI HASTUTI RATNA SETYANINGSIH RIDWAN AFFANDI RIKA INDRI ASTUTI Rika Indri Astuti ROB HARLING ROHANI CINTA BADIA GINTING Rustam, Yepy Hardi Satya, Andreas Adhi Sheila Sutanto Sheila Sutanto, Sheila SUMARDI Suryo Wiyono SUSAN SOKA SUSILOWATI1 SUSILOWATI1 T RESNAWATI P URWADARIA Tan Watumesa Agustina TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Tati Barus TEMMY DESILIYARNI TRESNAWATI PURWADARIA VICKY MEICY WALTER ERDELEN WIDANARNI WIDANARNI Wien Kusharyoto WILFADRI PUTRA JONESTI Yasinta Ratna Esti Wulandari YEPY HARDI RUSTAM Yepy Hardi Rustam Yogiara Yogiara YULIN LESTARI Yusminah Hala