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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
Antonius Suwanto
Department Of Biology, Faculty Of Mathematics And Natural Science, IPB University, Bogor, Indonesia
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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Abundance of Culturable Bacteria Isolated from Maize Rhizosphere Soil Using Four Different Culture Media ERNIN HIDAYATI; ARIS TRI WAHYUDI; ANTONIUS SUWANTO; RAHAYU WIDYASTUTI
Microbiology Indonesia Vol. 8 No. 1 (2014): March 2014
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (708.386 KB) | DOI: 10.5454/mi.8.1.5

Abstract

Composition and abundance of culturable bacteria of four soil samples (Ktr50II, D50II, G50II, and A50II) were analyzed. The soil samples were collected from maize rhizosphere that planted in dryland Lombok Island. Each soil sample give different growth performance of maize in greenhouse experiment. This study was to investigate the relation of maize growth performance with culturable bacterial community of their rhizosphere and the effect of culture media on number of bacterial isolates recovery. The rhizosphere bacteria were cultured and isolated on commercial media (SEA) and non commercial modification media (NAln, NAln-SE and NAln- RE). Thirty four strains rhizosphere bacteria were obtained from four maize rhizophere soil samples. D50II is the soil sample that caused the better growth performance to the maize, contrary to Ktr50II. D50II has significantly highest number of culturable bacterial types, while significantly lowest on Ktr50II. In D50II, at least 17 bacterial isolates contributed to better growth performance in maize and have relative abundance of dominant isolate not more than 35.34%. In comparing the rhizosphere bacteria recovered using different culture media, bacteria cultivated on SEA have different growth characteristic compared with bacteria cultivated on NAln, NAln SE and NAln-RE. Six bacterial isolates showed antagonistic ability when grew on SEA but not in all of three media. Compared with commercial media, non commercial modification media can increase total isolates recovery about 70.6%.
Genetic Profiles of Escherichia coli Isolated from Indonesian Tempeh Based on Enterobacterial Repetitive Intergenic Consensus- Polymerase Chain Reaction (ERIC-PCR) QURROTA A’YUN; ANTONIUS SUWANTO; TATI BARUS
Microbiology Indonesia Vol. 9 No. 2 (2015): June 2015
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1097.305 KB) | DOI: 10.5454/mi.9.2.2

Abstract

Tempeh is a famous Indonesian fermented food derived from soybeans inoculated with Rhizopus sp. Tempeh production varies depend on the producers and often conducted in an uncontrolled condition. This condition could lead to the growth of Escherichia coli which is known as bacterial indicators of environmental hygiene. Some strains of E. coli could induce diarrhea, acute gastroenteritis or gastrointestinal tract infections. The aim of this study was to compare genetic diversity of E. coli isolates from tempeh with medical isolates employing ERIC-PCR method. In this study, 63f and 1387r primers were used to amplify 16S rRNA genes, and ERIC 1R and ERIC 2 primers were used for ERIC-PCR analysis. Tempeh samples were obtained from four producers in Bogor. Thirty-three isolates of E. coli were successfully isolated from tempeh samples produced by only two producers, we could not obtain E. coli isolates from the other two producers. In addition, the same tempeh samples could carry different genotypes of E. coli. On the other hand, the same genotypes could be found in different tempeh samples. Based on phylogenetic tree analysis, E. coli from tempeh could be separated from medical isolates. We showed that E. coli isolates derived from tempeh were genetically different from those of medical or pathogenic isolates.
Komunitas Mikrob pada Hasil Fermentasi Nata De Coco Berdasarkan Marka Random Amplified Polymorphic DNA Raden Ajie Syahbarie; Antonius Suwanto; Aris Tri Wahyudi
Jurnal Ilmu Pertanian Indonesia Vol. 28 No. 4 (2023): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.28.4.620

Abstract

Traditional nata de coco fermentation often results in inconsistent nata thickness. From the producer's perspective, thin nata sheets are detrimental because most fermentation media will be wasted. The main cause of this condition may be that the microbial population in the starter culture is different in each batch. It is necessary to observe the cultured microbial community on various qualities of available thick and thin nata to design a better nata de coco starter culture. This study showed thick nata had more Komagataeibacter intermedius bacteria (pellicle forming) than thin nata. In traditional nata fermentation, K. intermedius always coexists with other microbes from the bacteria and yeast groups. Random Amplified Polymorphic DNA (RAPD) analysis indicated that the genetic diversity of bacteria was higher than that of the yeast group. Keywords: dendrogram of relationship, fermented food, microbial genetic diversity, nata de coco
Microbiological and Physicochemical Characteristics of Inasua Traditional Fish Fermented from Maluku Islands Ferymon Mahulette; Nisa Rachmania Mubarik; Antonius Suwanto; Widanarni Widanarni
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 2 (2018): August 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v10i2.13537

Abstract

Based on the raw materials, inasua consists of two types namely inasua with sap and inasua without sap. Research of inasua with sap has never been done and considered as the novelty of this research. The sensory characteristics and shelf life of two types of inasua were different. The research aims to analyze the microbiological and physicochemical characteristics of two types of inasua during fermentation. The microbiological analyzes include the total number of bacteria and lactic acid bacteria, while physicochemical analyzes include temperature, pH, water activity, proximate analysis, salt, alcohol, histamine, amino acids and fatty acids contents. The total number of bacteria and lactic acid bacteria has decreased during fermentation. At the end of the fermentation the total number of bacteria and lactic acid bacteria inasua with sap were 3.2x107 CFU/g and 3.0x107 CFU/g, while inasua without sap were 5.4x105CFU/g and 3.5x105 CFU/g, respectively. The moisture, protein, alcohol contents and water activity decreased, otherwise the salt, fat, ash, amino acids, and fatty acids contents increased during fermentation. Generally, microbiological and physicochemical characteristics of inasua with sap was better than inasua without sap. The results of this research to improve the quality of this fermentation product in the future.
GENETIC DIVERSITY ANALYSIS OF THERMOPHILIC BACTERIA FROM CANDRADIMUKA CRATER IN CENTRAL JAVA EMPLOYING PCR-RFLP OF 16S-rRNA GENE TEMMY DESILIYARNI; ANTONIUS SuwANTOAAAo; MAGGY T. SUHARTONO; TRESNAWATI PURWADARIA
BIOTROPIA No. 14 (1999)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (196.046 KB) | DOI: 10.11598/btb.1999.0.14.155

Abstract

The specific primers for bacteria (63f and 1387r) were used to amplify the 16S-rRNA genes from total community genomic DNA of thermophilic bacteria. The total community genomic DNA was obtained from muds and water samples of Candradimuka crater, Dieng Plateau, Central Java. PCR products were cloned into vector  pCR*2.1-TOPO (3.9 kb) and transformed into Escherichia coli TOPIC. Two  tetrameric restriction endonucleases  Rsal  and  Hhal  were employed to generate Restriction Fragment Length Polymorphisms (RFLP) paterns. These enzymes yielded 10 and 9 groups of 16S-rRNA profiles or OTU (Operational Taxonomic Units) from 27 16S-rRNA gene clones. Rsal was found to be more discriminative in differentiating the clones than Hhal. Rsal-RFLP indicated that OTU 7 and OTU 3 represented the most abundant clones, i.e. 6 and 5 clones respectively. The distribution of 16S-rRNA gene clones could  indicate relative distribution of  specific groups of  thermophilic  bacteria  in  their  natural habitat. Analysis of diversity at the DNA level could represent both culturable  and  unculturable bacteria in the  environment. Similarity analysis showed that  at level  0.600 there  were 8 different  groups from 10  RFLP  profiles generated by  Rsal  digestion. This study indicated that there were at least 8 groups of different thermophilic bacteria occupying Candradimuka crater. Key words: Thermophiles, 16S-rRNA, Candradimuka crater.
PRESENCE OF hemA-LIKE AND hemT-LlKE GENES IN A JSUMBER OF ANOXYGENIC PHOTOSYNTHETIC BACTERIAL ISOLATES FROM INDONESIA AND SOIL SAMPLES FROM BOGOR AREA NURUL AINI; ANTONIUS SUWANTO
BIOTROPIA No. 15 (2000)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (162.845 KB) | DOI: 10.11598/btb.2000.0.15.158

Abstract

The Rhodobacter sphaeroides hemA and hemT are known to encode a distinct 5-aminolevulinic acid (ALA)-synthase isozyme. This enzyme catalyzes the first and rate limiting step in ALA biosynthesis through the C4 pathway. This study was carried out to detect hemA-\\ke and hemT-\\ke genes in twenty Anoxygenic Photosynthetic Bacterial (APB) isolates from several wetland areas in Indonesia, and four DNA samples that were isolated from four soil samples obtained from Bogor area. Hybridization techniques of Southern and dot blot were used, using hemA and hemT fragment as probes. Southern hybridization analyses indicated the presence of hemA-\\ke gene in five of APB isolates, i.e., MB15, MB16, MB21.2, MB55 and MB6, whereas hemT-\\ke gene was detected only in MB15. Dot blot hybridization analyses suggested that the soil samples from waterlogged paddy-field, dry paddy-field as well as a mud pond were predominantly occupied by prokaryotic organisms which harboured hemA-]\ke gene. However, /iem7"-like sequences were also found in soil sample from dry paddy-field. Key words:    hemA-\\ks gene / hemT-\\ke gene / Southern hybridization analysis / dot blot hybridization analysis.
Identifikasi Aktinomiset Selulolitik dan Xilanolitik Indigenous Utarti, Esti; Suwanto, Antonius; Suhartono, Maggy T; Meryandini, Anja
BERKALA SAINSTEK Vol 8 No 1 (2020)
Publisher : Universitas Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/bst.v8i1.15941

Abstract

Lignoselulosa merupakan penyusun utama dinding sel tumbuhan, sehingga keberadaannya berlimpah di alam. Aktinomiset indigenous yang memiliki aktivitas selulolitik dan xilanolitik ekstraseluler berpeluang sebagai agens biokonversi limbah berlignoselulosa menjadi produk bermanfaat. Penelitian ini bertujuan untuk mendapatkan aktinomiset potensial yang memiliki aktivitas selulolitik dan xilanolitik. Penelitian ini diawali dari isolasi dan pemurnian aktinomiset indigenous asal lahan perkebunan kelapa sawit dan Taman Nasional Bukit Duabelas Jambi.Tahapan selanjutnya adalah penapisan aktivitas selulolitik dan xilanolitik dari aktinomiset, uji pertumbuhan aktinomiset pada mikrokristalin selulosa, dan identifikasi aktinomiset potensial berdasarkan karakter morfologi, fisiologi dan biokimia. Hasil penelitian menunjukkan bahwa aktinomiset isolat S2 yang diisolasi dari lahan perkebunan kelapa sawit mempunyai aktivitas selulolitik dan xilanolitik lebih baik dari keempat isolat lain. Aktinomiset isolat S2 juga mampu tumbuh secara lebih baik pada mikrokristalin selulosa. Aktivitas selulolitik, xilanolitik dan kemampuan tumbuh pada mikrokristalin selulosa dari aktinomiset isolat S2 menunjukkan potensinya sebagai agens pendegradasi material belignoselulosa. Berdasarkan identifikasi morfologi, fisiologi dan biokimia, aktinomiset isolat S2 tergolong dalam genus Streptomyces.
Bacterial and Fungal Communities in Tempeh as Reveal by Amplified Ribosomal Intergenic Sequence Analysis SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; RUSMANA, IMAN; SOLIHIN, DEDY DURYADI
HAYATI Journal of Biosciences Vol. 20 No. 2 (2013): June 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (142.073 KB) | DOI: 10.4308/hjb.20.2.65

Abstract

Tempeh is an Indonesian traditional fermented food produced using Rhizopus as a starter culture. In practice, however, the starter culture as well as fermentation processes would yield a polymicrobial fermentation, which generated a unique tempeh flavor and texture. This condition makes Indonesian tempeh as one of the most complex fermented food, while at the same time would make it difficult to scale up tempeh production with uniform quality and consistency. The aim of this study was to compare a number of tempeh microbial communities employing Amplified Ribosomal Intergenic Sequence Analysis (ARISA). Fresh tempeh samples were obtained from tempeh producers in Java and Moluccas. 16S rRNA gene libraries and DNA sequencing were employed to analyze further the nature of bacterial diversity in two selected tempeh samples. The results of our study showed that different tempeh producer possessed different Bacterial ARISA (BARISA) or fungi ARISA (FARISA) profiles.  However, BARISA profiles were found to be more discriminative than FARISA, and therefore BARISA would be more useful for tempeh genetic fingerprint or barcoding.
Effect of Synthetic Fertilizer on Diazotrophic Bacteria in Secondary Forest and Oil Palm Soils in Central Kalimantan Agustina, Delia; Purnamasari, Maria Indah; Karmawan, Listya Utami; Suwanto, Antonius
HAYATI Journal of Biosciences Vol. 32 No. 1 (2025): January 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.1.106-116

Abstract

Soil microorganisms, especially diazotrophic bacteria, are vital for ecosystem sustainability, significantly contributing to nitrogen cycling and biodiversity conservation. Understanding the impact of different land-use practices on soil microorganisms, especially synthetic fertilizer addition, is essential for sustainable agriculture. This study compares soil properties, bacterial densities, and responses to fertilization in secondary forest soils and adjacent oil palm plantation soils located in PT Kerry Sawit Indonesia, Central Kalimantan. A greenhouse experiment was conducted using both secondary forest and oil palm plantation soils to evaluate the impacts of different synthetic fertilizers on nitrogen-fixing bacteria and soybean agronomic performance. Total soil bacteria and diazotrophic bacteria, essential for nitrogen fixation, were analyzed through microbiological assays and qPCR focusing on the nifH gene. Our findings show that oil palm plantation soils had higher levels of nitrogen, phosphate, and nitrate, while secondary forest soils had a higher abundance of diazotrophic bacteria. Furthermore, excessive nitrogen fertilization was found to reduce microbial density, negatively impacting plant sustainability, highlighting the importance of customized fertilizer management. The study highlights the intricate connections between land-use practices and microbial populations, providing valuable insights for balancing agricultural productivity with ecological sustainability.
Effect of Multiple Gene Copy Number of Bacterial Lipase to Increase Lipase Production in Pichia pastoris Puspitasari, Esti; Rustam, Yepy Hardi; Satya, Andreas Adhi; Suwanto, Antonius; Wahyudi, Aris Tri; Astuti, Rika Indri
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.310-319

Abstract

Bacterial lipase poses potential challenges when expressed in eukaryotic protein expression systems such as Pichia pastoris. This research aims to increase extracellular T1.2RQ lipase secretion (free lipase) with multiple gene copy number strategies in Pichia pastoris and it was first performed on lipase from Geobacillus stearothermophilus T1.2. In this study, the T1.2RQ lipase gene from Geobacillus stearothermophilus T1.2 was expressed in Pichia pastoris GS115 through a strategy involving multiple copies of lipase, resulting in increased lipase activity. Three copies of the lipase gene in pPIC9K_T1.2RQ(3x) recombinant plasmid were integrated into the genome of Pichia pastoris GS115, and quantitative analysis using qPCR technique confirmed that the GS115 transformant strain contained six copies of T1.2RQ gene, indicating two integration events. Lipase activity measurement showed that the GS115/T1.2RQ(6x) strain exhibited a 111% increase compared to that containing a copy of the T1.2RQ gene. SDS-PAGE and Zymogram results showed a protein band with a size of 43kDa. Qualitative analysis in LA+TBN media of all strains containing the T1.2RQ gene showed clear zones. Lipase production in flask fermentation took at least 120 hours to produce the best lipase activity. Thus, strategies with multiple copy numbers of gene lipase have significantly increased the expression of the bacterial lipase gene in Pichia pastoris GS115.
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 ANJA MERYANDINI Anja Meryandini ARI SUSILOWATI Arifudin Rafif , Muhammad Ghildan Arild Ranlym Arifin Arina Amalia Putri Aris Tjahjoleksono Aris Tri Wahyudi ARTINI PANGASTUTI Asmini Budiani Basil J NIKOLAU BIBIANA W LAY BUDI TJAHJONO BUDI TJAHJONO Budi Tjahjono Budi Tjahjono Budinarta, Widyah C Hanny Wijaya 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 Dyah Kusuma Anggraini Edi Husen Edi Husen EDI HUSEN ERNIN HIDAYATI 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, Griselda Hajrial ASWIDINNOO HAJRIAL ASWIDINNOOR Hariyatun Hariyatun Hariyatun, Hariyatun Hermosaningtyas, Anastasia Aliesa Iman Rusmana Inez H.S. Loeddin Suharsono It Jamilah IVAN HANJAYA JOANITA SADELI KATHARINA JESSICA 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 THENAWIJAYA SUHARTONO Maria Dita Febriani Lumban Gaol 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. 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 RAHAYU WIDYASTUTI RASTI SARASWATI RASTI SARASWATI Rasti Saraswati Rasti Saraswati RATIH DEWI HASTUTI RATNA SETYANINGSIH RATNA SETYANINGSIH RIDWAN AFFANDI 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 Widanarni Widanarni Wien Kusharyoto Yasinta Ratna Esti Wulandari Yepy Hardi Rustam Yogiara Yogiara YULIN LESTARI Yusminah Hala