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All Journal HAYATI Journal of Biosciences Jurnal Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Akuakultur Indonesia Biospecies ILMU KELAUTAN: Indonesian Journal of Marine Sciences Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biogenesis: Jurnal Ilmiah Biologi Indonesian Journal of Agricultural Science Indonesian Journal of Biotechnology Jurnal Sumberdaya Hayati JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA ANNALES BOGORIENSES Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Biosaintifika: Journal of Biology & Biology Education Jurnal Iktiologi Indonesia (Indonesian Journal of Ichthyology) Media Akuatika: Jurnal Ilmiah Jurusan Budidaya Perairan Makara Journal of Science Annales Bogorienses

Aris Tri Wahyudi

Biology Department, Faculty Of Mathematics And Natural Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia, 16680

Author-ID : 410994

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology

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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

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

Exploration of Potential Actinomycetes from CIFOR Forest Origin as Antimicrobial, Antifungus, and Producing Extracellular Xylanase Sipriyadi Sipriyadi; Yulin Lestari; Aris Tri Wahyudi; Anja Meryandini; Maggy Thenawidjaja Suhartono
Biosaintifika: Journal of Biology & Biology Education Vol 8, No 1 (2016): March 2016
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.v8i1.5052

This study aimed to isolate and explore the actinomycetes of CIFOR forest origin as an antimicrobial and antifungal agent, to produce an extracellular xylanase, and to identify isolates based on 16S rRNA gene sequences. Actinomycetes were isolated using Humic-acid Vitamin-B agar (HV) media. Actinomycetes colonies that grow on the medium HV was subsequently purified by growing them on yeast malt agar (YMA) media), then an antagonistic test of selected bacteria against Bacillus sp., Escherichia coli, Fusarium oxysporum, and Sclerotium sp was performed. Xylanase activity test was detected by observing a clear zone, followed by identification. Total of 35 isolates of actinomycetes isolated based on their colony morphology characteristics and diverse types of spore chains showed Streptomyces spp. of isolates CFR-06, CFR-15, CFR-17, CFR-18, and CFR-19 were able to inhibit the growth of Bacillus sp.. The highest inhibition zone has a diameter of 10.1 mm (isolate CFR-17). Isolates CFR-01 and CFR-15 were able to inhibit the growth of E. coli with the highest inhibition zone diameter of 5.1 mm (isolate CFR-15). Isolates CFR-29 and CFR-12 were able to inhibit the growth of F. oxysporum while isolate CFR-35 were able to inhibit the growth of Sclerotium sp.. Xylanase activity test showed that isolates CFR-12, CFR-20, CFR-22, CFR-24, CFR-25, CFR-30, CFR-33, CFR-34 have an ability to produce extracellular xylanase enzyme. Actinomycetes isolate (Xyl_22) as a potential xylanase enzyme producer was closely related with Streptomyces drozdowicii by the maximum similarity of 99%.How to CiteSipriyadi, S., Lestari, Y., Wahyudi, A., Meryandini, A., Suhartono, M. T. (2016). Exploration Potential CIFOR Forest actinomycetes origin as Antimicrobial, Anti Fungus and Producing Enzymes Extracellular Xylanase. Biosaintifika: Journal of Biology Biology Education, 8(1), 94-102.

Antimicrobial Potential of an Actinomycete Gordonia terrae JSN1.9-Derived Orange Pigment Extract Siti Sholekha; Sri Budiarti; Akhmad Endang Zainal Hasan; Ni Putu Ratna Ayu Krishanti; Aris Tri Wahyudi
HAYATI Journal of Biosciences Vol. 31 No. 1 (2024): January 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.1.161-170

Actinomycetes are known to be a source of natural products and drugs. Gordonia terrae, an actinomycete pigment producer, shows potential in producing pigment with antimicrobial activity. This study aims to determine the antimicrobial activity of the active pigment fraction produced by the actinomycete G. terrae, assess the effects of the active pigment fraction on microbial cells, and identify the types of compounds present in the fraction. The pigment extract exhibited antimicrobial activity against Gram-positive bacteria and fungi. Specifically, it showed activity against Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 25293, and Candida albicans ATCC 10231. Furthermore, the study evaluated the antimicrobial activities of the active fractions, revealed the active fraction had better antimicrobial activity than the crude extract. Scanning electron microscopy (SEM) confirmed that the active fraction of the pigment causes damage to B. subtilis ATCC 6633 cells, inhibits the formation of filaments in C. albicans ATCC 10231, and alters the normal shape of the cells. LC-MS/MS results showed that the active fraction contained several compounds known for their antimicrobial activity. Among the dominant compounds identified were cholestyramine, aminopregnane, and sphinganine. Thus, this study demonstrated that the orange pigment extract derived from G. terrae JSN1.9 exhibits promising antimicrobial activity.

Diversity and the Composition of Fatty Acids of Lipolytic Bacteria Isolated from Soil and Aquatic Sediment in a Forest and on an Oil Palm Plantation Wijayanti, Marini; Meryandini, Anja; Wahyudi, Aris Tri; Yuhana, Munti
Makara Journal of Science Vol. 18, No. 3
Publisher : UI Scholars Hub

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The specific bacteria in forests and on oil palm plantations are lipolytic bacteria. Their enzymes have been applied in the agro-aquaculture, food, detergent, pharmaceutical, dairy, and biodiesel-biokerosene industries. This study describes the diversity of cultivable lipolytic bacteria from soil and aquatic sediment in a forest and on an oil palm plantation and their fatty acid products. Soil samples used in this research were obtained from topsoil in a lowland forest and on an oil palm plantation and from sediments in fresh water near these sites. The forest is located in Bukit Duabelas National Park, and the oil palm plantation is near the forest in Sarolangun District, Jambi Province, Indonesia. Twenty-two isolates of lypolitic bacteria were selected from 32 isolates grown in lipolytic selective medium. The 22 consisted of 11 isolates from topsoil and 11 from aquatic sediment from the forest and plantation area. These isolates were identified by 16S rRNA-sequence data analysis. Taxonomically, they belonged to five genera: Burkholderia, Cupriavidus, Serratia, Acinetobacter, and Kurthia. The maximum likelihood tree showed that they are phylogenetically distributed in three clusters. They were clustered into three groups: the Burkholderia-Cupriavidus group, the Serratia-Acinetobacter group, and the Kurthia group. Their lipolytic enzymes formed various fatty acids after analysis by gas chromatography-flame ionization detector (GC-FID). Some isolates formed essential fatty acids, such as linoleic, linolenic, arachidonic, eicosapentanoic acid (EPA), and docosahexanoic acid (DHA).

Xanthomonas oryzae pv. oryzae BAKTERI PENYEBAB HAWAR DAUN PADA PADI: ISOLASI, KARAKTERISASI, DAN TELAAH MUTAGENESIS DENGAN TRANSPOSON Wahyudi, Aris Tri; Meliah, Siti; Nawangsih, Abdjad Asih
Makara Journal of Science Vol. 15, No. 1
Publisher : UI Scholars Hub

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Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis. X. oryzae pv. oryzae (Xoo) causes bacterial leaf blight (BLB) of rice (Oryza sativa L.), a major disease that constrains production of the staple crop in many countries of the world. Identification of X. oryzae pv. oryzae (Xoo) was conducted based on the disease symptoms, pathogenicity, morphological, physiological, and genetic characteristics of bacterial cultures isolated from the infected plants. Fifty bacterial isolates predicted as Xoo have been successfully isolated. They are aerobic, rod shaped, and Gram negative bacteria. The isolates were evaluated for their hypersensitivity in tobacco and pathogenicity in rice plant. Fifty isolates induced hypersensitive reaction in tobacco and showed pathogenicity symptom in rice in different length. Based on physiological test, hypersensitivity and pathogenicity reactions, three bacterial isolates strongly predicted as Xoo, i.e. STG21, STG42, and STG46, were non indole formation, non pigment fluorescent, hydrolyzed casein, catalase activity positive, but negative oxidase. Partial sequencing of 16S rRNA genes of STG21 and STG42 showed 80% and 82% homology with X. oryzae, respectively, while STG46 showed 84% homology with X. campestris. Mini-Tn5 transposon mutagenesis of STG21 generated one of the mutants (M5) lossed it’s ability to induce hypersensitive reaction in tobacco plant and deficient in pathogenicity on rice. The lesion length of rice leaf caused by the mutant M5 decreased up to 80%.

Insilico analysis of adenylation and ketosynthase domain related to antifungal activity of rice phyllosphere bacteria Wiraswati, Sri Martina; Rusmana, Iman; Nawangsih, Abdjad Asih; Wahyudi, Aris Tri
Biogenesis: Jurnal Ilmiah Biologi Vol 11 No 2 (2023)
Publisher : Department of Biology, Faculty of Sci and Tech, Universitas Islam Negeri Alauddin Makassar

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24252/bio.v11i2.39872

The effectiveness of Liliaceae phyllospheric Actinomycetes as biocontrol agent of purple blotch disease (Alternaria porri Ell. Cif) on shallot Wati, Cheppy; Nawangsih, Abdjad Asih; Wahyudi, Aris Tri; Wiyono, Suryo; Munif, Abdul
Jurnal Hama dan Penyakit Tumbuhan Tropika Vol. 24 No. 2 (2024): SEPTEMBER, JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA: JOURNAL OF TROPICAL PLAN
Publisher : Universitas Lampung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23960/jhptt.224190-198

Purple blotch, caused by Alternaria porri, affects leaves and tubers, leading to reduced yields. Traditionally, synthetic chemical fungicides were heavily relied upon for control. As an alternative, biocontrol agents like actinomycetes have gained attention. Some actinomycetes can suppress plant pathogens by producing antifungal compounds. This research aimed to investigate the efficacy of phyllosphere actinomycetes from Liliaceae plants as biocontrol agents against purple blotch disease on shallots in the greenhouse. Conducted at the IPB University Plant Bacteriology and Mycology Laboratory and the greenhouse at Bogor Agricultural Development Polytechnic, West Java, the research involved several stages, including pathogen identification, preparation of actinomyces inoculum and A. porri, and application of actinomycetes biocontrol agents to shallots in the greenhouse. A. porri isolates were obtained from shallot production centers in the Brebes area, Central Java. The use of the actinomycetes from the phyllosphere effectively suppressed purple blotch disease, with the lowest area under the disease development curve (AUDPC) recorded at 635.9% for the CFS28 isolate. Lower AUDPC values indicated slower disease progression. Actinomycetes biocontrol agents showed promising efficacy, with the CFS28 isolate achieving the highest efficacy percentage of 78.37%. Additionally, plant growth was significantly enhanced by actinomycete application, with tuber sizes ranging from 1.44 to 2.06 g, fresh weights from 17.63 to 24.72 g, and dry weights of shallot bulbs from 5.43 to 17.96 g. The incubation period for A. porri could be extended by actinomycetes, ranging from 5.43 to 8.5 days for purple blotch symptoms to manifest on shallots. The use of Actinomyces phyllosphere biocontrol agents holds promise for disease control on other plants’ leaves, contributing to environmentally friendly and sustainable agricultural practices.

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

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.

Potency of sponge-associated bacteria producing bioactive compounds as biological control of vibriosis on shrimp Rini, Adityawati Fajar; Yuhana, Munti; Wahyudi, Aris Tri
Jurnal Akuakultur Indonesia Vol. 16 No. 1 (2017): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

ABSTRACT The aims of this study were to obtain sponge-associated bacteria as biocontrol to inhibit vibriosis in vitro and in vivo, to identify the bacterial isolates based on 16S-rRNA gene, and to detect the presence of nonribosomal peptide synthetase (NRPS), and polyketide synthase (PKS) genes to prove its ability of bioactive compounds synthesis. Aaptos sp. and Hyrtios sp. sponges were collected from Pramuka Island, Jakarta. The isolation using sea water complete (SWC) and zobel marine agar (ZMA) medium obtained 174 isolates. A total 69 isolates were screened successfully based on their antibacterial activity. 47 isolates showed negative haemolysis through hemolytic assays. The pathogenicity test used twelve selected isolates that have a broad spectrum of antibacterial activity and haemolysis negative. The result of pathogenicity test showed that 12 isolates were not pathogenic to the shrimp post larvae with no significantly different (P>0.05) between treatment and negative control. Results of challenge test with Vibrio harveyi have a significant difference survival (70±5.0–90±0.0%) (P<0.05) compared with positive control (38.3±2.9%). Genetic analysis based on 16S-rRNA revealed the groups of three genera belonged to Pseudomonas, Staphylococcus, and Alcaligenes. Based on amplification of NRPS and PKS genes, four bacterial isolates have been detected to have only NRPS gene, one isolate has only PKS, and one isolate has both genes. The results indicate that the potency of six sponge-associated bacteria as bioactive compounds producers. Keywords: NRPS, PKS, anti-vibriosis, Pacific white shrimp ABSTRAK Penelitian ini bertujuan untuk memperoleh isolat bakteri asosiasi spons yang mempunyai kemampuan dalam menghambat vibriosis secara in vitro, in vivo dan mendeteksi gen 16S-rRNA, nonribosomal peptide synthase (NRPS) serta polyketide synthase (PKS) untuk memastikan kemampuan mensintesis senyawa bioaktif. Spons Aaptos sp. dan Hyrtios sp. berhasil dikoleksi dari perairan Pulau Pramuka, Kep. Seribu Jakarta. Isolasi bakteri dengan menggunakan media sea water complete (SWC) dan zobel marine agar (ZMA) diperoleh 174 isolat. Sebanyak 69 isolat terdeteksi memiliki aktivitas antibakteri. Uji hemolisis menunjukkan 47 isolat adalah hemolisis negatif. Uji patogenisitas menggunakan 12 isolat terpilih yang memiliki spektrum luas dan hemolisis negatif. Hasil uji patogenisitas tehadap 12 isolat menunjukkan bahwa semua isolat tidak bersifat patogen terhadap pascalarva udang vaname. Hal ini dibuktikan dengan sintasan pascalarva udang vaname yang tidak berbeda nyata (P>0,05) dengan kontrol negatif. Hasil uji tantang terhadap Vibrio harveyi diketahui sintasan pascalarva udang vaname (70±5,0–90±0,0%) memiliki perbedaan yang signifikan jika dibandingkan dengan kontrol positif (38,3±2,9%). Berdasarkan analisis sekuen gen 16S-rRNA, menunjukkan bahwa isolat-isolat tersebut memiliki kemiripan dengan genus Pseudomonas, Staphylococcus, dan Alcaligenes. Deteksi gen NRPS dan PKS menggunakan PCR diperoleh empat isolat bakteri memiliki hanya gen NRPS, satu isolat memiliki hanya gen PKS, dan satu isolat memiliki kedua gen NRPS-PKS. Hal ini membuktikan bahwa keenam isolat memiliki potensi sebagai penghasil senyawa bioaktif. Kata kunci: NRPS, PKS, antivibriosis, udang vaname

Bacterial Communities in Aquatic Sediment from Bukit Duabelas Raintforest and Oil Palm Plantation at Sumatra Indonesia Wijayanti, Marini; Wahyudi, Aris Tri; Yuhana, Munti; Engelhaupt, Martin; Meryandini, Anja
HAYATI Journal of Biosciences Vol. 25 No. 2 (2018): April 2018
Publisher : Bogor Agricultural University, Indonesia

The diversity of bacterial communities in aquatic sediment of rainforest and oil palm plantation at Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used for revealing the community shift of bacterial phyla and genera in both areas. Ecological approach used soil pH, total Carbon (TC), total Nitrogen (TN), available Phosphorus (AP) measurement and bacterial diversity with Shanon and Simpson indices, and bacterial richness with Chao1-ACE indices and OTUs. Bacterial diversity and richness in aquatic sediment of forest area was higher than that ones in oil palm plantation area, although their pH, TC, and TN in both areas were not different significantly. The majority of sequences related to Proteobacteria (34.85%), Acidobacteria (32.67%), Nitrospirae (6.86%), Chloroflexi (4.31%), and Actinobacteria (4.02%) were from forest; whereas those related to Acidobacteria (46.10%), Proteobacteria (25.86%), Nitrospirae (9.20%), Chloroflexi (4.99%), and Actinobacteria (2.34%) invented from oil palm plantation. The genera of Alphaproteobacteria and Betaproteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed both aquatic sediment of forest and oil palm plantation. The most genera in the phylogenetic tree from aquatic sediment of both areas was Burkholderia. The bacterial community shift in aquatic sediment of forest transformation indicated higher bacterial diversity index, richness index, some of phyla and genera in aquatic sediment from forest than from oil palm plantation.

Co-Authors Abdjad Asih Nawangsih Abdjad Asih Nawangsih ABDUL MUNIF ABDUL MUNIF Akhmad Endang Zainal Hasan Alimuddin Alimuddin Alina Akhdiya ALINA AKHDIYA ANDINI PURNAWIJAYA Anja Meryandini Anja Meryandini Antonius Suwanto Ari Fina Bintarti Ari Fina Bintarti, Ari Fina ARI SUSILOWATI Aris Tjahjoleksono BRAMANTYO JATI PRASOJO Budi Tjahjono C Hanny Wijaya DIAH ISKANDRIATI Dina Aribah DINI NURDIANI Edi Husen EDI HUSEN Edi Husen Edi Husen EDI HUSEN Engelhaupt, Martin ERNIN HIDAYATI Hamim Hamim Hari KAPLI Hermawaty Abubakar Iman Rusmana Irmawati Jun Nomura LAKSMI AMBARSARI Latifah Kosim Darusman Maggy Thenawidjaja Suhartono Maggy Thenawidjaya Suhartono Marini Wijayanti Meliah, Siti Mia Setiawati MONA PRIMANITA MUHAMMAD AGUS SUPRAYUDI Muhammad Faiz Amri Muhammad Zairin Jr MUNTI YUHANA Mutiha Panjaitan NI PUTU RATNA AYU KRISHANTI Ni Putu Ratna Ayu Krishanti NISA RACHMANIA MUBARIK NURFITRIANI RINA Pamungkas, Joko Puspitasari, Esti Raden Ajie Syahbarie RAHAYU FITRIANI WANGSA PUTRIE RAHAYU WIDYASTUTI RASTI SARASWATI Rasti Saraswati Rasti Saraswati Rika Indri Astuti Rini, Adityawati Fajar Rury Eryna Putri Rustam, Yepy Hardi Sarah Asih Faulina Sarah Asih Faulina, Sarah Asih Satya, Andreas Adhi Sigit Tri Wibowo Sipriyadi Sipriyadi Sipriyadi Siska Tridesianti Siti Meliah Siti Sholekha Sri Budiarti Suryo Wiyono SUSILOWATI1 SUSILOWATI1 SYAMSUL BAHRI SYAMSUL BAHRI Tati Barus TEDJA IMAS Uci Cahlia Umi Fatmawati VINCENTIUS ARCA TESTAMENTI WAODE MUNAENI Wati, Cheppy WIDANARNI WIDANARNI Wiraswati, Sri Martina Yohanes Bernadino Putera Saju Yuli Siti Fatma YULIN LESTARI

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