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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) Journal of Multidisciplinary Applied Natural Science 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 Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics

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Molecular Identification of Genes Involved in Magnetosome Synthesis in Magnetospirillum magneticum AMB-1 Aris Tri Wahyudi
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 14, No 2 (2009): June 2009
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v14i2.2691

Satu mutan Magnetospirillum magneticum AMB-1 yang tidak bersifat magnetik, yang didesain NMA41, dikonstruksi melalui mutagenesis dengan transposon Mini-Tn5Km1 untuk mengidentifikasi gen yang terlibat dalam sintesis magnetosom. Mutagenesis dengan transposon dilakukan melalui konjugasi antara M. magneticum AMB-1 dan Escherichia coli S17-1 ( pir) yang membawa plasmid pUTmimi-Tn5Km1. Frekuensi transkonjugasi tertinggi berkisar 1.8 x 10-7 sel per resipien. NMA41 tidak respon terhadap bidang magnet dan kehilangan kemampuan dalam mensintesis magnetosom. Sekuens DNA/gen yang disisipi oleh transposon (dinamakan DNA pengapit) diisolasi dengan PCR yang dibalik (inverse PCR) dan diklon ke dalam plasmid pCR2.1. Penyejajaran sekuen DNA dari DNA pengapit terhadap sekuens DNA genom lengkap AMB-1 dapat mengidentifikasi sebuah kerangka baca terbuka (open reading frame, ORF2) dalam suatu operon yang terdiri dari 4 gen. Sekuen asam amino yang dideduksi dari ORF2 menunjukkan homologinya dengan protein domain GGDEF dari Magnetospirillum magnetotacticum MS-1 (identik 90%; kemiripan 95%) yang mempunyai fungsi dalam mekanisme transduksi sinyal. Gen atau operon ini diduga berfungsi selama proses sintesis magnetosom pada M. magneticum AMB-1.

Penapisan Bakteri Filosfer Penghasil Senyawa Bioaktif Anti Xanthomonas oryzae pv. oryzae Penyebab Penyakit Hawar Daun Bakteri pada Padi NURFITRIANI RINA; NI PUTU RATNA AYU KRISHANTI; ALINA AKHDIYA; ARIS TRI WAHYUDI
Jurnal Sumberdaya Hayati Vol. 2 No. 1 (2016)
Publisher : Departemen Biologi, Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jsdh.2.1.19-24

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the important diseases in rice crops in Indonesia. The disease is difficult to be controlled since it attacks the rice plant at different growth stages such as tillering, flowering and ripening. One of the alternatives that could be used to control the disease is by using phyllosphere bacteria as the biocontrol agents. This study aims to isolate, characterize and screen the rice phyllosphere bacteria producing bioactive compounds against Xoo. Phyllosphere bacteria isolated from healthy leaves of rice var. Ciherang by using 4 different media obtained 285 bacterial isolates which were consisted of the 65 isolates of King’s B agar, 86 isolates of Nutrient agar, 81 isolates of Luria-Bertani agar, and 53 isolates of Trypticase Soy agar media. Antagonist test using double layer method showed 58 isolates of phyllosphere bacteria produced bioactive compounds that inhibited the growth of Xoo. Pathogenicity test agaist rice leaf revealed 18 bacterial isolates did not perform their potencies as pathogenic bacteria. Among the 18 non-phytopathogenic bacterial isolates, 14 isolates belong to Gram-positive bacteria and 4 isolates belong to Gram-negative bacteria. Five isolates among Gram positive bacteria were predicted as Bacillus genera.

SOYBEAN SEEDLING ROOT GROWTH PROMOTION BY 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE-PRODUCING PSEUDOMONADS Edi Husen; Aris Tri Wahyudi; Antonius Suwanto; Rasti Saraswati
Indonesian Journal of Agricultural Science Vol 10, No 1 (2009): April 2009
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v10n1.2009.p19-25

Pseudomonad producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase (E.C.4.1.99.4) has been known to promote plant growth by lowering ethylene biosynthesis in higher plants, which can be induced by indole-3-acetic acid (IAA) production. The objective of this study was to examine the ability of IAAproducing Pseudomonas isolated from local soil environment (rhizosphere of soybean grown in Plumbon's agricultural areain Cirebon, West Java, Indonesia) to promote soybean root growth in relation to their ACC deaminase activities. The experiments were conducted in growth room and Laboratory of Soil Biology Research, Indonesian Soil Research Institute, Bogor, from January to August 2008. Soybean seeds were inoculated by immersing the seeds for 1 hour in bacterial cell suspension containing approximately 108-109 cells ml-1. The seeds were then germinatedfor 2 days before planting in growth pouches containing sterilized distilled water. All treated and untreated seeds were grown for 7 days in growth room at 24°C with 1300 lux of light intensity for 12-hour followed by a 12-hour dark period at 22°C. ACC deaminase activity of the isolates was assayed based on their ability to grow in Dworkin-Foster’s salt minimal medium containing ammonium sulfate or ACC as a source of nitrogen. Thirteen out of 81 isolates tested significantly increased soybean root length and weight, up to 50% from untreated plants. Of 13 isolates, 11 demonstrated ACC deaminase activities. Two isolates that did not show ACC deaminase activities had lower capacity to produce IAA. The results suggest that the effectiveness of IAA producing Pseudomonas in promoting the growth of the soybean seedlings is associated with their ACC deaminase activities or they produce IAA at low levels.

Role of Bacteria in Tempe Bitter Taste Formation: Microbiological and Molecular Biological Analysis Based on 16S rRNA Gene TATI BARUS; ANTONIUS SUWANTO; ARIS TRI WAHYUDI; HANNY WIJAYA
Microbiology Indonesia Vol. 2 No. 1 (2008): April 2008
Publisher : Indonesian Society for microbiology

Tempe is traditional Indonesian food. It has a variety of tastes, sometimes with a hint of bitterness, which may differ in intensity. The cause of bitterness in tempe has never been reported previously. In this study, the aim is to identify whether bacteria play a role in the formation of bitter tastes in tempe. Sensory tests were carried out in order to determine the scoresof bitter-taste-intensity in tempe. The sensory test on EMP, WJB, CLR, DRG, and MLB tempe shows that EMP tempe has the highest score (2.3) and WJB has the lowest (1.3). It is revealed that the processing method has no impact on the formation of the bitter taste in tempe. Plating analysis, showed that EMP soaking water contained a higher number of Enterobacteria groupbacteria, approximately 103-104 CFU ml-1 and spore-forming bacteria groups, 102 CFU ml-1, compared to WJB. Similarly, other bacteria groups in fresh EMP tempe was 102 CFU g-1 higher than those in fresh WJB tempe. Based on sequencing the16S rRNA gene, the dominant bacteria on PCA media in EMP tempe are Acetobacter indonesiensis, Klebsiella pneumoniae, Bacillus subtilis, and Flavobacterium sp. On the other hand those in WJB tempe were Klebsiella sp., Brevundimonas sp., Bacillus sp., Pseudomonas putida, and Acinetobacter sp. Bacillus, a group of proteolytic bacteria was found 105 CFU m-1 higher in the soaking water of EMP compared to WJB. Nevertheless, the types and numbers of fungi were not significantly different betweentempe types. Accordingly, it is concluded that the difference in the number and the types of bacteria involved in the tempe production process leads to the difference in the bitter taste intensity in both EMP and WJB tempe.

Rapid and Simple Amplification of Genomic DNA Sequences Flanking Transposon ARIS TRI WAHYUDI
Microbiology Indonesia Vol. 1 No. 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

A rapid and simple method to amplify genomic DNA sequences flanking mini-Tn5 transposon insertion was developed. This technique can be used to determine the location and orientation of the transposon insertion within genomic DNA of the bacteria. Based on the mini-Tn5Km1 transposon sequence, PCR primers can be designed to specifically amplify the DNA sequences flanking mini-Tn5 transposon by inverse polymerase chain reaction (inverse PCR) directly, upstream and downstream of the transposon insertion. The method involves: (i) digestion with a restriction enzyme that does not cut mini-Tn5Km1 sequence; (ii) self-ligation under conditionsfavoring the production of monomeric circles; and (iii) inverse PCR reaction using primers designed from mini-Tn5Km1 sequence to amplify the DNA sequences flanking mini-Tn5Km1 transposon insertion. Feasibility and reliability of this method were demonstrated with mini-Tn5Km1 mutants of the microaerobic magnetic bacterium Magnetospirillum magneticum AMB-1 which are defective in magnetosomes synthesis. The inverse PCR products amplified from these mutant genomes showed the correct fragments as determined through Southern hybridization and DNA sequence analysis.

Genetic Diversity of Antifungi-Producing Rhizobacteria of Pseudomonas sp. Isolated from Rhizosphere of Soybean Plant SUSILOWATI1 SUSILOWATI1; ARIS TRI WAHYUDI; YULIN LESTARI; SURYO WIYONO; ANTONIUS SUWANTO
Microbiology Indonesia Vol. 4 No. 1 (2010): April 2010
Publisher : Indonesian Society for microbiology

Antifungi-producing rhizobacteria have been recognized playing an important role in plant disease suppression. In our laboratory, 13 indigenous soybeans' rhizobacteria Pseudomonas sp. that showed strong growth inhibition of root pathogenic fungi, Rhizoctonia solani, Fusarium oxysporum and Sclerotium rolfsii, have been isolated from rhizosphere of soybean plant. For further understanding, the genetic diversity of the antifungi-producing Pseudomonas sp. was investigated using Amplified 16S rDNA Restriction Analysis (ARDRA) and 16S rRNA gene sequences analysis. 16S rDNA were amplified by PCR technique and digested with restriction endonuclease HaeIII, RsaI and AluI. Sequences of 16S rRNA gene were analyzed using the BLAST program for similarity searches on sequence databases. ARDRA based dendrogram analysis was carried out by neighbor-joining of TREECON 1.3b software package. ARDRA indicated the variability of Pseudomonas sp. based on the digestion sites. Dendrogram clustering analysis based on the restriction enzymes profile of the amplified rDNA distinguished Pseudomonas sp. into 7 ribotype groups. The sequences of 16S rRNA gene confirmed that the isolates belonging to Pseudomonas sp. and the phylogenetic tree formed 4 clusters. There was a quite overlap among ARDRA groups and 16S rRNA sequence clusters. This finding suggested that antifungal producing Pseudomonas sp. were present in the rhizosphere of soybean plant and the level of genetic diversity exist within these species. Sequence analysis of the 16S rRNA gene of the Pseudomonas sp. with an identical ARDRA pattern confirmed that members of an ARDRA group were closely related to each other.

Evidence for a Link Between Pathogenicity and the Role of ImpBacterial Transport Effector Proteins in Soybean Infection by Xanthomonas axonopodis pv. glycines ANTONIUS SUWANTO; ARIS TRI WAHYUDI; BUDI TJAHJONO
Microbiology Indonesia Vol. 1 No. 2 (2007): August 2007
Publisher : Indonesian Society for microbiology

Xanthomonas axonopodis pv. glycines (Xag) is the causal agent of bacterial pustule disease of soybeans. A nonpathogenic mutant of Xag (M715) was constructed employing transposon mutagenesis which showed similar epiphytic survival in planta to its wild type strain (YR32). The objective of this work was to identify and to analyze genes involved in pathogenicity in Xag YR32. Inverse Polymerase Chain Reaction (IPCR) was used to isolate the DNA flanking transposon insertion. A 1.3 kb flanking DNA fragment was sequenced and analyzed employing BLAST program to study homology, the position of transposon insertion and to predict the structure and function of the gene. One of the Open Reading Frames (ORFs) shared homology with inner membrane proteins (imps) of Xanthomonas axonopodis pv. citri (GenBank accession No. NC 003919). Northern blot analysis revealed that an imps gene was monocistronic and the size of imps mRNA in YR32 was slightly longer than in M715. Reverse Transcriptase- PCR analysis demonstrated that the imps transcript in M715 was much less abundant than in the wild type YR32. Transposon (mini-Tn5-Kmr-Tpr) was determined to be inserted close to the end of C-terminal region of imps gene and might be sufficient to destabilize the imps transcript in M715 and so influence effectors transportation from Xag to plant cell.

Characterization of Acid-Aluminium Sensitive Mutants of Soybean Symbiont Bradyrhizobium japonicum Generated by Transposon Mutagenesis ARIS TRI WAHYUDI; ANDINI PURNAWIJAYA; DINI NURDIANI; TEDJA IMAS
Microbiology Indonesia Vol. 1 No. 2 (2007): August 2007
Publisher : Indonesian Society for microbiology

Acid-aluminium sensitive mutants of symbiotic bacterium Bradyrhizobium japonicum BJ11 (designated as AAS11) and KDR15 (designated as AAS15) were constructed by mini-Tn5 transposon mutagenesis to study genes involved in acid-aluminium tolerance (AAT) in B. japonicum. Transposon delivery was carried out through conjugation between B. japonicum strains as recipients and Escherichia coli S17-1 (ë pir) carrying pUTmini- Tn5Km1 as a donor strain. The result showed that frequency of transconjugation was in the range of 6.7 x 10-7 to 7.1 x 10-6 cell per recipients. AAS11 and AAS15 mutants did not grow on Ayanaba media (pH 4.5) containing 50 μM Aluminium. These mutants remained able to form root nodules of Siratro (Macroptilium arthropurpureum) plants revealing genes interrupted by transposon which were responsible for acid-Al tolerance did not correlate with the nodulation genes. Strains tolerant to acid-aluminium and their mutants with a wild type sensitive to acidaluminium were characterized by accumulating phosphate and aluminium absorption. Compared to the wild type acid-aluminium tolerant B. japonicum, there was approximately a three- to eight-times decrease in phosphate accumulation and a five- to seven-times increase in aluminium absorption by these mutants. These results suggest that aluminium and phosphate contents in the bacterial cells may be involved in mechanisms of acid-Al tolerance of B. japonicum grown in acid-aluminium stress conditions.

Prospective Use of 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacteria for Plant Growth Promotion and Defense against Biotic and Abiotic Stresses in Peat-Soil-Agriculture EDI HUSEN; ARIS TRI WAHYUDI; ANTONIUS SUWANTO; RASTI SARASWATI
Microbiology Indonesia Vol. 2 No. 3 (2008): December 2008
Publisher : Indonesian Society for microbiology

The 1-aminocyclopropane-1-carboxylate (ACC) deaminase (EC4.1.99.4) is an enzyme produced by some soil bacteria to degrade ACC (the immediate precursor of ethylene) to reduce ethylene biosynthesis in higher plants. Increased concentrations of ethylene in plant tissues, which are triggered by various biotic and abiotic stresses, inhibits plant growth and weakens the plant defense against the stressors. Various findings on the successful use of ACC deaminase producing bacteria for plant growth under unfavorable soil conditions are inspiring their use in tropical peat-soil-agriculture, which possesses bio-physical constraints. It has been proven that inoculation of plants with ACC deaminase producing bacteria decreased ethylene inhibition generated by unfavorable environmental conditions, such as nutrient shortage, flooding, drought, high salts, and the presence of heavy metals and organic pollutants. Understanding the mechanisms by which ACC deaminase-producing bacteria act to reduce plant stress and the fitness of bacterial traits with the properties and constraints of peat-soils becomes a key to utilize these bacteria in improving crop productivity. The bacteria may ameliorate plant stress as well as promote plant growth under seasonal bio-physical changes of peat-soils that are usually encountered in the field.

Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis SYAMSUL BAHRI SYAMSUL BAHRI; ARIS TRI WAHYUDI; NISA RACHMANIA MUBARIK
Microbiology Indonesia Vol. 3 No. 1 (2009): April 2009
Publisher : Indonesian Society for microbiology

Plant-growth promoting rhizobacteria (PGPR) are rhizosphere associated soil-borne bacteria that can enhance plant growth and inhibit the development of root pathogens. Many soil bacteria have been used as PGPR, and one of them is Bacillus sp. The implementation of PGPR is constrained by genotype fluctuation that makes it inactive on the rhizosphere. Our previous study had characterized and revealed that 11 Bacillus sp. isolated from the soybean plant rhizosphere were PGPR. To asses and compare the genetic diversity of these isolates, Amplified Ribosomal DNA Restriction Analysis (ARDRA) and DNA sequence analysis of 16S rRNA were conducted. The construction of Neighbor-joining trees and bootstrap analysis of 100 resamples of ARDRA and 16S rRNA gene sequences were performed using Treecon software for windows ver. 1.3b. ARDRA analysis was done by using four restriction enzymes (RsaI, HaeIII, CfrI and HinfI), resulting in four phylotypes, respectively phylotype I (Bacillus sp. Cr24, Cr33, Cr64 and Cr68), phylotype II (Bacillus sp. Cr 31 and Cr66), phylotype III (Bacillus sp. Cr44 and Cr71) and phylotype IV (Bacillus sp. Cr67, Cr28 and Cr69). Results of BLASTN from 16S rRNA gene sequences showed that these isolates are genetically diversed. The evolution relationship of Bacillus sp. could be shown by the 16S rRNA gene sequences analysis, while ARDRA based on the digestion sites showed their variability.

Co-Authors Abdjad Asih Nawangsih Abdjad Asih Nawangsih ABDUL MUNIF ABDUL MUNIF Akhmad Endang Zainal Hasan Alimuddin Alimuddin Alina Akhdiya ALINA AKHDIYA Andi Ernawati 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 Dudi Hardianto, Dudi Edi Husen EDI HUSEN Edi Husen Edi Husen EDI HUSEN Efrida Martius 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 Nasution, Uli Julia 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 Sri Budiarti Poerwanto sri murtini . 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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