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

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Abstract

Pseudomonad producing 1-aminocyclopropane-1-carboxylate(ACC) deaminase (E.C.4.1.99.4) has been known to promoteplant 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 IAAproducingPseudomonas isolated from local soil environment(rhizosphere of soybean grown in Plumbons agricultural areain Cirebon, West Java, Indonesia) to promote soybean root growthin relation to their ACC deaminase activities. The experimentswere conducted in growth room and Laboratory of Soil BiologyResearch, Indonesian Soil Research Institute, Bogor, from Januaryto August 2008. Soybean seeds were inoculated by immersing theseeds for 1 hour in bacterial cell suspension containingapproximately 108-109 cells ml-1. The seeds were then germinatedfor 2 days before planting in growth pouches containing sterilizeddistilled water. All treated and untreated seeds were grown for7 days in growth room at 24°C with 1300 lux of light intensityfor 12-hour followed by a 12-hour dark period at 22°C. ACCdeaminase activity of the isolates was assayed based on their abilityto grow in Dworkin-Foster’s salt minimal medium containingammonium sulfate or ACC as a source of nitrogen. Thirteen outof 81 isolates tested significantly increased soybean root lengthand weight, up to 50% from untreated plants. Of 13 isolates,11 demonstrated ACC deaminase activities. Two isolates thatdid not show ACC deaminase activities had lower capacity toproduce IAA. The results suggest that the effectiveness of IAAproducingPseudomonas in promoting the growth of the soybeanseedlings is associated with their ACC deaminase activities orthey produce IAA at low levels.
Detection and Cloning of a Gene Involved in Zwitermicin A Synthesis from Plant Growth Promoting Rhizobacteria of Bacillus sp CR64 Wahyudi, Aris Tri; Astuti, Rika Indri; Mubarik, Nisa Rachmania; Faulina, Sarah Asih
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

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Abstract

Utilization of soil bacteria as biocontrol agent is becoming popular due to its valuable and effective mechanisms to suppress plant pathogenic microbes. We have previously isolated Bacillus sp, designated as Bacillus sp CR64, which exhibited effective plant growth promoting and antifungal activities. In this study, CR64 was examined in inhibiting the growth of Rhizoctonia solani, the causing agent of root rot disease. Partial sequence analysis of 16S rRNA gene revealed that this isolate similar with Bacillus cereus (94%). Furthermore, a gene designated zmaR was detected by means of specific amplification of DNA fragment approximately 950 bp. This fragment was then cloned onto pCRII-TOPO (3.9 kb) and sequenced using DNA sequencer ABI PRISM 310. Sequence analysis revealed that it had highest homology with the ZmaR protein (89% identity; 90% similarity) of B. thuringiensis serovar kurstaki (AAF82729.2). Alignment analysis with other ZmaR sequences from other antibiotic-producing Bacilli exhibited an almost fully conserved region within ZmaR sequences.Key words : PGPR, Bacillus sp CR64, Zwitermicin A, Cloning, Antifungal.
Exploration of Potential Actinomycetes from CIFOR Forest Origin as Antimicrobial, Antifungus, and Producing Extracellular Xylanase Sipriyadi, Sipriyadi; Lestari, Yulin; Wahyudi, Aris Tri; Meryandini, Anja; Suhartono, Maggy Thenawidjaja
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

Abstract

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.
Identification of nifD and nifH Genes of Methanotrophic Bacteria from Rice Field Bintarti, Ari Fina; Rusmana, Iman; Wahyudi, Aris Tri
ANNALES BOGORIENSES Vol 18, No 2 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (879.425 KB) | DOI: 10.1234/97

Abstract

Metanotrophic bacteria have ability to oxidize methane and fix atmospheric nitrogen, hence the bacteria has an important role as a nitrogen source provider on wetland area like rice fields. Nitrogen fixation process is catalyzed by the nitrogenase enzyme complex, encoded by nifD and nifH genes. However, characteristic of these genes from indigenous-methanotrophic bacteria still poorly understood. Hence, nifD and nifH genes of methanotrophic bacteria isolated from rice fields in Indonesia (BGM3, BGM9, SS1, SS3, SS10, ST18, SP3 and INP4) were identified and characterized. Detection of nifH and nifD genes was conducted by polymerase chain reaction (PCR) amplification. nifH and nifD gene sequences were analyzed using BLAST-X and phylogenetic trees were constructed using Neighbour Joining method. Based on nifH sequences analysis, SS1 closely related to Beijerinckia mobilis and SS3, SS10, ST 18 closely related to Beijerinckia indica subsp. indica ATCC 9039, while, BGM3, INP4, and BGM9 related to nifH of uncultured nitrogen-fixing bacterium. In other hand, sequence analysis of nifD gene showed that SS1, SS3, SS10, ST 18 closely related to B. indica subsp. indica ATCC 9039 and BGM3, BGM9, INP4 closely related to Xanthobacter autotrophicus Py2. Identification by 16 SrRNA indicated that SS1, SS3, SS10, and ST18 had closeness to Beijerinckia sp. P310-1, while INP4 closely related to Xanthobacter sp. M5C24.
Molecular Identification of Genes Involved in Magnetosome Synthesis in Magnetospirillum magneticum AMB-1 Wahyudi, Aris Tri
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 | Full PDF (267.758 KB) | DOI: 10.24002/biota.v14i2.2691

Abstract

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.
Pengaruh Ekstrak Bawang Hutan Eleutherine bulbosa (Mill.) Urb. Terhadap Perubahan pH Pada Stimulasi Pertumbuhan Probiotik Secara In Vitro Munaeni, Waode; Widanarni, Widanarni; Yuhana, Munti; Setiawati, Mia; Wahyudi, Aris Tri
Jurnal Media Akuatika Vol 6, No 3 (2021): Juli
Publisher : Universitas Halu Oleo

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (693.243 KB) | DOI: 10.33772/jma.v6i3.19875

Abstract

Bawang hutan Eleutherine bulbosa (Mill.) Urb.merupakan tanaman obat yang memiliki kandungan oligosakarida, berpotensi sebagai prebiotik yang mampu meningkatkan kesehatan usus udang vaname (Litopenaeus vannamei). Tujuan dari penelitian ini adalah menguji efek dari ekstrak bawang hutan dengan konsentrasi berbeda terhadap perubahan pH media pada stimulasi pertumbuhan probiotik secara in vitro. Konsentrasi ekstrak bawang hutan terdiri dari : 10, 5, 2.5, 1.25, 0.625, 0.313, 0.156 mg/mL. Bakteri probiotik yang digunakan adalah Pseudoalteromonas piscicida 1Ub dan Bacillus sp. NP5,sedangkan bakteri enterik menggunakan Vibrio parahaemolyticus. Waktu inkubasi selama 24 jam dengan pengamatan warna dan pH media dilakukan pada jam ke-0, 14, 18, dan 24. Hasil penelitian menunjukkan bahwa setelah inkubasi selama 24 jam terjadi perubahan warna dan pH media. Nilai pH pada perlakuan probiotik lebih rendah dibandingkan dengan bakteri enterik. Nilai pH pada P. piscicida 1Ub lebih rendah dibandingkan dengan Bacillus sp. NP5. Perubahan pH yang lebih rendah menandakan probiotik mampu memanfaatkan oligosakarida yang ada pada ekstrak bawang hutan.Kata kunci : Eleutherine bulbosa, oligosakarida, pH, prebiotik, probiotik. 
Involvement of a Gene Encoding Putative Acetate Kinase in Magnetosome Synthesis in Magnetospirillum magneticum AMB-1 ARIS TRI WAHYUDI
HAYATI Journal of Biosciences Vol. 13 No. 1 (2006): March 2006
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (93.295 KB) | DOI: 10.4308/hjb.13.1.26

Abstract

A nonmagnetic mutant of Magnetospirillum magneticum AMB-1, designated NMA40, was constructed by mini-Tn5 transposon mutagenesis to identify genes involved in magnetosome synthesis. Transposon delivery was carried out through conjugation between M. magneticum AMB-1 as a recipient and Escherichia coli S17-1 (λ pir) carrying pUTmini-Tn5Km1 as a donor strain. NAM40 did not respond to the magnetic fields and completely lacked of magnetosome in the cell. DNA sequence/gen interrupted by transposon (called flanking DNA) was isolated by inverse PCR and cloned into pGEM-T Easy. Alignment of the DNA sequence of the flanking DNA allowed the isolation of an open reading frame (ORF2) within an operon consisting of three genes. The amino acid sequence deduced from ORF2 showed homology with acetate kinase from Sinorhizobium meliloti (50% identity and 67% similarity), which function for acetate metabolism. Further analysis revealed that upstream of ORF2 is ORF1, had homology with phosphotransacetylase of S. meliloti (67% identity, 77% similarity), and ORF3 located downstream of ORF2, had homology with hypothetical protein of Thermotoga maritima (30% identity, 60% similarity). ORF2 was subsequently isolated, cloned, and overexpressed in Escherichia coli BL21 (DE3) pLysS as an ORF2-Histag fusion polypeptide. Key words: Magnetospirillum magneticum AMB-1, magnetosome synthesis, transposon mutagenesis, cloning, overexpression
Diversity of Antifungal Compounds-Producing Bacillus spp. Isolated from Rhizosphere of Soybean Plant Based on ARDRA and 16S rRNA ARIS TRI WAHYUDI; BRAMANTYO JATI PRASOJO; NISA RACHMANIA MUBARIK
HAYATI Journal of Biosciences Vol. 17 No. 3 (2010): September 2010
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (85.717 KB) | DOI: 10.4308/hjb.17.3.145

Abstract

Plant growth promoting rhizobacteria (PGPR) play an important role in improvement of seed germination, root development, and water utilization by plants. These rhizobacteria can stimulate plant growth directly by producing growth hormones or indirectly by producing antifungal compounds/antibiotics to suppress phytopathogenic fungi. The objective of this research was to analyze the diversity of 22 antifungal-producing rhizobacteria of Bacillus sp. isolated from rhizosphere of soybean plant based on Amplified rDNA Restriction Analysis (ARDRA) and 16S rRNA Sequence. Restriction enzymes in ARDRA analysis, HinfI, HaeIII, and RsaI were used to digest 22 16S rDNA amplified from Bacillus sp. genomes. Based on this analysis, genetic diversity of 22 Bacillus sp. producing antifungal compounds were classified into eight different groups. Moreover, six selected isolates randomly from each ARDRA group that have strong activity to suppress fungal growth were analyzed for their 16S rDNA sequences compared with reference strains. The distributions of these isolates were genetically diverse on several species of Bacillus sp. such as B. subtilis, B. cereus, and B. fusiformis. ARDRA is a reliable technique to analyze genetic diversity of Bacillus sp. community in the rhizosphere.
Potential Pseudomonas Isolated from Soybean Rhizosphere as Biocontrol against Soilborne Phytopathogenic Fungi ARI SUSILOWATI; ARIS TRI WAHYUDI; YULIN LESTARI; ANTONIUS SUWANTO; SURYO WIYONO
HAYATI Journal of Biosciences Vol. 18 No. 2 (2011): June 2011
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (105.133 KB) | DOI: 10.4308/hjb.18.2.51

Abstract

Plants are liable to be attacked by soilborne fungal pathogens which are responsible to reduce plant growth and losses in yield. In Indonesia, indigenous soybeans’ rhizobacteria such as antifungal producing Pseudomonas sp. have not many been reported yet. Therefore, the potential of the Pseudomonas sp. as biocontrol agent should be deeply explored. The aim of this study was to screen the indigenous soybeans’ rhizobacteria Pseudomonas sp. that possessing biocontrol characters against soilborne mainly i.e. Sclerotium rolfsii, Fusarium oxysporum, and Rhizoctonia solani, in vitro and in planta. Eleven isolates identified Pseudomonas sp. CRB numbered by CRB-3, CRB-16, CRB-17, CRB-31, CRB-44, CRB-75, CRB-80, CRB-86, CRB-102, CRB-109, and CRB-112 were affirmed to be candidates of biocontrol agents toward the soilborne fungal pathogens. Pseudomonas sp. CRB inhibited growth of the pathogenic fungi approximately 11.1-60.0% in vitro. Among of them, 7 isolates were also produced siderophore, 2 isolates produced chitinase, and 4 isolates produced hydrogen cyanide. Seed coating with the Pseudomonas sp. CRB accomplished disease suppression in planta about 14.3-100% in sterile soil condition and 5.2-52.6% in non sterile soil condition. Consistency in high performance more than 30% of disease suppression in non sterile soil condition suggested that 5 isolates i.e. CRB-16, CRB-44, CRB-86, CRB-102, and CRB-109 isolates have great promising to be developed as biocontrol agents of soilborne pathogenic fungi.
Characterization of an Endophytic Bacterium G062 Isolate with Beneficial Traits ALINA AKHDIYA; ARIS TRI WAHYUDI; ABDUL MUNIF; LATIFAH KOSIM DARUSMAN
HAYATI Journal of Biosciences Vol. 21 No. 4 (2014): December 2014
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1475.961 KB) | DOI: 10.4308/hjb.21.4.187

Abstract

An endophytic bacterium isolate G062 was characterized base on its molecular genetic potents, morphology, physiology, and biochemistry reactions. Analysis of 16S rDNA sequences of G062 showed the highest similarity to Paracoccus halophilus (98%). Detection of the phlD and prnC genes occurrence indicated that the bacterium had this antibiotic-like genes of Diacethylphloroglucinol (DAPG) and pyrrolnitrin. The cells are rod shaped (0.59-0.89 x 1.85-3.3 µm), aerobic, Gram negative, non motile, non spore forming,  positive catalase, positive oxydase, could reduce NO3 to N2, nitrogen fixing, producing siderophore and plant growth hormones-like compounds (IAA, Gibberellin, and zeatin), and solubilizing phosphate. The G062 isolate could grow on media containing 2.5% NaCl. Range of the temperature and pH growth were 15-40 and 5.0-9.5 oC, respectively. The bacterium did not cause red blood cells lysis. There was no hypersensitive response when it was injected into tobacco leaves, and it was not pathogenic against potato plantlets.  Moreover, the bacterium promoted the growth of the potato plant and had high colonization ability. These results suggested that the bacterium had beneficial and good traits as biological agent candidate to promote potato plant growth.
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