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Articles by issue : Vol 6, No 4 (2012): December 2012
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Enhanced Acetone, Butanol, and Ethanol Fermentation by Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) in a Chemically Defined Medium: Effect of Iron and Initial pH on ABE Ratio

AMBARSARI, HANIES AMBARSARI ( Institute of Environmental Technology (BTL) – Indonesian Agency for Assessment and Application of Technology (BPPT), Building 412 PUSPIPTEK Serpong, Banten 15314, Indonesia ) , SONOMOTO, KENJI ( Laboratory of Microbial Technology, Division of Microbial Science and Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Laborator )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

Batch studies were performed to investigate the performance of Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) in acetone-butanol-ethanol (ABE) fermentation as affected by iron and initial pH in defined TYA (Tryptone-Yeast extract-Acetate) media. Different concentrations of FeSO4.7H2O in the TYA media were found to influence the ABE fermentation process resulting in different ABE ratios. From the experiment with different concentrations of FeSO4.7H2O, it was also found that lag phases at initial pH of 4.4 were longer than those at initial pH of 6.5, however they could still have higher ABE productivity values. Addition of 0.003 g L-1 FeSO4.7H2O could give the highest ABE production with both initial pH of 6.5 and 4.4. With more than 0.01 g L-1 FeSO4.7H2O, ratios of acetone to butanol (0.50 - 0.53) were higher at initial pH of 4.4 than those (0.26 - 0.28) at initial pH of 6.5. Those differences were not obtained with low concentration of FeSO4.7H2O among the same initial pH. It was also confirmed that initial pH affected ABE production significantly more than FeSO4.7H2O by statistical analysis.

Isolation of root endophytic bacteria from tomato and its biocontrol activity againts fungal diseases

MUNIF, ABDUL ( Department of Plant Protection, Bogor Agricultural University (IPB), Jl. Kamper Kampus IPB Darmaga, Bogor, Indonesia 16680 ) , HALLMANN, JOHANNES ( Institut fur Pflanzenkrankheiten, University of Bonn, Nussallee 9, D 53119 Bonn, Germany ) , SIKORA, RICHARD A ( Institut fur Pflanzenkrankheiten, University of Bonn, Nussallee 9, D 53119 Bonn, Germany )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

Endophytic bacteria have gained attention due to their interesting features related to plant growth and health stimulation. The objective of this research was to determine the populations and spectrum of indigenous root endophytic bacteria from tomato (Lycopersicon esculentum) and the biocontrol activity of the bacteria for plant protection. The isolation procedure of these endophytic bacteria was done using surface-sterilization method using alcohol and sodium hypochlorite (NaOCl). General medium trypsic soy agar (TSA) was used as the growth medium for isolation. The total population density of endophytic bacteria recovered from tomato roots ranged from 1.0 to 4.4 (in log10  scale) CFU g-1 fresh root weight. A total of 564 strains of endophytic bacteria were isolated from tomato plants grown in West Java, Indonesia. Endophytic bacterial strains were identified based on their fatty acid profile using FAME-GC-MIDI system. Fifty species and 32 genera of endophytic bacteria were found in association with tomato root. The most abundant endophytic bacterial genera were Bacillus spp. and Pseudomonas spp. One hundred and eighty one  bacterial strains were tested for their in vitro antagonism towards Rhizoctonia solani, Fusarium oxysporum f.sp. radicis-lycopersici, and F. oxysporum f.sp. lycopersici. Fourteen strains showed antagonism against R. solani, nine strains against F. oxysporum f.sp. radicis-lycopersici and seven strains against F. oxysporum f. sp. lycopersici. The close relationship between endophytic bacteria and their hosts make them ideal candidates for biological control and plant growth promotion.

Adaptation of Oil Palm Seedlings Inoculated with Arbuscular Mycorrhizal Fungi and Mycorrhizal Endosymbiotic Bacteria Bacillus subtilis B10 towards Biotic Stress of Pathogen Ganoderma boninense Pat

BAKHTIAR, YENNI ( Biotech Center-Badan Pengkajian dan Penerapan Teknologi, Gedung 630 Kawasan Puspiptek, Serpong, Banten 15314, Indonesia Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor, Jalan Raya Darmaga, Bogor, West Java ) , YAHYA, SUDIRMAN ( Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor, Jalan Raya Darmaga, Bogor, West Java 16680, Indonesia ) , SUMARYONO, WAHONO ( Biotech Center-Badan Pengkajian dan Penerapan Teknologi, Gedung 630 Kawasan Puspiptek, Serpong, Banten 15314, Indonesia ) , SINAGA, MEITY SURADJI ( Department of Plant Protection, Faculty of Agriculture, Institut Pertanian Bogor, Jalan Raya Darmaga, Bogor, West Java 16680, Indonesia ) , BUDI, SRI WILARSO ( Department of Silviculture, Faculty of Forestry, Institut Pertanian Bogor, Jalan Raya Darmaga, Bogor, West Java 16680, Indonesia )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

The effects of mycorrhizal endosymbiotic bacteria Bacillus subtilis B10 and composite of arbuscular mycorrhizal fungal spores in green house experiment were examined in order to evaluate their effectiveness and compatibility with oil palm seedlings in the presence of a fungal pathogen Ganoderma boninense, the most serious pathogen in oil palm (Elaeis guineensis Jacq) in Indonesia. A three factors experiment were conducted, with mycorrhizal inoculation (M0 and M1), bacterial B. subtilis B10 inoculation (B0 and B1), and G. boninense inoculation (G0 and G1) as the first, second, and third factors, respectively. The results showed that disease severity index, plant height, root dry-weight, and phosphorus uptake were affected by co-inoculation of mycorrhizal endosymbiotic bacteria B. subtilis B10 and composite of arbuscular mycorrhizal fungi. Co-inoculation of mycorrhizal endosymbiotic bacteria B. subtilis B10 and arbuscular mycorrhizal fungi did not only reduce the percentage of basal stem rot incidence, but also significantly increased plant height and phosphorus uptake by oil palm seedlings. Our results suggest that in oil palm seedlings mycorrhizal endosymbiotic bacteria B. subtilis B10 worked synergistically with arbuscular mycorrhizal fungi in increasing plant adaptation toward biotic stress of pathogen G. boninese and could be promising biocontrol agents.

Genus Diversity of Actinomycetes in Cibinong Science Center, West Java, Indonesia

WIDYASTUTI, YANTYATI ( Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , LISDIYANTI, PUSPITA ( Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , RATNAKOMALA, SHANTI ( Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , KARTINA, GINA ( Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , RIDWAN, RONI ( Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , ROHMATUSSOLIHAT, ROHMATUSSOLIHAT ( Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , PRAYITNO, NITA ROSALINDA ( Research Center for Biotechnology,Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km 46, Bogor 16911Indonesian ) , TRIANA, EVI ( Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta-Bogor Km 46, Bogor 16911, Indonesia ) , WIDHYASTUTI, NUNUK ( Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta-Bogor Km 46, Bogor 16911, Indonesia ) , SARASWATI, RASTI ( Indonesia Soil Research Institute, Departement of Agricultutre, Jalan Tentara Pelajar No 12, Bogor 16114, Indonesia ) , HASTUTI, RATIH DEWI ( Indonesia Soil Research Institute, Departement of Agricultutre, Jalan Tentara Pelajar No 12, Bogor 16114, Indonesia ) , LESTARI, YULIN ( Faculty of Mathematics and Sciences, Institut Pertanian Bogor, Dramaga Campus, Bogor. 16680, Indonesia ) , OTOGURO, MISA ( NITE Biological Resource Center, National Instituite of Technology and Evaluation, Kazusakamatari, Kisarazu-shi, Chiba, Japan ) , MIYADOH, SHINJI ( NITE Biological Resource Center, National Instituite of Technology and Evaluation, Kazusakamatari, Kisarazu-shi, Chiba, Japan ) , YAMAMURA, HIDEKI ( NITE Biological Resource Center, National Instituite of Technology and Evaluation, Kazusakamatari, Kisarazu-shi, Chiba, Japan ) , TAMURA, TOMOHIKO ( NITE Biological Resource Center, National Instituite of Technology and Evaluation, Kazusakamatari, Kisarazu-shi, Chiba, Japan ) , ANDO, KATSUHIKO ( NITE Biological Resource Center, National Instituite of Technology and Evaluation, Kazusakamatari, Kisarazu-shi, Chiba, Japan )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

Actinomycetes are microorganisms that play important role to support human health and  known as soil microorganisms. The aim of the research was to describe genus diversity of actinomycetes in Cibinong Science Center (CSC), West Java. Samples for isolation were soil and plant litters. The samples were air dried and ground. We employed isolation methods: dry heat (DH), sodium dodecyl sulphates-yeast extract (SDS-YE), rehydration and centrifugation (RC), and oil separation (OS). A total of 263 isolates of actinomycetes were isolated in CSC, in 2004-2006. Totally 58, 144, 50, and 11 isolates were isolated under each isolation methods, respectively. All isolates were identified using the 16S rRNA gene sequencing method. The results showed that the isolates were belonged to the family Kineosporiaceae, Micromonosporaceae, Nocardiaceae, Pseudonocardiaceae, Streptomycetaceae, Streptosporangiaceae, Mycobacteriaceae, Nocardioidaceae, Nocardiopsaceae, and Thermomonosporaceae. There were 23 genera under those families. Homology value of the isolates based on BLAST search using 16S rRNA gene sequence data as queries showed that 136, 91, 30, and 6 isolates were ≥99, 98, 97, and ≤96%, respectively, compared to the known sequence in data base. The later 6 isolates were interesting for further identification leading to new taxa. Recognized species of Streptomyces genera under the member of the Streptomycetaceae were dominant among other isolates.

The Prevalence and Subtype Distribution of Hepatitis C Virus Infection among Hemodialysis Patients in a Private Hospital in Surabaya, Indonesia

AMIN, MOCHAMAD ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 6011 ) , ., JUNIASTUTI ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, Indonesia Indonesia-Japan ) , UTSUMI, TAKAKO ( Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo 65 ) , YANO, YOSHIHIKO ( Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo 650-0017, Japan ) , YUSUF, MOCHAMAD ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Cardiology, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, Indonesia ) , THAHA, MOCHAMMAD ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Internal Medicine Faculty of Medicine, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, In ) , PURWONO, PRIYO BUDI ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, Indonesia Indonesia-Japan ) , HANDAJANI, RETNO ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Biochemistry, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, Indonesia ) , ., SOETJIPTO ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Biochemistry, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, Indonesia Indonesia-Japan ) , HOTTA, HAK ( Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo 650-0017, Japan ) , HAYASHI, YOSHITAKE ( Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo 650-0017, Japan ) , LUSIDA, MARIA INGE ( Institute of Tropical Disease, Universitas Airlangga, Jalan Mulyoreijo, Surabaya 60115, Indonesia Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Jalan Mayjen Prof Dr Moestopo 47, Surabaya 60131, Indonesia Indonesia-Japan )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

The prevalence of hepatitis C virus (HCV) infection has been as high as approximately 80% in patients with maintenance hemodialysis in public hospitals in Indonesia. However, the prevalence in private hospitals has not been examined yet. The aim of  this study was  to  investigate  the prevalence of anti-HCV antibody and  the subtype distribution in patients with hemodialysis in a private hospital in Surabaya, Indonesia. Sera were obtained from 41 hemodialysis patients in a private hospital in Surabaya. The positive prevalence of anti-HCV antibody was carried out by  the enzyme-linked  immunosorbent assay (ELISA). Anti-HCV-positive sera were subjected  to  reverse transcription-PCR (RT-PCR) to detect HCV RNA and then direct sequencing. The HCV subtype was examined by phylogenetic analysis. Twenty five patients (61%) out of 41 were positive for anti-HCV antibody, and HCV-RNA was detected in 19 patients. The positive prevalence of anti-HCV antibody was 7.7% (one out of 13 patients) among patients who had undergone hemodialysis  for  less  than one year, whereas  it was 85.7%  (24 out of  28  patients)  among  patients who  had  undergone  hemodialysis  for  over  one  year.  Phylogenetic  analysis revealed HCV-1a  (52.6%) was  the most common  subtype,  followed by 1b  (15.8%), 1c  (15.8%), 2a  (5.3%), and 3k (5.3%). In conclusion,  the prevalence of HCV  infection among hemodialysis patients  in a private hospital was as high as  that  in general hospitals. The predominant subtype was HCV-1a, which  is  in accordance with  the previous studies  in general hospitals  in Surabaya,  Indonesia.

Optimization of Culture Conditions to Produce Thermostable Keratinolytic Protease of Brevibacillus thermoruber LII, Isolated from the Padang Cermin Hot Spring, Lampung, Indonesia

ZILDA, DEWI SESWITA ( Research and Development Center for Marine and Fishery Product Processing and Biotechnology (KKP), Jalan KS Tubun Petamburan VI, Jakarta 10260, Indonesia ) , HARMAYANI, ENI ( Biotechnology Study Program, Universitas Gadjah Mada, Jalan Teknika Utara, Barek Yogyakarta 55281, Indonesia ) , WIDADA, JAKA ( Biotechnology Study Program, Universitas Gadjah Mada, Jalan Teknika Utara, Barek Yogyakarta 55281, Indonesia ) , ASMARA, WIDYA ( Biotechnology Study Program, Universitas Gadjah Mada, Jalan Teknika Utara, Barek Yogyakarta 55281, Indonesia ) , IRIANTO, EKO ( Research and Development Center for Marine and Fishery Product Processing and Biotechnology (KKP), Jalan KS Tubun Petamburan VI, Jakarta 10260, Indonesia ) , PATANTIS, GINTUNG ( Research and Development Center for Marine and Fishery Product Processing and Biotechnology (KKP), Jalan KS Tubun Petamburan VI, Jakarta 10260, Indonesia ) , FAWZYA, YUSRO NURI ( Research and Development Center for Marine and Fishery Product Processing and Biotechnology (KKP), Jalan KS Tubun Petamburan VI, Jakarta 10260, Indonesia )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

Hot springs  represent one of  the most promising  sources  for  the  isolation of  thermostable enzyme producers.  The microorganisms living in a hot spring not only have to withstand elevated temperatures but also extreme environmental pH and certain chemical compounds that are often toxic to other microbes. A bacterial strain denoted  as  Brevibacillus  thermoruber  LII  has  been  isolated  from  Padang  Cermin  Hot  Spring,  Lampung,  Indonesia. Optimization of  the conditions  for protease production by  this strain  revealed  that  the  isolate produced a thermostable protease optimally at temperature and pH ranges 45-55  C and 6-7, respectively, with keratin as substrate. The strain’s keratinolytic activity was shown by the ability to degrade untreated chicken feathers after 24 h  incubation  in  liquid medium.

Biomining: an Established and Dynamic Biotechnology

JOHNSON, DAVID BARRIE ( College of Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

“Biomining” is generic term to describe the application of living organisms to extract and recover metals from mineral ores and waste materials. Since its inception as a crude technology (“dump leaching”) for treating “run of mine” rocks and boulders that contained too little copper to be processed by conventional processing, engineering options used  in biomining have become  increasingly  refined and diverse. Currently, microbiological processing is used to extract both base metals (copper, and to lesser extents nickel and zinc) and precious metals (mostly gold) from ores and mineral concentrates in heaps and stirred-tank bioreactors, as well as in dumps. Recent developments  include  the demonstration, at pilot-scale, of  indrect  leaching of zinc  sulfide concentrates,  in which the biological step (regeneration of ferric iron) is carried out independently of abiotic mineral oxidation, and  using microbiologically-mediated  reductive  dissolution  of  ferric  iron minerals  to  liberate  nickel  from lateritic ores.

Bacteria Associated with Arbuscula Mycorrhizal Spores Gigaspora margarita and Their Potential for Stimulating Root Mycorrhizal Colonization and Neem (Melia azedarach Linn) Seedling Growth

BUDI, SRI WILARSO ( Department of Silviculture Faculty of Forestry, Institut Pertanian Bogor , Campus IPB Darmaga. Bogor ) , BAKHTIAR, YENNI ( Center of Biotechnology, Badan Pengkajian dan Penerapan Teknologi, Gedung 630 Kawasan Puspitek Serpong Tangerang Selatan 15314, Indonesia ) , MAY, NUNANG LAMAEK ( Faculty of Forestry, Universitas Cendrawasih, Jalan Camp Wolker , Jayapura 99358, Papua, Indonesia )

Microbiology Indonesia Vol 6, No 4 (2012): December 2012
Publisher : Indonesian Society for microbiology

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Abstract

Four isolates (BGi1, BGi2, BGi3, and BGi4) bacteria were isolated from surface sterilized arbuscular mycorrhizal fungi (AMF) spores of Gigaspora margarita (Gm). Based on 16S rDNA analyses and phylogenetic tree, it was revealed that isolates BGi1, BGi3 and BGi4 belong to genus Bacillus, whereas BGi2 was very close  to Bacillus megaterium EG 24. Enzymatic activity test showed that all four isolates had cellulase and protease activities; while one isolate (Bacillus sp. BGi4) also has pectinase activity in addition to the celulase  and protease activities. Dual inoculation of Melia azedarch Linn roots by B. megaterium BGi2  and AMF spores G. margarita enhanced mycorrhizal root colonization by 58.3 %. Combination of Bacillus sp. BGi1 and G. margarita increased  height, diameter, shoot biomass, and root biomass of  M. azedarch by  353, 4.8, 4546, and 2810%, respectively,  in comparison to the uninoculated control plant.