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All Journal Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Jurnal Penelitian Hutan Tanaman Indonesian Journal of Biotechnology Jurnal Wana Tropika
SITI KABIRUN
Dosen Fakultas Pertanian Universitas PGRI Yogyakarta
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Decision Sciences, Operations Research & Management Environmental Science Immunology & microbiology Materials Science & Nanotechnology

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KAJIAN WATER TABLE PADA SEMAI PEREPAT(Combretocarpus rotundatus Miq dan JELUTUNG ( Dyera lowii Hook) DIINOKULASI Glomus sp 3 DI TANAH GAMBUT Burhanuddin, Burhanuddin; Kabirun, Siti; Radjagukguk, Bostang; Sumardi, Sumardi
Jurnal Penelitian Hutan Tanaman Vol 8, No 3 (2011): JURNAL PENELITIAN HUTAN TANAMAN
Publisher : Pusat Penelitian dan Pengembangan Peningkatan Produktivitas Hutan

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Abstract

KARAKTERISTIK MORFOLOGI DAN PEMBENTUKAN BINTILAKAR PADA CEMARA UDANG Atmanto, Winastuti Dwi; Sumardi, Sumardi; Kabirun, Siti
Jurnal Penelitian Hutan Tanaman Vol 9, No 3 (2012): JURNAL PENELITIAN HUTAN TANAMAN
Publisher : Pusat Penelitian dan Pengembangan Peningkatan Produktivitas Hutan

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ABSTRACTNitrogen fixation not only occurs in the symbiosis between legumes and Rhizobium bacteria, but also between non- legume plants and other type of microorganisms, for example symbiosis between Casuarina equisetifolia and Frankia. The morphological characteristics of C. equisefolia is not widely known yet, especially its nodule formation and its capacity to fix nitrogen. This research was aimed to 1) investigate the characteristics of Frankia root nodules of C. equsetifolia at pot and field experiment, 2) acquire the Frankia isolates which are fastest formed on C. equsetifolia. Observation of  the rate of root nodules formation carried out in pots with zeolite planting medium. Isolates used as treatments were derived from the selection of the different morphological characteristics of isolates from some coastal areas, namely: Madura (M1, M3, M4, M5, M6, M7, M8, M10, M11), Tepus (T1, T2, T3, T4), Samas (S1) and without inoculation (Kt) as control. Each of isolate was inoculated into 4 seedlings. The formation, development and amount of root nodules were observed every 2 weeks. The results found similar forms of  root nodules in the pot and field experiment. The outer part of root nodules performed soft colour but getting darker and harder inside the nodules. Root nodulation was observed at all isolates 4 weeks after inoculation, with mean number of nodules is 2.55 (34.86%). This study concluded that the isolates of M5 and M6 are best to use as a source of inoculum for the production of C. equisetifolia seedlings, because of its ability to form root nodule concurrently within 2 weeks.ABSTRAKMekanisme penambatan nitrogen tidak hanya terjadi pada simbiosis antara jenis Legum dengan Rhizobium, tetapi juga antara jenis non-legum dengan jenis mikroorganisma yang lain. Contohnya adalah antara jenis cemara udang dengan Frankia. Karakter morfologi jenis ini belum banyak diketahui terutama pada kemampuan pembentukan bintil akar dan kapasitasnya dalam menambat nitrogen. Penelitian ini bertujuan untuk 1) mengetahui tentang karakteristik bintil akar jenis cemara udang pada percobaan pot dan lapangan, 2) mendapatkan isolat Frankia dari bintil akar yang paling cepat membentuk bintil akar pada tanaman cemara udang. Pengamatan terhadap kecepatan pembentukan bintil akar dilakukan di dalam pot dengan media tanam zeolit. Isolat yang digunakan sebagai perlakuan diperoleh dari seleksi terhadap karakteristik morfologi isolat yang berbeda dari tanaman asal Madura (M1, M3, M4, M5, M6, M7, M8, M10, M11), Tepus (T1, T2, T3, T4), Samas (S1) dan tanpa inokulasi (Kt). Masing- masing isolat diinokulasikan pada 4 (empat) semai cemara udang. Pengamatan dilakukan setiap 2 (dua) minggu sekali, diamati perkembangan, pembentukan dan jumlah bintil akar. Hasil penelitian menunjukkan bahwa terdapat kesamaan ragam bentuk bintil akar cemara udang dalam percobaan pot dan lapangan. Bagian permukaan bintil akar dalam pertumbuhannya selalu berwarna lebih muda, makin ke arah dalam semakin gelap dan keras. Semua isolat yang diuji pada semai cemara udang mampu membentuk bintil akar setelah 4 (empat) minggu diinokulasi dengan rata-rata jumlah bintil akar yang terbentuk 2,55 buah (34,86%). Isolat M5 dan M6 paling baik digunakan sebagai sumber inokulum untuk pembuatan semai cemara udang, karena dalam waktu 2 (dua) minggu semua bibit serempak membentuk bintil akar.
Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Wedhastri, Sri; Fardhani, Dinar Mindrati; Kabirun, Siti; Widada, Jaka; Widianto, Donny; Evizal, Rusdi; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene.Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max
The Diversity of Legume-Nodulating Bacteria from Several Agroecosystems in Sumberjaya, Lampung Wedhastri, Sri; Yuliana Prahastiwi, Yuliana; Widada, Jaka; Widianto, Donny; Kabirun, Siti
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Bacteria that capable of forming root nodules on legumes are known as Rhizobia. They have also known as Legume- Nodulating Bacteria (LNB). They can fi x nitrogen from the atmosphere. Diversity of Legume-Nodulating Bacteria is affected by biotic factors (such as their genetic factors, plants, and competition with the other soil microbes) and abiotic factors (such as land use, soil’s temperature, pH, chemistry and soil’s properties). The aim of this experiment is to know the diversity of eleven Legume- Nodulating Bacteria based on their phenotypic and genotypic characters. The eleven LNB used in this experiments were isolated from several agroecosystems in Sumberjaya, Lampung. The analysis of these LNB diversity were carried out by characterizing both phenotypic and genotypic properties. The diversity analysis showed that the eleven LNB isolates had high diversity, based on nodule formation, and classifi ed into two groups of cross inoculation group.Key words: Rhizobia, phenotypic diversity, genotypic diversity
16s rRNA Sequence Analysis and Ammonium Excretion Ability of Nitrogen Fixing Bacteria Isolated from Mineral Acid Soil H, Hartono; Widada, Jaka; Kabirun, Siti
Indonesian Journal of Biotechnology Vol 14, No 2 (2009)
Publisher : Universitas Gadjah Mada

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Abstract

Nitrogen fixing bacteria defined as bacteria which is capable to transform free nitrogen molecules into ammonium v (PCR). Nitrogenase activity of these selected isolates was measured using Acetylene Reduction Assay (ARA). The ability of these selected isolates in ammonium excretion was qualitatively and quantitavely measured using Nessler reagent and spectrophotometry method respectively. Taxonomic position of the selected bacteria were determined based on their 16S rRNA sequence analysis. Genetic diversity analysis of these 15 isolates of nitrogen fixing bacteria yield eight selected bacteria for subsequent analysis. Sequence of nifH gene from all of these selected bacteria were successfully amplified. Nitrogenase assay of these selected bacteria revealed 6 isolates with high nitrogen fixation capasity namely GMA3, GMA5, GMA6, GMA9, GMA12 AND GMA 13.</div><div>Ammonium excretion analysis revealed 4 isolates which have remarkable ability of producing high level of ammonium namely GMA1, GMA3, GMA6, and GMA9. The 16S rRNA sequence analysis shown that isolates GMA3, GMA5, GMA11 and GMA12 had a close relationship with Brevibacillus formosus strain DSM 9885T, Flexibacter canadensis strain ISSDS-428, Rhizobium tropici strain rif 200849, and Azotobacter tropicalis strain RBS. Respectively, isolate GMA1 and GMA13 had a close relationship with Sthenotropphomonas sp. Strain MFC-C, while isolate GMA6 and GMA9 had a close relationship to Azotobacter vinelandii strain ISSDS-428.</div>, string),(105, en_US, subject, nitrogen fixing bacteria, ammonium excretion, identification, string),(105, en_US, sponsor, , string),(107, en_US, title, Effect of Probiotic Lactobacillus sp. Dad13 on Humoral Immune Response of Balb/C Mice Infected with Salmonella typhimurium, string),(107, en_US, abstract, An indigenous strain of lactic acid bacterium (LAB) identified as Lactobacillus spp. Dad13 (Dad13), isolated from traditional fermented buffalo milk, was found to be potential as probiotic. The aim of this research was to study the effect of probiotic Dad13 on humoral immune response of Balb/C mice infected with Salmonella typhimurium. Thespecific objective was to find out the effect of different Dad13 consumption time (before and along with infection of S. typhimurium) on the humoral immune response of Balb/C mice. The experiment was conducted by in vivo trial on 20<br />males of Balb/C mice, age of 6-8 weeks, fed with AIN-93 standard diet. The mice were assigned into 4 groups. Each group received the following treatments, ie. Dad13 only, Dad13 before infection, Dad13 along with infection and Salmonella infection only. A volume of 100 μl Dad13 cell suspensions (1010 CFU/ml) were given by oral forced feeding daily for a week, at week 3 for group before infection and at week 4 for group of Dad13 only and Dad13 along with infection. Salmonella infection (109 CFU/ml) was given once orally at week 4 to all groups except group treated with Dad13 only. The humoral immune response of Balb/C mice was detected 2 weeks after infection by measuring the titers of IgG and IgA specific from serum and mucosal intestinal liquid samples using Enzyme-linked Immunosorbent Assay (ELISA) method. The result indicated that humoral immune response of Balb/C mice consuming Dad13 before and along with Salmonella infection were significantly different (p<0.05). Dad13 consumption along with Salmonella infection increased circulated IgG and IgA as well as secretory IgA. It can be concluded that Dad13 probiotic feeding along with infection increased humoral immune response more significantly compared to that before infection.
Effect of AMF Inoculation on the Growth of Combretocarpus rotundatus (Miq) on a Peat Soil from Central Kalimantan (For Restoration Ex-Mega Rice Project Central Kalimantan) Burhanuddin, Burhanuddin; Kabirun, Siti; Radjagukguk, Bostang; Sumardi, Sumardi
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 15, No 1 (2010): February 2010
Publisher : Universitas Atma Jaya Yogyakarta

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Abstract

Diperlukan teknik silvikultur dengan memanfaatkan jamur mikoriza arbuskula (JMA) untuk memulihkan hutan rawa gambut yang terdegradasi. JMA berperan penting pada pertumbuhan dan ketahanan hidup pohon-pohonan. Penelitian ini bertujuan untuk mengetahui keberadaan dan bentuk dari JMA di hutan rawa gambut yang sudah terdegradasi pada blok C bekas pengembangan lahan gambut satu juta ha di Kelampangan Kalimantan Tengah. Kondisi lahan hanya ditumbuhi vegetasi jenis-jenis pioner. Contoh tanah diambil dibawah perakaran lima jenis tanaman pioner (Melastoma sp, Combretocarpus sp, Acacia sp, Cratoxylon sp, dan Nephrolepsis sp), kemudian contoh tanah dihitung jumlah spora dengan metode saringan basah. Jumlah spora terbanyak ada di bawah perakaran tanaman Melastoma sp, kemudian Acacia sp, dan Combretocarpus sp. Didapatkan tiga genus JMA: Glomus, Gigaspora, dan Acaulospora. Penelitian di rumah kaca bertujuan untuk mengetahui pengaruh inokulasi JMA jenis Glomus sp TD15, Glomus sp D32, dan Gigaspora sp pada semai perepat (C. rotundatus). Hasil penelitian menunjukkan JMA memberikan pengaruh pada parameter semai yang diukur. Jenis JMA Glomus sp TD15 meningkatkan pertumbuhan semai perepat yang ditunjukkan oleh parameter tinggi semai, diameter semai, dan jumlah daun per tanaman. Pada media gambut semai C. rotundatus sangat tergantung pada asosiasi JMA dalam meningkatkan pertumbuhan tanaman.
DEKOMPOSISI BERBAGAI JENIS SERESAH GAMAL DI HUTAN PENDIDIKAN WANAGAMA 1, GUNUNG KIDUL, YOGYAKARTA Nurjanto, Handojo H.; Supriyo, Haryono; Widyastuti, Siti M.; Kabirun, Siti
Jurnal Wana Tropika Vol 6 No 1 (2016)
Publisher : Fakultas Kehutanan Institut Pertanian STIPER Yogyakarta

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Abstract

Plant litter is the major source of organic matter in the forest floor and litter decomposition plays an important role in the organic matter and nutrient entry to the soil. The decomposition rate is strongly influenced by climatic conditions and initial chemical composition of the litter. Litter in the rehabilitated forest area of Wanagama 1 Education Forest is dominated by Gamal (Gliricidia sepium) litter which isconsisted of leaves, twigs and fruit pods. This study assessedthe decomposition rate of leaf, twig and fruit podlitter of Gamal in compartment 5 and 6 of Wanagama 1 Education Forest. To assess effect of season, the research was conducted in dry season (August to November 2012) and in rainy season (from January to March 2013). The results showed that the decomposition rates of leaf, twig and fruit pod litter of Gamal in dry season were moderate with k (decomposition index) = 0.0074 – 0.0065, slow (k = 0.0043 – 0.0040), andslow (k = 0.0031 – 0.0026), respectively.In the rainy season, the decomposition process was faster with decomposition rates were high (k = 0.0132 – 0.0161), moderate (k = 0.0073 – 0.0065) and moderate (k = 0.0055 – 0.0063), respectively. There was no effect of compartments which differed in the stand density. Keywords : Decomposition Rate, Kind of Litter, Gamal (Gliricidia sepium), Season
Co-Authors Bostang Radjagukguk Burhanuddin Burhanuddin Dinar Mindrati Fardhani Donny Widianto Handojo H. Nurjanto, Handojo H. Hartono H, Hartono Haryono Supriyo Irfan Dwidya Prijambada JAKA WIDADA Rusdi Evizal Sri Wedhastri Sumardi . Widyastuti, Siti M. Winastuti Dwi Atmanto Yuliana Yuliana Prahastiwi, Yuliana