Claim Missing Document
Check
Articles

Fluks Bentik dan Potensi Aktivitas Bakteri Terkait Siklus Nitrogen di Sedimen Perairan Mangrove Pulau Dua, Banten Iswantari, Aliati; Wardiatno, Yusli; Pratiwi, Niken T.M; Rusmana, Iman
JURNAL BIOLOGI INDONESIA Vol 10, No 1 (2014): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (265.728 KB) | DOI: 10.14203/jbi.v10i1.336

Abstract

Mangrove ecosystem has important role as source of nutrient particularly nitrogen in coastal area. Nitrogen (N) is alimiting factor in marine and coastal area. The aim of this research was to study benthic fluxes and potency ofbacterial activity in sediment of mangroves area, related to nitrogen cycle. This research was conducted in floodedmangroves area in Pulau Dua. The sediment and overlying water was sampled using sediment core sampler.Experimental treatment for flux analysis and sediment-slurry were conducted in three hours. Nutrient of NH3-N,NO2-N, and NO3-N and abundance of nitrifier, denitrifier, DNRA, and ammonifier were analyzed. The resultsshowed that the abundance of anaerobic bacteria was higher than aerobic bacteria. The dominance of bacterialgroups found in sediment was ammonification bacteria. The highest nutrient concentration in sediment was NH3-N. Benthic fluxes value showed higher NH3-N tends to release from the sediment to water than NO2-N and NO3-N. Generally, mangrove sediment in Pulau Dua has higher potency ofbacterial activity (Vmax and Km) in NO3reduction by anaerobic bacteria than NH3 oxidation by aerobic bacteria.Keywords: bacteria, benthic fluxes, mangrove, potency of bacterial activity, sediment
STRUKTUR KOMUNITAS BAKTERI PENGOKSIDASI AMONIA BERDASARKAN GEN amoA DI SITU SAWANGAN-BOJONGSARI, JAWA BARAT Novita, Lena; Rusmana, Iman; Widiyanto, Tri
LIMNOTEK - Perairan Darat Tropis di Indonesia Vol 21, No 1 (2014)
Publisher : Research Center for Limnology

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Salah satu permasalahan dalam pengelolaan perairan darat adalah penurunan kualitas air yang disebabkan oleh polusi senyawa nitrogen. Mekanisme transformasi senyawa nitrogen oleh bakteri indigenous menjadi langkah penting untuk mengatasi permasalahan tersebut. Aktivitas antropogenik di sekitar Situ Sawangan-Bojongsari memungkinkan terjadinya polusi senyawa nitrogen seperti amonia. Penelitian bertujuan untuk mengetahui struktur komunitas bakteri pengoksidasi amonia serta faktor fisika dan kimia yang mempengaruhinya di Situ Sawangan-Bojongsari. Kelimpahan dan keragaman bakteri pengoksidasi amonia dipengaruhi oleh faktor fisika dan kimia perairan. Kelimpahan tertinggi bakteri pengoksidasi amonia terdapat pada strata 0 cm (270 sel/mL) dan kelimpahan terendah terdapat pada strata 230 cm (73 sel/mL). Bakteri pengoksidasi amonia tidak ditemukan pada bagian sedimen. Gen amoA hanya teramplifikasi dari contoh air. Sebanyak 10 pita gen amoA dengan posisi yang berbeda dapat terdeteksi pada gel DGGE. Sebanyak enam isolat gen amoA memiliki kemiripan sekuen nukleotida dengan amo A dari uncultured bacterium (86-97%). Sekuen asam amino dari keenam isolat gen amo A menunjukkan kemiripan dengan protein ammonia monooxygenase (56-93%). Sebanyak lima isolat gen amo A teridentifikasi sebagai ammonia monooxygenase dari uncultured bacterium dan satu isolat sebagai ammonia monooxygenase dari Nitrosospira sp. III7. Berdasarkan analisis filogenetik, keenam isolat gen amoA termasuk ke dalam genus Nitrosospira.
The Effect of Biofertilizer on The Diversity of N2O Reducing Bacteria in Paddy Fields of Sukabumi, Indonesia Cahyadi, Alfan; Rusmana, Iman; Mubarik, Nisa Rachmania
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 3 (2017): December 2017
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.v9i3.9796

Abstract

Some of the methanotrophic bacteria and N2O reducing bacteria have been proven to be able to support the plant growth and increase the productivity of paddy. However effect of the methanotrophic and N2O reducing bacteria application as a biofertilizer to indigenous N2O reducing bacteria is still not well known yet. The aim of this study was to analyze the diversity of N2O reducing bacteria in lowland paddy soil based on a nosZ gene. Soil samples were taken from lowland paddy soils in Pelabuhan Ratu Sukabumi, West Java, Indonesia. There were two treatments for the paddy field soil, ie. biofertilizer-treated field 20% fertilizer (50 kg/ha) with the addition of biofertilizer and 100% fertilizer. PCR amplification of nosZ gene was successfully conducted using nosZF and nosZR primer pair. Denaturing Gradient Gel Electrophoresis (DGGE) process was conducted at 150 V for 5.5h. There were three differences nosZ bands were sequenced. The phylogenetic analysis showed that they were close to uncultured bacteria. Microbial diversity in the biofertilizer-treated field was higher than that of in the 100% fertilizer-treated field. The biofertilizer treatment has higher in microbial diversity than that of applied non-biofertilizer paddy fields. This research might have impact in the application of biofertilizers due to the emission of N2O as a green house gas from paddy fields farming activity. The biofertilizer has great potential application in sustainable environmental friendly agriculture systems.
Degradation of Polycyclic Aromatic Hydrocarbon Pyrene by Biosurfactant-Producing Bacteria Gordonia cholesterolivorans AMP 10 Kurniati, Tri Handayani; Rusmana, Iman; Suryani, Ani; Mubarik, Nisa Rachmania
Biosaintifika: Journal of Biology & Biology Education Vol 8, No 3 (2016): December 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.v8i3.6448

Abstract

Pyrene degradation and biosurfactant activity by a new strain identified as Gordonia cholesterolivorans AMP 10 were studied. The strain grew well and produced effective biosurfactants in the presence of glucose, sucrose, and crude oil. The biosurfactants production was detected by the decreased surface tension of the medium and emulsification activity. Analysis of microbial growth parameters showed that AMP10 grew best at 50gmL-1pyrene concentration, leading to 96% degradation of pyrene within 7days. The result of nested PCR analysis revealed that this isolate possessed the nahAc gene which encodes dioxygenase enzyme for initial degradation of Polycyclic Aromatic Hydrocarbon (PAH). Observation of both tensio-active and emulsifying activities indicated that biosurfactants which produced by AMP 10 when grown on glucose could lower the surface tension of medium from 71.3 mN/m to 24.7 mN/m and formed a stable emulsion in used lubricant oil with an emulsificationindex (E24) of 74%. According to the results, it is suggested that the bacterial isolates G. cholesterolivorans AMP10 are suitable candidates for bioremediation of PAH-contaminated environments.How to CiteKurniati, T. H., Rusmana, I. Suryani, A. & Mubarik, N. R. (2016). Degradation of Polycyclic Aromatic Hydrocarbon Pyrene by Biosurfactant-Producing Bacteria Gordonia cholesterolivorans AMP 10. Biosaintifika: Journal of Biology & Biology Education, 8(3), 336-343.
FLUKS BENTIK DAN POTENSI AKTIVITAS BAKTERI TERKAIT SIKLUS NITROGEN DI SEDIMEN PERAIRAN MANGROVE PULAU DUA, BANTEN Iswantari, Aliati; Wardiatno, Yusli; Pratiwi, Niken T.M; Rusmana, Iman
JURNAL BIOLOGI INDONESIA Vol 10, No 1 (2014): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v10i1.336

Abstract

Mangrove ecosystem has important role as source of nutrient particularly nitrogen in coastal area. Nitrogen (N) is alimiting factor in marine and coastal area. The aim of this research was to study benthic fluxes and potency ofbacterial activity in sediment of mangroves area, related to nitrogen cycle. This research was conducted in floodedmangroves area in Pulau Dua. The sediment and overlying water was sampled using sediment core sampler.Experimental treatment for flux analysis and sediment-slurry were conducted in three hours. Nutrient of NH3-N,NO2-N, and NO3-N and abundance of nitrifier, denitrifier, DNRA, and ammonifier were analyzed. The resultsshowed that the abundance of anaerobic bacteria was higher than aerobic bacteria. The dominance of bacterialgroups found in sediment was ammonification bacteria. The highest nutrient concentration in sediment was NH3-N. Benthic fluxes value showed higher NH3-N tends to release from the sediment to water than NO2-N and NO3-N. Generally, mangrove sediment in Pulau Dua has higher potency ofbacterial activity (Vmax and Km) in NO3reduction by anaerobic bacteria than NH3 oxidation by aerobic bacteria.Keywords: bacteria, benthic fluxes, mangrove, potency of bacterial activity, sediment
Candida Species Distribution of Clinical Specimens in Banda Aceh, Indonesia Suhartono, Suhartono; Mahdani, Wilda; Masthura, Aderiana; Rusmana, Iman
Biosaintifika: Journal of Biology & Biology Education Vol 12, No 2 (2020): August 2020
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.v12i2.23758

Abstract

Candidiasis has become increasingly widespread in the community alongside with the developing resistance of Candida sp. to some antifungals. A prevalence study in the present research is required to surveil the distribution of Candida-related infections to administrate the appropriate antifungal treatments. The objective of this research was to determine the species distribution of candidiasis with their antifungal susceptibility isolated from clinical specimens at the Zainoel Abidin Hospital (ZAH) Banda Aceh, Indonesia. The clinical specimens were from inpatients and outpatients in the hospital during January to June 2019. The identification of Candida species and antifungal sensitivity assay were conducted by using VITEK® 2 Compact. Of a total of 68 isolates, there were six species of Candida with the highest species prevalence was Candida tropicalis (52.94%). Additionally, the highest prevalence of candidiasis came from urine specimen (54.41%) and mostly from inpatients in the internal medicine unit (54.41%). Candidiasis occurred predominantly in men (58.82%) and during adulthood (55.88%). The antibiogram of Candida sp. shows a high percentage of sensitivity towards some antifungals including fluconazole (100%), voriconazole (100%), caspofungin (100%), micafungin (100%), amphotericin B (99.5%), and flucytosine (100%). From this result, it can be concluded that candidiasis cases in the ZAH Banda Aceh, Indonesia has prevalently occurred with the few antifungal therapies for candidiasis of were still effective empirically and definitively. This is an initial study of Candida prevalence within different clinical samples in Banda Aceh and the study is expected to be a basis for prevention and control of Candida-related infections in the area.
Comparison of DNA Extraction Methods for Microbial Community Analysis in Indonesian Tempe Employing Amplified Ribosomal Intergenic Spacer Analysis CECILIA ANNA SEUMAHU; ANTONIUS SUWANTO; IMAN RUSMANA; DEDY DURYADI SOLIHIN
HAYATI Journal of Biosciences Vol. 19 No. 2 (2012): June 2012
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (136.378 KB) | DOI: 10.4308/hjb.19.2.93

Abstract

Tempe fermentation involved complex microbial communities which are only revealed partially through culture dependent methods. Culture-independent methods would be potential to unravel this complex microbial fermentation. Appropriate DNA extraction is an essential tool to obtain reliable data from culture independent method. In this study, we employed two commercial DNA extraction methods to find the best one for microbial community characterization employing amplified ribosomal intergenic spacer analysis (ARISA). Our result showed that PowerFood Microbial DNA Isolation Kit-MOBIO (PFMDIK) is an excellent method for microbial DNA extraction from tempe. It gave high quantity and quality of DNA suitable for PCR amplification of 16S-23S rRNA intergenic spacer to yield a diverse and reproducible ARISA profile.
Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia ANIK KUSMIATUN; IMAN RUSMANA; SRI BUDIARTI
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (2344.168 KB) | DOI: 10.4308/hjb.22.1.27

Abstract

Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter), so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa.
Analysis of Intestinal Mucosal Immunoglobulin A in Sprague Dawley Rats Supplemented with Tempeh SUSAN SOKA; ANTONIUS SUWANTO; IMAN RUSMANA; DONDIN SAJUTHI; DIAH ISKANDRIATI; KATHARINA JESSICA
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1507.883 KB) | DOI: 10.4308/hjb.22.1.48

Abstract

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantified from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression.
Metagenomic of Actinomycetes Based on 16S rRNA and nifH Genes in Soil and Roots of Four Indonesian Rice Cultivars Using PCR-DGGE . Mahyarudin; Iman Rusmana; Yulin Lestari
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1377.267 KB) | DOI: 10.4308/hjb.22.3.113

Abstract

The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA) and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant.
Co-Authors Abdjad Asih Nawangsih Aceng Ruyani Achmad Dinoto Aderiana Masthura Alfan Cahyadi Alfisah, Rizal Khoirun Aliati Iswantari ALINA AKHDIYA ALINA AKHADIYA Alina Akhdiya Alina Akhdiya Alina Akhdiya ALINA AKHDIYA Amanda, Nisa Widya Andi Ernawati Andi Ernawati Angela Mariana Lusiastuti Angela Mariana Lusiastuti Ani Suryani Ani Suryani Ani Widiyati ANIK KUSMIATUN Anja Meryandini Antonius Suwanto Apon Zaenal Mustopa Ari Fina Bintarti Ari Fina Bintarti, Ari Fina Aris Tri Wahyudi Aris Tri Wahyudi Armanisa, Khafifah BAMBANG PRASETYA Baskoro S Wibowo CAHYA PRIHATNA Cahyadi, Alfan Cecep Kusmana CECILIA ANNA SEUMAHU CECILIA ANNA SEUMAHU Ciptadi Achmad YUSUP Daniel Djokosetiyanto Darmono Taniwiryono DEBI ARIVO DEDEN SUKMADJAJA Desniar - - Dewi Puspaningsih DIAH ISKANDRIATI Dian Hendrayanti DIETRIECH G. BENGEN Dinamella Wahjuningrum Dondin Sajuthi Dwi Andreas Santosa Dwi Ningsih Susilowati Eddy Supriyono Emei Widiyastuti ERMA SURYANTI Fachriyan Hasmi Pasaribu Fachriyan Hasmi Pasaribu Fahmi, Riziq Ilham Nur FATURRAHMAN FATURRAHMAN Faturrahman Faturrahman Ferbiyanto, Andri Fredinan Yulianda Frijona Fabiola Lokollo GALUH WENING PERMATASARI Gunawan Djajakirana HAFIZAH ILMI SUFA HAMIM Hamim Hamim Happy Widiastuti HEDI INDRA JANUAR Hefni Effendi HENI RISMIYATI Hessy Novita Hessy Novita I Komang Gede Wiryawan I MADE ARTIKA I Made Samudra IDA AYU PUTU SURYANTI Ifa Manzila Ika Roostika Tambunan, Ika Roostika Ika Setianingsih Indriyani, Yohanna Anisa Irmanida Batubara Irwan Cahyadi ISRAMILDA ISRAMILDA It Jamilah Jepri Agung Priyanto KATHARINA JESSICA Khairul Syahputra KOMANG G. WIRYAWAN Kukuh Nirmala Kuntari, Wahyu Budi Lena Novita Lena Novita Lizawati . Maggy Thenawidjaya Suhartono Maggy Thenawidjaya Suhartono Mahdani, Wilda Mahyarudin, Mahyarudin Majariana Krisanti Manguntungi, Baso MARIA INDAH PURNAMASARI Masrukhin Masrukhin Masthura, Aderiana Miftahudin . MITSUO SAKAMOTO MORIYA OHKUMA MUHAMMAD ZAIRIN JUNIOR Mukti Ali MUNTI YUHANA MUTTAQIN, MAFRIKHUL Nedwell, David B. Niken T.M Pratiwi, Niken T.M NISA RACHMANIA MUBARIK Nisa Widya Amanda Novita, Lena Nurhakiki Nurjanah Prihasto Setyanto PRIHASTO SETYANTO Priyo Handoyo Wicaksono Rahmad Lingga Rahmad Lingga Rahman Rahman Rahman Rahman Rahminovita Herlis RATNA SETYANINGSIH RATNANINGTYAS, SUSI Reza Wahyuni RIDWAN AFFANDI RIDWAN AFFANDI Rika Indri Astuti RIKA RAFFIUDIN Rina Hesti Utami RINI SUSILOWATI Risky Hadi Wibowo Risky Hadi Wibowo Risky Hadi wibowo Roedhy Poerwanto RONI RIDWAN Rosadela, Fitri SHEILAHRUSI SHEILAHRUSI Sipriyadi Sipriyadi Sipriyadi Sipriyadi Sipriyadi SISKA TRIDESIANTI Siti Nur Jannah Sobir Sobir SRI BUDIARTI Sri Budiarti SRI BUDIARTI Sri Budiarti Sri Budiarti Poerwanto SRI MARTINA WIRASWATI SRI MARTINA WIRASWATI Sri Murtini Suhartono Suhartono Sukarya Zaenal Arifin SUSAN SOKA Syaiful Anwar T. Widiyanto Taruna D. Satwika TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Thenawidjaya, Maggy Tri Eko WAHYONO Tri Handayani Kurniati Tri Handayani Kurniati Tri Muji Ermayanti Tri P. Priyatno Tri Panji Tri Puji Priyatno Tri Widiyanto Tridesianti, Siska Tuasalamony, Mutia Musdalifah Utut Widyastuti Wibowo, Risky Hadi WIDANARNI WIDANARNI Widiyanto, Tri Wildan Nurusallam Wiraswati, Sri Martina Yadi Suryadi Yani Aryati YANTYATI WIDYASTUTI Yohana A Dahliani Yohanna Anisa Indriyani Yuli Fatma Yuli Siti Fatma Yuli Siti Fatma YULIN LESTARI Yuni Puji Hastuti Yusli Wardiatno Zaenal Arifin, Sukarya Zulfarina Zulfarina Zulfarina,