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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Teknologi Industri Pertanian Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Akuatika Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Agrointek Jurnal Hortikultura Current Biochemistry BIOTIK: Jurnal Ilmiah Biologi Teknologi dan Kependidikan Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Indonesian Journal of Biotechnology Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat Jurnal Sumberdaya Hayati Journal of Tropical Biodiversity and Biotechnology Jurnal Bioteknologi & Biosains Indonesia (JBBI) Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Biosaintifika: Journal of Biology & Biology Education Jurnal Purifikasi Jurnal Pascapanen dan Bioteknologi Kelautan dan Perikanan Menara Perkebunan Jurnal Mangifera Edu Journal of Microbial Systematics and Biotechnology Konservasi Hayati Prosiding Seminar Nasional Biologi, Teknologi dan Kependidikan (Biotik) MADURANCH: JURNAL ILMU PETERNAKAN Makara Journal of Science International Journal of Oil Palm Biodiversitas Journal of Biological Diversity
NISA RACHMANIA MUBARIK
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Jl. Agathis 1, Darmaga-Bogor, Indonesia 16680
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Lipase-producing ability of bacteria from inasua (fish fermented product) from Central Moluccas, Indonesia Latusi Anggriani; SRI BUDIARTI; NISA RACHMANIA MUBARIK
Biodiversitas Journal of Biological Diversity Vol. 21 No. 2 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210226

Abstract

Abstract. Anggriani L, Budiarti S, Mubarik NR. 2020. Lipase-producing ability of bacteria from inasua (fish fermented product) from Central Moluccas, Indonesia. Biodiversitas 21: 622-628. One of fish preservation techniques through fermentation is Inasua which occurs spontaneously and involves various types of microorganisms. Isolates from Inasua are believed to have the ability to produce lipolytic enzymes. The purpose of this study was to identify potential bacterial isolates isolated from Inasua and to determine their lipase producing ability. The confirmation test of lipase-producing ability was conducted by inoculating the microbes into media containing Nutrient agar (NA), olive oil, and rhodamin-B. Lipolytic bacteria were detected using a screening method with UV light. From the results, there were 5 isolates of bacteria that showed lipolytic activity as IG 3.1, IG 6, IG 10, IG 12, IG 66. Lipase assay was determined using spectrophotometric method with p-nitrophenyl palmitate (pNPP) as a substrate and titration method with olive oil as a substrate. The enzyme showed maximum activity at pNPP as a substrate. IG 6 and IG 12 gave the highest activity from lipase assay. Growth and production curves were created before partial purification was carried out. The results of the curves showed that the optimum activity of IG 6 and IG 12 were in the stationary phase with value 38.16 U.mg-1 protein and 7.01 U.mg-1 protein, respectively. After ammonium sulfate precipitation, the activity of the lipase IG 6 and IG 12 were found to be 39.65 U.mL-1 and 37.05 U.mL-1, respectively. During optimization, the enzyme showed maximum activity at pH 8/70°C temperature. Molecular identification by using the 16S rRNA gene and phylogenetic analysis showed that isolates IG 6 and IG12 are closely related to Bacillus paramycoides and Bacillus kochii, respectively.
Characterization, identification, and analysis of bioactive compound of endophytic bacteria from Hoya multiflora Blume Dewinta Nur Alvionita; SRI RAHAYU; NISA RACHMANIA MUBARIK
Biodiversitas Journal of Biological Diversity Vol. 21 No. 1 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210125

Abstract

Hoya multiflora Blume has been used for various purposes. Extract hoya has been reported to have bioactivity but extraction from the plant has been inefficient because it requires large biomass. Therefore, one of the appropriate ways to extract its bioactive compounds is using endophytic bacteria. The purposes of this research were to isolate, characterize, test its antimicrobial activity against two pathogenic bacteria  and identify its bioactive compound. A total of 18 isolates from H. multiflora Blume were successfully obtained. Based on antimicrobial test, one isolate was able to inhibit Escherichia coli, one isolate inhibited Staphylococcus aureus and two isolates inhibited both of pathogenic bacteria. In addition, minimum inhibitory concentration (MIC) of ethyl acetate extract from HMB 1 was 62.5 ppm, while from HMD 4 was 125 ppm, both against E. coli and S. aureus. Based on 16S rRNA gene sequencing analysis, HMB 1 was the most similar (99.91%) with Bacillus siamensis KCTC-13613 and HMD 4 was the most similar (100%) with Bacillus aryabhattai B82W22. Using GC-MS, pyrollo[1,2-a]-pyrazine-1,4-dione was found to be dominant compound in the exctract  bacteria of HMB 1and HMD 4 while Stigmasterol was found in extract HMD 4 and extract leaves H. multiflora Blume, respectively.
Antagonistic activity of glucanolytic bacteria Bacillus subtilis W3.15 against Fusarium oxysporum and its enzyme characterization Rury Eryna Putri; Nisa Rachmania Mubarik; Laksmi Ambarsari; Aris Tri Wahyudi
Biodiversitas Journal of Biological Diversity Vol. 22 No. 9 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220956

Abstract

Abstract. Putri RE, Mubarik NR, Ambarsari L, Wahyudi AT. 2021. Antagonistic activity of glucanolytic bacteria Bacillus subtilis W3.15 against Fusarium oxysporum and its enzyme characterization. Biodiversitas 22: 4067-4077. Biocontrol of Fusarium oxysporum, a phytopathogenic fungus that causes plant wilt can be approached with cell-wall degrading enzymes such as ?-glucanase. The aim of this study was to evaluate the prospective ability in glucanase production from several soil bacterial isolates and to characterize its ?-glucanase activity of ammonium sulfate precipitation, and to determine its antifungal activity against F. oxysporum in vitro. Twenty bacterial isolates were screened qualitatively and quantitatively as ?-glucanase producers. The results showed that the prospective isolate W3.15 can produce ?-glucanase on glucan agar as the selection medium. From 16S rRNA sequences identification, the isolate belongs to the genus Bacillus, closely related to Bacillus subtilis. The enzyme activity of the ammonium sulfate fraction of isolate W3.15 is optimum at a pH of 7 and temperature range of 60-80oC. B. subtilis W3.15 exhibits high inhibition against the mycelial growth of F. oxysporum and significantly reduced fungal biomass.
Antioxidant activity of various solvent extracts from endophytic bacteria isolated from girang (Leea indica) leaves DEBI ARIVO; NISA RACHMANIA MUBARIK; IMAN RUSMANA; IRMANIDA BATUBARA
Biodiversitas Journal of Biological Diversity Vol. 24 No. 1 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240148

Abstract

Abstract. Arivo D, Mubarik NR, Rusmana I, Batubara I. 2023. Antioxidant activity of various solvent extracts from endophytic bacteria isolated from girang (Leea indica) leaves. Biodiversitas 24: 415-422. Girang (Leea indica) is one of the medicinal plants with various bioactive compounds that act as an antioxidant. However, isolating these bioactive compounds need a significant amount of biomass. Endophytic bacteria can be a good solution to produce the same bioactive compounds as their host. This study determined whether the potential isolate produces high antioxidant activity in various solvents, phytochemical screening, determination of total flavonoid and phenolic contents, and identification of the isolate. The BT4 isolate was isolated from L. indica leaves. The supernatant of BT4 was extracted in fractionated extraction. The antioxidant activity was determined using a DPPH assay. Folin-Ciocalteu and aluminum chloride colorimetric methods analyzed the total flavonoid and phenolic content. The isolate was identified using the 16S rRNA method. The best IC50 was obtained from n-butanol extract with a value of 59.021±0.541 ?g/mL. The flavonoid and phenolic contents from n-butanol extract have the value of 4.686±0.476 mgQE/g extract and 31.406±0.716 mgGAE/g extract, respectively. The BT4 isolate contained flavonoids, saponin, tannins, terpenoids, and steroids and was identical to Bacillus tequilensis with 99% similarity. This study revealed that endophytic bacteria from L. indica leaves could be a potential source of the novel natural antioxidant compound.
Bacterial selection and characterization of chitinase enzyme from bacteria controlling Fusarium proliferatum MIFTAHUL KHAIRAH; NISA RACHMANIA MUBARIK; LISDAR A. MANAF
Biodiversitas Journal of Biological Diversity Vol. 24 No. 3 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240370

Abstract

Abstract. Khairah M, Mubarik NR, Manaf LA. 2023. Bacterial selection and characterization of chitinase enzyme from bacteria controlling Fusarium proliferatum. Biodiversitas 24: 1926-1933. The phytopathogenic fungus Fusarium proliferatum causes wilt rot disease of onion bulbs and many agricultural losses. The biocontrol of F. proliferatum can be approached with chitinase from microorganisms, such as endophytic bacteria. The chitinase enzyme can inhibit and control fungus growth by degrading chitin, the main component of the fungal cell wall. This study aimed to select, characterize, and semi-purifying the chitinase produced by endophytic bacteria and to evaluate its antifungal activity against F. proliferatum. The results showed ABS 4.1.2 isolate produced chitinase and had antagonistic activity against F. proliferatum. The prospective ABS 4.1.2 isolate was identified based on 16S rRNA gene as Pseudomonas aeruginosa. The precipitated chitinase using 60% ammonium sulfate (w/v) showed a specific activity of 19.69 U/mg and increased the purity by 3.60 fold. SDS-PAGE analysis showed that chitinase had an estimated molecular weight of 32 kDa and 65 kDa. The chitinase activity of crude extract and precipitated chitinase were optimum at pH 7 and the temperature of 35°C and 45°C, respectively. The precipitated chitinase showed a higher inhibition compared to 12 hrs of cell culture and crude enzymes against F. proliferatum. The precipitated chitinase and crude enzymes significantly exhibited destructive activity toward F. proliferatum mycelium.
Whole genome sequencing of a siderophore-producing bacterium isolated from Simadu pineapple roots CUCU WIJAYANTI; PRAYOGA SURYADARMA; NISA RACHMANIA MUBARIK
Biodiversitas Journal of Biological Diversity Vol. 25 No. 12 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251222

Abstract

Abstract. Wijayanti C, Suryadarma P, Mubarik NR. 2024. Whole genome sequencing of a siderophore-producing bacterium isolated from Simadu pineapple roots. Biodiversitas 25: 4860-4869. Siderophores are organic compounds synthesized by bacteria that act as iron-chelating ligands, facilitating the solubilization and transport of iron into the cell. Siderophore-producing bacteria offer significant benefits across various fields of research and application. A recent study investigated a siderophore-producing bacterium, the M7 isolate, from Simadu pineapple roots in the Subang District of West Java, Indonesia. This study aimed to analyze the siderophore biosynthesis gene cluster (BGC) from the complete genome sequence of the M7 isolate through genome mining. Comparative genomic analysis with the strain Providencia manganoxydans LLDRA6 revealed that the M7 isolate has a similar guanine-cytosine (GC) content with a longer sequence length totaling 4,447,159 bp. Genome comparison using average nucleotide identity (ANI) calculations indicated that the M7 isolate had a genome similarity of 98.82% with strain P. manganoxydans LLDRA6. Additionally, the genome of the M7 isolate contains systems for iron acquisition and metabolism, which involve mechanisms for regulating iron. A specific region in the M7 isolate encodes the IucA/IucC family of siderophore biosynthesis proteins responsible for aerobactin biosynthesis through non-ribosomal peptide synthetase-independent siderophore (NIS) pathways. Regarding siderophore BGCs, this isolate showed the highest similarity to Providencia stuartii, with differences in genetic redundancy content. Additionally, pathogen prediction results for the M7 isolate indicate that it is not pathogenic to humans, unlike P. stuartii, which is known to be pathogenic. The new siderophore-producing bacterium, the M7 isolate, harbors a duplication of core biosynthesis genes, representing genetic redundancy that supports siderophore biosynthesis. This genetic feature may enable concurrent protein expression, potentially enhancing siderophore accumulation.
Genome mining, metabolite fractionation, and evaluation of antibiofilm activity of endophytic Priestia megaterium AJ5 against methicillin-resistant Staphylococcus aureus JEPRI AGUNG PRIYANTO; GENIA SOTYA SINARAWADI; MUHAMMAD EKA PRASTYA; ORHINTA MUTIARA JATI; NISA RACHMANIA; ZETRYANA PUTERI TACHRIM
Biodiversitas Journal of Biological Diversity Vol. 26 No. 6 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260634

Abstract

Abstract. Priyanto JA, Sinarawadi GS, Prastya ME, Jati OM, Rachmania N, Tachrim ZP. 2025. Genome mining, metabolite fractionation, and evaluation of antibiofilm activity of endophytic Priestia megaterium AJ5 against Methicillin-resistant Staphylococcus aureus. Biodiversitas 26: 2916-2925. Endophytic bacteria, particularly Priestia megaterium, are a source of secondary metabolites that are valuable for medicinal purposes. Therefore, this study aimed to mine the Secondary Metabolite Gene Clusters (SMGCs) within the complete genome of AJ5 strain, fractionate its secondary metabolites, and evaluate its antibiofilm activity against Methicillin-Resistant Staphylococcus aureus (MRSA). The bacterium had a complete genome length of 5,750,510 bp and was closely related to P. megaterium NCTC10342, with an Average Nucleotide Identity (ANI) of 98.37%. AntiSMASH analysis showed that the bacterium possessed 5 types of SMGCs, including Non-Ribosomal Peptide Synthetase (NRPS)-Independent (NI) siderophores, 3 types of terpenes, and type III Polyketide Synthase (PKS). In addition, 2 selected fractions obtained from thin-layer chromatography and column chromatography procedures exhibited strong anti-MRSA activity. F9 and F12 fractions had Minimum Inhibitory Concentrations (MIC) of 117.5 ?g/mL and 180 ?g/mL, respectively. Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) analysis indicated that these 2 fractions contained nigakilactone H, tetratriacontanamine, 2-(p-Anisyl)-5-methyl-1-hexene, and other unidentified compounds. The compounds were also capable of suppressing biofilm formation of MRSA by up to 81.54%±1.80 for the F9 and 77.01%±1.96 for F12 fraction after treatment with 1×MIC. All selected fractions also exhibited eradication activity against established MRSA biofilms up to 79.23±1.96%. In conclusion, this study showed the SMGCs profile and their metabolite products found within the genome of AJ5 strain, as well as its antibiofilm potential against MRSA. The thoroughness of our research process and the validity of our findings suggest that genome-based screening and in vitro assays could significantly accelerate the development of novel anti-MRSA agents.
Effects of lactic acid bacteria inoculants on fermentation characteristics and microbial community profiles of napier grass (Pennisetum purpureum) silage ROHMATUSSOLIHAT ROHMATUSSOLIHAT; RONI RIDWAN; AINISSYA FITRI; KI AGENG SARWONO; WULANSIH DWI ASTUTI; DUDI FIRMANSYAH; YANTYATI WIDYASTUTI; ARIO BETHA JUANSSILFERO; RUSLI FIDRIYANTO; MUHAMMAD RIDLA; NISA RACHMANIA MUBARIK; ANURAGA JAYANEGARA
Biodiversitas Journal of Biological Diversity Vol. 27 No. 4 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270438

Abstract

Abstract. Rohmatussolihat, Ridwan R, Fitri A, Sarwono KA, Astuti WD, Firmansyah D, Juanssilfero AB, Fidriyanto R, Ridla M, Mubarik NR, Jayanegara A. 2026. Effects of lactic acid bacteria inoculants on fermentation characteristics and microbial community profiles of napier grass (Pennisetum purpureum) silage. Biodiversitas 27 (4): d270438. https://doi.org/10.13057/biodiv/d270438. Napier grass (Pennisetum purpureum) is an important tropical forage; however, its high moisture content and low water-soluble carbohydrates (WSC) often impair silage fermentation. This study evaluated the effects of different lactic acid bacteria (LAB) inoculants on fermentation characteristics, nutrient preservation, and microbial community dynamics of napier grass silage. Four indigenous LAB strains, Companilactobacillus kimchii InaCC-B982, Lactiplantibacillus plantarum InaCC-B1028, Limosilactobacillus fermentum InaCC-B1024, and Levilactobacillus brevis InaCC-B1052, were applied individually and as a mixed inoculum and compared with an uninoculated control. Silage was sampled after 7, 14, and 28 days. LAB inoculation significantly improved fermentation quality compared with the control by accelerating acidification, lowering pH (3.69-3.86), increasing lactic acid concentration (2.38-4.90% DM), and suppressing yeasts and coliform bacteria. Among the inoculants, L. plantarum InaCC-B1028 showed the most consistent and superior performance, characterized by rapid and stable pH reduction (3.73-3.78), higher lactic acid production, minimal ammonia-N accumulation (≤0.08% DM), and improved crude protein retention (8.7-9.2% DM). In contrast, L. brevis and the mixed LAB treatment resulted in higher acetic acid concentrations, suggesting enhanced aerobic stability but less consistent nutrient preservation, whereas L. fermentum exhibited intermediate effects. Metagenomic analysis revealed that the bacterial community was dominated by Lactiplantibacillus and Companilactobacillus, with species such as L. plantarum, L. pentosus, L. paraplantarum, and C. kimchii contributing to fermentation dynamics. Genus-level dominance was consistent with species-level composition, indicating robust taxonomic structure across hierarchical levels. Overall, L. plantarum InaCC-B1028 is the most effective inoculant for improving fermentation efficiency, nutrient preservation, and microbial stability, highlighting its potential for enhancing silage quality in tropical forage systems.
Co-Authors . QATRUNNADA Aas Ratnasari Ahmad Suryadi Ainia Hanifitri AINISSYA FITRI Alfan Cahyadi Alfaridza, Annisa Nourma ALINA AKHDIYA Andreas Adhi Satya Andreas Adhi Satya ANGELIA REZTY FITRIANI SITUMORANG Anggreandari, Rizky Ani Suryani Ani Suryani Anja Meryandini Antonius Suwanto Anuraga Jayanegara ARIO BETHA JUANSSILFERO Aris Tjahjoleksono Aris Tri Wahyudi Atang Sutandi Ayni, Qurrotu Bambang - Riyanto Besty Maranatha BRAMANTYO JATI PRASOJO Budiasih Wahyuntari Budiasih Wahyuntari Budiasih Wahyuntari Cahyadi, Alfan CUCU WIJAYANTI Dadang Suhendar Dadang Suhendar DEBI ARIVO Delfi Trisnawati DERI YURATMOKO Desniar - - Dewi Seswita Zilda Dewi Seswita Zilda Dewinta Nur Alvionita Diah Ratnadewi Dian Syahfitri Dinamella Wahjuningrum Dudi Firmansyah Dwi Ambarawati Dwi Andreas Santosa Ekowati Chasanah Encah Ewi Mulyeti Esti Puspitasari ESTI PUSPITASARI Evi Damayanti Evi Damayanti, Evi Fahmi, Riziq Ilham Nur Fatmila Amirah Radwa Fauzy Rachman Fauzy Rachman Fauzy Rachman Ferymon Mahulette Ferymon Mahulette Ferymon Mahulette, Ferymon Fitratul Aini Fitratul Aini, Fitratul Fitriani Idham Galih Cendana Nabilasani Galih Cendana Nabilasani GENIA SOTYA SINARAWADI Hadi Susilo Hamim Hamim Hana Nurullita Prestisia Hasrul Satria Hasrul Satria, Hasrul HENDRA PARDEDE Hirmas Fuady Putra Idin Abidin Ika Roostika Tambunan, Ika Roostika Ika Setianingsih Iman Rusmana Irmanida Batubara Ismi Isti'anah Isna Rahma Dini Iswati, Ruma It Jamilah Ivan Permana Putra Jepri Agung Priyanto Jepri Agung Priyanto, Jepri Agung Jezila Amana Nousra Atsemani Karina Eku Dwinanda Gunawan KI AGENG SARWONO Kusuma Handayani LAKSMI AMBARSARI Latusi Anggriani Lia Siti Nur'amaliyah Lia Siti Nur'amaliyah LISDAR A. MANAF Lisdar Idwan Sudirman Listyowati, Sri lmiah, Sitti Nur Luky Adrianto Maggy Thenawidjaya Suhartono Maherani, Vincentia Fenice Angger Maranatha, Besty Maria Dita Febriani Lumban Gaol Marini Adani Mashudi Mashudi Masrukhin Masrukhin MIFTAHUL KHAIRAH Muhamad Azwar Syah MUHAMMAD EKA PRASTYA Muhammad Ridla Mulyorini Rahayuningsih Mutiha Panjaitan Nabilasani, Galih Cendana Nabilasani, Galih Cendana Ninda Ningtyas Nuraliah Rusman Nurul Hidayati ORHINTA MUTIARA JATI Partomuan Simanjuntak Partomuan Simanjuntak Partomuan Simanjuntak Popi Asri Kurniatin Prayoga SURYADARMA Puspita Lisdiyanti Rika Indri Astuti RIMA ERNIA Risky Hadi Wibowo Risky Hadi wibowo Rizky Anggreandari ROHMATUSSOLIHAT ROHMATUSSOLIHAT RONI RIDWAN Rury Eryna Putri Rury Eryna Putri RUSLI FIDRIYANTO Sarah Asih Faulina Sarah Asih Faulina, Sarah Asih Sipriyadi Sipriyadi Sipriyadi Siswa Setyahadi Siswodarsono, Trismilah Siswodarsono, Trismilah Siti Azzira Rahma Sitti Nur Ilmiah Sonya Tobing SRI BUDIARTI Sri Budiarti Poerwanto Sri Listyowati SRI RAHAYU Suhendar, Dadang Suhendar, Dadang Sukarya Zaenal Arifin SYAMSUL BAHRI SYAMSUL BAHRI TEDJA IMAS Thenawidjaya, Maggy Titi Candra Sunarti TRI ASMIRA DAMAYANTI Tri Handayani Kurniati Tri Handayani Kurniati Triadiati Triadiati Trismilah Trismilah Siswodarsono Untung Sudadi Wahyu Widosari Wibowo, Risky Hadi WIDANARNI WIDANARNI Widosari, Wahyu Wulandari Antika Putri WULANSIH DWI ASTUTI YANTYATI WIDYASTUTI Yoan Ramasita Yusro Nuri Fawzya Zaenal Arifin, Sukarya ZETRYANA PUTERI TACHRIM Zulfarina Zulfarina Zulfarina,