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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Teknologi Dan Industri Pangan Sainteks Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology Biotropika Indonesian Journal of Biotechnology Jurnal Sumberdaya Hayati Indonesian Journal of Chemistry ANNALES BOGORIENSES Marine Research in Indonesia Biosaintifika: Journal of Biology & Biology Education Menara Perkebunan Jurnal Tanah dan Iklim Makara Journal of Science Annales Bogorienses

YULIN LESTARI

Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus IPB Dramaga, Bogor 16680

Author-ID : 306475

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Immunology & microbiology Industrial & Manufacturing Engineering Materials Science & Nanotechnology Mechanical Engineering Medicine & Pharmacology Veterinary

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Characterization of Xylanase Streptomyces spp. SKK1-8 ANJA MERYANDINI; TRIO HENDARWIN; DEDEN SAPRUDIN; YULIN LESTARI
HAYATI Journal of Biosciences Vol. 13 No. 4 (2006): December 2006
Publisher : Bogor Agricultural University, Indonesia

Streptomyces spp. SKK1-8 producing xylanase was isolated from soil sample from Sukabumi West Java. The xylanase have an optimum condition at pH 6 and 50 0C. Addition of 5 mM Cu2+ decreased the xylanase activity up to about 77%, whereas not by other cations. The xylanase was stable at 3 0C for 48 hours, and the enzyme half lifetime was 1 hour 45 minute at 50 0C. This xylanase showed the highest activity on oatspelt xylan, and their molecular masses were estimated approximately 16.80, 15.21, and 13.86 kDa. HPLC analysis showed that xylosa and arabinosa were the main hydrolytic product of birchwood xylan. Key words: xilanase, Streptomyces spp., characterization, zymogram and SDS-PAGE, stability

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

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.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.19.4.155

Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight (BLB), is one of the most important pathogens of rice. The effectiveness of ten Streptomyces spp. isolates in suppressing Xoo disease was assessed in planta and in vitro. In planta experiments were carried out in a greenhouse and arranged in a randomized completely block design (RCBD) with three replications. Twenty treatments were tested which included plants inoculated with both Streptomyces spp. and Xoo, and plants inoculated with only Streptomyces spp. Plants inoculated with Xoo and sprayed with a chemical bactericide, and plants inoculated with only Xoo served as positive controls, whereas plants not inoculated with either Streptomyces spp. or Xoo were used as negative controls. The results showed that the effect of endophytic Streptomyces spp. on BLB disease expressed as area under disease progress curve (AUDPC) was not significantly different to that on control plants (P > 0.05). However, plants inoculated with endophytic Streptomyces spp. were significantly taller and produced higher tiller number than control plants (P < 0.05). Streptomyces spp. isolate AB131-1 gave the highest plant height. In vitro studies on biocontrol mechanisms of selected Streptomyces spp. isolates showed that isolate LBR02 gave the highest inhibition activity on Xoo growth, followed by AB131-1 and AB131-2. Two isolates (AB131-1 and LBR02) were able to produce chitinase, phosphatase, and siderophore which included biocontrol characteristics. Morphological and colonization studies under SEM and light microscopy confirmed that the three isolates were endophytic Streptomyces spp. from different species. These studies found that the paddy plant which was inoculated with endophytic Streptomyces spp. AB131-1 and infected by Xoo could increase the height of plant and number of tillers.

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

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.

Lipase Activity of Endophytic Actinobacteria from Medicinal Plants Yulin Lestari; Budi Wirawan; Sri Budiarti; Min Rahminiwati
HAYATI Journal of Biosciences Vol. 25 No. 1 (2018): January 2018
Publisher : Bogor Agricultural University, Indonesia

Endophytic bacteria are known to reside within host plant tissue without giving a harmfull effect. The endophytes may play an important role, as they may produce similar bioactive compounds as produced by the host plant. Various medicinal plants have long been used to cure diseases. Traditionally, leaves extract of Guazuma ulmifolia, Psidium guajava, or the rhizome of Curcuma xanthorrhiza can be used to treat disease, e.g. hyperlipidemic. The mechanism can be through lipase activity, where the lipase catalyzes the hydrolysis of triacylglycerol to fatty acids and acylglycerol. The objective of this research was to assess potency of endophytic bacteria as anti-hyperlipidemic compounds producer through their lipase activity. Sixty nine endophytic bacteria which comprised of 22, 27 and 20 isolates were isolated from the leaves of G. ulmifolia, P. guajava, and the rhizome of C. xanthorrhiza, respectively. Eight out of the 69 isolates showed lipase activity, and the two selected isolates, i.e. DPG 3(2) and AJB 4(4) were considered as good lipase producers. The highest specific lipase activity of DPG 3(2) isolate was observed for 0.874 units per mg at 38 h, whereas AJB 4(4) isolates had the specific lipase activity at 1.139 units per mg after 72 h observation. These data indicate that the two selected isolates have the potency as antihyperlipidemic compounds producer through their lipase activity.

The Existence of Endophytic Actinobacteria from Rhododendron zoelerri Revealed by Culture-Dependent and Culture-Independent Approaches Yulin Lestari; Lia Aseptin Murdini; Dedy Duryadi Solihin
HAYATI Journal of Biosciences Vol. 25 No. 2 (2018): April 2018
Publisher : Bogor Agricultural University, Indonesia

Endophytic actinobacteria from medicinal plant may play a significant role in producing bioactive compounds. The information regarding their diversity is an important. Rhododendron are traditionally used for treating human disorders. One of the selected Rhododendron used in this study was R. zoelleri from Papua origin, which has been conserved and grown in Cibodas Botanical Garden, West Java, Indonesia. The aim of this study was to assess the existence of endophytic actinobacteria from R. zoelleri based on a culture-dependent and their community structure based on a culture-independent approach. Culturable actinobacteria were isolated and cultured on HV medium. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) targeting the metagenomic 16S rRNA was used to analyse the structure of the actinobacterial community. Six culturable endophytic actinobacteria (200 cfu/g fresh weight) from R. zoelleri were successfully isolated, three isolates from leaf, and the other isolates were obtained from stem. The six culturable isolates were RZP 1.3, RZP 1.1, RZP 2.2, RZPB 1.1, RZPB 7.1, RZPB 4.1. Based on their morphological characteristics, the endophytes have Streptomyces characters. The existence of Streptomyces spp. were also confirmed with molecular analysis based on 16S rRNA gene. The phylogenetic analysis based on 16S rRNA gene to the reference strains available in EzTaxon-e database showed that six isolates were closely related to S. djakartensis strains of NBRC 15409ᵀ(99.19%), S. tritolerans strains of DAS 165T(99.90%), S. coelicoflavus strains of NBRC 15399T(99.59). However, they showed differences in morphological characteristics as compared with the reference strains. The metagenomic analysis of the DGGE profile based on 16S rRNA gene showed the community structure of endophytic actinobacteria from R. zoelleri which was represented by 13 DGGE bands. The bands were closely related to Agromyces, Gordonia, Microbacterium, Micromonospora, Propionibacterium, Saccharomonospora, Streptomyces which have 93.18%-100% similarity. Based on the data, it showed diversity of endophytic actinobacteria from R. zoelleri which may be further assess for their novelty and bioprospecting.

Community of Soil Actinobacteria in PTPN VI Oil Palm Plantation Jambi (Sumatra, Indonesia) Based on Amplicon Sequencing of 16S rRNA Gene Mazidah Noer Inayah; Yulin Lestari; Anja Meryandini
HAYATI Journal of Biosciences Vol. 29 No. 3 (2022): May 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.3.389-398

In Sumatra, Indonesia, increased oil palm production encourages land expansion for oil palm plantations. And soil Actinobacteria have a potential role in agriculture and plantations ecosystems. The use of fertilizer and herbicide affects soil microbial diversity, including Actinobacteria. This research analyzed and investigated the community composition and diversity of Actinobacteria in soils of oil palm plantations in Jambi Sumatra. Amplicon-based analysis of the 16S rRNA gene (V3-V4 hypervariable region) was used to amplify actinobacterial full-length 16S sequences. The V3-V4 actinobacterial specific 16S rRNA gene sequencing was done using Next-Generation Sequencing. This study confirmed that actinobacterial specific 16S rRNA gene primer could amplify the actinobacterial 16S rRNA gene. Frankiales dominated the community composition of soilborne Actinobacteria. The diversity and community composition of soilborne Actinobacteria were not significantly affected by the interaction between fertilization and weed treatments. Furthermore, the use of NPK fertilizer significantly affected the abundance of Kineosporiales, whose abundance increased with the increasing concentration of NPK fertilizer. The interaction between fertilization and weeding treatments in the oil palm plantations has no impact on soil Actinobacteria's community composition and diversity.

Identification, Characterization and Antioxidant Activity of Yellowish-Orange Pigments Actinobacteria Farhana Halimah Rusyda; Irmanida Batubara; Yulin Lestari
HAYATI Journal of Biosciences Vol. 31 No. 1 (2024): January 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.1.200-210

Actinobacteria are Gram-positive bacteria that can produce various secondary metabolites, including pigments that have potential as antioxidants. This study assessed the characteristics of yellowish-orange pigmented actinobacteria. The antioxidant activity of their extract pigment was tested by DPPH and analyzed by LC-MS. The identification results based on the 16S rRNA gene showed that the HRA isolate had 99.91% similarity value to Streptomyces gramineus JR-43, the HVA isolate had 99.22% similarities value to S. tendae ATCC 19812 and the HVB isolate had 81.18% similarities value to Rhodococcus ruber DSM 43338. Meanwhile, AGM 2.2 and 2.3 isolates had similarities to S. xanthophaeus NRRL B-5414 with similarity values of 98.95% and 99.82%, respectively. The Inhibitory Concentration (IC50) of actinobacterial crude extract pigments ranges from 53.38 µg/ml to 184.38 µg/ml. The HVB isolates with the major compound luteolin, have the highest antioxidant activity. The crude extract pigment of HVB isolates may consider rich in luteolin and has potency as an antioxidant.

Characterization of Antibacterial Compounds from Marine Sponge-associated Streptomyces spp. against Some Pathogenic Bacteria Efendi, Firda Sri; Budiarti, Sri; Lestari, Yulin
HAYATI Journal of Biosciences Vol. 32 No. 1 (2025): January 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.1.55-69

The increasing trend of antibiotic resistance among pathogenic bacteria is a worldwide problem. Streptomyces produce a number of bioactive compounds such as antibacterial. This study aimed to investigate the effect of different media and incubation time in increasing the antibacterial activity of marine sponge-associated Streptomyces spp. and characterize antibacterial compounds of marine sponge-associated Streptomyces spp. against pathogenic bacteria. Among the three tested media and some days of incubation times, Streptomyces spp. produce more antibacterial activity when grown using modified molasses medium at 15 days incubation. The ethyl acetate extracts of Dbi28t exhibited a significant inhibitory zone against Extended Spectrum β-Lactamase (ESBL)-producing Escherichia coli, Providencia rettgeri then followed by Proteus mirabilis and Pseudomonas putida and the results were higher than some commercial antibiotics. This study has identified nine antibacterial compounds in Dbi28t using Liquid Chromatography-tandem Mass Spectrometric (LC-MS/MS) analysis, with the most abundance belonging to pumilacidin A, then followed by pumilacidin B, surfactin B, surfactin A, phenazostatin B, chalcomycin B, neopyrrolomycin C, saquayamycin A and saphenamycin. This work provides the first report from a Streptomyces sp. Dbi28t produced pumilacidin, surfactin and other bioactive compounds with the modified molasses medium for optimization of characterization of its antibacterial compounds.

Bacterial Community in Apis cerana and Heterotrigona itama Honey Using a Metabarcoding Approach Nurjanah, Nurjanah; Raffiudin, Rika; Lestari, Yulin
HAYATI Journal of Biosciences Vol. 33 No. 2 (2026): March 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.2.310-320

Honey is a healthy, natural product with high nutritional value that is converted from sugar in nectar by bacteria in the honey stomach of the bees. Several beneficial bacteria in honey produce bioactive compounds, such as Lactobacillus in Apis mellifera honey, which synthesizes lactic acid, bacteriocins, and enzymes. Here, we employed the metabarcoding technique using the 16S rRNA gene to identify the bacterial community in honey from A. cerana and Heterotrigona itama collected in Sukabumi Regency, West Java, Indonesia. Genomic DNA from both honey samples was isolated using the ZymoBIOMICSTM DNA miniprep kit before sequencing with the Oxford Nanopore Technologies (ONT) platform. Our studies showed that the most dominant bacteria in the honey of A. cerana and H. itama were Paenibacillus glucanolyticus and Limosilactobacillus, respectively. In both types of honey, Gram-positive and Gram-negative bacteria were also detected, as well as lactic acid bacteria, including Acetilactobacillus jinshanensis and Limosilactobacillus. We also found Actinobacteria in A. cerana and H. itama honey. This genomic data showed that A. cerana honey has a higher bacterial diversity than H. itama. Our finding is the first genomic study of bacterial diversity found in the honey of A. cerana and H. itama that live sympatrically in a bee farm.

Co-Authors A. HAITAMI Abdjad Asih Nawangsih Alifian Ariansyah Amor Tresna Karyawati, Amor Tresna Anas Dinurrohman Susila Ando Katsuhiko ANDO KATSUHIKO Anja Meryandini Anja Meryandini Anja Meryandini Antonius Suwanto ARI SUSILOWATI Ariansyah, Alifian Aris Tri Wahyudi ARTINI PANGASTUTI Arum Asiyanti Suhastyo, Arum Asiyanti Arum Asriyanti Suhastyo BAMBANG MARWOTO Batara, Lily Noviani Budi Wirawan Deden Saprudin Dedy Duryadi Solihin Didy Sopandie DITA, SASMIATI FARACH DWI ANDREAS SANTOSA Dyah Iswantini DYAH NOOR HIDAYATI Efendi, Firda Sri Egra, Saat Elisa Sopiatul Fitriani Endang Sukara EVI TRIANA Evi Triana Farhana Halimah Rusyda Ferry Mutia Fitriandini, Risa Gina Kartina GINA KARTINA GINA KARTINA Hamim Hamim Hastuti, Ratih Dwi HIDEKI YAMAMURA Iman Rusmana Inayah, Mazidah Noer Indah Puspita SARI Irmanida Batubara Isra Janatiningrum Iswandi Anas Iswandi Anas KATSUHIKO ANDO KATSUHIKO ANDO Laksmita Prima SANTI Lenni Fitri Lenni Fitri Lia Aseptin Murdini Lilis Nuraida Maggy T. Suhartono Maggy Thenawidjaja Suhartono Mahyarudin, Mahyarudin MISA OTOGURO MISA OTOGURO MONA PRIMANITA Munif Ghulamahdi N. Nurjanah Niken Financia Gusmawati NITA ROSALINDA PRAYITNO NITA ROSALINDA PRAYITNO Nunuk Widhyastuti NUNUK WIDHYASTUTI NUNUK WIDHYASTUTI PUSPITA LISDIYANTI Puspita Lisdiyanti PUSPITA LISDIYANTI Rahminiwati, Min RASTI SARASWATI RASTI SARASWATI RATIH DEWI HASTUTI RATIH DEWI HASTUTI Ratte, Marina RIKA RAFFIUDIN Risa Fitriandini ROHMATUSSOLIHAT ROHMATUSSOLIHAT Roni Ridwan RONI RIDWAN RONI RIDWAN Saat Egra Shanti Ratnakomala SHANTI RATNAKOMALA SHANTI RATNAKOMALA SHINJI MIYADOH Sipriyadi Sipriyadi Sipriyadi Sri Budiarti Sri Budiarti Poerwanto Suryo Wiyono SUSILOWATI1 SUSILOWATI1 TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Titi Candra Sunarti TOMOHIKO TAMURA Tomohiko Tamura TOMOHIKO TAMURA TRI RATNA SULISTIYANI TRIO HENDARWIN Umi Fatmawati Winanda, Witri Witri Winanda Yantyati Widyastuti YANTYATI WIDYASTUTI Yantyati Widyastuti Zaenal Abidin

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