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Biodecolorization of Remazol Brilliant Blueâ€“R dye by Tropical White-Rot Fungi and Their Enzymes in The Presence of Guaiacol Sita Heris Anita; Fitria Ningsih; Dede Heri Yuli Yanto
Jurnal Riset Kimia Vol. 12 No. 2 (2021): September
Publisher : Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jrk.v12i2.388

The ability of the tropical white-rot fungi and their enzyme to decolorize synthetic dyes was investigated. Production of lignin-modifying enzymes (LMEs) from the three new isolated fungi, namely Trametes hirsuta D7, Ceriporia sp. BIOM 3, and Cymatoderma dendriticum WM01 were observed for 9 days incubation under static condition. The results showed that the LMEs production enhanced in the present of guaiacol. T. hirsuta D7 produced only laccase (Lac), with the highest activity was 22.6 U/L on the 5th-day of the cultivation. At the same time, Ceriporia sp. BIOM 3 and C. dendriticum WM01 secreted both laccases (Lac) with the activities 0.2 U/L and 1.0 U/L, respectively, and manganese peroxidase (MnP) with the activities 0.1 U/L and 1.0 U/L, respectively. Among the fungi, T. hirsuta D7 efficiently degraded 65% Remazol Brilliant Blueâ€“R (RBBR) dye within 72 h using the only laccase. This study shows that laccase may have a major role in synthetic dyes' decolorization process, followed by MnP and LiP.

DETECTION OF ANTIMICROBIAL COMPOUNDS FROM THERMOPHILIC ACTINOMYCETES USING ONE STRAIN MANY COMPOUNDS (OSMAC) APPROACH Endah Wati Zahroh; Fitria Ningsih; Wellyzar Sjamsuridzal
BIOLINK (Jurnal Biologi Lingkungan Industri Kesehatan) Vol 9, No 1 (2022): August
Publisher : Universitas Medan Area

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31289/biolink.v9i1.6438

Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.

DETECTION OF ANTIMICROBIAL COMPOUNDS FROM THERMOPHILIC ACTINOMYCETES USING ONE STRAIN MANY COMPOUNDS (OSMAC) APPROACH Endah Wati Zahroh; Fitria Ningsih; Wellyzar Sjamsuridzal
BIOLINK (Jurnal Biologi Lingkungan Industri Kesehatan) Vol. 9 No. 1 (2022): August 2022
Publisher : Universitas Medan Area

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31289/biolink.v9i1.6438

Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.

Screening for amylolytic activity and characterization of thermophilic Actinobacteria isolated from a Geothermal Area in West Java, Indonesia WINDA AYU SYAFITRI; FITRIA NINGSIH; PUTRI PRATIWI SETYANINGSIH; MAZYTHA KINANTI RACHMANIA; DHIAN CHITRA AYU FITRIA SARI; SHUHEI YABE; AKIRA YOKOTA; ARIYANTI OETARI; WELLYZAR SJAMSURIDZAL
Biodiversitas Journal of Biological Diversity Vol. 20 No. 7 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200720

Abstract. Syafitri WA, Ningsih F, Setyaningsih PP, Rachmania MK, Sari DCAF, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. 2019. Screening for amylolytic activity and characterization of thermophilic Actinobacteria isolated from a geothermal area in West Java, Indonesia. Biodiversitas 20: 1929-1938. In this study, we describe the screening for amylolytic activity of 17 thermophilic Actinobacteria isolates obtained from the soil of Cisolok geysers, a geothermal area in West Java, Indonesia. All isolates were screened for amylolytic activity by the starch-agar plate method at various temperatures. The results showed that all of isolates were able to grow at 45oC. The growth abilities of the isolates grown in ISP 1 medium varied at temperatures from 45 to 60oC. Fifteen of the 17 isolates showed amylolytic activity at 45oC, 13 showed such activity at 50oC, and four showed activity at 55oC. Only three isolates, designated SL1-2-R-2, SL1-2-R-3, and SL1-2-R-4, showed growth and amylolytic activity at 60oC. These three isolates were selected for molecular identification. The nearly full-length of 16S rRNA gene sequences data showed that these three isolates have a similarity of 99.93-100% with Actinomadura keratinilytica WCC-2265T and of 98.74-98.91% with A. miaoliensis BC 44T-5T. Phylogenetic tree shows that all three isolates are clustered together in a monophyletic group with the type strain of A. keratinilytica WCC-2265T as their most closely related species, with 100% bootstrap support. Based on sequencing of the 16S rRNA gene, phylogenetic comparison, and phenotypic characterization, the three isolates were identified as A. keratinilytica.

Cellulolytic enzyme-producing thermophilic Actinobacteria isolated from the soil of Cisolok Geysers, West Java, Indonesia PUTRI PRATIWI SETYANINGSIH; FITRIA NINGSIH; MAZYTHA KINANTI RACHMANIA; WINDA AYU SYAFITRI; DHIAN CHITRA AYU FITRIA SARI; SHUHEI YABE; AKIRA YOKOTA; ARIYANTI OETARI; Wellyzar Sjamsuridzal
Biodiversitas Journal of Biological Diversity Vol. 20 No. 11 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201105

Abstract. Setyaningsih PP, Ningsih F, Rachmania MK, Syafitri WA, Sari DCAF, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. 2019. Cellulolytic enzyme-producing thermophilic Actinobacteria isolated from the soil of Cisolok Geysers, West Java, Indonesia. Biodiversitas 20: 3134-3141. This study investigated 17 thermophilic Actinobacteria isolated from the soil of geysers in the Cisolok geothermal area, West Java, as potential producers of cellulase. Screening for cellulase was performed on minimal (Mm) agar medium with and without the addition of 1% (w/v) carboxymethylcellulose (CMC) and microcrystalline cellulose (MCC), then incubated at 45, 50, 55 and 60°C for up to 7 days. Formation of clear zones around colonies indicated cellulose hydrolysis. The results showed that 15, 14, 4, and 3 isolates showed cellulolytic activity on CMC agar medium at 45, 50, 55, and 60°C, respectively, after 7 days of incubation. Three potential isolates showed cellulolytic activity on MCC agar medium after being incubated for 7 days at 45°C. Molecular identification based on the 16S rRNA gene was performed for three isolates with positive cellulolytic activity at 60°C. The results showed that the three isolates are closely related to Actinomadura keratinilytica WCC-2265T with 99.93-100% sequence similarities. A phylogenetic tree based on 16S rRNA gene sequences confirmed that the three isolates were clustered together with Actinomadura keratinilytica WCC-2265T with 100% bootstrap value. The tree also showed that cellulase producers and non-cellulase producers in Thermomonosporaceae are grouped into different clades.

Xylan-degrading ability of thermophilic Actinobacteria from soil in a geothermal area MAZYTHA KINANTI RACHMANIA; FITRIA NINGSIH; PUTRI PRATIWI SETYANINGSIH; WINDA AYU SYAFITRI; DHIAN CHITRA AYU FITRIA SARI; SHUHEI YABE; AKIRA YOKOTA; ARIYANTI OETARI; Wellyzar Sjamsuridzal
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/d210119

Abstract. Rachmania MK, Ningsih F, Setyaningsih PP, Syafitri WA, Sari DCAF, Yabe S, Yokota A, Oetari A, Sjamsuridjal W. 2020. Xylan-degrading ability of thermophilic Actinobacteria isolated from soil in a geothermal area. Biodiversitas 21: 144-154. This study was conducted to obtain the potential isolates of xylan-degrading thermophilic Actinobacteria. Seventeen isolates were obtained from the soil samples collected from Cisolok geysers in West Java, Indonesia. These isolates were screened for their xylan-degrading ability on minimal medium with the addition of 0.5% xylan as substrate, and were incubated at various temperatures for 7 days. A total of 15, 14, 4, and 3 isolates showed a xylan-degrading ability at 45°C, 50°C, 55°C, and 60°C, respectively. The three isolates (SL1-2-R-2, SL1-2-R-3, and SL1-2-R-4) that showed xylan-degrading ability at 60°C on 0.5% xylan were further tested by using minimal medium with the addition of 0.1% RBB-xylan as a substrate. The results showed that these isolates were also able to utilized RBB-xylan at 45 to 60°C. The xylanolytic activity of the crude enzymes from the three isolates on minimal medium containing 0.5% xylan or 0.1% RBB-xylan as substrates, indicated that these isolates were able to produce extracellular xylanase. This study revealed that the soil of Cisolok geysers served as an ideal source for finding the thermophilic Actinobacteria which produced xylanase at high temperatures.

Potential secondary metabolite biosynthetic gene clusters and antibacterial activity of novel taxa Gandjariella Fitria Ningsih; Dhian Chitra Ayu Fitria Sari; Shuhei Yabe; Akira Yokota; Wellyzar Sjamsuridzal
Biodiversitas Journal of Biological Diversity Vol. 21 No. 12 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d211225

Abstract. Ningsih F, Sari DCAF, Yabe S, Yokota A, Sjamsuridzal W. 2020. Potential secondary metabolite biosynthetic gene clusters and antibacterial activity of novel taxa Gandjariella. Biodiversitas 21: 5674-5684. Microbial resistance to available antibiotics has gained increasing attention in recent years and led to the urgent search for active secondary metabolites from novel microbial taxa. This study aimed to assess putative secondary metabolite biosynthetic gene clusters (BGCs) in the genome of a novel thermophilic Actinobacteria type strain Gandjariella thermophila SL3-2-4T and screen for its antibacterial activity. Four other related novel candidate Actinobacteria strains, isolated from forest soil in the Cisolok geothermal area (West Java, Indonesia), were also screened for antibacterial activity in various media solidified with gellan gum. The genome of the SL3-2-4T strain contained 21 antiSMASH-identified secondary metabolite regions harboring BGCs. These BGCs were for polyketide synthase, non-ribosomal peptide synthase, and ribosomally synthesized and post-translationally modified peptide family clusters. Three BGC regions displayed 50-100% similarity with known secondary metabolites. Thirteen and five regions displayed low (4-35%) and no similarity with known BGCs for secondary metabolites, respectively. Strains SL3-2-4T and SL3-2-7 on MM 2 medium solidified with gellan gum at 45 °C for 14 days demonstrated inhibitory activity against all Gram-positive, but not Gram-negative bacteria. Strain SL3-2-10 on ISP 3 gellan gum medium incubated for seven days only active against K. rhizophila NBRC 12078. Strains SL3-2-6 and SL3-2-9 did not exhibit any antibacterial activity against the tested bacterial strains on the three tested media. The results indicated that novel taxa have the potential for the discovery of active secondary metabolites.

Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia MAZYTHA KINANTI RACHMANIA; FITRIA NINGSIH; DHIAN CHITRA AYU FITRIA SARI; YURIZA ESHANANDA; YASUTERU SAKAI; SHUHEI YABE; AKIRA YOKOTA; WELLYZAR SJAMSURIDZAL
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230935

Abstract. Rachmania MK, Ningsih F, Sari DCAF, Eshananda Y, Sakai Y, Yabe S, Yokota A, Sjamsuridzal W. 2022. Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia. Biodiversitas 23: 4686-4695. This study aimed to provide information on culturable Ktedonobacteria from forest soil in the Cisolok geothermal area and their potential as enzyme producers. Twelve ktedonobacterial isolates were obtained from this study and identified based on full-sequence of the 16S rRNA gene. Seventeen isolates (including five isolates from previous studies) were used for enzymatic screening and phylogenetic analyses. Screening of amylolytic (0.5% soluble starch) and cellulolytic (0.5% carboxymethylcellulose) (CMC) activities from ktedonobacterial isolates was performed on a ten-fold diluted R2A agar medium, and were incubated at 30 °C for 21 days. The EzBioCloud search revealed that all isolates showed low sequence similarities with Dictyobacter aurantiacus S-27T (97.82 to 98.18%) as their closest related species. The phylogenetic tree showed that all isolates belong to the genus Dictyobacter (family Dictyobacteraceae of the class Ktedonobacteria). All isolates formed a monophyletic group and were placed as the sister clade to D. aurantiacus, as supported by a very strong bootstrap value (99%). Screening of amylolytic and cellulolytic abilities showed that most isolates (88.23%) were able to degrade both 0.5% starch and 0.5% CMC as substrates. This study revealed the presence of Ktedonobacteria with amylolytic and cellulolytic abilities in the forest soil of Cisolok geothermal area.

Next Generation Sequencing (NGS) for Cyanobacterial study in Agung and Sunter Barat Lakes, North Jakarta, Indonesia DIAN HENDRAYANTI; NINING BETAWATI PRIHANTINI; FITRIA NINGSIH; FADHLURAHMAN MAULANA
Biodiversitas Journal of Biological Diversity Vol. 24 No. 2 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240251

Abstract. Hendrayanti D, Prihantini NB, Ningsih F, Maulana F. 2023. Next Generation Sequencing (NGS) for Cyanobacterial study in Agung and Sunter Barat Lakes, North Jakarta, Indonesia. Biodiversitas 24: 1117-1124. The Next Generation Sequences (NGS) is one of the established metabarcoding methods for analyzing microbial communities. Investigation of the cyanobacterial community in eutrophic freshwater habitats is important, especially for those known as toxic-released cyanobacteria. This study aimed to analyze the structure community of cyanobacteria in Agung and Sunter Barat Lakes in North Jakarta, DKI Jakarta Province using the NGS method. The physico-chemical parameters were also measured. Sampling plots were selected by purposive sampling method. The result of the study successfully analyzed the bacterial community structure and portrayed the dominancy of the cyanobacterial population on the two lakes. Several cyanobacteria genera previously reported in 2008 research were found, including Arthrospira and Planktothrix. The diversity index in Agung Lake (4.7) was higher than in Sunter Barat Lake (3.7). Two dominant populations were found, which were Raphidiopsis (in Agung Lake) and Planktothrix (in Sunter Barat Lake). Both genera have been acknowledged as toxin-releasing cyanobacteria, which could be harmful to the water-biotic community as well as human health. The presence of potentially toxic cyanobacteria in the recreation area of Agung Lake should be taken into consideration for biomonitoring management.

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