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All Journal Jurnal Biologi Tropis BIODIVERS - BIOTROP Scientific Magazine
Pamungkas, Edo Agam
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Energy Environmental Science Immunology & microbiology

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Effectiveness of DNA Barcoding Primers in Red Algae (Rhodophyta) Identification Khan, Aidil Zaid; Fernando, Ardian Putra; Pamungkas, Edo Agam; Andhira, Ayu; Ishlah, Rifa Nur; Resmi, Denia Dwi Citra; Damayanti, Farida; Rahmawati, Dewi
BIODIVERS - BIOTROP Science Magazine Vol. 4 No. 1 (2025): Vol. 4 No. 1 (2025): BIODIVERS Volume 4 No. 1 (2025)
Publisher : SEAMEO BIOTROP

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Abstract

Red algae (Rhodophyta) are vital primary producers in marine ecosystems and are economically significant due to their wide use in food, pharmaceutical, and cosmetic industries. The significant utilization of red algae indicates that these organisms require conservation and protection from extinction, therefore, accurate identification is a must. Traditional morphological approaches face challenges due to their simplicity and plasticity; however, molecular techniques, such as DNA barcoding can overcome these limitations. This study evaluated the effectiveness of using ITS1, Cox2-3, rbcL 1, and rbcL 2 primers for barcoding seven red algae species, focusing on amplification success and sequencing quality. All of the above-mentioned primers have demonstrated a noteworthy amplification rate of success, with 100% efficacy observed for ITS1 and rbcL 2. However, only Cox2-3, rbcL 1, and rbcL 2 primers exhibited a high-quality read based on the sequencing quality score, indicating their reliability in capturing the target sequence for identification. The results strongly suggested that rbcL 2 is the optimal choice for identifying Rhodophyta due to its high amplification rate and high-quality sequencing results.
Direct Pellet PCR: Rapid Extraction-Free Method for Identification of Cellulolytic Bacteria from Empty Fruit Bunch Pamungkas, Edo Agam; Madusari, Sylvia; Putri, Halida Adistya; Rosita, Risa
Jurnal Biologi Tropis Vol. 26 No. 1 (2026): Januari-Maret
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v26i1.11225

Abstract

Oil Palm (Elaeis guineensis Jacq.) is a major industrial crop producing large amounts of empty fruit bunches (EFB), which necessitate rapid molecular methods to support microbial biodiversity studies and biotechnology applications. This study evaluated the effectiveness of Direct Pellet PCR as a rapid, extraction-free method for the molecular identification of cellulolytic bacteria isolated from EFB. Bacterial cell pellets were directly used as PCR templates to amplify the 16S rRNA gene without prior DNA extraction. The method consistently produced clear and specific amplicons of approximately 1500 bp for all isolates, indicating reliable PCR amplification. Sequence analysis showed similarity values ranging from 68.82% to 80.43% compared with reference sequences in the NCBI database, suggesting low similarity to currently available references. These findings demonstrate that Direct Pellet PCR is an efficient and cost-effective approach for rapid DNA amplification and preliminary molecular screening of cellulolytic bacteria from lignocellulosic substrates.
Co-Authors Andhira, Ayu DEWI RAHMAWATI Farida Damayanti Fernando, Ardian Putra Ishlah, Rifa Nur Khan, Aidil Zaid Putri, Halida Adistya Resmi, Denia Dwi Citra ROSITA, Risa Sylvia Madusari