Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits Zen Ladestam Siallagan, Muhammad Fadli, Charlie Ester de Fretes, Rafidha Dh Ahmad Opier, R. Dwi Susanto, Zexun Wei, V. Sri Harjati Suhardi, Husna Nugrahapraja, Ocky Karna Radjasa, Fenny M. Dwivany Scientific Reports, 2024 The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.
From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential Ocky K. Radjasa, Ray Steven, Yosua Natanael, Husna Nugrahapraja, Septhy K. Radjasa, Tati Kristianti, Maelita R. Moeis, Joko P. Trinugroho, Haekal B. Suharya, Alfito O. Rachmatsyah, Ari Dwijayanti, Mutiara R. Putri, Charlie E. de Fretes, Zen L. Siallagan, Muhammad Fadli, Rafidha D. A. Opier, Jandinta D. Farahyah, Viana Rahmawati, Meirifa Rizanti, Zalfa Humaira, Ary S. Prihatmanto, Nugroho D. Hananto, R. Dwi Susanto, Agus Chahyadi, Elfahmi, Neil Priharto, Kamarisima, Fenny M. Dwivany BMC Genomics, 2024 BACKGROUND: The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods. RESULTS: Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4 Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (α < 1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes. CONCLUSIONS: This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.
Salinity and temperature regulations on the genus Trichodesmium in Pombo Island national marine park environment, Central Maluku, during the easterly monsoon Aacl Bioflux, 2024
Composition, abundance, and structure community of larva fish in Ambon Bay Aacl Bioflux, 2023
Abundance and biovolume of gelatinous zooplankton in Inner Ambon Bay during the northwest monsoon 2022 Aacl Bioflux, 2023
Why many Indonesian marine species remain undescribed: a case study using polychaete species discovery Zen L. Siallagan, Conni M. Sidabalok, Muhammad Masrur Islami, Nova Mujiono, Simon Wilson, et al. Raffles Bulletin of Zoology, 2023 Siallagan, Zen L., Sidabalok, Conni M., Islami, Muhammad M., Mujiono, Nova, Wilson, Simon P., Abstract, Joko Pamungkas, hotspot, Even though it is a global marine biodiversity, small, the contribution of Indonesia to marine species discovery has been disproportionately, scientists, and despite the amount of biodiversity research conducted by local, undescribed, many species in this country remain, article, In this, country, we used the discovery rate of Indonesian polychaete species as a case example to investigate the contributory factors leading to the slow rate of marine species discovery in the, addition, In, evaluated, we (2023): Why many Indonesian marine species remain undescribed: a case study using polychaete species discovery. Raffles Bulletin of Zoology 71: 337-365, DOI: 10.26107/RBZ-2023-0026
Vertical profile of culturable bacteria from the Makassar Strait, Indonesia Zen Ladestam Siallagan, Tati Kristianti, Fenny Martha Dwivany, Husna Nugrahapraja, Charlie Ester de Fretes, et al. Biodiversitas, 2023 Abstract. Siallagan ZL, Kristianti T, Dwivany FM, Nugrahapraja H, Fretes CED, Fadli M, Trinugroho JP, Radjasa OK, Susanto RD. 2023. Vertical profile of culturable bacteria from the Makassar Strait, Indonesia. Biodiversitas 24: 1356-1365. Indonesia's extensive maritime background is a rich biological and chemical diversity source. This diversity has become as source of unique chemical compounds with the potential for industrial development as enzymes, molecular probes, chemicals, pharmaceuticals, cosmetics, nutritional supplements, and agrochemicals. The present study aimed to analyze the community composition of culturable bacteria from three different layers of depth from Makassar Strait using high throughput DNA Illumina sequencing of 16S rRNA. Bioinformatic analysis has rendered 140336 high-quality sequences with an average of 124127 sequences per sample and a mean read length of 428 bp. Results showed that Firmicutes and Proteobacteria were the two most abundant phyla. Taxonomic analysis showed that Firmicutes dominated all samples. Genus Streptomycetes and Psychrobacter occurred mainly in the culture from the surface layer. Species richness and diversity for the bacterial communities at 100 m were higher than those at 5 m and 200 m. PCA plot, NMDS plot, and UPGMA clustering demonstrated that the culturable bacterial community compositions of 100 and 200 ms were highly similar and distinct from those in 5 m. This research discovered microbes with potential as sources of marine natural products, including Streptomyces, Paenibacillus, Bacillus, Psychrobacter, Arthrobacter, Bradyrhizobium, Gemmatimonas, and Acidobacteria.
Symbiotic performance of several leguminous plants with legume nodule bacteria isolated from siratro (macroptilium atropurpureum) at Mount Merapi Eruption, Indonesia Zen Ladestam Siallagan, Endah Retnaningrum, Irfan Dwidya Prijambada Aip Conference Proceedings, 2020 Legume nodule bacteria (LNB) have the host specific nodulation in forming a symbiosis with leguminous plants. This research was conducted to investigate the symbiotic performance of 27 LNB isolates from Siratro (Macroptilium atropurpureum) at Mount Merapi Eruption, Indonesia with six legumes species such as Medicago sativa, Pisum sativum, Phaseolus vulgaris, Glycine max, Arachis hypogeal and M. atropurpureum. The successful cross inoculation group of LNB were further identified phenotypically. This research was designed with a completely randomized design using plastic pouch method for analyzing their symbiotic performance with three replications. The symbiotic relationship with those leguminous plants species were observed by the root nodule formations. The results revealed significant the root nodule formations in G. max which inoculating of each 4 isolates (MPB8, MPB9, MPB25 and MPB27), whereas the successful root nodule formation of M. atropurpureum was only observed which inoculating of MPB25 isolate. Furthermore, acetylene reduction assay of M. atropurpureum root nodules which inoculating MPB25 isolate showed the highest nitrogenase activity (0.0087 mmol N2 g-1 hour−1). In contrast, the lowest nitrogenase activity was measured at G. max nodules which inoculated by MPB25 isolate (0.0004 mmol N2 g-1 hour-1). Those nodule diameter results showed positive correlation significantly between fresh weight (r= 0.9) and dry weight of their nodules (r= 0.8), while nitrogenase activity showed negatively correlation between nodule diameter (r=-0.6), nodule number (r=-0.3) and fresh weight of nodule(r=- 0.7). Based on the phenotypic characterization, MPB8 and MPB9 isolates were identified genus Rhizobium, whereas MPB25 and MPB27 isolates were identified genus Ensifer.
RECENT SCHOLAR PUBLICATIONS
STEM Trends in Physics Education Research at The Secondary School Level In Indonesia: A Bibliometric Perspective (2010–2024) CSA Barus, SS Ringo, JE Sitepu, ZL Siallagan Jurnal Pendidikan Fisika Indonesia 21 (2), 179-191 , 2025 2025 Citations: 2
From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential OK Radjasa, R Steven, Y Natanael, H Nugrahapraja, SK Radjasa, ... BMC genomics 25 (1), 1259 , 2024 2024 Citations: 1
Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits OKRFMD Siallagan ZL, Muhammad Fadli, Charlie Ester de Fretes, Rafidha Dh ... Scientific Reports , 2024 2024 Citations: 6
Water Quality Analysis Based on Total Coliform Bacteria in Ambon Bay ZL Siallagan, CE de Fretes Proceedings of the 9th Mathematics, Science, and Computer Science Education … , 2024 2024
Salinity and temperature regulations on the genus Trichodesmium in Pombo Island national marine park environment, Central Maluku, during the easterly monsoon S Likumahua, F Ruli, D Patty, AK Yamko, ZL Siallagan Aquaculture, Aquarium, Conservation & Legislation 17 (4), 1480-1489 , 2024 2024
Composition, abundance, and structure community of larva fish in Ambon Bay A Romdon, M Fadli, RDA Opier, F Ruli, ZL Siallagan, T Widodo, ... Aquaculture, Aquarium, Conservation & Legislation 16 (6), 3240-3249 , 2023 2023 Citations: 2
Abundance and biovolume of gelatinous zooplankton in Inner Ambon Bay during the northwest monsoon 2022 FR Nining B. Prihantini, Sem Likumahua, Marsya J. Rugebregt, Rafidha D ... http://www.bioflux.com.ro/docs/2023.989-999.pdf, 989-999 , 2023 2023 Citations: 3
Vertical profile of culturable bacteria from the Makassar Strait, Indonesia ZENL SIALLAGAN, T KRISTIANTI, FM DWIVANY, H NUGRAHAPRAJA, ... https://smujo.id/biodiv/article/view/12525/6623 24, 1356-1365 , 2023 2023 Citations: 1
Why many Indonesian marine species remain undescribed: a case study using polychaete species discovery JP Zen L Siallagan, Conni M Sidabalok, Muhammad M Islami, Nova Mujiono ... Raffles Bulletin of Zoology (https://lkcnhm.nus.edu.sg/wp-content/uploads … , 2023 2023 Citations: 9
KERAGAMAN BAKTERI PENDEGRADASI POLIETILENA DI HUTAN MANGROVE AMBON SBJ Rizki Estiningtyas , I Putu Sastra Negara , Dwi Andreas Santosa , I Made ... https://e-journal.biologi.lipi.go.id/index.php/berita_biologi/article/view … , 2022 2022 Citations: 1
Review Article Biodiversitas Lichens Laut dan Prospeknya sebagai Kandidat Antiviral ZLS Yosmina Tapilatu ITB Press , 2020 2020
Symbiotic performance of several leguminous plants with legume nodule bacteria isolated from siratro ( Macroptilium atropurpureum ) at Mount Merapi Eruption … ZL Siallagan, E Retnaningrum, ID Prijambada AIP Conference Proceedings 2260 (1), 020019 , 2020 2020 Citations: 2
UJI SILANG BAKTERI PEMBENTUK BINTIL AKAR LEGUM DARI LAHAN PEKARANGAN TERDAMPAK ERUPSI MERAPI ZENL SIALLAGAN Universitas Gadjah Mada , 2015 2015
MOST CITED SCHOLAR PUBLICATIONS
Why many Indonesian marine species remain undescribed: a case study using polychaete species discovery JP Zen L Siallagan, Conni M Sidabalok, Muhammad M Islami, Nova Mujiono ... Raffles Bulletin of Zoology (https://lkcnhm.nus.edu.sg/wp-content/uploads … , 2023 2023 Citations: 9
Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits OKRFMD Siallagan ZL, Muhammad Fadli, Charlie Ester de Fretes, Rafidha Dh ... Scientific Reports , 2024 2024 Citations: 6
Abundance and biovolume of gelatinous zooplankton in Inner Ambon Bay during the northwest monsoon 2022 FR Nining B. Prihantini, Sem Likumahua, Marsya J. Rugebregt, Rafidha D ... http://www.bioflux.com.ro/docs/2023.989-999.pdf, 989-999 , 2023 2023 Citations: 3
STEM Trends in Physics Education Research at The Secondary School Level In Indonesia: A Bibliometric Perspective (2010–2024) CSA Barus, SS Ringo, JE Sitepu, ZL Siallagan Jurnal Pendidikan Fisika Indonesia 21 (2), 179-191 , 2025 2025 Citations: 2
Composition, abundance, and structure community of larva fish in Ambon Bay A Romdon, M Fadli, RDA Opier, F Ruli, ZL Siallagan, T Widodo, ... Aquaculture, Aquarium, Conservation & Legislation 16 (6), 3240-3249 , 2023 2023 Citations: 2
Symbiotic performance of several leguminous plants with legume nodule bacteria isolated from siratro ( Macroptilium atropurpureum ) at Mount Merapi Eruption … ZL Siallagan, E Retnaningrum, ID Prijambada AIP Conference Proceedings 2260 (1), 020019 , 2020 2020 Citations: 2
From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential OK Radjasa, R Steven, Y Natanael, H Nugrahapraja, SK Radjasa, ... BMC genomics 25 (1), 1259 , 2024 2024 Citations: 1
Vertical profile of culturable bacteria from the Makassar Strait, Indonesia ZENL SIALLAGAN, T KRISTIANTI, FM DWIVANY, H NUGRAHAPRAJA, ... https://smujo.id/biodiv/article/view/12525/6623 24, 1356-1365 , 2023 2023 Citations: 1
KERAGAMAN BAKTERI PENDEGRADASI POLIETILENA DI HUTAN MANGROVE AMBON SBJ Rizki Estiningtyas , I Putu Sastra Negara , Dwi Andreas Santosa , I Made ... https://e-journal.biologi.lipi.go.id/index.php/berita_biologi/article/view … , 2022 2022 Citations: 1
Water Quality Analysis Based on Total Coliform Bacteria in Ambon Bay ZL Siallagan, CE de Fretes Proceedings of the 9th Mathematics, Science, and Computer Science Education … , 2024 2024
Salinity and temperature regulations on the genus Trichodesmium in Pombo Island national marine park environment, Central Maluku, during the easterly monsoon S Likumahua, F Ruli, D Patty, AK Yamko, ZL Siallagan Aquaculture, Aquarium, Conservation & Legislation 17 (4), 1480-1489 , 2024 2024
Review Article Biodiversitas Lichens Laut dan Prospeknya sebagai Kandidat Antiviral ZLS Yosmina Tapilatu ITB Press , 2020 2020
UJI SILANG BAKTERI PEMBENTUK BINTIL AKAR LEGUM DARI LAHAN PEKARANGAN TERDAMPAK ERUPSI MERAPI ZENL SIALLAGAN Universitas Gadjah Mada , 2015 2015
