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- Ship Hull‑Fouling Diatoms on Korean Research Vessels Revealed by Morphological and Molecular Methods, and Their Environmental Implications
- Jaeyeong Park , Taehee Kim , Buhari Lawan Muhammad , Jang-Seu Ki
- J. Microbiol. 2023;61(6):615-626. Published online May 25, 2023
- DOI: https://doi.org/10.1007/s12275-023-00055-3
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Abstract
- Ship biofouling is one of the main vectors for the introduction and global spread of non-indigenous organisms. Diatoms were the early colonizers of ship hulls; however, their community composition on ships is poorly understood. Herein, we investigated the diatom community on the hull samples collected from two Korean research vessels Isabu (IRV) and Onnuri (ORV) on September 2 and November 10, 2021, respectively. IRV showed low cell density (345 cells/cm2) compared to ORV (778 cells/cm2). We morphologically identified more than 15 species of diatoms from the two research vessels (RVs). The microalgae in both RVs were identified as Amphora, Cymbella, Caloneis, Halamphora, Navicula, Nitzschia, and Plagiogramma. Of them, the genus Halamphora was found to be predominant. However, both RVs had a varied dominant species with a significant difference in body size; Halamphora oceanica dominated at IRV, and Halamphora sp. at ORV, respectively. Molecular cloning showed similar results to morphological analysis, in which Halamphora species dominated in both RVs. The hull-attached species were distinct from species found in the water column. These results revealed diatoms communities that are associated with ship hull-fouling at an early stage of biofilm formation. Moreover, ships arriving from different regions could show some variation in species composition on their hull surfaces, with the potential for nonindigenous species introduction.
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Citations
Citations to this article as recorded by
- Invasion and ecological impact of the biofouling tube worm Hydroides elegans (Polychaeta: Serpulidae) in Korean coastal waters
Sang Lyeol Kim, Ok Hwan Yu
Frontiers in Marine Science.2025;[Epub] CrossRef - High haplotype diversity and strong phylogeographic structure in the invasive jellyfish Blackfordia virginica population highlight its complex demographic history in Korea
Buhari Lawan Muhammad, Jinho Chae, Jang-Seu Ki
Marine Biodiversity.2024;[Epub] CrossRef
- Invasion and ecological impact of the biofouling tube worm Hydroides elegans (Polychaeta: Serpulidae) in Korean coastal waters
Review
- [Minireview]Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches
- Dae-Wi Kim , Jae-Hyung Ahn , Chang-Jun Cha
- J. Microbiol. 2022;60(10):969-976. Published online September 27, 2022
- DOI: https://doi.org/10.1007/s12275-022-2313-7
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- 24 Web of Science
- 20 Crossref
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Abstract
- Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.
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Citations
Citations to this article as recorded by- Molecular docking and metagenomics assisted mitigation of microplastic pollution
Dinesh Parida, Konica Katare, Atmaadeep Ganguly, Disha Chakraborty, Oisi Konar, Regina Nogueira, Kiran Bala
Chemosphere.2024; 351: 141271. CrossRef - Recent advances in screening and identification of PET-degrading enzymes
Shengwei Sun
Environmental Reviews.2024; 32(3): 294. CrossRef - Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation
Akhilesh Kumar, Sudarshan Singh Lakhawat, Kashmir Singh, Vikram Kumar, Kumar Sambhav Verma, Umesh Kumar Dwivedi, S.L. Kothari, Naveen Malik, Pushpender Kumar Sharma
Journal of Hazardous Materials.2024; 480: 135804. CrossRef - PEZy-miner: An artificial intelligence driven approach for the discovery of plastic-degrading enzyme candidates
Renjing Jiang, Zhenrui Yue, Lanyu Shang, Dong Wang, Na Wei
Metabolic Engineering Communications.2024; 19: e00248. CrossRef - Mining strategies for isolating plastic-degrading microorganisms
Ziyao Zhang, Qi Zhang, Huihui Yang, Li Cui, Haifeng Qian
Environmental Pollution.2024; 346: 123572. CrossRef - Microenvironment of Landfill-Mined Soil-Like Fractions (LMSF): Evaluating the Polymer Composting Potential Using Metagenomics and Geoenvironmental Characterization
Arnab Banerjee, Charakho N. Chah, Manoj Kumar Dhal, Kshitij Madhu, Kiran Vilas Dhobale, Bharat Rattan, Vimal Katiyar, Sreedeep Sekharan
International Journal of Environmental Research.2024;[Epub] CrossRef - Progress in polystyrene biodegradation by insect gut microbiota
Luhui Xu, Zelin Li, Liuwei Wang, Zihang Xu, Shulin Zhang, Qinghua Zhang
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef - Recent trends in microbial and enzymatic plastic degradation: a solution for plastic pollution predicaments
Swagata Lakshmi Dhali, Dinesh Parida, Bikash Kumar, Kiran Bala
Biotechnology for Sustainable Materials.2024;[Epub] CrossRef - Deconstructing PET: Advances in enzyme engineering for sustainable plastic degradation
Jiaxin Yao, Yao Liu, Zhenghua Gu, Liang Zhang, Zhongpeng Guo
Chemical Engineering Journal.2024; 497: 154183. CrossRef - Mechanistic Insights into Cellular and Molecular Basis of Protein‐Nanoplastic Interactions
Goutami Naidu, Nupur Nagar, Krishna Mohan Poluri
Small.2024;[Epub] CrossRef - Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach
Beat Frey, Margherita Aiesi, Basil M. Rast, Joel Rüthi, Jérôme Julmi, Beat Stierli, Weihong Qi, Ivano Brunner, Sinosh Skarlyachan
PLOS ONE.2024; 19(4): e0300503. CrossRef - Discovery and characterization of two novel polyethylene terephthalate hydrolases: One from a bacterium identified in human feces and one from the Streptomyces genus
Zhengyang Han, Mario Roque Huanca Nina, Xiaoyan Zhang, Hanyao Huang, Daidi Fan, Yunpeng Bai
Journal of Hazardous Materials.2024; 472: 134532. CrossRef - Synthesis of Renewable and Cost-Effective Bioplastic from Apple Waste: Physicochemical and Biodegradability Studies
Nicholas Yung Li Loh, Hui Ying Pang, Wan Ting Tee, Billie Yan Zhang Hiew, Svenja Hanson, Siewhui Chong, Suchithra Thangalazhy-Gopakumar, Suyin Gan, Lai Yee Lee
Waste and Biomass Valorization.2023; 14(10): 3235. CrossRef - Validated High-Throughput Screening System for Directed Evolution of Nylon-Depolymerizing Enzymes
Hendrik Puetz, Christoph Janknecht, Francisca Contreras, Mariia Vorobii, Tetiana Kurkina, Ulrich Schwaneberg
ACS Sustainable Chemistry & Engineering.2023; 11(43): 15513. CrossRef - Perspectives on biorefineries in microbial production of fuels and chemicals
Stephen R. Decker, Roman Brunecky, John M. Yarbrough, Venkataramanan Subramanian
Frontiers in Industrial Microbiology.2023;[Epub] CrossRef - Microbial Enzyme Biotechnology to Reach Plastic Waste Circularity: Current Status, Problems and Perspectives
Marco Orlando, Gianluca Molla, Pietro Castellani, Valentina Pirillo, Vincenzo Torretta, Navarro Ferronato
International Journal of Molecular Sciences.2023; 24(4): 3877. CrossRef - Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET
Sandhya K. Jayasekara, Hriday Dhar Joni, Bhagya Jayantha, Lakshika Dissanayake, Christopher Mandrell, Manuka M.S. Sinharage, Ryan Molitor, Thushari Jayasekara, Poopalasingam Sivakumar, Lahiru N. Jayakody
Computational and Structural Biotechnology Journal.2023; 21: 3513. CrossRef - From waste to resource: Metagenomics uncovers the molecular ecological resources for plastic degradation in estuaries of South China
Lei Zhou, Shilei Sang, Jiajie Li, Yusen Li, Dapeng Wang, Lihong Gan, Zelong Zhao, Jun Wang
Water Research.2023; 242: 120270. CrossRef - Biodegradation of Different Types of Bioplastics through Composting—A Recent Trend in Green Recycling
Wazir Aitizaz Ahsan, Adnan Hussain, Chitsan Lin, Minh Ky Nguyen
Catalysts.2023; 13(2): 294. CrossRef - Biodegradation of Poly(ethylene terephthalate) by Bacillus safensis YX8
Caiting Zeng, Fanghui Ding, Jie Zhou, Weiliang Dong, Zhongli Cui, Xin Yan
International Journal of Molecular Sciences.2023; 24(22): 16434. CrossRef
- Molecular docking and metagenomics assisted mitigation of microplastic pollution
Journal Article
- Structural and biochemical analysis of the PTPN4 PDZ domain bound to the C-terminal tail of the human papillomavirus E6 oncoprotein
- Hye Seon Lee , Hye-Yeoung Yun , Eun-Woo Lee , Ho-Chul Shin , Seung Jun Kim , Bonsu Ku
- J. Microbiol. 2022;60(4):395-401. Published online January 28, 2022
- DOI: https://doi.org/10.1007/s12275-022-1606-1
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- 8 Web of Science
- 7 Crossref
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Abstract
- High-risk genotypes of human papillomaviruses (HPVs) are directly implicated in various abnormalities associated with cellular hyperproliferation, including cervical cancer. E6 is one of two oncoproteins encoded in the HPV genome, which recruits diverse PSD-95/Dlg/ZO-1 (PDZ) domain-containing human proteins through its C-terminal PDZ-binding motif (PBM) to be degraded by means of the proteasome pathway. Among the three PDZ domain-containing protein tyrosine phosphatases, protein tyrosine phosphatase non-receptor type 3 (PTPN3) and PTPN13 were identified to be recognized by HPV E6 in a PBM-dependent manner. However, whether HPV E6 associates with PTPN4, which also has a PDZ domain and functions as an apoptosis regulator, remains undetermined. Herein, we present structural and biochemical evidence demonstrating the direct interaction between the PBM of HPV16 E6 and the PDZ domain of human PTPN4 for the first time. X-ray crystallographic structure determination and binding measurements using isothermal titration calorimetry demonstrated that hydrophobic interactions in which Leu158 of HPV16 E6 plays a key role and a network of intermolecular hydrogen bonds sustain the complex formation between PTPN4 PDZ and the PBM of HPV16 E6. In addition, it was verified that the corresponding motifs from several other highrisk HPV genotypes, including HPV18, HPV31, HPV33, and HPV45, bind to PTPN4 PDZ with comparable affinities, suggesting that PTPN4 is a common target of various pathogenic HPV genotypes.
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Citations
Citations to this article as recorded by- Bioinformatics Analysis of Human Papillomavirus 16 Integration in Cervical Cancer: Changes in MAGI-1 Expression in Premalignant Lesions and Invasive Carcinoma
Oscar Catalán-Castorena, Olga Lilia Garibay-Cerdenares, Berenice Illades-Aguiar, Rocio Castillo-Sánchez, Ma. Isabel Zubillaga-Guerrero, Marco Antonio Leyva-Vazquez, Sergio Encarnacion-Guevara, Eugenia Flores-Alfaro, Mónica Ramirez-Ruano, Luz del Carmen Al
Cancers.2024; 16(12): 2225. CrossRef - Comparative structural studies on Bovine papillomavirus E6 oncoproteins: Novel insights into viral infection and cell transformation from homology modeling and molecular dynamics simulations
Lucas Alexandre Barbosa de Oliveira Santos, Tales de Albuquerque Leite Feitosa, Marcus Vinicius de Aragão Batista
Genetics and Molecular Biology.2024;[Epub] CrossRef - Crystal Structures of Plk1 Polo-Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2-Derived Peptide
Sujin Jung, Hye Seon Lee, Ho-Chul Shin, Joon Sig Choi, Seung Jun Kim, Bonsu Ku
Journal of Microbiology.2023; 61(8): 755. CrossRef - The effects of HPV oncoproteins on host communication networks: Therapeutic connotations
Josipa Skelin, Ho Yin Luk, Dražan Butorac, Siaw Shi Boon, Vjekoslav Tomaić
Journal of Medical Virology.2023;[Epub] CrossRef - Structural analysis of human papillomavirus E6 interactions with Scribble PDZ domains
Bryce Z. Stewart, Sofia Caria, Patrick O. Humbert, Marc Kvansakul
The FEBS Journal.2023; 290(11): 2868. CrossRef - Viral manipulation of cell polarity signalling
Airah Javorsky, Patrick O. Humbert, Marc Kvansakul
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research.2023; 1870(7): 119536. CrossRef - Mechanistic role of HPV-associated early proteins in cervical cancer: Molecular pathways and targeted therapeutic strategies
Rahul Bhattacharjee, Sabya Sachi Das, Smruti Sudha Biswal, Arijit Nath, Debangshi Das, Asmita Basu, Sumira Malik, Lamha Kumar, Sulagna Kar, Sandeep Kumar Singh, Vijay Jagdish Upadhye, Danish Iqbal, Suliman Almojam, Shubhadeep Roychoudhury, Shreesh Ojha, J
Critical Reviews in Oncology/Hematology.2022; 174: 103675. CrossRef
- Bioinformatics Analysis of Human Papillomavirus 16 Integration in Cervical Cancer: Changes in MAGI-1 Expression in Premalignant Lesions and Invasive Carcinoma
Research Support, Non-U.S. Gov't
- Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing
- Da-Eun Lee , Jinhwan Lee , Young-Mog Kim , Jeong-In Myeong , Kyoung-Ho Kim
- J. Microbiol. 2016;54(4):296-304. Published online April 1, 2016
- DOI: https://doi.org/10.1007/s12275-016-5571-4
- 55 View
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- 30 Crossref
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Abstract
- Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.
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Citations
Citations to this article as recorded by- Bacterial community in African catfish (Clarias gariepinus) recirculating aquaculture systems under different stocking densities
Júlia Clols-Fuentes, Julien A. Nguinkal, Patrick Unger, Bernd Kreikemeyer, Harry W. Palm
Frontiers in Marine Science.2023;[Epub] CrossRef - Effects of Dietary Bacillus licheniformis and Combined Herbs Extracts Supplementation on Physiological and Immune Characteristics, Microbial Community, and Vibriosis Resistance of Apostichopus japonicus
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Maria Kyritsi, Antiopi Tsoureki, Konstantinos Koukaras, Nikolaos Kamidis, Grigorios Krey, Sofia Michailidou, Anagnostis Argiriou
Journal of Marine Science and Engineering.2023; 11(7): 1332. CrossRef - Seasonal and Spatial Variations of Bacterial Community Structure in the Bailang River Estuary
Wenxun Dong, Zhengguo Cui, Mengjuan Zhao, Junfeng Li
Journal of Marine Science and Engineering.2023; 11(4): 825. CrossRef - Microalgae simultaneously promote antibiotic removal and antibiotic resistance genes/bacteria attenuation in algal-bacterial granular sludge system
Wenhao Liu, Wenli Huang, Zhenhua Cao, Yuan Ji, Dongfang Liu, Weiwei Huang, Yanjing Zhu, Zhongfang Lei
Journal of Hazardous Materials.2022; 438: 129286. CrossRef - Abundance and Diversity of Nitrifying Microorganisms in Marine Recirculating Aquaculture Systems
Qintong Li, Ryo Hasezawa, Riho Saito, Kunihiro Okano, Kazuya Shimizu, Motoo Utsumi
Water.2022; 14(17): 2744. CrossRef - Dynamic changes in the microbial community in the surface seawater of Jiaozhou Bay after crude oil spills: An in situ microcosm study
Yumiao Zhou, Qiang Kong, Xinyu Zhao, Zhihao Lin, Huanxin Zhang
Environmental Pollution.2022; 307: 119496. CrossRef - Endosymbiotic microbes from entomopathogenic nematode (EPNs) and their applications as biocontrol agents for agro-environmental sustainability
Preety Tomar, Neelam Thakur, Ajar Nath Yadav
Egyptian Journal of Biological Pest Control.2022;[Epub] CrossRef - Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae
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Journal of Microbiology.2021; 59(6): 546. CrossRef - Temporal dynamics of bacterial communities in the water and sediments of sea cucumber (Apostichopus japonicus) culture ponds
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Aquaculture.2020; 528: 735498. CrossRef - Pukyongia salina gen. nov., sp. nov., a novel genus in the family Flavobacteriaceae
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Archaea.2020; 2020: 1. CrossRef - Nitrogen Removal Characteristics in a Biofilm System for Recirculating Aquaculture Wastewater Treatment under High-Salinity Conditions and Oligotrophic Stress
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Spieck Eva
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