Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea
Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA g...
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description | Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G+ C Gram-positive bacteria, cyanobacteria, low G+ C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes.Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity ( |
doi_str_mv | 10.1007/s00248-011-9896-6 |
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Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G+ C Gram-positive bacteria, cyanobacteria, low G+ C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes.Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (<97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of spongeassociated bacteria and contributes to the growing database of the bacterial communities within sponges.</description><identifier>ISSN: 0095-3628</identifier><identifier>EISSN: 1432-184X</identifier><identifier>DOI: 10.1007/s00248-011-9896-6</identifier><identifier>PMID: 21728038</identifier><identifier>CODEN: MCBEBU</identifier><language>eng</language><publisher>New York: Springer Science + Business Media</publisher><subject>Actinobacteria - classification ; Actinobacteria - genetics ; Actinobacteria - isolation & purification ; Animals ; Antibiosis ; Bacillus ; Bacteria ; Biodiversity ; Biological and medical sciences ; Biomedical and Life Sciences ; Chemical analysis ; Coastal waters ; Community structure ; Cultivation ; Cyanobacteria ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial - genetics ; Ecology ; ENVIRONMENTAL MICROBIOLOGY ; Fundamental and applied biological sciences. Psychology ; Gelliodes ; Gelliodes carnosa ; Gene Library ; Geoecology/Natural Processes ; Gram positive bacteria ; Life Sciences ; Marine ; Marine environment ; Microbial Ecology ; Microbiology ; Microorganisms ; Nature Conservation ; Phylogenetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Porifera - microbiology ; Proteobacteria ; Proteobacteria - classification ; Proteobacteria - genetics ; Proteobacteria - isolation & purification ; RNA, Ribosomal, 16S - genetics ; rRNA genes ; Sea water ; Seawater ; Sequence Analysis, DNA ; Sponge divers ; Sponges ; Vibrio ; Water analysis ; Water Quality/Water Pollution</subject><ispartof>Microbial ecology, 2011-11, Vol.62 (4), p.800-812, Article 800</ispartof><rights>2011 Springer Science+Business Media, LLC.</rights><rights>Springer Science+Business Media, LLC 2011</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c486t-2c443ec7abc109d25d1fc2d285cc8ee6bc3ecde89544f8bdb364f0e84a28e1aa3</citedby><cites>FETCH-LOGICAL-c486t-2c443ec7abc109d25d1fc2d285cc8ee6bc3ecde89544f8bdb364f0e84a28e1aa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/41489196$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/41489196$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,27903,27904,41466,42535,51296,57994,58227</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24785514$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21728038$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Chang-Qing</creatorcontrib><creatorcontrib>Liu, Wen-Chao</creatorcontrib><creatorcontrib>Zhu, Ping</creatorcontrib><creatorcontrib>Yang, Jin-Ling</creatorcontrib><creatorcontrib>Cheng, Ke-Di</creatorcontrib><title>Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea</title><title>Microbial ecology</title><addtitle>Microb Ecol</addtitle><addtitle>Microb Ecol</addtitle><description>Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G+ C Gram-positive bacteria, cyanobacteria, low G+ C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes.Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (<97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of spongeassociated bacteria and contributes to the growing database of the bacterial communities within sponges.</description><subject>Actinobacteria - classification</subject><subject>Actinobacteria - genetics</subject><subject>Actinobacteria - isolation & purification</subject><subject>Animals</subject><subject>Antibiosis</subject><subject>Bacillus</subject><subject>Bacteria</subject><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Chemical analysis</subject><subject>Coastal waters</subject><subject>Community structure</subject><subject>Cultivation</subject><subject>Cyanobacteria</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial - genetics</subject><subject>Ecology</subject><subject>ENVIRONMENTAL MICROBIOLOGY</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gelliodes</subject><subject>Gelliodes carnosa</subject><subject>Gene Library</subject><subject>Geoecology/Natural Processes</subject><subject>Gram positive bacteria</subject><subject>Life Sciences</subject><subject>Marine</subject><subject>Marine environment</subject><subject>Microbial Ecology</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Nature Conservation</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymorphism, Restriction Fragment Length</subject><subject>Porifera - microbiology</subject><subject>Proteobacteria</subject><subject>Proteobacteria - classification</subject><subject>Proteobacteria - genetics</subject><subject>Proteobacteria - isolation & purification</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA genes</subject><subject>Sea water</subject><subject>Seawater</subject><subject>Sequence Analysis, DNA</subject><subject>Sponge divers</subject><subject>Sponges</subject><subject>Vibrio</subject><subject>Water analysis</subject><subject>Water Quality/Water Pollution</subject><issn>0095-3628</issn><issn>1432-184X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqNkkGP0zAQhS0EYkvhB3AAWUiIU8B2HMc5LgV2V1oEUkFwi6bOZOsqjbueBNQfw3_FoWVX4gCcfJjvveexH2OPpXgphShfkRBK20xImVW2Mpm5w2ZS5yqTVn-9y2ZCVEWWG2VP2AOijRCyNCq_z06ULJUVuZ2xHx_X-y5cYY-Dd_yN_4aR_LDnoeWvwQ0YPfBTouA8DNjw735Y82GN_D1E3yNf7kJ_hfwMu86HBok7iH0g4IvQdegmSRvD9pfkHHwPPb-gDvomAUADdPxL8o005U3MMowpYLFOJF8iPGT3WugIHx3POfv87u2nxXl2-eHsYnF6mTltzZApp3WOroSVk6JqVNHI1qlG2cI5i2hWLk0btFWhdWtXzSo3uhVoNSiLEiCfsxcH310M1yPSUG89ubQU9BhGqitj05OWtvw3qYy1Jjf_QQolEilMIp_9QW7CGPu0cIJkLlVKTpA8QC4GoohtvYt-C3FfS1FPbagPbahTG-qpDfVk_PRoPK622Nwofn9_Ap4fASAHXRuhd55uuRRcFKlRc6YOHKVR-vB4e8O_pT85iDY0hHhjqqW2laxM_hOJvNet</recordid><startdate>20111101</startdate><enddate>20111101</enddate><creator>Li, Chang-Qing</creator><creator>Liu, Wen-Chao</creator><creator>Zhu, Ping</creator><creator>Yang, Jin-Ling</creator><creator>Cheng, Ke-Di</creator><general>Springer Science + Business Media</general><general>Springer New York</general><general>Springer</general><general>Springer Nature B.V</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7SN</scope><scope>7T7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>F1W</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>H95</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>L.G</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><scope>7TG</scope><scope>7TN</scope><scope>H99</scope><scope>KL.</scope><scope>L.F</scope></search><sort><creationdate>20111101</creationdate><title>Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea</title><author>Li, Chang-Qing ; Liu, Wen-Chao ; Zhu, Ping ; Yang, Jin-Ling ; Cheng, Ke-Di</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c486t-2c443ec7abc109d25d1fc2d285cc8ee6bc3ecde89544f8bdb364f0e84a28e1aa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Actinobacteria - classification</topic><topic>Actinobacteria - genetics</topic><topic>Actinobacteria - isolation & purification</topic><topic>Animals</topic><topic>Antibiosis</topic><topic>Bacillus</topic><topic>Bacteria</topic><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Chemical analysis</topic><topic>Coastal waters</topic><topic>Community structure</topic><topic>Cultivation</topic><topic>Cyanobacteria</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial - genetics</topic><topic>Ecology</topic><topic>ENVIRONMENTAL MICROBIOLOGY</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gelliodes</topic><topic>Gelliodes carnosa</topic><topic>Gene Library</topic><topic>Geoecology/Natural Processes</topic><topic>Gram positive bacteria</topic><topic>Life Sciences</topic><topic>Marine</topic><topic>Marine environment</topic><topic>Microbial Ecology</topic><topic>Microbiology</topic><topic>Microorganisms</topic><topic>Nature Conservation</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Polymorphism, Restriction Fragment Length</topic><topic>Porifera - microbiology</topic><topic>Proteobacteria</topic><topic>Proteobacteria - classification</topic><topic>Proteobacteria - genetics</topic><topic>Proteobacteria - isolation & purification</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA genes</topic><topic>Sea water</topic><topic>Seawater</topic><topic>Sequence Analysis, DNA</topic><topic>Sponge divers</topic><topic>Sponges</topic><topic>Vibrio</topic><topic>Water analysis</topic><topic>Water Quality/Water Pollution</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Chang-Qing</creatorcontrib><creatorcontrib>Liu, Wen-Chao</creatorcontrib><creatorcontrib>Zhu, Ping</creatorcontrib><creatorcontrib>Yang, Jin-Ling</creatorcontrib><creatorcontrib>Cheng, Ke-Di</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Oceanic Abstracts</collection><collection>ASFA: Marine Biotechnology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Marine Biotechnology Abstracts</collection><jtitle>Microbial ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Chang-Qing</au><au>Liu, Wen-Chao</au><au>Zhu, Ping</au><au>Yang, Jin-Ling</au><au>Cheng, Ke-Di</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea</atitle><jtitle>Microbial ecology</jtitle><stitle>Microb Ecol</stitle><addtitle>Microb Ecol</addtitle><date>2011-11-01</date><risdate>2011</risdate><volume>62</volume><issue>4</issue><spage>800</spage><epage>812</epage><pages>800-812</pages><artnum>800</artnum><issn>0095-3628</issn><eissn>1432-184X</eissn><coden>MCBEBU</coden><abstract>Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G+ C Gram-positive bacteria, cyanobacteria, low G+ C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes.Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (<97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of spongeassociated bacteria and contributes to the growing database of the bacterial communities within sponges.</abstract><cop>New York</cop><pub>Springer Science + Business Media</pub><pmid>21728038</pmid><doi>10.1007/s00248-011-9896-6</doi><tpages>13</tpages></addata></record> |
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subjects | Actinobacteria - classification Actinobacteria - genetics Actinobacteria - isolation & purification Animals Antibiosis Bacillus Bacteria Biodiversity Biological and medical sciences Biomedical and Life Sciences Chemical analysis Coastal waters Community structure Cultivation Cyanobacteria Deoxyribonucleic acid DNA DNA, Bacterial - genetics Ecology ENVIRONMENTAL MICROBIOLOGY Fundamental and applied biological sciences. Psychology Gelliodes Gelliodes carnosa Gene Library Geoecology/Natural Processes Gram positive bacteria Life Sciences Marine Marine environment Microbial Ecology Microbiology Microorganisms Nature Conservation Phylogenetics Phylogeny Polymorphism, Restriction Fragment Length Porifera - microbiology Proteobacteria Proteobacteria - classification Proteobacteria - genetics Proteobacteria - isolation & purification RNA, Ribosomal, 16S - genetics rRNA genes Sea water Seawater Sequence Analysis, DNA Sponge divers Sponges Vibrio Water analysis Water Quality/Water Pollution |
title | Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Gelliodes carnosa Collected from the Hainan Island Coastal Waters of the South China Sea |
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