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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Veröffentlicht in:Microbial ecology 2011-11, Vol.62 (4), p.800-812, Article 800
Hauptverfasser: Li, Chang-Qing, Liu, Wen-Chao, Zhu, Ping, Yang, Jin-Ling, Cheng, Ke-Di
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Zhu, Ping
Yang, Jin-Ling
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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 (
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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 (&lt;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. 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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. 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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 (&lt;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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