Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis
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{"title"=>"Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis", "type"=>"journal", "authors"=>[{"first_name"=>"Patrícia", "last_name"=>"Martins"}, {"first_name"=>"Daniel F. R.", "last_name"=>"Cleary"}, {"first_name"=>"Ana C. C.", "last_name"=>"Pires"}, {"first_name"=>"Ana Maria", "last_name"=>"Rodrigues"}, {"first_name"=>"Victor", "last_name"=>"Quintino"}, {"first_name"=>"Ricardo", "last_name"=>"Calado"}, {"first_name"=>"Newton C. M.", "last_name"=>"Gomes"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0080847", "pmid"=>"24278329", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)"}, "id"=>"058923b8-623c-32f6-926a-ecd3dfefd300", "abstract"=>"The present study combined a DGGE and barcoded 16S rRNA pyrosequencing approach to assess bacterial composition in the water of a recirculating aquaculture system (RAS) with a shallow raceway system (SRS) for turbot (Scophthalmus maximus) and sole (Solea senegalensis). Barcoded pyrosequencing results were also used to determine the potential pathogen load in the RAS studied. Samples were collected from the water supply pipeline (Sup), fish production tanks (Pro), sedimentation filter (Sed), biofilter tank (Bio), and protein skimmer (Ozo; also used as an ozone reaction chamber) of twin RAS operating in parallel (one for each fish species). Our results revealed pronounced differences in bacterial community composition between turbot and sole RAS, suggesting that in the systems studied there is a strong species-specific effect on water bacterial communities. Proteobacteria was the most abundant phylum in the water supply and all RAS compartments. Other important taxonomic groups included the phylum Bacteriodetes. The saltwater supplied displayed a markedly lower richness and appeared to have very little influence on bacterial composition. The following potentially pathogenic species were detected: Photobacterium damselae in turbot (all compartments), Tenacibaculum discolor in turbot and sole (all compartments), Tenacibaculum soleae in turbot (all compartments) and sole (Pro, Sed and Bio), and Serratia marcescens in turbot (Sup, Sed, Bio and Ozo) and sole (only Sed) RAS. Despite the presence of these pathogens, no symptomatic fish were observed. Although we were able to identify potential pathogens, this approach should be employed with caution when monitoring aquaculture systems, as the required phylogenetic resolution for reliable identification of pathogens may not always be possible to achieve when employing 16S rRNA gene fragments.", "link"=>"http://www.mendeley.com/research/molecular-analysis-bacterial-communities-detection-potential-pathogens-recirculating-aquaculture-sys-3", "reader_count"=>61, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>14, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>18, "Student > Master"=>13, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>14, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>18, "Student > Master"=>13, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>1, "Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>34, "Veterinary Science and Veterinary Medicine"=>3, "Chemistry"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>4, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>8}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"Netherlands"=>1, "Denmark"=>1, "Chile"=>1, "Portugal"=>3, "Germany"=>1}, "group_count"=>1}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1292504"], "description"=>"<p>A) in all sampling compartments (water supply (Sup), turbot production tank (TurPro), turbot sedimentation tank (TurSed), turbot biofilter tank (TurBio), turbot ozone tank (TurOzo), sole production tank (SolPro), sole sedimentation tank (SolSed), sole biofilter tank (SolBio), sole ozone tank (SolOzo)); B) only in turbot and sole sampling compartments (without water supply). </p>", "links"=>[], "tags"=>["diagrams", "bacterial", "dgge"], "article_id"=>859984, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ordination_diagrams_PCO_of_the_bacterial_community_based_on_DGGE_profile_/859984", "title"=>"Ordination diagrams (PCO) of the bacterial community based on DGGE profile.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 04:43:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1292505"], "description"=>"<p>Rarefied OTU richness in all sampling compartments (water supply (Sup), turbot production tank (TurPro), turbot sedimentation tank (TurSed), turbot biofilter tank (TurBio), turbot ozone tank (TurOzo), sole production tank (SolPro), sole sedimentation tank (SolSed), sole biofilter tank (SolBio), sole ozone tank (SolOzo)).</p>", "links"=>[], "tags"=>[], "article_id"=>859985, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_richness_/859985", "title"=>"Bacterial richness.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 04:43:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1292506"], "description"=>"<p>(A) in all sampling compartments; (B) the most abundant OTU’s associated to all sampling points; (C) only in turbot and the sole sampling compartments (without water supply); (D) the most abundant OTUs associated to turbot and the sole sampling compartments.</p>", "links"=>[], "tags"=>["diagrams", "bacterial", "barcoded", "pyrosequencing"], "article_id"=>859986, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ordination_diagrams_PCO_of_the_bacterial_community_based_on_barcoded_pyrosequencing_data_/859986", "title"=>"Ordination diagrams (PCO) of the bacterial community based on barcoded pyrosequencing data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 04:43:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1292507"], "description"=>"<p>Relative abundance of the most dominant bacterial groups (2 phyla, 8 classes and 10 orders) in each sampling compartments (water supply (Sup), turbot production tank (TurPro), turbot sedimentation tank (TurSed), turbot biofilter tank (TurBio), turbot ozone tank (TurOzo), sole production tank (SolPro), sole sedimentation tank (SolSed), sole biofilter tank (SolBio), sole ozone tank (SolOzo)). Groups are present from the most abundant to the least abundant.</p>", "links"=>[], "tags"=>["bacterial"], "article_id"=>859987, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dominant_bacterial_groups_/859987", "title"=>"Dominant bacterial groups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 04:43:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1292508"], "description"=>"<p>Bootstrap values generated from 500 replicates. Values lower than 50% were omitted.</p>", "links"=>[], "tags"=>["phylogenetic", "rrna", "otus", "turbot", "ras", "relatives"], "article_id"=>859988, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbour_joining_phylogenetic_tree_16S_rRNA_gene_sequences_of_the_most_dominant_OTUs_in_turbot_and_sole_RAS_and_their_closest_relatives_accession_number_species_/859988", "title"=>"Neighbour-joining phylogenetic tree (16S rRNA gene sequences) of the most dominant OTUs in turbot and sole RAS and their closest relatives (accession number-species).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 04:43:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1292509"], "description"=>"<p>Black circles indicate the most frequent pathogens described in literature. Bootstrap values generated from 500 replicates. Values lower than 50% were omitted.</p>", "links"=>[], "tags"=>["phylogenetic", "rrna", "otus", "pathogens", "relatives", "accession"], "article_id"=>859989, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbour_joining_phylogenetic_tree_16S_rRNA_gene_sequences_of_OTUs_related_potential_fish_pathogens_and_their_closest_relatives_with_accession_number_/859989", "title"=>"Neighbour-joining phylogenetic tree (16S rRNA gene sequences) of OTUs related potential fish pathogens and their closest relatives (with accession number).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-21 04:43:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1292510", "https://ndownloader.figshare.com/files/1292511", "https://ndownloader.figshare.com/files/1292512"], "description"=>"<div><p>The present study combined a DGGE and barcoded 16S rRNA pyrosequencing approach to assess bacterial composition in the water of a recirculating aquaculture system (RAS) with a shallow raceway system (SRS) for turbot (<i>Scophthalmus maximus</i>) and sole (<i>Solea senegalensis</i>). Barcoded pyrosequencing results were also used to determine the potential pathogen load in the RAS studied. Samples were collected from the water supply pipeline (Sup), fish production tanks (Pro), sedimentation filter (Sed), biofilter tank (Bio), and protein skimmer (Ozo; also used as an ozone reaction chamber) of twin RAS operating in parallel (one for each fish species). Our results revealed pronounced differences in bacterial community composition between turbot and sole RAS, suggesting that in the systems studied there is a strong species-specific effect on water bacterial communities. <i>Proteobacteria</i> was the most abundant phylum in the water supply and all RAS compartments. Other important taxonomic groups included the phylum <i>Bacteriodetes</i>. The saltwater supplied displayed a markedly lower richness and appeared to have very little influence on bacterial composition. The following potentially pathogenic species were detected: <i>Photobacterium damselae</i> in turbot (all compartments), <i>Tenacibaculum discolor</i> in turbot and sole (all compartments), <i>Tenacibaculum soleae</i> in turbot (all compartments) and sole (Pro, Sed and Bio), and <i>Serratia marcescens</i> in turbot (Sup, Sed, Bio and Ozo) and sole (only Sed) RAS. Despite the presence of these pathogens, no symptomatic fish were observed. Although we were able to identify potential pathogens, this approach should be employed with caution when monitoring aquaculture systems, as the required phylogenetic resolution for reliable identification of pathogens may not always be possible to achieve when employing 16S rRNA gene fragments.</p> </div>", "links"=>[], "tags"=>["molecular", "bacterial", "communities", "detection", "pathogens", "recirculating", "aquaculture"], "article_id"=>859990, "categories"=>["Biological Sciences"], "users"=>["Patrícia Martins", "Daniel F. R. Cleary", "Ana C. C. Pires", "Ana Maria Rodrigues", "Victor Quintino", "Ricardo Calado", "Newton C. M. Gomes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080847.s001", "https://dx.doi.org/10.1371/journal.pone.0080847.s002", "https://dx.doi.org/10.1371/journal.pone.0080847.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Analysis_of_Bacterial_Communities_and_Detection_of_Potential_Pathogens_in_a_Recirculating_Aquaculture_System_for_Scophthalmus_maximus_and_Solea_senegalensis_/859990", "title"=>"Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for <i>Scophthalmus maximus</i> and <i>Solea senegalensis</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-21 04:43:56"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"13", "full-text"=>"16", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
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Relative Metric

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