Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat
Publication Date
September 19, 2007
Journal
PLOS ONE
Authors
Ana Belen Martín Cuadrado, Purificación López García, Juan Carlos Alba, David Moreira, et al
Volume
2
Issue
9
Pages
e914
DOI
https://dx.plos.org/10.1371/journal.pone.0000914
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000914
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/17878949
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976395
Europe PMC
http://europepmc.org/abstract/MED/17878949
Web of Science
000207455700022
Scopus
39149124249
Mendeley
http://www.mendeley.com/research/metagenomics-deep-mediterranean-warm-bathypelagic-habitat
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Mendeley | Further Information

{"title"=>"Metagenomics of the deep Mediterranean, a warm bathypelagic habitat", "type"=>"journal", "authors"=>[{"first_name"=>"Ana Belen", "last_name"=>"Martín-Cuadrado", "scopus_author_id"=>"6507045993"}, {"first_name"=>"Purificación", "last_name"=>"López-García", "scopus_author_id"=>"7003921637"}, {"first_name"=>"Juan Carlos", "last_name"=>"Alba", "scopus_author_id"=>"13409561000"}, {"first_name"=>"David", "last_name"=>"Moreira", "scopus_author_id"=>"7005854171"}, {"first_name"=>"Luis", "last_name"=>"Monticelli", "scopus_author_id"=>"8580879000"}, {"first_name"=>"Axel", "last_name"=>"Strittmatter", "scopus_author_id"=>"7004373431"}, {"first_name"=>"Gerhard", "last_name"=>"Gottschalk", "scopus_author_id"=>"7103072625"}, {"first_name"=>"Francisco", "last_name"=>"Rodríguez-Valera", "scopus_author_id"=>"7004876728"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"17878949", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0000914", "pui"=>"351445308", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "scopus"=>"2-s2.0-39149124249", "sgr"=>"39149124249"}, "id"=>"633ce4ce-0256-3c61-8c14-46e9eae369d1", "abstract"=>"BACKGROUND: Metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. Most marine metagenomic analyses have been nearly exclusively devoted to photic waters.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We constructed a metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which is much warmer (approximately 14 degrees C) than waters of similar depth in open oceans (approximately 2 degrees C). We analyzed the library both by phylogenetic screening based on 16S rRNA gene amplification from clone pools and by sequencing both insert extremities of ca. 5,000 fosmids. Genome recruitment strategies showed that the majority of high scoring pairs corresponded to genomes from Rhizobiales within the Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria, Chloroflexi and Gammaproteobacteria. We have found a community structure similar to that found in the aphotic zone of the Pacific. However, the similarities were significantly higher to the mesopelagic (500-700 m deep) in the Pacific than to the single 4000 m deep sample studied at this location. Metabolic genes were mostly related to catabolism, transport and degradation of complex organic molecules, in agreement with a prevalent heterotrophic lifestyle for deep-sea microbes. However, we observed a high percentage of genes encoding dehydrogenases and, among them, cox genes, suggesting that aerobic carbon monoxide oxidation may be important in the deep ocean as an additional energy source.\\n\\nCONCLUSIONS/SIGNIFICANCE: The comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding pressure at least over 4000 m deep. Several chemolithotrophic metabolic pathways could supplement organic matter degradation in this most depleted habitat.", "link"=>"http://www.mendeley.com/research/metagenomics-deep-mediterranean-warm-bathypelagic-habitat", "reader_count"=>257, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>23, "Student > Doctoral Student"=>13, "Researcher"=>69, "Student > Ph. D. Student"=>66, "Student > Postgraduate"=>6, "Student > Master"=>37, "Other"=>8, "Student > Bachelor"=>15, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>23, "Student > Doctoral Student"=>13, "Researcher"=>69, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/945964"], "description"=>"<p>Hallmark proteins in the Km3 metagenome compared to the deep ALOHA water column.</p>", "links"=>[], "tags"=>["proteins", "km3", "metagenome", "compared", "aloha"], "article_id"=>616318, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.t003", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hallmark_proteins_in_the_Km3_metagenome_compared_to_the_deep_ALOHA_water_column_/616318", "title"=>"Hallmark proteins in the Km3 metagenome compared to the deep ALOHA water column.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 12:01:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/944976"], "description"=>"<p>A, Phylogenetic tree of 16S rRNA genes amplified from the metagenomic library Km3. The tree was constructed by maximum likelihood using PhyML and a total of 704 non ambiguously aligned positions. Non-parametric bootstrapping was performed upon 1,000 replicates. Only bootstrap values above 50 are shown. Km3 and ALOHA water column sequences are indicated in red and blue, respectively. B, Comparative taxonomic distribution obtained by best BLAST hit (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000914#s4\" target=\"_blank\">methods</a>) of archaeal fosmid-ends in KM3 and ALOHA deep-sea libraries <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000914#pone.0000914-DeLong2\" target=\"_blank\">[14]</a>. Marine group I and environmental samples are non-taxonomic designations as used in databases.</p>", "links"=>[], "tags"=>["archaeal"], "article_id"=>615355, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomy_of_archaeal_fosmids_/615355", "title"=>"Taxonomy of archaeal fosmids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:49:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/945920"], "description"=>"*<p>BLASTX cut off value1e-50</p>", "links"=>[], "tags"=>["genomes", "recruited", "km3", "fosmid-end"], "article_id"=>616282, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.t002", "stats"=>{"downloads"=>6, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hallmark_genomes_recruited_by_Km3_fosmid_end_sequences_/616282", "title"=>"Hallmark genomes recruited by Km3 fosmid-end sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 12:01:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/945136"], "description"=>"<p>A, Phylogenetic tree of 16S rRNA genes amplified from the metagenomic library Km3 whose adjacent intergenic spacers differ in size from those of <i>Escherichia coli</i>. The tree was constructed by maximum likelihood using PhyML and a total of 1128 non ambiguously aligned positions. Non-parametric bootstrapping was performed upon 1,000 replicates. Only bootstrap values above 50 are shown. Km3 and ALOHA water column sequences are indicated in red and blue, respectively. Unc., uncultured. [*], AA0D00000000 genome sequence underway. B, Comparative taxonomic distribution of bacterial fosmid-ends by best BLAST hits in KM3 and ALOHA deep-sea libraries <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000914#pone.0000914-DeLong2\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["bacterial"], "article_id"=>615509, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomy_of_bacterial_fosmids_/615509", "title"=>"Taxonomy of bacterial fosmids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:50:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/945294"], "description"=>"<p>Individual fosmid-end sequences were aligned to the sequenced strain genome and the alignment-sequence conservation visualized in the form of percent identity plot. Each dot of the graph represents an individual fosmid-end sequence aligned along its homologous region in <i>C. symbiosum</i> A genome. <i>Y</i> axis reflects its nucleotide percent identity to the syntenic region. Both Km3 and ALOHA water column datasets were used.</p>", "links"=>[], "tags"=>["recruitment"], "article_id"=>615668, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g004", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_recruitment_by_Cenarchaeum_symbiosum_A_/615668", "title"=>"Genome recruitment by <i>Cenarchaeum symbiosum</i> A.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:51:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/945463"], "description"=>"<p>Fosmid-ends were classified according to the COG database both Km3 and ALOHA <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000914#pone.0000914-DeLong2\" target=\"_blank\">[14]</a> datasets were analyzed (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000914#s4\" target=\"_blank\">methods</a>).</p>", "links"=>[], "tags"=>["cog", "fosmid-ends", "km3", "aloha"], "article_id"=>615806, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g005", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_COG_distribution_of_fosmid_ends_in_Km3_and_ALOHA_water_column_/615806", "title"=>"Comparison of COG distribution of fosmid-ends in Km3 and ALOHA water column.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:52:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/946001"], "description"=>"<p>BLAST cut-off values used in each case are shown in brackets.</p>a<p>Considering average insert sizes of 35 kbp</p>b<p>Only fosmids containing bacterial ITS regions different in size of that from <i>E. coli</i> were identified.</p>c<p>GOS, Global Ocean Surveyor database {Rusch, 2007 #16}</p>", "links"=>[], "tags"=>["km3"], "article_id"=>616367, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.t001", "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_the_Km3_metagenome_/616367", "title"=>"General features of the Km3 metagenome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 12:01:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/945752"], "description"=>"<p>For normalization, a total of 6,853 sequences (size of the smallest library compared, ALOHA 130 m) from each library were randomly selected and compared. A, Neighbour joining analysis of fosmid-end sequences in Km3 and different depths in ALOHA. Temperature, salinity, and the total number of sequences available for each library are shown on the right; Jackknife values, at nodes. B, Normalized MUMmer plots showing the number of maximal unique matches (MUMs) shared by the 3000 m deep Km3 and the different ALOHA metagenomic libraries. MUMs are distributed as a function of their identity (ordinates) and the type of COG to which they belong (abscises). Average identity values are indicated for each pair of libraries compared. The number of MUMs having more that 80% identity are given to the right of each panel.</p>", "links"=>[], "tags"=>["metagenome", "3000", "m-deep", "mediterranean", "km3", "pacific", "aloha"], "article_id"=>616112, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g007", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Normalized_metagenome_comparison_of_3000_m_deep_Mediterranean_Km3_and_Pacific_ALOHA_water_column_/616112", "title"=>"Normalized metagenome comparison of 3000 m-deep Mediterranean Km3 and Pacific ALOHA water column.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:00:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/944800"], "description"=>"<p>Relative abundances of PCR-amplified 16S rRNA genes in environmental libraries are from Ref.4. For bacteria in the Km3 metagenomic library (central panel), only 16S rRNA genes whose adjacent ITS can be distinguished in size from that of <i>E. coli</i> were detected.</p>", "links"=>[], "tags"=>["taxa", "km3", "m-deep", "plankton", "inferred", "fosmid-ends", "16s", "rrna", "detection", "metagenomic"], "article_id"=>615164, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prokaryotic_taxa_identified_in_Km3_3_000_m_deep_plankton_inferred_from_fosmid_ends_and_16S_rRNA_detection_in_environmental_and_metagenomic_libraries_/615164", "title"=>"Prokaryotic taxa identified in Km3 3,000 m-deep plankton inferred from fosmid-ends and 16S rRNA detection in environmental and metagenomic libraries.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:48:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/945884"], "description"=>"<p>Values shown are those from the same CTD casts as the samples (DeLong <i>et al.</i> 2006 and this work). *Archival data are from ALOHA HOT-DOGS© database (<a href=\"http://hahana.soest.hawaii.edu/hot/hot-dogs/\" target=\"_blank\">http://hahana.soest.hawaii.edu/hot/hot-dogs/</a>) or in the case of Km3 from the ICES oceanographic database (<a href=\"http://www.ices.dk/ocean\" target=\"_blank\">http://www.ices.dk/ocean</a>) and correspond to several datasets collected at the depth and approximate location (less than 50 NM away) as the samples. Values in parentheses are the average value±standard deviation. Abbreviations are Temp, Temperature; Chl, chlorophyll; DOC, dissolved organic carbon; DIP, dissolved inorganic phosphate; N+N, nitrate plus nitrite; SLCA, silicate; HPP, heterotrophic picoplankton (DAPI counts); POC, particulate organic carbon.</p>", "links"=>[], "tags"=>["km3", "oceanographic"], "article_id"=>616248, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.t004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ALOHA_and_Km3_oceanographic_data_/616248", "title"=>"ALOHA and Km3 oceanographic data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 12:01:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/945574"], "description"=>"<p>A, Detailed KEGG categories. B, Major KEGG categories and classification by type of substrate of Km3 fosmid-ends identified as transporters. * Other transporters.</p>", "links"=>[], "tags"=>["km3", "fosmid-ends", "kegg"], "article_id"=>615941, "categories"=>["Microbiology", "Genetics", "Ecology"], "users"=>["Ana-Belen Martín-Cuadrado", "Purificación López-García", "Juan-Carlos Alba", "David Moreira", "Luis Monticelli", "Axel Strittmatter", "Gerhard Gottschalk", "Francisco Rodriguez-Valera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000914.g006", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Km3_fosmid_ends_in_KEGG_categories_/615941", "title"=>"Distribution of Km3 fosmid-ends in KEGG categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:59:19"}

PMC Usage Stats | Further Information

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Relative Metric

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