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A Molecular Study of Microbe Transfer between Distant Environments

Publication Date: July 09, 2008
Journal: PLOS ONE
Authors: Sean D. Hooper, Jeroen Raes, Konrad U. Foerstner, Eoghan D. Harrington, et al
Volume: 3
Issue: 7
Pages: e2607
DOI: https://dx.plos.org/10.1371/journal.pone.0002607
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0002607
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/18612393
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442867
Europe PMC: http://europepmc.org/abstract/MED/18612393
Web of Science: 000264065800013
Scopus: 50249091464
Mendeley: http://www.mendeley.com/research/molecular-study-microbe-transfer-between-distant-environments

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{"title"=>"A molecular study of microbe transfer between distant environments", "type"=>"journal", "authors"=>[{"first_name"=>"Sean D.", "last_name"=>"Hooper", "scopus_author_id"=>"9941819700"}, {"first_name"=>"Jeroen", "last_name"=>"Raes", "scopus_author_id"=>"8602126700"}, {"first_name"=>"Konrad U.", "last_name"=>"Foerstner", "scopus_author_id"=>"9740594200"}, {"first_name"=>"Eoghan D.", "last_name"=>"Harrington", "scopus_author_id"=>"8970878200"}, {"first_name"=>"Daniel", "last_name"=>"Dalevi", "scopus_author_id"=>"7801377410"}, {"first_name"=>"Peer", "last_name"=>"Bork", "scopus_author_id"=>"7103061421"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"352219181", "doi"=>"10.1371/journal.pone.0002607", "sgr"=>"50249091464", "scopus"=>"2-s2.0-50249091464", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"18612393"}, "id"=>"253605d2-2a2d-3e1a-9554-f13ce1eedd96", "abstract"=>"BACKGROUND: Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances. METHODOLOGY: By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water. CONCLUSIONS: Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.", "link"=>"http://www.mendeley.com/research/molecular-study-microbe-transfer-between-distant-environments", "reader_count"=>75, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>28, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>4, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>28, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>4, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>49, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>49}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>2, "Sweden"=>2, "United States"=>5, "Brazil"=>4, "Mexico"=>1, "France"=>2, "Germany"=>2, "Spain"=>2}, "group_count"=>5}

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Figshare 7526 Apr 10:12 UTC

Figshare

{"files"=>["https://ndownloader.figshare.com/files/458544", "https://ndownloader.figshare.com/files/458568", "https://ndownloader.figshare.com/files/458585", "https://ndownloader.figshare.com/files/458602", "https://ndownloader.figshare.com/files/458620", "https://ndownloader.figshare.com/files/458635", "https://ndownloader.figshare.com/files/458687", "https://ndownloader.figshare.com/files/458720", "https://ndownloader.figshare.com/files/458780", "https://ndownloader.figshare.com/files/458824"], "description"=>"<div><h3>Background</h3><p>Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances.</p><h3>Methodology</h3><p>By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water.</p><h3>Conclusions</h3><p>Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.</p></div>", "links"=>[], "tags"=>["molecular", "microbe", "environments"], "article_id"=>150338, "categories"=>["Biological Sciences"], "users"=>["Sean D. Hooper", "Konrad U. Förstner", "Jeroen Raes", "Eoghan D. Harrington", "Daniel Dalevi", "Peer Bork"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0002607.s001", "https://dx.doi.org/10.1371/journal.pone.0002607.s002", "https://dx.doi.org/10.1371/journal.pone.0002607.s003", "https://dx.doi.org/10.1371/journal.pone.0002607.s004", "https://dx.doi.org/10.1371/journal.pone.0002607.s005", "https://dx.doi.org/10.1371/journal.pone.0002607.s006", "https://dx.doi.org/10.1371/journal.pone.0002607.s007", "https://dx.doi.org/10.1371/journal.pone.0002607.s008", "https://dx.doi.org/10.1371/journal.pone.0002607.s009", "https://dx.doi.org/10.1371/journal.pone.0002607.s010"], "stats"=>{"downloads"=>11, "page_views"=>52, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Molecular_Study_of_Microbe_Transfer_between_Distant_Environments/150338", "title"=>"A Molecular Study of Microbe Transfer between Distant Environments", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-07-09 00:05:38"}
{"files"=>["https://ndownloader.figshare.com/files/926974"], "description"=>"<p>Distributions of GC3s for each of 1216 ORF pairs with closer similarity in the foreign environment. Using GC3s% = 48% as a separator (dotted lines), the ORF pairs are classified based on the GC content of its two members. Category A (upper right) is the quadrant where we expect to find possible transfer events from soil to sea, since these pairs have high GC3%s values for both members. Pairs in category B (lower left) have low GC3%s scores for both Genes, which could suggest a transfer from a sea-like environment to soil. Category C (lower right) has typical GC3s% values for both members of ORF pairs. These pairs are likely to be ancient conserved sequences. Finally, Category D (upper left) has atypical values for both Genes, close to the expected given the shape of the GC3% distribution (28 observed, 24 expected). Unsaturated Ks values are green, and pairs with Kn/Ks>1 are red.</p>", "links"=>[], "tags"=>["orthologous"], "article_id"=>597419, "categories"=>["Biological Sciences"], "users"=>["Sean D. Hooper", "Jeroen Raes", "Konrad U. Foerstner", "Eoghan D. Harrington", "Daniel Dalevi", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002607.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GC3s_distribution_of_orthologous_Genes_/597419", "title"=>"GC3s distribution of orthologous Genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-09 02:03:39"}
{"files"=>["https://ndownloader.figshare.com/files/927189"], "description"=>"<p>Distributions of genes in quadrants A and B. Key: <b>S</b>: sample number, <b>nA</b>; number of gene pairs in A, with the average expected number in parenthesis, <b>nB</b>; number of gene pairs in B, also with expected in parenthesis, <b>aA</b>; number of gene pairs in A with <i>Kn/Ks</i>>1, <b>aB</b>; number of gene pairs in B with <i>Kn/Ks</i>>1, <b>sA</b>; number of gene pairs in A with <i>Ks</i><2, <b>sB</b>; number of gene pairs in B with <i>Ks</i><2.</p>", "links"=>[], "tags"=>["computational biology/metagenomics"], "article_id"=>597643, "categories"=>["Biological Sciences"], "users"=>["Sean D. Hooper", "Jeroen Raes", "Konrad U. Foerstner", "Eoghan D. Harrington", "Daniel Dalevi", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002607.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Resampling_of_sea_set_/597643", "title"=>"Resampling of sea set.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-09 02:07:23"}
{"files"=>["https://ndownloader.figshare.com/files/927112"], "description"=>"<p>Note the similarities between A and soil, and B and sea respectively. Figure intensities have been normalized for clarity. CGR plots are a way of visualizing chain processes, such as oligomer patterns. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002607#s4\" target=\"_blank\">methods</a> for details.</p>", "links"=>[], "tags"=>["oligomer", "frequencies"], "article_id"=>597566, "categories"=>["Biological Sciences"], "users"=>["Sean D. Hooper", "Jeroen Raes", "Konrad U. Foerstner", "Eoghan D. Harrington", "Daniel Dalevi", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002607.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chaos_Game_Representation_CGR_plot_of_oligomer_frequencies_of_A_and_B_vs_soil_and_sea_patterns_/597566", "title"=>"Chaos Game Representation (CGR) plot of oligomer frequencies of A and B vs soil and sea patterns.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-09 02:06:06"}

PMC Usage Stats 127417 Nov 14:42 UTC

PMC Usage Stats | Further Information

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Relative Metric 191027010 May 16:16 UTC

Relative Metric

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F1000Prime04 Dec 11:48 UTC

F1000Prime

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