A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities
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{"title"=>"A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities", "type"=>"journal", "authors"=>[{"first_name"=>"David", "last_name"=>"Emerson", "scopus_author_id"=>"7102272741"}, {"first_name"=>"Jeremy A.", "last_name"=>"Rentz", "scopus_author_id"=>"6701378704"}, {"first_name"=>"Timothy G.", "last_name"=>"Lilburn", "scopus_author_id"=>"6602880137"}, {"first_name"=>"Richard E.", "last_name"=>"Davis", "scopus_author_id"=>"56390441700"}, {"first_name"=>"Henry", "last_name"=>"Aldrich", "scopus_author_id"=>"7007143877"}, {"first_name"=>"Clara", "last_name"=>"Chan", "scopus_author_id"=>"35848124100"}, {"first_name"=>"Craig L.", "last_name"=>"Moyer", "scopus_author_id"=>"7006276356"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"351314878", "sgr"=>"39849101191", "pmid"=>"17668050", "scopus"=>"2-s2.0-39849101191", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "arxiv"=>"NIHMS150003", "doi"=>"10.1371/journal.pone.0000667", "issn"=>"19326203"}, "id"=>"cc0c3ff8-b871-30cd-9c82-e8ea6d1640c4", "abstract"=>"<sec><title>Background</title><p>For decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano.</p></sec><sec><title>Methodology/Principle Findings</title><p>Using gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe<sup>0</sup> were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the <italic>Proteobacteria</italic>. The most similar sequence (85.3% similarity) from a cultivated isolate came from <italic>Methylophaga marina</italic>. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the <italic>Proteobacteria</italic>. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi.</p></sec><sec><title>Conclusions</title><p>On the basis of phylogenetic and physiological data, it is proposed that isolate PV-1<sup>T</sup> ( = ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, <italic>Mariprofundus ferrooxydans</italic> gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the <italic>Proteobacteria</italic> that is widely distributed in deep-sea environments, Candidatus ζ <italic>(zeta)</italic>-<italic>Proteobacteria</italic> cl. nov.</p></sec>", "link"=>"http://www.mendeley.com/research/novel-lineage-proteobacteria-involved-formation-marine-feoxidizing-microbial-mat-communities", "reader_count"=>185, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>14, "Student > Doctoral Student"=>8, "Researcher"=>47, "Student > Ph. D. Student"=>49, "Student > Postgraduate"=>4, "Student > Master"=>28, "Other"=>5, "Student > Bachelor"=>12, "Lecturer"=>3, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>14, "Student > Doctoral Student"=>8, "Researcher"=>47, "Student > Ph. D. Student"=>49, "Student > Postgraduate"=>4, "Student > Master"=>28, "Other"=>5, "Student > Bachelor"=>12, "Lecturer"=>3, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Engineering"=>7, "Environmental Science"=>23, "Biochemistry, Genetics and Molecular Biology"=>15, "Materials Science"=>1, "Agricultural and Biological Sciences"=>90, "Medicine and Dentistry"=>2, "Chemical Engineering"=>1, "Chemistry"=>4, "Computer Science"=>1, "Immunology and Microbiology"=>3, "Earth and Planetary Sciences"=>26}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>7}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>26}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>90}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>23}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Austria"=>1, "United States"=>9, "Egypt"=>1, "United Kingdom"=>1, "Portugal"=>2, "Germany"=>3, "Russia"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/947897"], "description"=>"<p>Two groups of communities have been identified and designated Loihi Group 1 (from lower temperature vents with enhanced ferrous iron) and Loihi Group 2 (from higher temperature vents with enhanced sulphide; (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000667#pone.0000667-Davis1\" target=\"_blank\">[37]</a>). Triangles indicate T-RFs associated with <i>Mariprofundus ferrooxydans</i> from restriction digests with Hinf I and Msp I (176 bp and 449 bp, respectively). T-RF scales range from 50 to 500 base pairs. Numbers at the nodes indicate the cophenetic correlation value of the cluster. Dendrogram scale bar units are r value ×100.</p>", "links"=>[], "tags"=>["product-moment", "t-rflp", "bacterial", "fingerprints", "digest", "treatments", "iron-dominated", "mats", "loihi", "seamount"], "article_id"=>618209, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000667.g005", "stats"=>{"downloads"=>3, "page_views"=>53, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_UPGMA_Pearson_product_moment_cluster_analysis_of_T_RFLP_bacterial_community_fingerprints_using_eight_restriction_digest_treatments_from_iron_dominated_mats_from_Loihi_Seamount_including_the_isolate_Mariprofundus_ferrooxydans_/618209", "title"=>"UPGMA/Pearson product-moment cluster analysis of T-RFLP bacterial community fingerprints using eight restriction digest treatments from iron-dominated mats from Loihi Seamount including the isolate <i>Mariprofundus ferrooxydans.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-01 02:16:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/466399", "https://ndownloader.figshare.com/files/466458", "https://ndownloader.figshare.com/files/466504", "https://ndownloader.figshare.com/files/466521"], "description"=>"<div><h3>Background</h3><p>For decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano.</p><h3>Methodology/Principle Findings</h3><p>Using gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe<sup>0</sup> were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the <em>Proteobacteria</em>. The most similar sequence (85.3% similarity) from a cultivated isolate came from <em>Methylophaga marina</em>. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the <em>Proteobacteria</em>. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi.</p><h3>Conclusions</h3><p>On the basis of phylogenetic and physiological data, it is proposed that isolate PV-1<sup>T</sup> ( = ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, <em>Mariprofundus ferrooxydans</em> gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the <em>Proteobacteria</em> that is widely distributed in deep-sea environments, Candidatus ζ <em>(zeta)</em>-<em>Proteobacteria</em> cl. nov.</p></div>", "links"=>[], "tags"=>["lineage", "proteobacteria", "fe-oxidizing", "microbial", "mat", "communities"], "article_id"=>151926, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000667.s001", "https://dx.doi.org/10.1371/journal.pone.0000667.s002", "https://dx.doi.org/10.1371/journal.pone.0000667.s003", "https://dx.doi.org/10.1371/journal.pone.0000667.s004"], "stats"=>{"downloads"=>10, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Novel_Lineage_of_Proteobacteria_Involved_in_Formation_of_Marine_Fe_Oxidizing_Microbial_Mat_Communities/151926", "title"=>"A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-08-01 00:32:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/947636"], "description"=>"<p>Scale bar represents 5 nucleotide substitutions per 100 positions.</p>", "links"=>[], "tags"=>["phylogenetic", "evolutionary", "pv-1", "belonging", "zeta-proteobacteria", "representatives", "classes"], "article_id"=>617959, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000667.g003", "stats"=>{"downloads"=>4, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_tree_showing_the_evolutionary_placement_of_Mariprofundus_ferrooxydans_strains_PV_1_and_JV_1_belonging_to_the_novel_class_of_zeta_Proteobacteria_along_with_representatives_from_other_previously_described_classes_of_Proteoba/617959", "title"=>"Maximum-likelihood phylogenetic tree showing the evolutionary placement of <i>Mariprofundus ferrooxydans</i> (strains PV-1 and JV-1) belonging to the novel class of zeta-Proteobacteria along with representatives from other previously described classes of Proteobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-01 02:12:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/947996"], "description"=>"1<p>16∶1 w7c/15 iso 2OH</p>2<p>19∶0 CYCLO w10c/19w6</p>", "links"=>[], "tags"=>["fatty", "acids"], "article_id"=>618329, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000667.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FAME_Analysis_showing_fatty_acids_8805_2_of_total_/618329", "title"=>"FAME Analysis, showing fatty acids ≥2% of total.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-08-01 02:18:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/947453"], "description"=>"<p>A control (σ) with agarose but no FeS was included. Cell numbers were determined by direct counts and errors are based on duplicate samples.</p>", "links"=>[], "tags"=>["pv-1", "gradient", "plates", "fes"], "article_id"=>617786, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000667.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_curve_of_PV_1_on_gradient_plates_with_FeS_or_Fe_0_9675_as_the_iron_source_/617786", "title"=>"Growth curve of PV-1 on gradient plates with FeS (□) or Fe<sup>0</sup> (○) as the iron source.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-01 02:09:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/947727"], "description"=>"<p>Figures A and B show trees inferred from the amino acid sequences of the widely conserved RecA and GyrB proteins, respectively. The shaded clusters represent the recognized classes of <i>Proteobacteria</i>. The number of sequences representing each class is shown inside the cluster. The numbers at the nodes represent the per cent support for that group. The scale bar represents the estimated number of substitutions along the branches.</p>", "links"=>[], "tags"=>["trees", "phylogenetic", "pv-1", "conserved"], "article_id"=>618062, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000667.g004", "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_maximum_likelihood_trees_showing_the_phylogenetic_relationship_of_Mariprofundus_ferrooxydans_PV_1_to_other_Proteobacteria_based_on_conserved_protein_sequences_/618062", "title"=>"Two maximum likelihood trees showing the phylogenetic relationship of <i>Mariprofundus ferrooxydans</i> PV-1 to other <i>Proteobacteria</i> based on conserved protein sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-01 02:14:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/947546"], "description"=>"<p>A–D, Light micrographs showing cells attached at the end of the filaments; the cells have been stained with Syto and composite epifluoresence and phase contrast images produced to show the cells stained green. The bar = 5 µm. E TEM image of the cells, note the Gram-negative type cell wall and the fibers of Fe-oxides in the lower left corner. The bar = 0.5 µm. F. A HRTEM image of the Fe-oxide filament showing its composition as a bundle of conjoined fibers of Fe-oxide. The bar = 0.63 µm.</p>", "links"=>[], "tags"=>["microbiology/environmental microbiology"], "article_id"=>617871, "categories"=>["Microbiology"], "users"=>["David Emerson", "Jeremy A. Rentz", "Timothy G. Lilburn", "Richard E. Davis", "Henry Aldrich", "Clara Chan", "Craig L. Moyer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000667.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Micrographs_of_strain_PV_1_/617871", "title"=>"Micrographs of strain PV-1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-01 02:11:11"}

PMC Usage Stats | Further Information

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Relative Metric

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