Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia
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{"title"=>"Modern subsurface bacteria in pristine 2.7 Ga-old fossil stromatolite drillcore samples from the fortescue group, Western Australia", "type"=>"journal", "authors"=>[{"first_name"=>"Emmanuelle", "last_name"=>"Gérard", "scopus_author_id"=>"8729288400"}, {"first_name"=>"David", "last_name"=>"Moreira", "scopus_author_id"=>"7005854171"}, {"first_name"=>"Pascal", "last_name"=>"Philippot", "scopus_author_id"=>"56218599000"}, {"first_name"=>"Martin J.", "last_name"=>"Van Kranendonk", "scopus_author_id"=>"6701618227"}, {"first_name"=>"Purificación", "last_name"=>"López-García", "scopus_author_id"=>"7003921637"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"65449117967", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "issn"=>"19326203", "pmid"=>"19396360", "pui"=>"354554897", "doi"=>"10.1371/journal.pone.0005298", "scopus"=>"2-s2.0-65449117967"}, "id"=>"106203ec-7a50-3bc1-8736-1b78009744a2", "abstract"=>"BACKGROUND: Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper \"fresh\" samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth.\\n\\nCONCLUSIONS/SIGNIFICANCE: The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life remains and makes claims for morphological, chemical, isotopic, and biomarker traces syngenetic with the rock unreliable in the absence of detailed contextual analyses at microscale.", "link"=>"http://www.mendeley.com/research/modern-subsurface-bacteria-pristine-27-gaold-fossil-stromatolite-drillcore-samples-fortescue-group-w", "reader_count"=>50, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Other"=>5, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Other"=>5, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>23, "Earth and Planetary Sciences"=>20}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>20}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "Sweden"=>1, "Belgium"=>1, "United States"=>1, "United Kingdom"=>2, "Mexico"=>2, "Chile"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/445673"], "description"=>"<div><h3>Background</h3><p>Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible.</p><h3>Methodology/Principal Findings</h3><p>In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper “fresh” samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth.</p><h3>Conclusions/Significance</h3><p>The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life remains and makes claims for morphological, chemical, isotopic, and biomarker traces syngenetic with the rock unreliable in the absence of detailed contextual analyses at microscale.</p></div>", "links"=>[], "tags"=>["subsurface", "pristine", "ga-old", "fossil", "stromatolite", "drillcore", "samples", "fortescue", "australia"], "article_id"=>147840, "categories"=>["Microbiology", "Ecology"], "users"=>["Emmanuelle Gérard", "David Moreira", "Pascal Philippot", "Martin J. Van Kranendonk", "Purificación López-García"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005298", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Modern_Subsurface_Bacteria_in_Pristine_2_7_Ga_Old_Fossil_Stromatolite_Drillcore_Samples_from_the_Fortescue_Group_Western_Australia/147840", "title"=>"Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-27 02:10:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/899624"], "description"=>"<p>Black triangles indicate the regions in the schematic lithological PDP1 log <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005298#pone.0005298-VanKranendonk1\" target=\"_blank\">[13]</a> where samples for microbiology analyses were retrieved from. Photographs showing the samples analyzed are shown on the left. The scale bar corresponds to 1 cm.</p>", "links"=>[], "tags"=>["pilbara", "drilling", "drillcore"], "article_id"=>570075, "categories"=>["Microbiology", "Ecology"], "users"=>["Emmanuelle Gérard", "David Moreira", "Pascal Philippot", "Martin J. Van Kranendonk", "Purificación López-García"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005298.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Samples_analyzed_from_the_Pilbara_Drilling_Project_drillcore_PDP1_/570075", "title"=>"Samples analyzed from the Pilbara Drilling Project drillcore PDP1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-27 00:01:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/899800"], "description"=>"<p>Relative abundance of contaminant and indigenous SSU rDNA sequences in the different PDP1 drillcore sample libraries.</p>", "links"=>[], "tags"=>["abundance", "contaminant", "ssu", "rdna", "sequences", "pdp1", "drillcore"], "article_id"=>570247, "categories"=>["Microbiology", "Ecology"], "users"=>["Emmanuelle Gérard", "David Moreira", "Pascal Philippot", "Martin J. Van Kranendonk", "Purificación López-García"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005298.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_contaminant_and_indigenous_SSU_rDNA_sequences_in_the_different_PDP1_drillcore_sample_libraries_/570247", "title"=>"Relative abundance of contaminant and indigenous SSU rDNA sequences in the different PDP1 drillcore sample libraries.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-27 00:04:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/899903"], "description"=>"<p>The tree was constructed including the closest possible cultivated members to our sequences. The number of phylotype counts in SSU rDNA libraries from different samples is given on the right. Phylotypes are color-coded attending to their classification along a gradient going from indigenous and potentially indigenous to laboratory contaminants. Clones considered indigenous or potentially indigenous were found exclusively in PDP1 drillcores, having no close relatives (>95% identical) in control contaminant libraries or in the sawing fluid-associated library. Only bootstrap values above 50% are given at nodes.</p>", "links"=>[], "tags"=>["phylogenetic", "otus", "pdp1", "drillcore", "drilling", "sawing"], "article_id"=>570350, "categories"=>["Microbiology", "Ecology"], "users"=>["Emmanuelle Gérard", "David Moreira", "Pascal Philippot", "Martin J. Van Kranendonk", "Purificación López-García"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005298.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_tree_showing_the_position_of_different_OTUs_identified_in_PDP1_drillcore_and_control_laboratory_drilling_fluid_sawing_fluid_samples_/570350", "title"=>"Maximum likelihood phylogenetic tree showing the position of different OTUs identified in PDP1 drillcore and control (laboratory, drilling fluid, sawing fluid) samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-27 00:05:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/899698"], "description"=>"<p>The number of operational taxonomic units (OTUs) accumulated can be observed as a function of the number of total sequences obtained. OTUs were defined as clusters of SSU rDNA sequences >97% identical.</p>", "links"=>[], "tags"=>["curves", "drillcore", "ssu", "rdna"], "article_id"=>570154, "categories"=>["Microbiology", "Ecology"], "users"=>["Emmanuelle Gérard", "David Moreira", "Pascal Philippot", "Martin J. Van Kranendonk", "Purificación López-García"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005298.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_curves_of_drillcore_and_control_SSU_rDNA_libraries_/570154", "title"=>"Rarefaction curves of drillcore and control SSU rDNA libraries.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-27 00:02:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/900015"], "description"=>"*<p>(PCR+DNA extraction kit) associated contaminants</p><p><b>nd</b> not done</p><p>OTU, operational taxonomic unit.</p>", "links"=>[], "tags"=>["rdna", "libraries", "clones", "yielded", "pdp1", "drillcores"], "article_id"=>570465, "categories"=>["Microbiology", "Ecology"], "users"=>["Emmanuelle Gérard", "David Moreira", "Pascal Philippot", "Martin J. Van Kranendonk", "Purificación López-García"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005298.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SSU_rDNA_amplification_libraries_generated_and_clones_yielded_and_or_analyzed_in_PDP1_drillcores_of_different_depths_/570465", "title"=>"SSU rDNA amplification, libraries generated, and clones yielded and/or analyzed in PDP1 drillcores of different depths.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-27 00:07:45"}

PMC Usage Stats | Further Information

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