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Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon P, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert R, Knott GJ, Lapinaite A, Pausch P, Cofsky J, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res 2024; 52:D590-D596. [PMID: 37889041 PMCID: PMC10767948 DOI: 10.1093/nar/gkad890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
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Affiliation(s)
- Benjamin A Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elaine Zhang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Hannah M Karp
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Rachel F Weissman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
| | - Tomas Hessler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Colognori
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ron Boger
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Connor A Tsuchida
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan V Tran
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Laura Hofman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Graduate School of Life Sciences, Utrecht University, 3584 CS Utrecht, UT, The Netherlands
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Kevin M Wasko
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Zehan Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Chenglong Xia
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Muntathar J Al-Shimary
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jaymin R Patel
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Vienna C J X Thomas
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Rithu Pattali
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew J Kan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, CA 94158, USA
| | - Anna Vardapetyan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Alana Yang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Micaela F Maxwell
- Department of Chemistry and Biochemistry, Hampton University, Hampton, VA 23668, USA
| | - Andrew G Murdock
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Glenn C Ramit
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Hope R Henderson
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Roland W Calvert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rebecca S Bamert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Patrick Pausch
- LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Joshua C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Genetics Otago, University of Otago, Dunedin 9016, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9016, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, 2629 HZ Delft, The Netherlands
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | | | | | | | - Rodolphe Barrangou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Virginius Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The University of Melbourne, Parkville, VIC 3052, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94158, USA
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2
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Alexander LM, Aliaga Goltsman DS, Liu J, Lin JL, Temoche-Diaz MM, Laperriere SM, Neerincx A, Bednarski C, Knyphausen P, Cohnen A, Albers J, Gonzalez-Osorio L, Fregoso Ocampo R, Oki J, Devoto AE, Castelle CJ, Lamothe RC, Cost GJ, Butterfield CN, Thomas BC, Brown CT. Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability. CRISPR J 2023; 6:261-277. [PMID: 37272861 DOI: 10.1089/crispr.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 nucleases have been extensively used in biotechnology and therapeutics. However, many applications are not possible owing to the size, targetability, and potential off-target effects associated with currently known systems. In this study, we identified thousands of CRISPR type II effectors by mining an extensive, genome-resolved metagenomics database encompassing hundreds of thousands of microbial genomes. We developed a high-throughput pipeline that enabled us to predict tracrRNA sequences, to design single guide RNAs, and to demonstrate nuclease activity in vitro for 41 newly described subgroups. Active systems represent an extensive diversity of protein sequences and guide RNA structures and require diverse protospacer adjacent motifs (PAMs) that collectively expand the known targeting capability of current systems. Several nucleases showed activity levels comparable to or significantly higher than SpCas9, despite being smaller in size. In addition, top systems exhibited low levels of off-target editing in mammalian cells, and PAM-interacting domain engineered chimeras further expanded their targetability. These newly discovered nucleases are attractive enzymes for translation into many applications, including therapeutics.
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Affiliation(s)
| | | | - Jason Liu
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | - Jyun-Liang Lin
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | | | | | - Andreas Neerincx
- Bayer AG, Research & Development, Pharmaceuticals, Leverkusen, Germany
| | | | | | - Andre Cohnen
- Bayer AG, Research & Development, Pharmaceuticals, Leverkusen, Germany
| | - Justine Albers
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | | | | | - Jennifer Oki
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | - Audra E Devoto
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | | | | | - Gregory J Cost
- Metagenomi Inc., Pre-clinical, Emeryville, California, USA
| | | | - Brian C Thomas
- Metagenomi, Inc., Discovery, Emeryville, California, USA
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3
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Lamothe RC, Storlie MD, Espinosa DA, Rudlaff R, Browne P, Liu J, Rivas A, Devoto A, Oki J, Khoubyari A, Goltsman DSA, Lin JL, Butterfield CN, Brown CT, Thomas BC, Cost GJ. Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering. CRISPR J 2023. [PMID: 37219969 DOI: 10.1089/crispr.2022.0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Development of medicines using gene editing has been hampered by enzymological and immunological impediments. We described previously the discovery and characterization of improved, novel gene-editing systems from metagenomic data. In this study, we substantially advance this work with three such gene-editing systems, demonstrating their utility for cell therapy development. All three systems are capable of reproducible, high-frequency gene editing in primary immune cells. In human T cells, disruption of the T cell receptor (TCR) alpha-chain was induced in >95% of cells, both paralogs of the TCR beta-chain in >90% of cells, and >90% knockout of β2-microglobulin, TIGIT, FAS, and PDCD1. Simultaneous double knockout of TRAC and TRBC was obtained at a frequency equal to that of the single edits. Gene editing with our systems had minimal effect on T cell viability. Furthermore, we integrate a chimeric antigen receptor (CAR) construct into TRAC (up to ∼60% of T cells), and demonstrate CAR expression and cytotoxicity. We next applied our novel gene-editing tools to natural killer (NK) cells, B cells, hematopoietic stem cells, and induced pluripotent stem cells, generating similarly efficient cell-engineering outcomes including the creation of active CAR-NK cells. Interrogation of our gene-editing systems' specificity reveals a profile comparable with or better than Cas9. Finally, our nucleases lack preexisting humoral and T cell-based immunity, consistent with their sourcing from nonhuman pathogens. In all, we show these new gene-editing systems have the activity, specificity, and translatability necessary for use in cell therapy development.
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Affiliation(s)
| | | | | | | | | | - Jason Liu
- Metagenomi, Inc., Emeryville, California, USA
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4
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Aliaga Goltsman DS, Alexander LM, Lin JL, Fregoso Ocampo R, Freeman B, Lamothe RC, Perez Rivas A, Temoche-Diaz MM, Chadha S, Nordenfelt N, Janson OP, Barr I, Devoto AE, Cost GJ, Butterfield CN, Thomas BC, Brown CT. Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes. Nat Commun 2022; 13:7602. [PMID: 36522342 PMCID: PMC9755519 DOI: 10.1038/s41467-022-35257-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. However, to further expand the therapeutic application of these tools there is a need for targetable systems that are small enough to be delivered efficiently. Here, we mined an extensive genome-resolved metagenomics database and identified families of uncharacterized RNA-guided, compact nucleases (between 450 and 1,050 aa). We report that Cas9d, a new CRISPR type II subtype, contains Zinc-finger motifs and high arginine content, features that we also found in nucleases related to HEARO effectors. These enzymes exhibit diverse biochemical characteristics and are broadly targetable. We show that natural Cas9d enzymes are capable of genome editing in mammalian cells with >90% efficiency, and further engineered nickase variants into the smallest base editors active in E. coli and human cells. Their small size, broad targeting potential, and translatability suggest that Cas9d and HEARO systems will enable a variety of genome editing applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Ian Barr
- Metagenomi Inc. 1545 Park Ave, Emeryville, CA 94608 USA
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5
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Aliaga Goltsman DS, Alexander LM, Devoto AE, Albers JB, Liu J, Butterfield CN, Brown CT, Thomas BC. Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities. CRISPR J 2020; 3:454-461. [PMID: 33146573 PMCID: PMC7757703 DOI: 10.1089/crispr.2020.0043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cas12a enzymes are quickly being adopted for use in a variety of genome-editing applications. These programmable nucleases are part of adaptive microbial immune systems, the natural diversity of which has been largely unexplored. Here, we identified novel families of Type V-A CRISPR nucleases through a large-scale analysis of metagenomes collected from a variety of complex environments, and developed representatives of these systems into gene-editing platforms. The nucleases display extensive protein variation and can be programmed by a single-guide RNA with specific motifs. The majority of these enzymes are part of systems recovered from uncultivated organisms, some of which also encode a divergent Type V effector. Biochemical analysis uncovered unexpected protospacer adjacent motif diversity, indicating that these systems will facilitate a variety of genome-engineering applications. The simplicity of guide sequences and activity in human cell lines suggest utility in gene and cell therapies.
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Affiliation(s)
| | | | | | | | - Jason Liu
- Metagenomi, Inc., Emeryville, California, USA
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6
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Mu A, Thomas BC, Banfield JF, Moreau JW. Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph. Environ Microbiol Rep 2020; 12:525-533. [PMID: 32633030 DOI: 10.1111/1758-2229.12868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO2 (scCO2 ) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO-utilizing anaerobe Carboxydocella, which decreased in relative abundance post-scCO2 injection. Here, we present results from more detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella. We demonstrate a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment. We discuss the potential impacts of scCO2 on subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO).
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Affiliation(s)
- Andre Mu
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Melbourne, Australia
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7
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Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF. Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nat Microbiol 2019; 4:1356-1367. [PMID: 31110364 PMCID: PMC6784897 DOI: 10.1038/s41564-019-0449-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/03/2019] [Indexed: 12/15/2022]
Abstract
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.
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Affiliation(s)
- Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhou Li
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Katherine R Lane
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
- School of Computer Science and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
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8
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Lavy A, McGrath DG, Matheus Carnevali PB, Wan J, Dong W, Tokunaga TK, Thomas BC, Williams KH, Hubbard SS, Banfield JF. Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock. Ecol Evol 2019; 9:6869-6900. [PMID: 31380022 PMCID: PMC6662431 DOI: 10.1002/ece3.5254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/01/2023] Open
Abstract
Watersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharge through soils and underlying weathered rock, yet there is limited information regarding the structure and function of these communities. Within the East River, CO watershed, we conducted a depth-resolved, hillslope to riparian zone transect study to identify factors that control how microorganisms are distributed and their functions. Metagenomic and geochemical analyses indicate that distance from the East River and proximity to groundwater and underlying weathered shale strongly impact microbial community structure and metabolic potential. Riparian zone microbial communities are compositionally distinct, from the phylum down to the species level, from all hillslope communities. Bacteria from phyla lacking isolated representatives consistently increase in abundance with increasing depth, but only in the riparian zone saturated sediments we found Candidate Phyla Radiation bacteria. Riparian zone microbial communities are functionally differentiated from hillslope communities based on their capacities for carbon and nitrogen fixation and sulfate reduction. Selenium reduction is prominent at depth in weathered shale and saturated riparian zone sediments and could impact water quality. We anticipate that the drivers of community composition and metabolic potential identified throughout the studied transect will predict patterns across the larger watershed hillslope system.
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Affiliation(s)
- Adi Lavy
- Earth and Planetary ScienceUniversity of CaliforniaBerkeleyCalifornia
- Earth and Environmental SciencesLawrence Berkeley National LabBerkeleyCalifornia
| | | | | | - Jiamin Wan
- Earth and Environmental SciencesLawrence Berkeley National LabBerkeleyCalifornia
| | - Wenming Dong
- Earth and Environmental SciencesLawrence Berkeley National LabBerkeleyCalifornia
| | - Tetsu K. Tokunaga
- Earth and Environmental SciencesLawrence Berkeley National LabBerkeleyCalifornia
| | - Brian C. Thomas
- Earth and Planetary ScienceUniversity of CaliforniaBerkeleyCalifornia
| | - Kenneth H. Williams
- Earth and Environmental SciencesLawrence Berkeley National LabBerkeleyCalifornia
| | - Susan S. Hubbard
- Earth and Environmental SciencesLawrence Berkeley National LabBerkeleyCalifornia
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9
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Goltsman DSA, Sun CL, Proctor DM, DiGiulio DB, Robaczewska A, Thomas BC, Shaw GM, Stevenson DK, Holmes SP, Banfield JF, Relman DA. Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. Genome Res 2018; 28:1467-1480. [PMID: 30232199 PMCID: PMC6169887 DOI: 10.1101/gr.236000.118] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/28/2018] [Indexed: 12/22/2022]
Abstract
Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.
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Affiliation(s)
- Daniela S Aliaga Goltsman
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christine L Sun
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Diana M Proctor
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Daniel B DiGiulio
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Anna Robaczewska
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Gary M Shaw
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - David K Stevenson
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.,Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - David A Relman
- March of Dimes Prematurity Research Center at Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
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10
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Abstract
Recent data indicate one or more moderately nearby supernovae in the Early Pleistocene, with additional events likely in the Miocene. This has motivated more detailed computations, using new information about the nature of supernovae and the distances of these events to describe in more detail the sorts of effects that are indicated at the Earth. This short communication/review is designed to describe some of these effects so that they may possibly be related to changes in the biota around these times.
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Affiliation(s)
- Adrian L Melott
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA,
| | - Brian C Thomas
- Department of Physics and Astronomy, Washburn University, 1700 SW College Avenue Topeka, Kansas 66621, USA,
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11
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Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 2018; 3:836-843. [PMID: 29807988 PMCID: PMC6786971 DOI: 10.1038/s41564-018-0171-1] [Citation(s) in RCA: 603] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/27/2018] [Indexed: 11/30/2022]
Abstract
Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.
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Affiliation(s)
- Christian M K Sieber
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Allison Sharrar
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Matthias Hess
- Department of Animal Science, University of California, Davis, CA, USA
| | - Susannah G Tringe
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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12
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Brooks B, Olm MR, Firek BA, Baker R, Geller-McGrath D, Reimer SR, Soenjoyo KR, Yip JS, Dahan D, Thomas BC, Morowitz MJ, Banfield JF. The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms. Microbiome 2018; 6:112. [PMID: 29925423 PMCID: PMC6011520 DOI: 10.1186/s40168-018-0493-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 06/06/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants. RESULTS Over 2832 swabs, wipes, and air samples were collected from 16 private-style NICU rooms housing very low birth weight (< 1500 g), premature (< 31 weeks' gestation) infants. For each infant, room samples were collected daily, Monday through Friday, for 1 month. The first samples from the first infant and the last samples from the last infant were collected 383 days apart. Twenty-two NICU locations spanning room surfaces, hands, electronics, sink basins, and air were collected. Results point to an incredibly simple room community where 5-10 taxa, mostly skin-associated, account for over 50% of the amplicon reads. Biomass estimates reveal four to five orders of magnitude difference between the least to the most dense microbial communities, air, and sink basins, respectively. Biomass trends from bioaerosol samples and petri dish dust collectors suggest occupancy to be a main driver of suspended biological particles within the NICU. Using a machine learning algorithm to classify the origin of room samples, we show that each room has a unique microbial fingerprint. Several important taxa driving this model were dominant gut colonizers of infants housed within each room. CONCLUSIONS Despite regular cleaning of hospital surfaces, bacterial biomass was detectable at varying densities. A room-specific microbiome signature was detected, suggesting microbes seeding NICU surfaces are sourced from reservoirs within the room and that these reservoirs contain actively dividing cells. Collectively, the data suggests that hospitalized infants, in combination with their caregivers, shape the microbiome of NICU rooms.
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Affiliation(s)
- Brandon Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Brian A Firek
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robyn Baker
- Division of Newborn Medicine, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - David Geller-McGrath
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Sophia R Reimer
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Karina R Soenjoyo
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Jennifer S Yip
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Dylan Dahan
- Department of Biology, Bard College, Annandale-on-Hudson, NY, USA
- Present address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | | | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA.
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13
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Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J 2018; 12:1715-1728. [PMID: 29467397 PMCID: PMC6018805 DOI: 10.1038/s41396-018-0078-0] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 11/16/2022]
Abstract
A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, Berkeley, CA, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Sean P Jungbluth
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adi Lavy
- Department of Earth and Planetary Science, Berkeley, CA, USA
| | - Lesley A Warren
- Department of Civil Engineering, University of Toronto, Toronto, ON, Canada
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Brian C Thomas
- Department of Earth and Planetary Science, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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14
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Abstract
We investigated the potential biological impacts at Earth's surface of stratospheric O3 depletion caused by nearby supernovae known to have occurred about 2.5 and 8 million years ago at about 50 pc distance. New and previously published atmospheric chemistry modeling results were combined with radiative transfer modeling to determine changes in surface-level solar irradiance and biological responses. We find that UVB irradiance is increased by a factor of 1.1 to 2.8, with large variation in latitude, and seasonally at high-latitude regions. Changes in UVA and PAR (visible light) are much smaller. DNA damage (in vitro) is increased by factors similar to UVB, while other biological impacts (erythema, skin cancer, cataracts, marine phytoplankton photosynthesis inhibition, and plant damage) are increased by smaller amounts. We conclude that biological impacts due to increased UV irradiance in this SN case are not mass-extinction level but might be expected to contribute to changes in species abundances; this result fits well with species turnover observed around the Pliocene-Pleistocene boundary. Key Words: UV radiation-Supernovae-Ozone-Radiative transfer. Astrobiology 18, 481-490.
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Affiliation(s)
- Brian C Thomas
- Department of Physics and Astronomy, Washburn University , Topeka, Kansas
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15
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West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res 2018; 28:569-580. [PMID: 29496730 PMCID: PMC5880246 DOI: 10.1101/gr.228429.117] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/27/2018] [Indexed: 11/24/2022]
Abstract
Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.
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Affiliation(s)
- Patrick T West
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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16
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Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M. A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. Environ Microbiol 2018; 20:800-814. [PMID: 29194919 PMCID: PMC5812793 DOI: 10.1111/1462-2920.14013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 01/09/2023]
Abstract
Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.
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Affiliation(s)
- Adi Lavy
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Israel
- Earth and Planetary Science, 369 McCone Hall, University of California, Berkeley, USA
| | - Ray Keren
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Israel
- Department of Civil and Environmental Engineering, University of California, Berkeley, USA
| | - Ke Yu
- Department of Civil and Environmental Engineering, University of California, Berkeley, USA
| | - Brian C. Thomas
- Earth and Planetary Science, 369 McCone Hall, University of California, Berkeley, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California, Berkeley, USA
| | - Jillian F. Banfield
- Earth and Planetary Science, 369 McCone Hall, University of California, Berkeley, USA
| | - Micha Ilan
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Israel
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17
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Dudek NK, Sun CL, Burstein D, Kantor RS, Aliaga Goltsman DS, Bik EM, Thomas BC, Banfield JF, Relman DA. Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome. Curr Biol 2017; 27:3752-3762.e6. [PMID: 29153320 DOI: 10.1016/j.cub.2017.10.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/13/2017] [Accepted: 10/13/2017] [Indexed: 12/28/2022]
Abstract
The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named "Candidatus Delphibacteria" and "Candidatus Fertabacteria"). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. We uncovered a rich diversity of predicted Cas9 proteins, including the two longest predicted Cas9 proteins to date. Notably, we identified the first type II CRISPR-Cas systems encoded by members of the Candidate Phyla Radiation. Using their spacer sequences, we subsequently identified and assembled a complete Saccharibacteria phage genome. These findings underscore the immense microbial diversity and functional potential that await discovery in previously unexplored environments.
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Affiliation(s)
- Natasha K Dudek
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christine L Sun
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniela S Aliaga Goltsman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisabeth M Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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18
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Ino K, Hernsdorf AW, Konno U, Kouduka M, Yanagawa K, Kato S, Sunamura M, Hirota A, Togo YS, Ito K, Fukuda A, Iwatsuki T, Mizuno T, Komatsu DD, Tsunogai U, Ishimura T, Amano Y, Thomas BC, Banfield JF, Suzuki Y. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. ISME J 2017; 12:31-47. [PMID: 28885627 DOI: 10.1038/ismej.2017.140] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 07/06/2017] [Accepted: 07/25/2017] [Indexed: 01/14/2023]
Abstract
Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.
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Affiliation(s)
- Kohei Ino
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Alex W Hernsdorf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Uta Konno
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsunori Yanagawa
- Graduate School of Environmental Engineering, The University of Kitakyushu, Kitakyushu, Fukuoka, Japan
| | - Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC (Japan Agency for Marine-Earth Science and Technology), Yokosuka City, Kanagawa, Japan
| | - Michinari Sunamura
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akinari Hirota
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Yoko S Togo
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Kazumasa Ito
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Akari Fukuda
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.,Japan Atomic Energy Agency, Naka-gun, Ibaraki, Japan
| | | | | | - Daisuke D Komatsu
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Toyoho Ishimura
- National Institute of Technology, Ibaraki College, Hitachinaka-shi, Ibaraki, Japan
| | - Yuki Amano
- Japan Atomic Energy Agency, Naka-gun, Ibaraki, Japan
| | - Brian C Thomas
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yohey Suzuki
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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19
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Finstad KM, Probst AJ, Thomas BC, Andersen GL, Demergasso C, Echeverría A, Amundson RG, Banfield JF. Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics. Front Microbiol 2017; 8:1435. [PMID: 28804480 PMCID: PMC5532433 DOI: 10.3389/fmicb.2017.01435] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at the highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.
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Affiliation(s)
- Kari M. Finstad
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
| | - Alexander J. Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, BerkeleyCA, United States
| | - Brian C. Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, BerkeleyCA, United States
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States
| | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del NorteAntofagasta, Chile
| | - Alex Echeverría
- Centro de Biotecnología, Universidad Católica del NorteAntofagasta, Chile
| | - Ronald G. Amundson
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
| | - Jillian F. Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
- Department of Earth and Planetary Sciences, University of California, Berkeley, BerkeleyCA, United States
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20
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Abstract
Recent 60Fe results have suggested that the estimated distances of supernovae in the last few million years should be reduced from ∼100 to ∼50 pc. Two events or series of events are suggested, one about 2.7 million years to 1.7 million years ago, and another about 6.5-8.7 million years ago. We ask what effects such supernovae are expected to have on the terrestrial atmosphere and biota. Assuming that the Local Bubble was formed before the event being considered, and that the supernova and the Earth were both inside a weak, disordered magnetic field at that time, TeV-PeV cosmic rays (CRs) at Earth will increase by a factor of a few hundred. Tropospheric ionization will increase proportionately, and the overall muon radiation load on terrestrial organisms will increase by a factor of ∼150. All return to pre-burst levels within 10 kyr. In the case of an ordered magnetic field, effects depend strongly on the field orientation. The upper bound in this case is with a largely coherent field aligned along the line of sight to the supernova, in which case, TeV-PeV CR flux increases are ∼104; in the case of a transverse field they are below current levels. We suggest a substantial increase in the extended effects of supernovae on Earth and in the "lethal distance" estimate; though more work is needed. This paper is an explicit follow-up to Thomas et al. We also provide more detail on the computational procedures used in both works.
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Affiliation(s)
- A L Melott
- Department of Physics and Astronomy, University of Kansas, Lawrence, KS 66045, USA
| | - B C Thomas
- Department of Physics and Astronomy, Washburn University, Topeka, KS 66621, USA
| | | | - D V Semikoz
- APC, Universite Paris Diderot, CNRS/IN2P3, CEA/IRFU, Observatoire de Paris, Sorbonne Paris Cite, 119 F-75205 Paris, France
- National Research Nuclear University "MEPHI" (Moscow Engineering Physics Institute), Kashirskoe Highway 31, M4, 115409, Russia
| | - A C Overholt
- Department of Science and Mathematics, MidAmerica Nazarene University, Olathe, KS 66062, USA
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21
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Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF. Potential for microbial H 2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J 2017; 11:1915-1929. [PMID: 28350393 PMCID: PMC5520028 DOI: 10.1038/ismej.2017.39] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/02/2017] [Accepted: 02/05/2017] [Indexed: 01/24/2023]
Abstract
Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.
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Affiliation(s)
- Alex W Hernsdorf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.,Horonobe Underground Research Center, Japan Atomic Energy Agency, Horonobe, Hokkaido, Japan
| | - Kazuya Miyakawa
- Horonobe Underground Research Center, Japan Atomic Energy Agency, Horonobe, Hokkaido, Japan
| | - Kotaro Ise
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Yohey Suzuki
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | | | - David Burstein
- Department of Earth and Planetary Sciences, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
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22
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Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison STL, Banfield JF. Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation. Environ Sci Technol 2017; 51:2944-2953. [PMID: 28139919 DOI: 10.1021/acs.est.6b04477] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN-), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN- loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN-. A second reactor was fed ammonium sulfate to mimic breakdown products of SCN-. Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN- reactor, Thiobacillus strains capable of SCN- degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN- reactor expressed proteins involved in SCN- degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.
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Affiliation(s)
- Rose S Kantor
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Robert J Huddy
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town , Rondebosch, 7701, South Africa
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
| | - Susannah Tringe
- Joint Genome Institute , Walnut Creek, California 94598, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town , Rondebosch, 7701, South Africa
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
- Department of Environmental Science, Policy, and Management, University of California , Berkeley, California 94720, United States
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23
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Olm MR, Butterfield CN, Copeland A, Boles TC, Thomas BC, Banfield JF. The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis. mBio 2017; 8:e01969-16. [PMID: 28223457 PMCID: PMC5358914 DOI: 10.1128/mbio.01969-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/25/2017] [Indexed: 12/21/2022] Open
Abstract
In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples. D. acidovorans was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods.IMPORTANCE It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.
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Affiliation(s)
| | | | - Alex Copeland
- Joint Genome Institute, Walnut Creek, California, USA
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24
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Rahman SF, Kantor RS, Huddy R, Thomas BC, van Zyl AW, Harrison STL, Banfield JF. Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings. Microbiologyopen 2017; 6. [PMID: 28215046 PMCID: PMC5458468 DOI: 10.1002/mbo3.446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
Thiocyanate (SCN−) is a toxic compound that forms when cyanide (CN−), used to recover gold, reacts with sulfur species. SCN−‐degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory‐based reactors operated without suspended solids. Despite minor upsets during the acclimation period, the SCN− degradation performance was largely unchanged under stable operating conditions. Here, we characterized the microbial community in the SCN− degrading bioreactor that included solid particulate tailings and determined how it differed from the biofilm‐based communities in solids‐free reactor systems inoculated from the same source. Genome‐based analysis revealed that the presence of solids decreased microbial diversity, selected for different strains, suppressed growth of thiobacilli inferred to be primarily responsible for SCN− degradation, and promoted growth of Trupera, an organism not detected in the reactors without solids. In the solids reactor community, heterotrophy and aerobic respiration represent the dominant metabolisms. Many organisms have genes for denitrification and sulfur oxidation, but only one Thiobacillus sp. in the solids reactor has SCN− degradation genes. The presence of the solids prevented floc and biofilm formation, leading to the observed reduced microbial diversity. Collectively the presence of the solids and lack of biofilm community may result in a process with reduced resilience to process perturbations, including fluctuations in the influent composition and pH. The results from this investigation have provided novel insights into the community composition of this industrially relevant community, giving potential for improved process control and operation through ongoing process monitoring.
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Affiliation(s)
- Sumayah F Rahman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Robert Huddy
- Department of Chemical Engineering, Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Andries W van Zyl
- Department of Chemical Engineering, Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Susan T L Harrison
- Department of Chemical Engineering, Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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25
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Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res 2017; 27:601-612. [PMID: 28073918 PMCID: PMC5378178 DOI: 10.1101/gr.213256.116] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/09/2017] [Indexed: 12/22/2022]
Abstract
The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity.
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Affiliation(s)
- Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brandon Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Robyn Baker
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, Pennsylvania 15213, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Karina Soenjoyo
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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26
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Neale PJ, Thomas BC. Inhibition by ultraviolet and photosynthetically available radiation lowers model estimates of depth-integrated picophytoplankton photosynthesis: global predictions for Prochlorococcus and Synechococcus. Glob Chang Biol 2017; 23:293-306. [PMID: 27178715 DOI: 10.1111/gcb.13356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 06/05/2023]
Abstract
Phytoplankton photosynthesis is often inhibited by ultraviolet (UV) and intense photosynthetically available radiation (PAR), but the effects on ocean productivity have received little consideration aside from polar areas subject to periodic enhanced UV-B due to depletion of stratospheric ozone. A more comprehensive assessment is important for understanding the contribution of phytoplankton production to the global carbon budget, present and future. Here, we consider responses in the temperate and tropical mid-ocean regions typically dominated by picophytoplankton including the prokaryotic lineages, Prochlorococcus and Synechococcus. Spectral models of photosynthetic response for each lineage were constructed using model strains cultured at different growth irradiances and temperatures. In the model, inhibition becomes more severe once exposure exceeds a threshold (Emax ) related to repair capacity. Model parameters are presented for Prochlorococcus adding to those previously presented for Synechococcus. The models were applied to estimate midday, water column photosynthesis based on an atmospheric model of spectral radiation, satellite-derived spectral water transparency and temperature. Based on a global survey of inhibitory exposure severity, a full-latitude section of the mid-Pacific and near-equatorial region of the east Pacific were identified as representative regions for prediction of responses over the entire water column. Comparing predictions integrated over the water column including versus excluding inhibition, production was 7-28% lower due to inhibition depending on strain and site conditions. Inhibition was consistently greater for Prochlorococcus compared to two strains of Synechococcus. Considering only the surface mixed layer, production was inhibited 7-73%. On average, including inhibition lowered estimates of midday productivity around 20% for the modeled region of the Pacific with UV accounting for two-thirds of the reduction. In contrast, most other productivity models either ignore inhibition or only include PAR inhibition. Incorporation of Emax model responses into an existing spectral model of depth-integrated, daily production will enable efficient global predictions of picophytoplankton productivity including inhibition.
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Affiliation(s)
- Patrick J Neale
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Brian C Thomas
- Department of Physics and Astronomy, Washburn University, 1700 SW College Ave, Topeka, KS, 66604, USA
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Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature 2016; 542:237-241. [PMID: 28005056 PMCID: PMC5300952 DOI: 10.1038/nature21059] [Citation(s) in RCA: 350] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA1,2. Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences3,4. The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research5. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms6,7. Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet identified. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in E. coli. Interrogation of environmental microbial communities combined with in vivo experiments allows access to an unprecedented diversity of genomes whose content will expand the repertoire of microbe-based biotechnologies.
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Affiliation(s)
- David Burstein
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Steven C Strutt
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.,Department of Chemistry, University of California, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Innovative Genomics Initiative, University of California, Berkeley, California 94720, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA
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28
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Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 2016; 4:e2687. [PMID: 27843720 PMCID: PMC5103831 DOI: 10.7717/peerj.2687] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 01/03/2023] Open
Abstract
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
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Affiliation(s)
- Cristina N Butterfield
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Peter F Andeer
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Susan Spaulding
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Andrea Singh
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Kenwyn B Suttle
- Department of Ecology and Evolutionary Biology, University of California , Santa Cruz , CA , United States
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | | | - Trent Northen
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotechnol 2016; 34:1256-1263. [PMID: 27819664 DOI: 10.1038/nbt.3704] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/20/2016] [Indexed: 12/22/2022]
Abstract
Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication. We apply this method to show that microbial replication rates increase after antibiotic administration in human infants. We also show that uncultivated, groundwater-associated, Candidate Phyla Radiation bacteria only rarely replicate quickly in subsurface communities undergoing substantial changes in geochemistry. Our method can be applied to any genome-resolved microbiome study to track organism responses to varying conditions, identify actively growing populations and measure replication rates for use in modeling studies.
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Affiliation(s)
- Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Thomas BC, Goracke BD, Dalton SM. Atmospheric constituents and surface-level UVB: Implications for a paleoaltimetry proxy and attempts to reconstruct UV exposure during volcanic episodes. Earth Planet Sci Lett 2016; 453:141-151. [PMID: 30034018 PMCID: PMC6052448 DOI: 10.1016/j.epsl.2016.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chemical and morphological features of spores and pollens have been linked to changes in solar ultraviolet radiation (specifically UVB, 280-315 nm) at Earth's surface. Variation in UVB exposure as inferred from these features has been suggested as a proxy for paleoaltitude; such proxies are important in understanding the uplift history of high altitude plateaus, which in turn is important for testing models of the tectonic processes responsible for such uplift. While UVB irradiance does increase with altitude above sea level, a number of other factors affect the irradiance at any given place and time. In this modeling study we use the TUV atmospheric radiative transfer model to investigate dependence of surface-level UVB irradiance and relative biological impact on a number of constituents in Earth's atmosphere that are variable over long and short time periods. We consider changes in O3 column density, and SO2 and sulfate aerosols due to periods of volcanic activity, including that associated with the formation of the Siberian Traps. We find that UVB irradiance may be highly variable under volcanic conditions and variations in several of these atmospheric constituents can easily mimic or overwhelm changes in UVB irradiance due to changes in altitude. On the other hand, we find that relative change with altitude is not very sensitive to different sets of atmospheric conditions. Any paleoaltitude proxy based on UVB exposure requires confidence that the samples under comparison were located at roughly the same latitude, under very similar O3 and SO2 columns, with similar atmospheric aerosol conditions. In general, accurate estimates of the surface-level UVB exposure at any time and location require detailed radiative transfer modeling taking into account a number of atmospheric factors; this result is important for paleoaltitude proxies as well as attempts to reconstruct the UV environment through geologic time and to tie extinctions, such as the end-Permian mass extinction, to UVB irradiance changes.
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Affiliation(s)
- Brian C. Thomas
- Correspondence to: 1700 SW College Ave., Topeka, KS 66604, United States. (B.C. Thomas)
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Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219. [PMID: 27774985 PMCID: PMC5079060 DOI: 10.1038/ncomms13219] [Citation(s) in RCA: 572] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Christopher T. Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Laura A. Hug
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Alexander J. Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Michael J. Wilkins
- School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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32
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Thomas BC, Müller A, Auffarth GU, Holzer MP. [Duration of Examination and Patient Comfort with a New Biometric Device, in Comparison to Three Established Devices]. Klin Monbl Augenheilkd 2016; 233:933-7. [PMID: 27560200 DOI: 10.1055/s-0042-105566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE The aim of this study was to evaluate the duration of the preoperative examination and patient comfort in measurements with an Image Guided System (Verion, Alcon), which is used for the calculation and intraoperative alignment of toric intraocular lenses, in comparison to established keratometry devices. PATIENTS AND METHODS In a prospective, monocentric, open, ethics committee controlled study, 150 eyes of 150 ophthalmologically healthy volunteers were examined by a single examiner. Three measurements were performed with the Verion Image Guided System and - for comparison - one measurement each with IOLMaster 500, Lenstar LS900 and Pentacam HR. The measurement time was recorded with a stopwatch. For the analysis, patients were divided into three age groups (young, middle, old). Patient comfort was assessed using a questionnaire, which focussed on grading the whole measurement, as well as brightness of light, head posture and subjective duration. RESULTS The mean age of the volunteers was 40.5 years (18-78 years). The mean duration of measurement was as follows: first Verion measurement 54.0 ± 42.7 seconds (n = 149), second Verion measurement 42.0 ± 20.5 s (n = 144), third Verion measurement 44.7 ± 25.2 s (n = 143), IOLMaster 500 46.3 ± 22.4 s (n = 147), Lenstar LS900 46.6 ± 14.4 s (n = 146) and Pentacam HR 46.6 ± 25.5 s (n = 147). Only the first and second Verion measurements were statistically different (p < 0.01). There were no statistical differences between the age groups, with the single exception of young versus old with the Pentacam (p < 0.01). Subjective patient comfort (n = 143) was very high for all devices and rated as "not uncomfortable" or "slightly uncomfortable". CONCLUSION The duration of the preoperative examination with the Verion Image Guided System is comparable to established keratometry devices. However, IOL calculation with the Verion requires measurement of axial length and anterior chamber depth with another biometric device, which requires additional time. No age dependent differences were found. The examination can be easily integrated into clinical routine and is well tolerated by patients.
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Affiliation(s)
- B C Thomas
- International Vision Correction Research Centre (IVCRC), Universitätsaugenklinik Heidelberg
| | - A Müller
- International Vision Correction Research Centre (IVCRC), Universitätsaugenklinik Heidelberg
| | - G U Auffarth
- International Vision Correction Research Centre (IVCRC), Universitätsaugenklinik Heidelberg
| | - M P Holzer
- International Vision Correction Research Centre (IVCRC), Universitätsaugenklinik Heidelberg
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Thomas BC, Engler EE, Kachelrieß M, Melott AL, Overholt AC, Semikoz DV. TERRESTRIAL EFFECTS OF NEARBY SUPERNOVAE IN THE EARLY PLEISTOCENE. Astrophys J Lett 2016; 826:L3. [PMID: 30034771 PMCID: PMC6052446 DOI: 10.3847/2041-8205/826/1/l3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent results have strongly confirmed that multiple supernovae happened at distances of ∼100 pc, consisting of two main events: one at 1.7-3.2 million years ago, and the other at 6.5-8.7 million years ago. These events are said to be responsible for excavating the Local Bubble in the interstellar medium and depositing 60Fe on Earth and the Moon. Other events are indicated by effects in the local cosmic ray (CR) spectrum. Given this updated and refined picture, we ask whether such supernovae are expected to have had substantial effects on the terrestrial atmosphere and biota. In a first look at the most probable cases, combining photon and CR effects, we find that a supernova at 100 pc can have only a small effect on terrestrial organisms from visible light and that chemical changes such as ozone depletion are weak. However, tropospheric ionization right down to the ground, due to the penetration of ⩾TeV CRs, will increase by nearly an order of magnitude for thousands of years, and irradiation by muons on the ground and in the upper ocean will increase twentyfold, which will approximately triple the overall radiation load on terrestrial organisms. Such irradiation has been linked to possible changes in climate and increased cancer and mutation rates. This may be related to a minor mass extinction around the Pliocene-Pleistocene boundary, and further research on the effects is needed.
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Affiliation(s)
- B C Thomas
- Department of Physics and Astronomy, Washburn University, Topeka, KS 66621, USA
| | - E E Engler
- Department of Physics and Astronomy, Washburn University, Topeka, KS 66621, USA
| | | | - A L Melott
- Department of Physics and Astronomy, University of Kansas, Lawrence, KS 66045, USA
| | - A C Overholt
- Department of Science and Mathematics, MidAmerica Nazarene University, Olathe, KS 66062, USA
| | - D V Semikoz
- APC, Universite Paris Diderot, CNRS/IN2P3, CEA/IRFU, Observatoire de Paris, Sorbonne Paris Cite, F-119 75205 Paris, France
- National Research Nuclear University "MEPHI" (Moscow Engineering Physics Institute), Kashirskoe Highway 31, Moscow, 115409, Russia
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Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Burstein D, Emerson JB, Thomas BC, Banfield JF. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2 concentrations. Environ Microbiol 2016; 19:459-474. [PMID: 27112493 DOI: 10.1111/1462-2920.13362] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As in many deep underground environments, the microbial communities in subsurface high-CO2 ecosystems remain relatively unexplored. Recent investigations based on single-gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO2 -saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high-quality genomes from 150 microbial species affiliated with 46 different phylum-level lineages. Bacteria from two novel phylum-level lineages have the capacity for CO2 fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood-Ljungdahl pathway and the Calvin-Benson-Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO2 -concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H2 is an important inter-species energy currency even under gaseous CO2 -saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO2 saturation.
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Affiliation(s)
- Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Andrea Singh
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Laura A Hug
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - David Burstein
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Joanne B Emerson
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, 307 McCone Hall, CA, 94720, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
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35
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Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Sharon I, Williams KH, Tabita FR, Banfield JF. RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. ISME J 2016; 10:2702-2714. [PMID: 27137126 PMCID: PMC5113843 DOI: 10.1038/ismej.2016.53] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 02/29/2016] [Accepted: 03/04/2016] [Indexed: 11/23/2022]
Abstract
Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates and WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete (>93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency.
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Affiliation(s)
- Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Vanessa A Varaljay
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Michael J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Kenneth H Williams
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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Neale PJ, Thomas BC. Solar Irradiance Changes and Phytoplankton Productivity in Earth's Ocean Following Astrophysical Ionizing Radiation Events. Astrobiology 2016; 16:245-258. [PMID: 27027533 DOI: 10.1089/ast.2015.1360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Two atmospheric responses to simulated astrophysical ionizing radiation events significant to life on Earth are production of odd-nitrogen species, especially NO2, and subsequent depletion of stratospheric ozone. Ozone depletion increases incident short-wavelength ultraviolet radiation (UVB, 280-315 nm) and longer (>600 nm) wavelengths of photosynthetically available radiation (PAR, 400-700 nm). On the other hand, the NO2 haze decreases atmospheric transmission in the long-wavelength UVA (315-400 nm) and short-wavelength PAR. Here, we use the results of previous simulations of incident spectral irradiance following an ionizing radiation event to predict changes in terran productivity focusing on photosynthesis of marine phytoplankton. The prediction is based on a spectral model of photosynthetic response, which was developed for the dominant genera in central regions of the ocean (Synechococcus and Prochlorococcus), and on remote-sensing-based observations of spectral water transparency, temperature, wind speed, and mixed layer depth. Predicted productivity declined after a simulated ionizing event, but the effect integrated over the water column was small. For integrations taking into account the full depth range of PAR transmission (down to 0.1% of utilizable PAR), the decrease was at most 2-3% (depending on strain), with larger effects (5-7%) for integrations just to the depth of the surface mixed layer. The deeper integrations were most affected by the decreased utilizable PAR at depth due to the NO2 haze, whereas shallower integrations were most affected by the increased surface UV. Several factors tended to dampen the magnitude of productivity responses relative to increases in surface-damaging radiation, for example, most inhibition in the modeled strains is caused by UVA and PAR, and the greatest relative increase in damaging exposure is predicted to occur in the winter when UV and productivity are low.
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Affiliation(s)
- Patrick J Neale
- 1 Smithsonian Environmental Research Center , Edgewater, Maryland
| | - Brian C Thomas
- 2 Department of Physics and Astronomy, Washburn University , Topeka, Kansas
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Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, Probst AJ, Thomas BC, Banfield JF. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. Nat Commun 2016; 7:10613. [PMID: 26837824 PMCID: PMC4742961 DOI: 10.1038/ncomms10613] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/04/2016] [Indexed: 12/24/2022] Open
Abstract
Current understanding of microorganism–virus interactions, which shape the evolution and functioning of Earth's ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides. It is thought that CRISPR-Cas systems, which confer acquired immunity to phage and archaeal viruses, are widespread among bacteria and archaea. Here, Burstein et al. show that entire lineages of uncultivated microorganisms are essentially devoid of CRISPR-Cas systems.
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Affiliation(s)
- David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Christine L Sun
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.,Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
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38
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Anantharaman K, Brown CT, Burstein D, Castelle CJ, Probst AJ, Thomas BC, Williams KH, Banfield JF. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PeerJ 2016; 4:e1607. [PMID: 26844018 PMCID: PMC4736985 DOI: 10.7717/peerj.1607] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/28/2015] [Indexed: 01/08/2023] Open
Abstract
Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California , Berkeley, California , United States
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California , Berkeley, California , United States
| | - David Burstein
- Department of Earth and Planetary Sciences, University of California , Berkeley, California , United States
| | - Cindy J Castelle
- Department of Earth and Planetary Sciences, University of California , Berkeley, California , United States
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California , Berkeley, California , United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley, California , United States
| | - Kenneth H Williams
- Earth Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California , United States
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States
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Abstract
Astrophysical ionizing radiation events such as supernovae, gamma-ray bursts, and solar proton events have been recognized as a potential threat to life on Earth, primarily through depletion of stratospheric ozone and subsequent increase in solar UV radiation at Earth's surface and in the upper levels of the ocean. Other work has also considered the potential impact of nitric acid rainout, concluding that no significant threat is likely. Not yet studied to date is the potential impact of ozone produced in the lower atmosphere following an ionizing radiation event. Ozone is a known irritant to organisms on land and in water and therefore may be a significant additional hazard. Using previously completed atmospheric chemistry modeling, we examined the amount of ozone produced in the lower atmosphere for the case of a gamma-ray burst and found that the values are too small to pose a significant additional threat to the biosphere. These results may be extended to other ionizing radiation events, including supernovae and extreme solar proton events.
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Affiliation(s)
- Brian C Thomas
- Department of Physics and Astronomy, Washburn University , Topeka, Kansas
| | - Byron D Goracke
- Department of Physics and Astronomy, Washburn University , Topeka, Kansas
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40
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Kantor RS, van Zyl AW, van Hille RP, Thomas BC, Harrison STL, Banfield JF. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 2015; 17:4929-41. [DOI: 10.1111/1462-2920.12936] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Rose S. Kantor
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
| | - A. Wynand van Zyl
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Robert P. van Hille
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Brian C. Thomas
- Department of Earth and Planetary Sciences; University of California; Berkeley CA USA
| | - Susan T. L. Harrison
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences; University of California; Berkeley CA USA
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
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Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, Wilkins MJ, Williams KH, Singh A, Banfield JF. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol 2015; 18:159-73. [DOI: 10.1111/1462-2920.12930] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Laura A. Hug
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | - Itai Sharon
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | | | - Ritin Sharma
- Oak Ridge National Laboratory; Oak Ridge; TN USA
| | | | - Michael J. Wilkins
- Department of Microbiology; Ohio State University; Columbus OH USA
- School of Earth Sciences; Ohio State University; Columbus OH USA
| | - Kenneth H. Williams
- Department of Geophysics, Division of Earth Sciences; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Andrea Singh
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science; UC Berkeley; Berkeley CA USA
- Department of Environmental Science, Policy, and Management; UC Berkeley; Berkeley CA USA
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Auerbach FN, Holzer MP, Auffarth GU, Khoramnia R, Thomas BC, Saure D, Rabsilber TM. [Influence of corneal pachymetric changes on functional results after cataract surgery]. Ophthalmologe 2015; 112:834-9. [PMID: 26040794 DOI: 10.1007/s00347-015-0009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND In the early postoperative period following uncomplicated cataract surgery, the correlation of corrected distance visual acuity (CDVA) and the increase in corneal thickness and anterior chamber depth (ACD) are investigated. PATIENTS AND METHODS A total of 54 cataract patients with a mean age of 70 ± 8.4 years were included in this prospective study. Surgery was carried out on one eye of each patient according to the study protocol. Refraction, CDVA and ACD were evaluated 1 day and 1 week postoperatively and compared with the pachymetry results measured with the Pentacam. RESULTS The mean postoperative CDVA significantly improved from 0.31 ± 0.24 logMAR to 0.18 ± 0.22 logMAR after one day and up to 0.06 ± 0.13 logMAR one week after surgery (p < 0.05). The mean spherical equivalent was - 0.52 ± 0.69 D after one day and - 0.50 ± 0.82 D one week after surgery and showed only minimal differences compared to the mean target refraction of - 0.39 ± 0.70 D. Postoperative corneal thickness showed a significant increase compared to the preoperative results (p < 0.05) on both visits: the mean difference was 33.26 ± 50.20 µm (- 17 to 315 µm) on the first day and 20.22 ± 23.15 µm (- 10 to 99 µm) one week after surgery. Up to 7 days postoperatively the increase in corneal thickness and CDVA showed only moderate or no correlations (r = 0.465 vs. r = 0.072, respectively). Regarding pachymetry and ACD values, no or only low correlations were found. CONCLUSION The significant increase in corneal thickness on the first and seventh day shows no to moderate correlation to the CDVA. Nevertheless, a good and early rehabilitation of visual acuity following uncomplicated cataract surgery is possible. Intraocular pressure measurement can lead to false high results due to an increase in corneal thickness.
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Affiliation(s)
- F N Auerbach
- International Vision Correction Research Centre, Universitäts-Augenklinik Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Deutschland
| | - M P Holzer
- International Vision Correction Research Centre, Universitäts-Augenklinik Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Deutschland
| | - G U Auffarth
- International Vision Correction Research Centre, Universitäts-Augenklinik Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Deutschland
| | - R Khoramnia
- International Vision Correction Research Centre, Universitäts-Augenklinik Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Deutschland
| | - B C Thomas
- International Vision Correction Research Centre, Universitäts-Augenklinik Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Deutschland
| | - D Saure
- Institut für Medizinische Biometrie und Informatik, Universitätsklinikum Heidelberg, 69120, Heidelberg, Deutschland
| | - T M Rabsilber
- International Vision Correction Research Centre, Universitäts-Augenklinik Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Deutschland.
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43
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Emerson JB, Thomas BC, Alvarez W, Banfield JF. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environ Microbiol 2015; 18:1686-703. [DOI: 10.1111/1462-2920.12817] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/31/2015] [Accepted: 02/12/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Joanne B. Emerson
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Walter Alvarez
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
- Department of Environmental Science, Policy, and Management; University of California, Berkeley; Berkeley CA 94720-4767 USA
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44
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Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res 2015; 25:534-43. [PMID: 25665577 PMCID: PMC4381525 DOI: 10.1101/gr.183012.114] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/06/2015] [Indexed: 01/18/2023]
Abstract
Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.
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Affiliation(s)
- Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Michael Kertesz
- Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Laura A Hug
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Dmitry Pushkarev
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | | | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Mojgan Amirebrahimi
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA
| | - Susannah G Tringe
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA; Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Aliaga Goltsman DS, Comolli LR, Thomas BC, Banfield JF. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J 2015; 9:1014-23. [PMID: 25361394 PMCID: PMC4817702 DOI: 10.1038/ismej.2014.200] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/08/2014] [Accepted: 09/16/2014] [Indexed: 12/21/2022]
Abstract
A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ∼ 254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent 'omic' analyses is not simplicity but rather the high dominance by a few taxa. We conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time.
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Affiliation(s)
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian C Thomas
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 2015; 4. [PMID: 25735037 PMCID: PMC4384745 DOI: 10.7554/elife.05477] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/10/2015] [Indexed: 12/11/2022] Open
Abstract
Premature infants are highly vulnerable to aberrant gastrointestinal tract
colonization, a process that may lead to diseases like necrotizing enterocolitis.
Thus, spread of potential pathogens among hospitalized infants is of great concern.
Here, we reconstructed hundreds of high-quality genomes of microorganisms that
colonized co-hospitalized premature infants, assessed their metabolic potential, and
tracked them over time to evaluate bacterial strain dispersal among infants. We
compared microbial communities in infants who did and did not develop necrotizing
enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same
species colonized many infants, our genome-resolved analysis revealed that strains
colonizing each baby were typically distinct. In particular, no strain was common to
all infants who developed necrotizing enterocolitis. The paucity of shared gut
colonizers suggests the existence of significant barriers to the spread of bacteria
among infants. Importantly, we demonstrate that strain-resolved comprehensive
community analysis can be accomplished on potentially medically relevant time
scales. DOI:http://dx.doi.org/10.7554/eLife.05477.001 The spread of potentially harmful bacteria is a major source of disease in patients
staying in hospitals. Premature babies—born before 37 weeks of
pregnancy—can be particularly vulnerable to these infections because their
organs may not yet be fully developed. Also, young babies do not have the fully
established populations of beneficial microbes that help to protect us from dangerous
bacteria. Necrotizing enterocolitis—a life-threatening disease that can cause portions
of the bowel to die—is mostly seen in extremely premature babies. Although it
is not known what causes this serious condition, research has suggested that a
contagious microbe may be responsible. The development of methods that can sequence DNA from whole communities of microbes,
known as metagenomics, allows researchers to identify the presence of individual
strains of bacteria within these communities. This makes it possible to compare and
contrast the strains of bacteria present in both diseased and healthy individuals, to
help identify the bacteria responsible for a disease. Here, Raveh-Sadka et al. used a metagenomics approach to study the communities of
microbes present in premature babies in a hospital unit during an outbreak of
necrotizing enterocolitis. The study found that very few bacterial strains were
present in more than one baby, suggesting that bacterial strains are not readily
transferred between the babies while they are in the hospital. Furthermore,
Raveh-Sadka et al. reveal that no single bacterial strain was shared among all the
babies who developed necrotizing enterocolitis. These findings indicate that necrotizing enterocolitis is not caused by a single
strain of bacterium. Instead, if bacteria do contribute to the disease, it maybe that
it is caused by a variety of potentially harmful bacteria colonizing the gut at the
cost of beneficial bacteria. In future, better understanding of the barriers that
limit the transfer of bacteria between premature babies could help inform efforts to
reduce the spread of infections between patients in hospitals. DOI:http://dx.doi.org/10.7554/eLife.05477.002
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Affiliation(s)
- Tali Raveh-Sadka
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Brandon Brooks
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Robyn Baker
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States
| | - Misty Good
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
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Thomas BC, Neale PJ, Snyder BR. Solar irradiance changes and photobiological effects at earth's surface following astrophysical ionizing radiation events. Astrobiology 2015; 15:207-220. [PMID: 25692406 DOI: 10.1089/ast.2014.1224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Astrophysical ionizing radiation events have been recognized as a potential threat to life on Earth, primarily through depletion of stratospheric ozone and subsequent increase in surface-level solar ultraviolet radiation. Simulations of the atmospheric effects of a variety of events (such as supernovae, gamma-ray bursts, and solar proton events) have been previously published, along with estimates of biological damage at Earth's surface. In this work, we employed the Tropospheric Ultraviolet and Visible (TUV) radiative transfer model to expand and improve calculations of surface-level irradiance and biological impacts following an ionizing radiation event. We considered changes in surface-level UVB, UVA, and photosynthetically active radiation (visible light) for clear-sky conditions and fixed aerosol parameter values. We also considered a wide range of biological effects on organisms ranging from humans to phytoplankton. We found that past work overestimated UVB irradiance but that relative estimates for increase in exposure to DNA-damaging radiation are still similar to our improved calculations. We also found that the intensity of biologically damaging radiation varies widely with organism and specific impact considered; these results have implications for biosphere-level damage following astrophysical ionizing radiation events. When considering changes in surface-level visible light irradiance, we found that, contrary to previous assumptions, a decrease in irradiance is only present for a short time in very limited geographical areas; instead we found a net increase for most of the modeled time-space region. This result has implications for proposed climate changes associated with ionizing radiation events.
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Affiliation(s)
- Brian C Thomas
- 1 Department of Physics and Astronomy, Washburn University , Topeka, Kansas
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48
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Luef B, Frischkorn KR, Wrighton KC, Holman HYN, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 2015; 6:6372. [DOI: 10.1038/ncomms7372] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/23/2015] [Indexed: 02/04/2023] Open
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Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol 2015; 25:690-701. [PMID: 25702576 DOI: 10.1016/j.cub.2015.01.014] [Citation(s) in RCA: 334] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/30/2014] [Accepted: 01/06/2015] [Indexed: 01/23/2023]
Abstract
BACKGROUND Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown. RESULTS We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles. CONCLUSIONS The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.
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Affiliation(s)
- Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Laura A Hug
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Michael J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA; School of Earth Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Kyle R Frischkorn
- Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, NY 10964 USA
| | - Susannah G Tringe
- Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Ronald C Taylor
- Environmental Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Kenneth H Williams
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720 USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720 USA.
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50
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Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe SG, Banfield JF. Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J 2015; 9:1846-56. [PMID: 25647349 DOI: 10.1038/ismej.2015.2] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 12/17/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Little is known about the biogeography or stability of sediment-associated microbial community membership because these environments are biologically complex and generally difficult to sample. High-throughput-sequencing methods provide new opportunities to simultaneously genomically sample and track microbial community members across a large number of sampling sites or times, with higher taxonomic resolution than is associated with 16 S ribosomal RNA gene surveys, and without the disadvantages of primer bias and gene copy number uncertainty. We characterized a sediment community at 5 m depth in an aquifer adjacent to the Colorado River and tracked its most abundant 133 organisms across 36 different sediment and groundwater samples. We sampled sites separated by centimeters, meters and tens of meters, collected on seven occasions over 6 years. Analysis of 1.4 terabase pairs of DNA sequence showed that these 133 organisms were more consistently detected in saturated sediments than in samples from the vadose zone, from distant locations or from groundwater filtrates. Abundance profiles across aquifer locations and from different sampling times identified organism cohorts that comprised subsets of the 133 organisms that were consistently associated. The data suggest that cohorts are partly selected for by shared environmental adaptation.
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Affiliation(s)
- Laura A Hug
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | | | - Kyle R Frischkorn
- Department of Earth and Environmental Science, Columbia University, New York, NY, USA
| | - Kenneth H Williams
- Geophysics Department, Earth Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Susannah G Tringe
- Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Jillian F Banfield
- 1] Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA [2] Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
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