DOCSLIB.ORG

Assessing the Diversity of Freshwater Bacteria and Viruses

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Assessing the Diversity of Freshwater Bacteria and Viruses ASSESSING THE DIVERSITY OF FRESHWATER BACTERIA AND VIRUSES EMPLOYING METAGENOMICS TO CAPTURE THE DYNAMICS AND THE DIVERSITY OF FRESHWATER BACTERIA AND VIRUSES By MOHAMMAD MOHIUDDIN, M.Sc., Hons. B.Sc. A Thesis Submitted to the School of Graduate Studies in Partial Fulfilment of the Requirements for the Degree Doctor of Philosophy McMaster University © Copyright by Mohammad Mohiuddin, July 2019 DOCTOR OF PHILOSOPHY (2019) McMaster University Department of Biology Hamilton, Ontario, Canada TITLE: Employing Metagenomics to Capture the Dynamics and the Diversity of Freshwater Bacteria and Viruses AUTHOR: Mohammad Mohiuddin, M.Sc., Hons. B.Sc. (University of Dhaka, Bangladesh) SUPERVISOR: Professor Herb E. Schellhorn NUMBER OF PAGES: xx, 241 ii Lay Abstract Bacteria and viruses are abundant in freshwaters, yet our understanding of bacterial and viral communities in freshwaters remains inadequate. In addition, the changing patterns of waterborne diseases in recent years have warranted strong monitoring of recreational freshwaters across the globe. The goals of this thesis were to assess the dynamics and the diversity of freshwater bacterial and viral communities of the lower Great Lakes region and identify pathogenic bacterial and viral species. Employing a metagenomic approach, I have investigated the spatial and temporal distribution of bacterial and viral communities in recreational freshwaters. Using computational approaches, I have identified pathogenic bacteria and viruses and investigated the link between connected habitats. My research advances our understanding of bacterial and viral communities of the lower Great Lakes region and provides useful information to water quality decision makers for the optimization of municipal sampling programs currently employed in the Great Lakes area. iii Abstract Microbial water communities are a complex consortium of bacteria, viruses and protozoa. These complex microbial and viral communities may contain pathogens that cannot be detected by conventional methods. Next-generation sequencing (NGS) offers the potential to exhaustively characterize all microbial and viral components of a given water sample and facilitates the identification and quantification of pathogens of interest. The goals of this thesis were to assess the dynamics and the diversity of freshwater bacterial and viral communities of the lower Great Lakes region and identify pathogenic bacterial and viral species. We first assessed the diversity of viral communities in six different beaches of Lake Ontario and Lake Erie, two of the largest freshwater reservoirs in North America. We employed a robust and routinely applicable approach that can provide a comprehensive analysis of bacterial and viral community composition. Our analysis suggests that the viral communities of the lower Great Lakes region are dominated by bacteriophages but also contained viruses of plants and animals. Exhaustive characterization of bacterial communities indicates that the bacterial community composition is highly diverse, and the diversity differs between recreational waters and beach sands. In addition, we identified sequences of pathogens that are not currently included in traditional water monitoring schemes in both recreational water and beach sand. To investigate the impact of spatiotemporal and environmental factors on the distribution of bacterial species, we employed a computational approach and our analysis suggests that dissolved oxygen (DO) level is strongly associated with bacterial iv community diversity. Using a computational approach, we have also identified habitat- specific bacterial species and a possible link between inter-connected habitats. The findings of this thesis aid in our understanding of bacterial and viral community diversity in recreational waters and provide useful information to water quality decision makers. v Acknowledgements First and foremost, I would like to thank Dr. Herb Schellhorn for giving me the opportunity to work with him and for being an outstanding advisor and mentor. His patience and guidance have helped me grow intellectually, both as a researcher and as a person. I am truly grateful for my time learning from him. I am also thankful for the freedom and resources I have received from him to complete my graduate studies. I would also like to thank my supervisory committee members, Dr. Radhey Gupta and Dr. Brian Golding, for their guidance and support throughout my graduate studies. Thank you for meeting with me and for thoughtful discussions. Thanks are due to the collaborators, Dr. Tom Edge, Joshua Diamond, Glen Hudgin, for providing samples and resources throughout my graduate studies. I am grateful for the generous financial support I received from Norgen Biotek, Natural Sciences and Engineering Research Council (NSERC) of Canada, Niagara Peninsula Conservation Authority (NPCA), WaterSmart Niagara, MacWater and Niagara Region Public Health, for my research. Throughout my time in the Schellhorn lab, I have enjoyed the company of dynamic lab members. Thank you all for your support, for the creative ideas and for all the fun I had in and outside the lab. Special thanks go to Dr. Athanasios Paschos, Steven Botts and Yasser Salama for their input in my research. Finally, thank you to all my family, friends and loved ones, for their support and encouragement throughout my graduate studies. vi Table of Contents Lay Abstract ................................................................................................................. iii Abstract ......................................................................................................................... iv Acknowledgements ....................................................................................................... vi Table of Contents ......................................................................................................... vii List of Figures .............................................................................................................. xii List of Tables............................................................................................................. xviii Declaration of Academic Achievement ...................................................................... xix Chapter 1: Assessing the diversity of freshwater bacteria and viruses in the metagenomic era ............................................................................................................ 1 Abstract ....................................................................................................................... 2 1. Introduction .............................................................................................................. 3 2. Freshwater bacterial communities............................................................................. 5 2.1 Bacterial community structure ............................................................................ 5 2.2 Diversity of bacterial communities .................................................................... 13 3. Freshwater viruses .................................................................................................. 15 3.1 Viral community structure ................................................................................ 15 3.2 Diversity of viral communities .......................................................................... 20 4. Metagenomics- advantages and limitations ............................................................. 21 4.1 Factors that impact metagenomic studies .......................................................... 22 5. Conclusion ............................................................................................................. 37 References ................................................................................................................. 40 Chapter 2: Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analyses .......................................................... 59 Abstract ..................................................................................................................... 60 1. Introduction ............................................................................................................ 61 2. Materials and methods ............................................................................................ 64 2.1 Sampling sites and sample collection ................................................................ 64 2.2 Sample fractionation ......................................................................................... 64 2.3 Extraction of DNA from bacterial and VLP fraction ......................................... 65 vii 2.4 Preparation of DNA samples for sequencing ..................................................... 66 2.5 Bioinformatic analyses ...................................................................................... 66 3. Results ................................................................................................................... 68 3.1 Efficiency of the fractionation scheme .............................................................. 68 3.2 DNA in the environmental water samples ......................................................... 68 3.3 Abundance of bacterial and viral genome copies in freshwater .......................... 69 3.4 Overview of the viromes ..................................................................................
Load more

Recommended publications
  • Resilience of Microbial Communities After Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
    microorganisms Article Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms Tim Piel 1,†, Giovanni Sandrini 1,†,‡, Gerard Muyzer 1 , Corina P. D. Brussaard 1,2 , Pieter C. Slot 1, Maria J. van Herk 1, Jef Huisman 1 and Petra M. Visser 1,* 1 Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; [email protected] (T.P.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (C.P.D.B.); [email protected] (P.C.S.); [email protected] (M.J.v.H.); [email protected] (J.H.) 2 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands * Correspondence: [email protected]; Tel.: +31-20-5257073 † These authors have contributed equally to this work. ‡ Current address: Department of Technology & Sources, Evides Water Company, 3006 AL Rotterdam, The Netherlands. Abstract: Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little Citation: Piel, T.; Sandrini, G.; is known about the impacts of these H2O2 treatments on other members of the microbial com- Muyzer, G.; Brussaard, C.P.D.; Slot, munity. In this study, we investigated changes in microbial community composition during two P.C.; van Herk, M.J.; Huisman, J.; −1 lake treatments with low H2O2 concentrations (target: 2.5 mg L ) and in two series of controlled Visser, P.M.
    [Show full text]
  • Dissertation Implementing Organic Amendments To
    DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO.
    [Show full text]
  • Systema Naturae 2000 (Phylum, 6 Nov 2017)
    The Taxonomicon Systema Naturae 2000 Classification of Domain Bacteria (prokaryotes) down to Phylum Compiled by Drs. S.J. Brands Universal Taxonomic Services 6 Nov 2017 Systema Naturae 2000 - Domain Bacteria - Domain Bacteria Woese et al. 1990 1 Genus †Eoleptonema Schopf 1983, incertae sedis 2 Genus †Primaevifilum Schopf 1983, incertae sedis 3 Genus †Archaeotrichion Schopf 1968, incertae sedis 4 Genus †Siphonophycus Schopf 1968, incertae sedis 5 Genus Bactoderma Tepper and Korshunova 1973 (Approved Lists 1980), incertae sedis 6 Genus Stibiobacter Lyalikova 1974 (Approved Lists 1980), incertae sedis 7.1.1.1.1.1 Superphylum "Proteobacteria" Craig et al. 2010 1.1 Phylum "Alphaproteobacteria" 1.2.1 Phylum "Acidithiobacillia" 1.2.2.1 Phylum "Gammaproteobacteria" 1.2.2.2.1 Candidate phylum Muproteobacteria (RIF23) Anantharaman et al. 2016 1.2.2.2.2 Phylum "Betaproteobacteria" 2 Phylum "Zetaproteobacteria" 7.1.1.1.1.2 Phylum "Deltaproteobacteria_1" 7.1.1.1.2.1.1.1 Phylum "Deltaproteobacteria" [polyphyletic] 7.1.1.1.2.1.1.2.1 Phylum "Deltaproteobacteria_2" 7.1.1.1.2.1.1.2.2 Phylum "Deltaproteobacteria_3" 7.1.1.1.2.1.2 Candidate phylum Dadabacteria (CSP1-2) Hug et al. 2015 7.1.1.1.2.2.1 Candidate phylum "MBNT15" 7.1.1.1.2.2.2 Candidate phylum "Uncultured Bacterial Phylum 10 (UBP10)" Parks et al. 2017 7.1.1.2.1 Phylum "Nitrospirae_1" 7.1.1.2.2 Phylum Chrysiogenetes Garrity and Holt 2001 7.1.2.1.1 Phylum "Nitrospirae" Garrity and Holt 2001 [polyphyletic] 7.1.2.1.2.1.1 Candidate phylum Rokubacteria (CSP1-6) Hug et al.
    [Show full text]
  • Libros Sobre Enfermedades Autoinmunes: Tratamientos, Tipos Y Diagnósticos- Profesor Dr
    - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS . AUTOR: PROFESOR DR. ENRIQUE BARMAIMON.- - Doctor en Medicina.- - Cátedras de: - Anestesiología - Cuidados Intensivos - Neuroanatomía - Neurofisiología - Psicofisiología - Neuropsicología. - 9 TOMOS - - TOMO VI - -AÑO 2020- 1ª Edición Virtual: (.2020. 1)- - MONTEVIDEO, URUGUAY. 1 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - Queda terminantemente prohibido reproducir este libro en forma escrita y virtual, total o parcialmente, por cualquier medio, sin la autorización previa del autor. -Derechos reservados. 1ª Edición. Año 2020. Impresión [email protected]. - email: [email protected].; y [email protected]; -Montevideo, 15 de enero de 2020. - BIBLIOTECA VIRTUAL DE SALUD del S. M.U. del URUGUAY; y BIBLIOTECA DEL COLEGIO MÉDICO DEL URUGUAY. 0 0 0 0 0 0 0 0. 2 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - TOMO V I - 3 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - ÍNDICE.- - TOMO I . - - ÍNDICE. - PRÓLOGO.- - INTRODUCCIÓN. - CAPÍTULO I: -1)- GENERALIDADES. -1.1)- DEFINICIÓN. -1.2)- CAUSAS Y FACTORES DE RIESGO. -1.2.1)- FACTORES EMOCIONALES. -1.2.2)- FACTORES AMBIENTALES. -1.2.3)- FACTORES GENÉTICOS. -1.3)- Enterarse aquí, como las 10 Tipos de semillas pueden mejorar la salud. - 1.4)- TIPOS DE TRATAMIENTO DE ENFERMEDADES AUTOINMUNES. -1.4.1)- Remedios Naturales. -1.4.1.1)- Mejorar la Dieta.
    [Show full text]
  • Marine Sediments Illuminate Chlamydiae Diversity and Evolution
    Supplementary Information for: Marine sediments illuminate Chlamydiae diversity and evolution Jennah E. Dharamshi1, Daniel Tamarit1†, Laura Eme1†, Courtney Stairs1, Joran Martijn1, Felix Homa1, Steffen L. Jørgensen2, Anja Spang1,3, Thijs J. G. Ettema1,4* 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden 2 Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway 3 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, The Netherlands 4 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. † These authors contributed equally * Correspondence to: Thijs J. G. Ettema, Email: [email protected] Supplementary Information Supplementary Discussions ............................................................................................................................ 3 1. Evolutionary relationships within the Chlamydiae phylum ............................................................................. 3 2. Insights into the evolution of pathogenicity in Chlamydiaceae ...................................................................... 8 3. Secretion systems and flagella in Chlamydiae .............................................................................................. 13 4. Phylogenetic diversity of chlamydial nucleotide transporters. ....................................................................
    [Show full text]
  • The Bright Side of Microbial Dark Matter: Lessons Learned
    Available online at www.sciencedirect.com ScienceDirect The bright side of microbial dark matter: lessons learned from the uncultivated majority 1 2 1 Lindsey Solden , Karen Lloyd and Kelly Wrighton Microorganisms are the most diverse and abundant life forms The first realizations of just how diverse and unexplored on Earth. Yet, in many environments, only 0.1–1% of them have microorganisms are came from analyzing microbial small been cultivated greatly hindering our understanding of the subunit ribosomal RNA (SSU or 16S rRNA) gene sequences microbial world. However, today cultivation is no longer a directly from environmental samples [7]. These analyses requirement for gaining access to information from the revealed that less than half of the known microbial phyla uncultivated majority. New genomic information from contained a single cultivated representative. Phyla com- metagenomics and single cell genomics has provided insights posed exclusively of uncultured representatives are referred into microbial metabolic cooperation and dependence, to as Candidate Phyla (CP). Borrowing language from generating new avenues for cultivation efforts. Here we astronomy, microbiologists operationally define these CP summarize recent advances from uncultivated phyla and as microbial dark matter, because these organisms likely discuss how this knowledge has influenced our understanding account for a large portion of the Earth’s biomass and of the topology of the tree of life and metabolic diversity. biodiversity, yet their basic metabolic and ecological prop- erties are not known. This uncultivated majority represents Addresses 1 a grand challenge to the scientific community and until we Department of Microbiology, The Ohio State University, Columbus, OH solve the mysteries of the CP, our knowledge of the micro- 43210, USA 2 Department of Microbiology, University of Tennessee, Knoxville, TN bial world around us is profoundly skewed by what we have 37996, USA cultivated in the laboratory [8 ].
    [Show full text]
  • Biological Capacities Clearly Define a Major Subdivision in Domain Bacteria 4 5 Raphaël Méheust+,1,2, David Burstein+,1,3,8, Cindy J
    bioRxiv preprint doi: https://doi.org/10.1101/335083; this version posted May 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Research article 2 3 Biological capacities clearly define a major subdivision in Domain Bacteria 4 5 Raphaël Méheust+,1,2, David Burstein+,1,3,8, Cindy J. Castelle1,2,4 and Jillian F. Banfield1,2,4,5,6,7,*,# 6 7 1Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA 8 2Innovative Genomics Institute, Berkeley, CA, USA 9 3 California Institute for Quantitative Biosciences (QB3), University of California Berkeley, CA USA 10 4Chan Zuckerberg Biohub, San Francisco, CA, USA 11 5University of Melbourne, Melbourne, VIC, Australia 12 6Lawrence Berkeley National Laboratory, Berkeley, CA, USA 13 7Department of Environmental Science, Policy and Management, University of California, Berkeley, 14 Berkeley, CA, USA 15 8Present address: School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of 16 Life Sciences, Tel Aviv University, Tel Aviv, Israel 17 +These authors contributed equally to this work 18 *Correspondence: [email protected] 19 #Lead Contact 20 21 Resume 22 Phylogenetic analyses separate candidate phyla radiation (CPR) bacteria from other bacteria, but 23 the degree to which their proteomes are distinct remains unclear. Here, we leveraged a proteome 24 database that includes sequences from thousands of uncultivated organisms to identify protein 25 families and examine their organismal distributions. We focused on widely distributed protein 26 families that co-occur in genomes, as they likely foundational for metabolism.
    [Show full text]
  • Biosynthetic Capacity, Metabolic Variety and Unusual Biology in the CPR and DPANN Radiations Cindy J
    Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations Cindy J. Castelle 1,2, Christopher T. Brown 1, Karthik Anantharaman 1,5, Alexander J. Probst 1,6, Raven H. Huang3 and Jillian F. Banfield 1,2,4* 1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 2Chan Zuckerberg Biohub, San Francisco, CA, USA. 3Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA. 4Department of Environmental Science, Policy, and Management, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5Department of Bacteriology, University of WisconsinMadison, Madison, WI, USA. 6Department of Chemistry, Biofilm Center, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany. *e-mail: [email protected] Abstract Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth’s environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living.
    [Show full text]
  • Evidence of Independent Acquisition and Adaption of Ultra-Small Bacteria to Human Hosts Across the Highly Diverse Yet Reduced Genomes of the Phylum Saccharibacteria
    bioRxiv preprint doi: https://doi.org/10.1101/258137; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria Jeffrey S. McLeana,b,1 , Batbileg Borc#, Thao T. Toa#, Quanhui Liua, Kristopher A. Kernsa, Lindsey Soldend, Kelly Wrightond, Xuesong Hec, Wenyuan Shic a Department of Periodontics, University of Washington, Seattle, WA, 98195, USA b Department of Microbiology, University of Washington, Seattle, WA, 98195, USA c Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts 02142 dDepartment of Microbiology, The Ohio State University, Columbus, OH, USA Short title: Host Adaptation of the Saccharibacteria Phylum Keywords: TM7, Saccharibacteria, Candidate Phyla Radiation, epibiont, oral microbiome, # These authors contributed equally to this work. 1To whom correspondence should be addressed. Email: [email protected] Author contribution: JSM, XH, BB and WS conceived the study and designed experiments. XH, JSM, BB, TT, KK, LS, KW, QL conducted experiments. All authors listed analyzed the data. JSM, XH, BB wrote the paper with input from all other authors. All authors have read and approved the manuscript. This research was funded by NIH NIGMS R01GM095373 (J.S.M.), NIH NIDCR Awards 1R01DE023810 (W.S., X.H., and J.M.), 1R01DE020102 (W.S., X.H., and J.S.M.), F32DE025548-01 (B.B.), T90DE021984 (T.T.) 1R01DE026186 (W.S., X.H., and J.S.M.).
    [Show full text]
  • A New View of the Tree of Life
    LETTERS PUBLISHED: 11 APRIL 2016 | ARTICLE NUMBER: 16048 | DOI: 10.1038/NMICROBIOL.2016.48 OPEN A new view of the tree of life Laura A. Hug1†, Brett J. Baker2, Karthik Anantharaman1, Christopher T. Brown3, Alexander J. Probst1, Cindy J. Castelle1,CristinaN.Butterfield1,AlexW.Hernsdorf3, Yuki Amano4,KotaroIse4, Yohey Suzuki5, Natasha Dudek6,DavidA.Relman7,8, Kari M. Finstad9, Ronald Amundson9, Brian C. Thomas1 and Jillian F. Banfield1,9* The tree of life is one of the most important organizing prin- Contributing to this expansion in genome numbers are single cell ciples in biology1. Gene surveys suggest the existence of an genomics13 and metagenomics studies. Metagenomics is a shotgun enormous number of branches2, but even an approximation of sequencing-based method in which DNA isolated directly from the the full scale of the tree has remained elusive. Recent depic- environment is sequenced, and the reconstructed genome fragments tions of the tree of life have focused either on the nature of are assigned to draft genomes14. New bioinformatics methods yield deep evolutionary relationships3–5 or on the known, well-classi- complete and near-complete genome sequences, without a reliance fied diversity of life with an emphasis on eukaryotes6. These on cultivation or reference genomes7,15. These genome- (rather than approaches overlook the dramatic change in our understanding gene) based approaches provide information about metabolic poten- of life’s diversity resulting from genomic sampling of previously tial and a variety of phylogenetically informative sequences that can unexamined environments. New methods to generate genome be used to classify organisms16. Here, we have constructed a tree sequences illuminate the identity of organisms and their meta- of life by making use of genomes from public databases and 1,011 bolic capacities, placing them in community and ecosystem con- newly reconstructed genomes that we recovered from a variety of texts7,8.
    [Show full text]
  • Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR
    Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication Charles Bernard, Romain Lannes, Yanyan Li, Éric Bapteste, Philippe Lopez To cite this version: Charles Bernard, Romain Lannes, Yanyan Li, Éric Bapteste, Philippe Lopez. Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication. mSystems, 2020, 5 (5), 10.1128/mSystems.00414-20. hal-02967400 HAL Id: hal-02967400 https://hal.archives-ouvertes.fr/hal-02967400 Submitted on 14 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. RESEARCH ARTICLE Ecological and Evolutionary Science crossm Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication Downloaded from Charles Bernard,a,b Romain Lannes,a* Yanyan Li,b Éric Bapteste,a Philippe Lopeza aInstitut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, Paris, France bUnité Molécules de Communication et Adaptation des Micro-organismes (MCAM), CNRS, Museum National d’Histoire Naturelle, Paris, France ABSTRACT The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity.
    [Show full text]
  • Genome-Resolved Metagenomics Reveals Site-Specific Diversity of Episymbiotic CPR Bacteria and DPANN Archaea in Groundwater Ecosystems
    ARTICLES https://doi.org/10.1038/s41564-020-00840-5 Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems Christine He 1, Ray Keren 2, Michael L. Whittaker3,4, Ibrahim F. Farag 1, Jennifer A. Doudna 1,5,6,7,8, Jamie H. D. Cate 1,5,6,7 and Jillian F. Banfield 1,4,9 ✉ Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host associa- tion of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproduc- ibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.
    [Show full text]