in

Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth

  • 1.

    Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus genome (MIUVIG). Nat Biotechnol 2019;37:29–37.

    PubMed 

    Google Scholar 

  • 2.

    Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. Uncovering Earth’s virome. Nature. 2016;536:425–30.

    PubMed 

    Google Scholar 

  • 3.

    Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell. 2019;177:1109–23.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 4.

    Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome. 2019;7:1–15.

    Google Scholar 

  • 5.

    Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, et al. Hidden diversity of soil giant viruses. Nat Commun 2018;9:1–9.

    Google Scholar 

  • 6.

    Trubl G, Jang H Bin, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems 2018;3:e00076–18.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 7.

    Guerin E, Shkoporov A, Stockdale SR, Clooney AG, Ryan FJ, Sutton TDS, et al. Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut. Cell Host Microbe. 2018;24:653–664.e6.

    PubMed 

    Google Scholar 

  • 8.

    Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, et al. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun 2017;8:1–13.

    Google Scholar 

  • 9.

    Aguirre de Cárcer D, Angly FE, Alcamí A. Evaluation of viral genome assembly and diversity estimation in deep metagenomes. BMC Genomics. 2014;15:1–12.

    Google Scholar 

  • 10.

    Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 2017;5:e3817.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D. Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature. 2011;474:604–8.

    PubMed 

    Google Scholar 

  • 12.

    Rodriguez-Valera F, Martin-Cuadrado A-B, Rodriguez-Brito B, Pasic L, Thingstad TF, Rohwer F, et al. Explaining microbial population genomics through phage predation. Nat Rev Microbiol 2009;7:828–36.

    PubMed 

    Google Scholar 

  • 13.

    Marston MF, Pierciey FJ, Shepard A, Gearin G, Qi J, Yandava C, et al. Rapid diversification of coevolving marine Synechococcus and a virus. Proc Natl Acad Sci USA 2012;109:4544–9.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 14.

    Enav H, Kirzner S, Lindell D, Mandel-Gutfreund Y, Béjà O. Adapt sub-Optim hosts is a Driv viral Diversif ocean Nat Comm 2018;9:1–11.

    Google Scholar 

  • 15.

    Boon M, Holtappels D, Lood C, van Noort V, Lavigne R. Host range expansion of pseudomonas virus LUZ7 is driven by a conserved tail fiber mutation. PHAGE. 2020;1:87–90.

    Google Scholar 

  • 16.

    Bernheim A, Sorek R. The pan-immune system of bacteria: antiviral defence as a community resource. Nat Rev Microbiol 2020;18:113–9.

    PubMed 

    Google Scholar 

  • 17.

    Sørensen MA, Kurland CG, Pedersen S. Codon usage determines translation rate in Escherichia coli. J Mol Biol 1989;207:365–77.

    PubMed 

    Google Scholar 

  • 18.

    Varenne S, Buc J, Lloubes R, Lazdunski C. Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J Mol Biol 1984;180:549–76.

    PubMed 

    Google Scholar 

  • 19.

    Yu CH, Dang Y, Zhou Z, Wu C, Zhao F, Sachs MS, et al. Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Mol Cell. 2015;59:744–54.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 20.

    Plotkin JB, Kudla G. Synonymous but not the same: The causes and consequences of codon bias. Nat Rev Genet 2011;12:32–42.

    PubMed 

    Google Scholar 

  • 21.

    Chu D, Wei L. Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation. BMC Cancer. 2019;19:359.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 22.

    Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, et al. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 2014;513:242–5.

    PubMed 

    Google Scholar 

  • 23.

    Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, et al. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019;4:1727–36.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nat. Microbiol. 2019;5:1–7.

  • 25.

    Coutinho FH, Rosselli R, Rodríguez-Valera F. Trends of microdiversity reveal depth-dependent evolutionary strategies of viruses in the Mediterranean. mSystems. 2019;4:1–17.

    Google Scholar 

  • 26.

    Needham DM, Sachdeva R, Fuhrman JA. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME J. 2017;11:1614–29.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Martinez-Hernandez F, Fornas Ò, Lluesma Gomez M, Garcia-Heredia I, Maestre-Carballa L, López-Pérez M, et al. Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean. ISME J. 2019;13:232–6.

    PubMed 

    Google Scholar 

  • 28.

    McMullen A, Martinez‐Hernandez F, Martinez‐Garcia M. Absolute quantification of infecting viral particles by chip‐based digital polymerase chain reaction. Environ Microbiol Rep. 2019;11:855–60.

    PubMed 

    Google Scholar 

  • 29.

    Marston MF, Amrich CG. Recombination and microdiversity in coastal marine cyanophages. Environ Microbiol. 2009;11:2893–903.

    PubMed 

    Google Scholar 

  • 30.

    Marston MF, Martiny JBH. Genomic diversification of marine cyanophages into stable ecotypes. Environ Microbiol 2016;18:4240–53.

    PubMed 

    Google Scholar 

  • 31.

    Cordero OX. Endemic cyanophages and the puzzle of phage-bacteria coevolution. Environ Microbiol 2017;19:420–2.

    PubMed 

    Google Scholar 

  • 32.

    Shannon CE. The mathematical theory of communication. 1963. MD Comput. 1997;14:306–17.

    PubMed 

    Google Scholar 

  • 33.

    Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 2016;537:689–93.

    PubMed 

    Google Scholar 

  • 34.

    Bobay L-M, Ochman H. Biological species in the viral world. Proc Natl Acad Sci USA 2018;115:6040–5.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 35.

    Henson MW, Lanclos VC, Faircloth BC, Thrash JC. Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. ISME J. 2018;12:1846–60.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Paez-Espino D, Roux S, Chen I-MA, Palaniappan K, Ratner A, Chu K, et al. IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. Nucleic Acids Res. 2019;47:D678–D686.

    PubMed 

    Google Scholar 

  • 37.

    Brum JR, Ignacio-Espinoza JC, Kim E-H, Trubl G, Jones RM, Roux S, et al. Illuminating structural proteins in viral ‘dark matter’ with metaproteomics. Proc Natl Acad Sci USA 2016;113:2436–41.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 38.

    Sakowski EG, Arora-Williams K, Tian F, Zayed AA, Zablocki O, Sullivan MB, et al. Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR. Nat. Microbiol. 2021;6:1–13.

  • 39.

    Alonso-Sáez L, Morán XAG, Clokie MR. Low activity of lytic pelagiphages in coastal marine waters. ISME J. 2018;12:2100–2.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 40.

    Martinez‐Hernandez F, Luo E, Tominaga K, Ogata H, Yoshida T, DeLong EF, et al. Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses in Earth. Environ Microbiol Rep. 2020;12:214–219

  • 41.

    Mruwat N, Carlson MCG, Goldin S, Ribalet F, Kirzner S, Hulata Y, et al. A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances. ISME J. 2021;15:41–54.

    PubMed 

    Google Scholar 

  • 42.

    de Avila e Silva S, Echeverrigaray S, Gerhardt GJL. BacPP: bacterial promoter prediction-A tool for accurate sigma-factor specific assignment in enterobacteria. J Theor Biol 2011;287:92–99.

    PubMed 

    Google Scholar 

  • 43.

    Sampaio M, Rocha M, Oliveira H, Dias O. Predicting promoters in phage genomes using PhagePromoter. Bioinformatics. 2019;35:5301–2.

    PubMed 

    Google Scholar 

  • 44.

    Allert M, Cox JC, Hellinga HW. Multifactorial determinants of protein expression in prokaryotic open reading frames. J Mol Biol. 2010;402:905–18.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

    Dressaire C, Picard F, Redon E, Loubière P, Queinnec I, Girbal L, et al. Role of mRNA stability during bacterial adaptation. PLoS ONE 2013;8:e59059.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 46.

    Deana A, Belasco JG. Lost in translation: The influence of ribosomes on bacterial mRNA decay. Genes Dev. 2005;19:2526–33.

    PubMed 

    Google Scholar 

  • 47.

    Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, Landry ZC, et al. Abundant SAR11 viruses in the ocean. Nature. 2013;494:357–60.

    PubMed 

    Google Scholar 

  • 48.

    Zhang Z, Qin F, Chen F, Chu X, Luo H, Zhang R, et al. Culturing novel and abundant pelagiphages in the ocean. Environ Microbiol 2020;1462-2920:15272.

    Google Scholar 

  • 49.

    Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, et al. Pelagiphages in the Podoviridae family integrate into host genomes. Environ Microbiol. 2018;21:1989–2001.

  • 50.

    Morris RM, Cain KR, Hvorecny KL, Kollman JM. Lysogenic host–virus interactions in SAR11 marine bacteria. Nat Microbiol 2020;5:1011–5.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 51.

    Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc Lond, B, Biol Sci 2006;361:1929–40.

    Google Scholar 

  • 52.

    Rosselló-Mora R. Updating prokaryotic taxonomy. J Bacteriol. 2005;187:6255–7.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2017;2:1533–42.

    PubMed 

    Google Scholar 

  • 54.

    Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009;106:19126–31.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 55.

    Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, et al. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 2015;4:e06416.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 56.

    Gregory AC, Solonenko SA, Ignacio-Espinoza JC, LaButti K, Copeland A, Sudek S, et al. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC genomics. 2016;17:930.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 57.

    Martinez-Hernandez F, Garcia-Heredia I, Lluesma Gomez M, Maestre-Carballa L, Martínez Martínez J, Martinez-Garcia M. Droplet digital PCR for estimating absolute abundances of widespread Pelagibacter viruses. Front Microbiol 2019;10:1226.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, et al. Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. 2019;7:e6800.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 59.

    Beaulaurier J, Luo E, Eppley JM, Uyl P Den, Dai X, Burger A, et al. Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. Genome Res. 2020;30:437–46.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 60.

    Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, Harliwong I, et al. Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience 2020;9:giaa146.

  • 61.

    Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol 2019;37:1155–62.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 62.

    Martínez Martínez J, Martinez-Hernandez F, Martinez-Garcia M. Single-virus genomics and beyond. Nat Rev Microbiol. 2020;18:705–16.

    PubMed 

    Google Scholar 

  • 63.

    Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, et al. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J. 2015;9:2386–99.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 64.

    Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R. Expanding the marine virosphere using metagenomics. PLoS Genet. 2013;9:e1003987.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 65.

    Mizuno CM, Ghai R, Saghaï A, López-García P, Rodriguez-Valera F. Genomes of abundant and widespread viruses from the deep ocean. mBio. 2016;7:e00805–16.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 66.

    Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinforma. 2012;13:134.

    Google Scholar 

  • 67.

    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 68.

    Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.

    PubMed 

    Google Scholar 

  • 69.

    Philosof A, Yutin N, Flores-Uribe J, Sharon I, Koonin EV, Béjà O. Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota. Curr Biol. 2017;27:1362–8.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 70.

    Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ. 2017;5:e3428.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 71.

    Bin Jang H, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol 2019;37:632–9.

    Google Scholar 

  • 72.

    Bobay L-M, Ellis BS-H, Ochman H. ConSpeciFix: classifying prokaryotic species based on gene flow. Bioinformatics. 2018;34:3738–40.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 73.

    Bobay L-M, Ochman H. Biological species are universal across life’s domains. Genome Biol Evol. 2017;9:491–501.

    PubMed Central 

    Google Scholar 

  • 74.

    Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.

    Google Scholar 

  • 75.

    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 76.

    Harris CD, Torrance EL, Raymann K, Bobay L-M. CoreCruncher: Fast and robust construction of core genomes in large prokaryotic data sets. Mol. Biol. Evol. 2020;38:727–734.

  • 77.

    Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 78.

    Rice P, Longden L, Bleasby A EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000. Elsevier Ltd., 16: 276–7

  • 79.

    Džunková M, Low SJ, Daly JN, Deng L, Rinke C, Hugenholtz P. Defining the human gut host–phage network through single-cell viral tagging. Nat Microbiol 2019;4:2192–203.

    PubMed 

    Google Scholar 

  • 80.

    Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 81.

    Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 82.

    Swan BK, Ehrhardt CJ, Reifel KM, Moreno LI, Valentine DL. Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a california hypersaline lake, the Salton Sea. Appl Environ Microbiol 2010;76:757–68.

    PubMed 

    Google Scholar 

  • 83.

    Baran N, Goldin S, Maidanik I, Lindell D. Quantification of diverse virus populations in the environment using the polony method. Nat Microbiol 2018;3:62–72.

    PubMed 

    Google Scholar 


  • Source: Ecology - nature.com

    MIT makes strides on climate action plan

    Forest fires and climate-induced tree range shifts in the western US