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Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification

  • Prosser JI, Hink L, Gubry-Rangin C, Nicol GW. Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies. Glob Chang Biol. 2020;26:103–18.

    Article 
    PubMed 

    Google Scholar 

  • Huang L, Chakrabarti S, Cooper J, Perez A, John SM, Daroub SH, et al. Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil. ISME Commun. 2021;1:19.

    Article 

    Google Scholar 

  • Hink L, Gubry-Rangin C, Nicol GW, Prosser JI. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J. 2018;12:1084–93.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Li Y, Chapman SJ, Nicol GW, Yao H. Nitrification and nitrifiers in acidic soils. Soil Biol Biochem. 2018;116:290–301.

    Article 
    CAS 

    Google Scholar 

  • Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J 2019;13:618–31.

    Article 
    PubMed 
    CAS 

    Google Scholar 

  • Kim J-G, Kim S-J, Cvirkaite-Krupovic V, Yu W-J, Gwak J-H, López-Pérez M, et al. Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea. Proc Natl Acad Sci USA. 2019;116:15645–50.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Emerson JB. Soil Viruses: A New Hope. mSystems 2019;4:e00120–19.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Santos-Medellín C, Estera-Molina K, Yuan M, Pett-Ridge J, Firestone MK, Emerson JB. Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands. Proc Natl Acad Sci USA. 2022;119:e2209132119.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wu R, Davison MR, Gao Y, Nicora CD, Mcdermott JE, Burnum-Johnson KE, et al. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun Biol. 2021;4:992.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Braga LPP, Spor A, Kot W, Breuil M-C, Hansen LH, Setubal JC, et al. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Microbiome 2020;8:52.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Albright MBN, Gallegos-Graves LV, Feeser KL, Montoya K, Emerson JB, Shakya M, et al. Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition. ISME Commun. 2022;2:24.

    Article 

    Google Scholar 

  • Starr EP, Shi S, Blazewicz SJ, Koch BJ, Probst AJ, Hungate BA, et al. Stable-isotope-informed, genome-resolved metagenomics uncovers potential cross-kingdom interactions in rhizosphere soil. mSphere 2021;6:e0008521.

    Article 
    PubMed 

    Google Scholar 

  • Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 2021;9:208.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Lee S, Sieradzki ET, Nicolas AM, Walker RL, Firestone MK, Hazard C, et al. Methane-derived carbon flows into host–virus networks at different trophic levels in soil. Proc Natl Acad Sci USA. 2021;118:e2105124118.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Nicol GW, Leininger S, Schleper C, Prosser JI. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol. 2008;10:2966–78.

    Article 
    PubMed 
    CAS 

    Google Scholar 

  • Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020;36:1925–7.

    CAS 

    Google Scholar 

  • Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun. 2018;9:1517.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cardinale DJ, Duffy S. Single-stranded genomic architecture constrains optimal codon usage. Bacteriophage 2011;1:219–24.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lee S, Sorensen JW, Walker RL, Emerson JB, Nicol GW, Hazard C. Soil pH influences the structure of virus communities at local and global scales. Soil Biol Biochem. 2022;166:108569.

    Article 
    CAS 

    Google Scholar 

  • Jang HB, 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.

    Article 

    Google Scholar 

  • Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinformatics 2017;33:2379–80.

    Article 
    PubMed 
    CAS 

    Google Scholar 

  • Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, et al. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proc Natl Acad Sci Usa 2016;113:7937–46.

    Article 

    Google Scholar 

  • Reyes C, Hodgskiss LH, Kerou M, Pribasnig T, Abby SS, Bayer B, et al. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation. ISME J 2020;14:2659–74.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • Sieradzki ET, Greenlon A, Nicolas AM, Firestone MK, Pett-Ridge J, Blazewicz SJ, et al. Functional succession of actively growing soil microorganisms during rewetting is shaped by precipitation history. bioRxiv. 2022; 2022.06.28.498032.


  • Source: Ecology - nature.com

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