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Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

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  • 1.

    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. 2016;18:1686–703.

    CAS 
    PubMed 

    Google Scholar 

  • 2.

    Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, et al. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol. 2016;18:159–73.

    CAS 
    PubMed 

    Google Scholar 

  • 3.

    Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:1–11.

    Google Scholar 

  • 4.

    Lu X, Seuradge BJ, Neufeld JD. Biogeography of soil Thaumarchaeota in relation to soil depth and land usage. FEMS Microbiol Ecol. 2017;93:fiw246.

    PubMed 

    Google Scholar 

  • 5.

    Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota dominate subsurface ammonia-oxidizing communities in semi-arid floodplains in the western United States. Micro Ecol. 2020;80:778–92.

    CAS 

    Google Scholar 

  • 6.

    Tolar BB, Boye K, Bobb C, Maher K, Bargar JR, Francis CA. Stability of floodplain subsurface microbial communities through seasonal hydrological and geochemical cycles. Front Earth Sci. 2020;8:338.

    Google Scholar 

  • 7.

    Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. PNAS. 2005;102:14683–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 8.

    Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk H-P, Schleper C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol. 2005;7:1985–95.

    CAS 
    PubMed 

    Google Scholar 

  • 9.

    Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature. 2006;442:806–9.

    CAS 
    PubMed 

    Google Scholar 

  • 10.

    Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P, et al. Archaeal nitrification in the ocean. PNAS. 2006;103:12317–22.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Prosser JI, Nicol GW. Archaeal and bacterial ammonia-oxidisers in soil:the quest for niche specialisation and differentiation. Trends Microbiol. 2012;20:523–31.

    CAS 
    PubMed 

    Google Scholar 

  • 12.

    Mußmann M, Brito I, Pitcher A, Damste JSS, Hatzenpichler R, Richter A, et al. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. PNAS. 2011;108:16771–6.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 13.

    Weber EB, Lehtovirta-Morley LE, Prosser JI, Gubry-Rangin C, Laanbroek R. Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota. FEMS Microbiol Ecol. 2015;91:fiv001.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 14.

    Lin X, Handley KM, Gilbert JA, Kostka JE. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J. 2015;9:2740–4.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 15.

    Kato S, Itoh T, Yuki M, Nagamori M, Ohnishi M, Uematsu K, et al. Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. ISME J. 2019;13:2465–74.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 16.

    Aylward FO, Santoro AE. Heterotrophic Thaumarchaea with small genomes are widespread in the dark ocean. mSystems. 2020;5:e00415–20.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 17.

    Reji L, Francis CA. Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME J. 2020;14:2105–15.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 18.

    Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, et al. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J. 2019;13:2150–61.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 19.

    Kerou M, Alves RJE, Schleper C. Nitrososphaerales. In: Bergeys manual of systematics of archaea and bacteria ed. Bergey’s Manual Trust (Hoboken, NJ: John Wiley & Sons). 2016. https://doi.org/10.1002/9781118960608.cbm00055.

  • 20.

    Qin W, Martens-Habbena W, Kobelt JN, Stahl DA. Candidatus nitrosopumilales. In: Bergeys manual of systematics of archaea and bacteria ed. Bergey’s Manual Trust (Hoboken, NJ: John Wiley & Sons). 2016. https://doi.org/10.1002/9781118960608.gbm01290.

  • 21.

    Prosser JI, Nicol GW. Candidatus Nitrosotaleales. In: Bergeys manual of systematics of archaea and bacteria ed. Bergey’s Manual Trust (Hoboken, NJ: John Wiley & Sons). 2016. https://doi.org/10.1002/9781118960608.obm00123.

  • 22.

    Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, et al. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. PNAS. 2015;112:9370–5.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 23.

    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.

    CAS 
    PubMed 

    Google Scholar 

  • 24.

    Szukics U, Abell GCJ, Hödl V, Mitter B, Sessitsch A, Hackl E, et al. Nitrifiers and denitrifiers respond rapidly to changed moisture and increasing temperature in a pristine forest soil. FEMS Microbiol Ecol. 2010;72:395–406.

    CAS 
    PubMed 

    Google Scholar 

  • 25.

    Höfferle Š, Nicol GW, Pal L, Hacin J, Prosser JI, Mandić-Mulec I. Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile. FEMS Microbiol Ecol. 2010;74:302–15.

    PubMed 

    Google Scholar 

  • 26.

    Tourna M, Freitag TE, Nicol GW, Prosser JI. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol. 2008;10:1357–64.

    CAS 
    PubMed 

    Google Scholar 

  • 27.

    He J-Z, Shen J-P, Zhang L-M, Zhu Y-G, Zheng Y-M, Xu M-G, et al. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol. 2007;9:2364–74.

    CAS 
    PubMed 

    Google Scholar 

  • 28.

    Marusenko Y, Bates ST, Anderson I, Johnson SL, Soule T, Garcia-Pichel F. Ammonia-oxidizing archaea and bacteria are structured by geography in biological soil crusts across North American arid lands. Ecol Process. 2013;2:9.

    Google Scholar 

  • 29.

    Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol. 2014;90:39–53.

    CAS 
    PubMed 

    Google Scholar 

  • 30.

    Purkamo L, Kietäväinen R, Miettinen H, Sohlberg E, Kukkonen I, Itävaara M, et al. Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater. FEMS Microbiol Ecol. 2018;94.

  • 31.

    Bushnell B BBTools software package. 2014. http://bbtools.jgi.doe.gov.

  • 32.

    Li H. BFC:correcting Illumina sequencing errors. Bioinformatics. 2015;31:2885–7.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.

    CAS 
    PubMed 

    Google Scholar 

  • 34.

    Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, et al. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.

    CAS 
    PubMed 

    Google Scholar 

  • 35.

    Kang D, Li F, Kirton ES, Thomas A, Egan RS, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2:26.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 37.

    Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0:an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.

    CAS 
    PubMed 

    Google Scholar 

  • 38.

    Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6:158.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, et al. Assembling genomes and mini-metagenomes from highly chimeric reads. In: Deng M, Jiang R, Sun F, Zhang X, editors. Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science, Springer; Berlin, Heidelberg. 2013;7821:158–70.

  • 40.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 41.

    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 

  • 42.

    Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;38:1079–86.

    CAS 
    PubMed 

    Google Scholar 

  • 43.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.

    CAS 
    PubMed 

    Google Scholar 

  • 44.

    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

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

    Google Scholar 

  • 46.

    Seemann T. Prokka:rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS 
    PubMed 

    Google Scholar 

  • 47.

    Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726–31.

    CAS 
    PubMed 

    Google Scholar 

  • 48.

    Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 49.

    Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Mering von C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34:2115–22.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 50.

    Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–14.

    CAS 

    Google Scholar 

  • 51.

    Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2013;42:D206–14.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 52.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Elbourne LDH, Tetu SG, Hassan KA, Paulsen IT. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Res. 2016;45:D320–4.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 54.

    Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997;10:1–6.

    CAS 
    PubMed 

    Google Scholar 

  • 55.

    Armenteros JJA, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37:420–3.

    Google Scholar 

  • 56.

    Sonnhammer EL, Heijne G, von, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998;6:175–82.

    CAS 
    PubMed 

    Google Scholar 

  • 57.

    Krogh A, Larsson B, Heijne G, von, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 59.

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

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 60.

    Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Nucleic Acids Res. 2009;25:1972–3.

    Google Scholar 

  • 61.

    Nguyen L-T, Schmidt HA, Haeseler von A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Nucleic Acids Res. 2015;32:268–74.

    CAS 

    Google Scholar 

  • 62.

    Hoang DT, Chernomor O, Haeseler von A, Minh BQ. Le Sy Vinh. UFBoot2: improving the ultrafast bootstrap approximation. Nucleic Acids Res. 2017;35:518–22.

    Google Scholar 

  • 63.

    Kalyaanamoorthy S, Minh BQ, Wong TKF, Haeseler von A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 64.

    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 

  • 65.

    Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539–9.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 66.

    Chen I-MA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 2021;49:D751–63.

    CAS 
    PubMed 

    Google Scholar 

  • 67.

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

    PubMed 
    PubMed Central 

    Google Scholar 

  • 68.

    Tolar BB, Mosier AC, Lund MB, Francis CA. Nitrosarchaeum. In: Bergeys manual of systematics of archaea and bacteria ed. Bergey’s Manual Trust (Hoboken, NJ: John Wiley & Sons). 2019:1–9. https://doi.org/10.1002/9781118960608.gbm01289.

  • 69.

    Park S-J, Kim J-G, Jung M-Y, Kim S-J, Cha I-T, Ghai R, et al. Draft genome sequence of an ammonia-oxidizing archaeon, “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in the Arctic Circle. J Bacteriol. 2012;194:6948–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 70.

    Kim BK, Jung M-Y, Yu DS, Park S-J, Oh TK, Rhee S-K, et al. Genome sequence of an ammonia-oxidizing soil archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1. J Bacteriol. 2011;193:5539–40.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 71.

    Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol. 2003;5:787–97.

    CAS 
    PubMed 

    Google Scholar 

  • 72.

    Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Prosse, Nicol GW. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. PNAS. 2011;108:15892–7.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 73.

    Lehtovirta-Morley LE, Ross J, Hink L, Weber EB, Gubry-Rangin C, Thion C, et al. Isolation of “Candidatus Nitrosocosmicus franklandus,” a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiol Ecol. 2016;92:fiw057.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 74.

    Könneke M, Bernhard AE, la Torre de JR, Walker CB, Waterbury JB, Stahl DA. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 2005;437:543–6.

    PubMed 

    Google Scholar 

  • 75.

    Qin W, Amin SA, Martens-Habbena W, Walker CB, Urakawa H, Devol AH, et al. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. PNAS. 2014;111:12504–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 76.

    Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, et al. Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: an ammonia-oxidizing archaeon from the open ocean. PNAS. 2015;112:1173–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 77.

    Bayer B, Vojvoda J, Offre P, Alves RJE, Elisabeth NH, Garcia JA, et al. Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. ISME J. 2015;10:1051–63.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 78.

    Larentis M, Psenner R, Alfreider A. Prokaryotic community structure in deep bedrock aquifers of the Austrian Central Alps. Antonie van Leeuwenhoek. 2015;107:687–701.

    PubMed 

    Google Scholar 

  • 79.

    Lazar CS, Stoll W, Lehmann R, Herrmann M, Schwab VF, Akob DM, et al. Archaeal diversity and CO2 fixers in carbonate-/siliciclastic-rock groundwater ecosystems. Archaea. 2017;2136287.

  • 80.

    Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Williams TA, et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Commun. 2020;11:1–12.

    Google Scholar 

  • 81.

    Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, et al. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. PNAS. 2014;111:8239–44.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 82.

    Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y-I, Sugahara J, et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. PNAS. 2006;103:18296–301.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 83.

    Spang A, Poehlein A, Offre P, Zumbr a gel S, Haider S, Rychlik N, et al. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol. 2012;14:3122–45.

    CAS 
    PubMed 

    Google Scholar 

  • 84.

    Kamanda Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, et al. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. ISME J. 2015;9:396–411.

    CAS 
    PubMed 

    Google Scholar 

  • 85.

    Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, et al. Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome. Front Microbiol. 2018;9:28.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 86.

    Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T, et al. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. PNAS. 2011;108:8420–5.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 87.

    Johnson WV, Anderson PM. Bicarbonate is a recycling substrate for cyanase. J Biol Chem. 1987;262:9021–5.

    CAS 
    PubMed 

    Google Scholar 

  • 88.

    Palatinszky M, Herbold C, Jehmlich N, Pogoda M, Han P, Bergen von M, et al. Cyanate as an energy source for nitrifiers. Nature. 2015;524:105–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 89.

    Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, et al. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol. 2019;4:234–43.

    CAS 
    PubMed 

    Google Scholar 

  • 90.

    Pace HC, Brenner C. The nitrilase superfamily: classification, structure and function. Genome Biol. 2001;2:REVIEWS0001. https://doi.org/10.1186/gb-2001-2-1-reviews0001.

  • 91.

    Ramteke PW, Maurice NG, Joseph B, Wadher BJ. Nitrile-converting enzymes: an eco-friendly tool for industrial biocatalysis. Biotechnol Appl Biochem. 2013;60:459–81.

    CAS 
    PubMed 

    Google Scholar 

  • 92.

    Walker CB, la Torre de JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. PNAS. 2010;107:8818–23.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 93.

    Mosier AC, Lund MB, Francis CA. Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Micro Ecol. 2012;64:955–63.

    CAS 

    Google Scholar 

  • 94.

    Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, et al. Enrichment and genome sequence of the group i.1a ammonia-oxidizing archaeon “Ca. Nitrosotenuis uzonensis” representing a clade globally distributed in thermal habitats. PLoS ONE. 2013;8:e80835.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 95.

    Daebeler A, Herbold C, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, et al. Cultivation and genomic analysis of “Candidatus Nitrosocaldus islandicus,” an obligately thermophilic, ammonia-oxidizing thaumarchaeon from a hot spring biofilm in Graendalur valley, Iceland. Front Microbiol. 2018;9:193.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 96.

    Beam JP, Jay ZJ, Kozubal MA, Inskeep WP. Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME J. 2014;8:938–51.

    CAS 
    PubMed 

    Google Scholar 

  • 97.

    Kim J-G, Park S-J, Damste JSS, Schouten S, Rijpstra WIC, Jung M-Y, et al. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea. PNAS. 2016;113:7888–93.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 98.

    Imlay JA. Cellular defenses against superoxide and hydrogen peroxide. Annu Rev Biochem. 2008;77:755–76.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 99.

    Zhalnina KV, Dias R, Leonard MT, de Quadros PD, Camargo FAO, Drew JC, et al. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from everglades soil reveals novel genomic features of the ammonia-oxidizing archaea. PLoS ONE. 2014;9:e101648.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 100.

    Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, et al. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME J. 2017;11:1142–57.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 101.

    Tolar BB, Powers LC, Miller WL, Wallsgrove NJ, Popp BN, Hollibaugh JT. Ammonia oxidation in the ocean can be inhibited by nanomolar concentrations of hydrogen peroxide. Front Mar Sci. 2016;3:237.

    Google Scholar 

  • 102.

    Bayer B, Pelikan C, Bittner MJ, Reinthaler T, Könneke M, Herndl GJ, et al. Proteomic response of three marine ammonia-oxidizing archaea to hydrogen peroxide and their metabolic interactions with a heterotrophic alphaproteobacterium. mSystems. 2019;4:e00181–19.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 103.

    Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zhayed AAF, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560:49–54.

    CAS 
    PubMed 

    Google Scholar 

  • 104.

    Yang Y, Herbold CW, Jung M-Y, Qin W, Cai M, Du H, et al. Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration. Water Res. 2021;191:116798.

    CAS 
    PubMed 

    Google Scholar 

  • 105.

    Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, et al. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 2016;10:761–77.

    CAS 
    PubMed 

    Google Scholar 

  • 106.

    Ma K, Schicho RN, Kelly RM, Adams MW. Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase:evidence for a sulfur-reducing hydrogenase ancestor. PNAS. 1993;90:5341–4.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 107.

    Finney AJ, Sargent F. Formate hydrogenlyase:A group 4 [NiFe]-hydrogenase in tandem with a formate dehydrogenase. Adv Micro Physiol. 2019;74:465–86.

    Google Scholar 

  • 108.

    Baker BJ, Saw JH, Lind AE, Lazar CS, Hinrichs KU, Teske AP, et al. Genomic inference of the metabolism of cosmopolitan subsurface archaea, Hadesarchaea. Nat Microbiol. 2016;1:1–9.

    Google Scholar 

  • 109.

    He Y, Li M, Perumal V, Feng X, Fang J, Xie J, et al. Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments. Nat Microbiol. 2016;1:1–9.

    Google Scholar 

  • 110.

    Lazar CS, Baker BJ, Seitz KW, Teske AP. Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME J. 2017;11:1118–29.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 111.

    Farag IF, Biddle JF, Zhao R, Martino AJ, House CH, León-Zayas RI. Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments. ISME J. 2020;14:1345–58.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 112.

    Orsi WD, Vuillemin A, Rodriguez P, Coskun ÖK, Gomez-Saez GV, Lavik G, et al. Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments. Nat Microbiol. 2020;5:248–55.

    CAS 
    PubMed 

    Google Scholar 

  • 113.

    Adam PS, Borrel G, Gribaldo S. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. PNAS. 2018;115:E1166–73.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 114.

    Köpke M, Held C, Hujer S, Liesegang H, Wiezer A, Wollherr A, et al. Clostridium ljungdahlii represents a microbial production platform based on syngas. PNAS. 2010;107:13087–92.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 115.

    Lazar CS, Baker BJ, Seitz KW, Hyde AS, Dick GJ, Hinrichs KU, et al. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Nucleic Acids Res. 2015;18:1200–11.

    Google Scholar 

  • 116.

    Debnar-Daumler C, Seubert A, Schmitt G, Heider J. Simultaneous involvement of a tungsten-containing aldehyde:ferredoxin oxidoreductase and a phenylacetaldehyde dehydrogenase in anaerobic phenylalanine metabolism. J Bacteriol. 2014;196:483–92.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 117.

    Kletzin A, Mukund S, Kelley-Crouse TL, Chan MK, Rees DC, Adams MW. Molecular characterization of the genes encoding the tungsten-containing aldehyde ferredoxin oxidoreductase from Pyrococcus furiosus and formaldehyde ferredoxin oxidoreductase from Thermococcus litoralis. J Bacteriol. 1995;177:4817–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 118.

    Arndt F, Schmitt G, Winiarska A, Saft M, Seubert A, Kahnt J, et al. Characterization of an aldehyde oxidoreductase from the mesophilic bacterium Aromatoleum aromaticum ebn1, a member of a new subfamily of tungsten-containing enzymes. Front Microbiol. 2019;10. https://doi.org/10.3389/fmicb.2019.00071.

  • 119.

    Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, et al. Predominant archaea in marine sediments degrade detrital proteins. Nature. 2013;496:215–8.

    CAS 
    PubMed 

    Google Scholar 

  • 120.

    Dimapilis JRR. Tungsten is essential for long-term maintenance of members of candidate archaeal genus Aigarchaeota Group 4. [dissertation on the Internet]. San Bernardino, California State University; 2019. https://scholarworks.lib.csusb.edu/etd/927/.

  • 121.

    Anthony C. The quinoprotein dehydrogenases for methanol and glucose. Arch Biochem Biophys. 2004;428:2–9.

    CAS 
    PubMed 

    Google Scholar 

  • 122.

    Jaffe AL, Castelle CJ, Dupont CL, Banfield JF. Lateral gene transfer shapes the distribution of rubisco among candidate phyla radiation bacteria and DPANN archaea. Nucleic Acids Res. 2019;36:435–46.

    CAS 

    Google Scholar 

  • 123.

    Herbold CW, Lehtovirta-Morley LE, Jung M-Y, Jehmlich N, Hausmann B, Han P, et al. Ammonia-oxidising archaea living at low pH: insights from comparative genomics. Environ Microbiol. 2017;19:4939–52.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 124.

    Aono R, Sato T, Imanaka T, Atomi H. A pentose bisphosphate pathway for nucleoside degradation in Archaea. Nat Chem Biol. 2015;11:355–60.

    CAS 
    PubMed 

    Google Scholar 

  • 125.

    Chadwick GL, Hemp J, Fischer WW, Orphan VJ. Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications. ISME J. 2018;12:2668–80.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 126.

    Cai C, Leu AO, Xie G-J, Guo J, Feng Y, Zhao J-X, et al. A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J. 2018;12:1929–39.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 127.

    Leu AO, McIlroy SJ, Ye J, Parks DH, Orphan VJ, Tyson GW. Lateral gene transfer drives metabolic flexibility in the anaerobic methane-oxidizing archaeal family Methanoperedenaceae. mBio. 2020;11:e01325–20.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 128.

    Zhou Z, L Y, Xu W, Pan J, Luo Z-H, Li M. Genome- and community-level interaction insights into carbon utilization and element cycling functions of Hydrothermarchaeota in hydrothermal sediment. mSystems. 2020;5:e00795–19.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 129.

    Tully BJ, Graham ED, Heidelberg JF. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci Data. 2018;5:170203.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 


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