[1] |
DeLong EF (1992) Archaea in coastal marine environments. P Natl Acad Sci USA 89: 5685–5689. doi: 10.1073/pnas.89.12.5685 |
[2] |
Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507. doi: 10.1038/35054051 |
[3] |
Bintrim SB, Donohue TJ, Handelsman J, et al. (1997) Molecular phylogeny of Archaea from soil. P Natl Acad Sci USA 94: 277–282. doi: 10.1073/pnas.94.1.277 |
[4] |
Adam PS, Borrel G, Brochier-Armanet C, et al. (2017) The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J 11: 2407. doi: 10.1038/ismej.2017.122 |
[5] |
Spang A, Caceres EF, Ettema TJ (2017) Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357: eaaf3883. doi: 10.1126/science.aaf3883 |
[6] |
Spang A, Saw JH, Jørgensen SL, et al. (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521: 173–179. doi: 10.1038/nature14447 |
[7] |
Dombrowski N, Teske AP, Baker BJ (2018) Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nature Comm 9: 4999. doi: 10.1038/s41467-018-07418-0 |
[8] |
Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, et al. (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541: 353–358. doi: 10.1038/nature21031 |
[9] |
Wong HL, White RA, Visscher PT, et al. (2018) Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. ISME J 12: 2619. doi: 10.1038/s41396-018-0208-8 |
[10] |
Narrowe AB, Spang A, Stairs CW, et al. (2018) Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids. Genome Biol Evol 10: 2380–2393. doi: 10.1093/gbe/evy154 |
[11] |
Seitz KW, Lazar CS, Hinrichs KU, et al. (2016) Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J 10: 1696. doi: 10.1038/ismej.2015.233 |
[12] |
Liu Y, Zhou Z, Pan J, et al. (2018) Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. ISME J 12: 1021. |
[13] |
Tully BJ, Graham ED, Heidelberg JF (2018) The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci Data 5: 170203. doi: 10.1038/sdata.2017.203 |
[14] |
Pushkarev A, Inoue K, Larom S, et al. (2018) A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. Nature: 558: 595–599. doi: 10.1038/s41586-018-0225-9 |
[15] |
Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. P Natl Acad Sci USA 74: 5088–5090. doi: 10.1073/pnas.74.11.5088 |
[16] |
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. P Natl Acad Sci USA 87: 4576–4579. doi: 10.1073/pnas.87.12.4576 |
[17] |
Iwabe N, Kuma K, Hasegawa M, et al. (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. P Natl Acad Sci USA 86: 9355–9359. doi: 10.1073/pnas.86.23.9355 |
[18] |
Lake JA, Henderson E, Oakes M, et al. (1984) Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. P Natl Acad Sci USA 81: 3786–3790. doi: 10.1073/pnas.81.12.3786 |
[19] |
Rivera MC, Lake JA (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257: 74–76. doi: 10.1126/science.1621096 |
[20] |
Eme L, Spang A, Lombard J, et al. (2017) Archaea and the origin of eukaryotes. Nat Rev Microbiol 15: 711. doi: 10.1038/nrmicro.2017.133 |
[21] |
Vetriani C, Jannasch HW, MacGregor BJ, et al. (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microb 65: 4375–4384. |
[22] |
Takai K, Horikoshi K (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152: 1285–1297. |
[23] |
Inagaki F, Suzuki M, Takai K, et al. (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microb 69: 7224–7235. doi: 10.1128/AEM.69.12.7224-7235.2003 |
[24] |
Jørgensen SL, Thorseth IH, Pedersen RB, et al. (2013) Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge. Front Microbiol 4: 299. |
[25] |
Braga RM, Dourado MN, Araújo WL (2016) Microbial interactions: ecology in a molecular perspective. Braz J Microbiol 47: 86–98. doi: 10.1016/j.bjm.2016.10.005 |
[26] |
Weiss S, Van Treuren W, Lozupone C, et al. (2016) Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J 10: 1669. doi: 10.1038/ismej.2015.235 |
[27] |
Saghaï A, Gutiérrez‐Preciado A, Deschamps P, et al. (2017) Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond. Environ Microbiol 19: 2405–2421. doi: 10.1111/1462-2920.13754 |
[28] |
Baker BJ, Lazar CS, Teske AP, et al. (2015) Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome 3: 14. doi: 10.1186/s40168-015-0077-6 |
[29] |
Sousa FL, Neukirchen S, Allen JF, et al. (2016) Lokiarchaeon is hydrogen dependent. Nat Microbiol 1: 16034. doi: 10.1038/nmicrobiol.2016.34 |
[30] |
Sousa FL, Martin WF (2014) Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. BBA-Bioenergetics 1837: 964–981. doi: 10.1016/j.bbabio.2014.02.001 |
[31] |
Borrel G, Adam PS, Gribaldo S (2016) Methanogenesis and the Wood-Ljungdahl pathway: an ancient, versatile, and fragile association. Genome Biol Evol 8: 1706–1711. doi: 10.1093/gbe/evw114 |
[32] |
Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428: 726–731. doi: 10.1016/j.jmb.2015.11.006 |
[33] |
Ragsdale SW, Pierce E (2008) Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. BBA-Proteins Proteom 1784: 1873–1898. doi: 10.1016/j.bbapap.2008.08.012 |
[34] |
Sato T, Atomi H, Imanaka T (2007) Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315: 1003–1006. doi: 10.1126/science.1135999 |
[35] |
Aono R, Sato T, Yano A, et al. (2012) Enzymatic characterization of AMP phosphorylase and ribose-1, 5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J Bacteriol 194: 6847–6855. doi: 10.1128/JB.01335-12 |
[36] |
Li R, Chai M, Qiu GY (2016) Distribution, fraction, and ecological assessment of heavy metals in sediment-plant system in Mangrove Forest, South China Sea. PLoS One 11: e0147308. doi: 10.1371/journal.pone.0147308 |
[37] |
Oremland RS, Stolz JF, Hollibaugh JT (2004) The microbial arsenic cycle in Mono Lake, California. FEMS Microbiol Ecol 48: 15–27. doi: 10.1016/j.femsec.2003.12.016 |
[38] |
Jackson CR, Dugas SL (2003) Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol Biol 3: 18. doi: 10.1186/1471-2148-3-18 |
[39] |
Da Cunha V, Gaia M, Gadelle D, et al. (2017) Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet 13: e1006810. doi: 10.1371/journal.pgen.1006810 |
[40] |
Spang A, Eme L, Saw JH, et al. (2018) Asgard archaea are the closest prokaryotic relatives of eukaryotes. PLoS Genet 14: e1007080. doi: 10.1371/journal.pgen.1007080 |
[41] |
Klinger CM, Spang A, Dacks JB, et al. (2016) Tracing the archaeal origins of eukaryotic membrane-trafficking system building blocks. Mol Biol Evol 33: 1528–1541. doi: 10.1093/molbev/msw034 |
[42] |
Xue B, Robinson RC (2013) Guardians of the actin monomer. Eur J Cell Biol 92: 316–332. doi: 10.1016/j.ejcb.2013.10.012 |
[43] |
Akıl C, Robinson RC (2018) Genomes of Asgard archaea encode profilins that regulate actin. Nature 562: 439. doi: 10.1038/s41586-018-0548-6 |
[44] |
Gunning PW, Ghoshdastider U, Whitaker S, et al. (2015) The evolution of compositionally and functionally distinct actin filaments. J Cell Sci 128: 2009–2019. doi: 10.1242/jcs.165563 |
[45] |
Javaux EJ, Knoll AH, Walter MR (2001) Morphological and ecological complexity in early eukaryotic ecosystems. Nature 412: 66. doi: 10.1038/35083562 |
[46] |
Parfrey LW, Lahr DJ, Knoll AH, et al. (2011) Estimating the timing of early eukaryotic diversification with multigene molecular clocks. P Natl Acad Sci USA 108: 13624–13629. doi: 10.1073/pnas.1110633108 |
[47] |
Nunoura T, Takaki Y, Kakuta J, et al. (2010) Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39: 3204–3223. |
[48] |
James RH, Caceres EF, Escasinas A, et al. (2017) Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon. Nature Comm 8: 1120. doi: 10.1038/s41467-017-01162-7 |
[49] |
Stock T, Rother M (2009) Selenoproteins in Archaea and Gram-positive bacteria. BBA-Gen Subjects 1790: 1520–1532. doi: 10.1016/j.bbagen.2009.03.022 |
[50] |
Yoshizawa S, Böck A (2009) The many levels of control on bacterial selenoprotein synthesis. BBA-Gen Subjects 1790: 1404–1414. doi: 10.1016/j.bbagen.2009.03.010 |
[51] |
Labunskyy VM, Hatfield DL, Gladyshev VN (2014) Selenoproteins: molecular pathways and physiological roles. Physiol Rev 94: 739–777. doi: 10.1152/physrev.00039.2013 |
[52] |
Mariotti M, Lobanov AV, Manta B, et al. (2016) Lokiarchaeota marks the transition between the archaeal and eukaryotic selenocysteine encoding systems. Mol Biol Evol 33: 2441–2453. doi: 10.1093/molbev/msw122 |