Woese, C. R., Kandler, O. & Wheelis, M. L. In direction of a pure system of organisms: proposal for the domains Archaea, Micro organism, and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990).
Article
CAS
Google Scholar
Hedlund, B. P., Zhang, C., Wang, F., Rinke, C. & Martin, W. F. Editorial: ecology, metabolism and evolution of archaea-perspectives from Proceedings of the Worldwide Workshop on Geo-Omics of Archaea. Entrance. Microbiol. 12, 827229 (2021).
Article
Google Scholar
DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685–5689 (1992).
Article
CAS
Google Scholar
Fuhrman, J. A., McCallum, Ok. & Davis, A. A. Novel main archaebacterial group from marine plankton. Nature 356, 148–149 (1992).
Article
CAS
Google Scholar
DeLong, E. F. Exploring marine planktonic archaea: then and now. Entrance. Microbiol. 11, 616086 (2021).
Article
Google Scholar
Karimi, B. et al. Biogeography of soil micro organism and archaea throughout France. Sci. Adv. 4, eaat1808 (2018).
Article
Google Scholar
Tahon, G., Geesink, P. & Ettema, T. J. G. Increasing archaeal variety and phylogeny: previous, current, and future. Annu. Rev. Microbiol. 75, 359–381 (2021).
Article
Google Scholar
Baker, B. J. et al. Range, ecology and evolution of Archaea. Nat. Microbiol. 5, 887–900 (2020).
Article
CAS
Google Scholar
Needham, D. M. & Fuhrman, J. A. Pronounced each day succession of phytoplankton, archaea and micro organism following a spring bloom. Nat. Microbiol. 1, 16005 (2016).
Article
CAS
Google Scholar
Shu, W. S. & Huang, L. N. Microbial variety in excessive environments. Nat. Rev. Microbiol. 20, 219–235 (2021).
Article
Google Scholar
Adam, P. S., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. The rising tree of Archaea: new views on their variety, evolution and ecology. ISME J. 11, 2407–2425 (2017).
Article
Google Scholar
Zaremba-Niedzwiedzka, Ok. et al. Asgard archaea illuminate the origin of eukaryotic mobile complexity. Nature 541, 353–358 (2017).
Article
CAS
Google Scholar
Imachi, H. et al. Isolation of an archaeon on the prokaryote-eukaryote interface. Nature 577, 519–525 (2020).
Article
CAS
Google Scholar
Liu, Y. et al. Expanded variety of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021).
Article
CAS
Google Scholar
Angel, R., Soares, M. I., Ungar, E. D. & Gillor, O. Biogeography of soil archaea and micro organism alongside a steep precipitation gradient. ISME J. 4, 553–563 (2010).
Article
Google Scholar
Auguet, J. C., Barberan, A. & Casamayor, E. O. International ecological patterns in uncultured Archaea. ISME J. 4, 182–190 (2010).
Article
Google Scholar
Bates, S. T. et al. Analyzing the worldwide distribution of dominant archaeal populations in soil. ISME J. 5, 908–917 (2011).
Article
CAS
Google Scholar
Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).
Article
CAS
Google Scholar
Offre, P., Spang, A. & Schleper, C. Archaea in biogeochemical cycles. Annu. Rev. Microbiol. 67, 437–457 (2013).
Article
CAS
Google Scholar
Leininger, S. et al. Archaea predominate amongst ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006).
Article
CAS
Google Scholar
Danovaro, R., Rastelli, E., Corinaldesi, C., Tangherlini, M. & Dell’Anno, A. Marine archaea and archaeal viruses below international change. F1000Research 6, 1241 (2017).
Article
Google Scholar
Goberna, M., Garcia, C., Insam, H., Hernandez, M. T. & Verdu, M. Burning fire-prone Mediterranean shrublands: instant modifications in soil microbial neighborhood construction and ecosystem features. Microb. Ecol. 64, 242–255 (2012).
Article
CAS
Google Scholar
Gschwendtner, S. et al. Local weather change induces shifts in abundance and exercise sample of micro organism and archaea catalyzing main transformation steps in nitrogen turnover in a soil from a mid-European beech forest. PLoS ONE 9, e114278 (2014).
Article
Google Scholar
Hayden, H. L. et al. Modifications within the microbial neighborhood construction of micro organism, archaea and fungi in response to elevated CO2 and warming in an Australian native grassland soil. Environ. Microbiol. 14, 3081–3096 (2012).
Article
CAS
Google Scholar
Guo, X. et al. Local weather warming results in divergent succession of grassland microbial communities. Nat. Clim. Change 8, 813–818 (2018).
Article
Google Scholar
Guo, X. et al. Local weather warming accelerates temporal scaling of grassland soil microbial biodiversity. Nat. Ecol. Evol. 3, 612–619 (2019).
Article
Google Scholar
Wu, L. et al. Discount of microbial variety in grassland soil is pushed by long-term local weather warming. Nat. Microbiol. 7, 1054–1062 (2022).
Article
CAS
Google Scholar
Yuan, M. M. et al. Local weather warming enhances microbial community complexity and stability. Nat. Clim. Change 11, 343–348 (2021).
Article
Google Scholar
Cavicchioli, R. Archaea–timeline of the third area. Nat. Rev. Microbiol. 9, 51–61 (2011).
Article
CAS
Google Scholar
Prach, Ok. & Walker, L. R. 4 alternatives for research of ecological succession. Traits Ecol. Evol. 26, 119–123 (2011).
Article
Google Scholar
Xu, X., Sherry, R. A., Niu, S. L., Li, D. J. & Luo, Y. Q. Internet major productiveness and rain-use effectivity as affected by warming, altered precipitation, and clipping in a mixed-grass prairie. Glob. Change Biol. 19, 2753–2764 (2013).
Article
Google Scholar
Kerou, M., Alves, R. J. E. & Schleper, C. in Bergey’s Handbook of Systematics of Archaea and Micro organism (eds Trujillo, M. E. et al.) https://doi.org/10.1002/9781118960608.obm00124 (John Wiley & Sons, 2018).
Nkamga, V. D. & Drancourt, M. in Bergey’s Handbook of Systematics of Archaea and Micro organism (eds Trujillo, M. E. et al.) https://doi.org/10.1002/9781118960608.gbm01365 (John Wiley & Sons, 2016).
Zhou, J. et al. Excessive-throughput metagenomic applied sciences for advanced microbial neighborhood evaluation: open and closed codecs. mBio 6, e02288-14 (2015).
Article
CAS
Google Scholar
Zhou, J. et al. Random sampling course of results in overestimation of beta-diversity of microbial communities. mBio 4, e00324-13 (2013).
Article
CAS
Google Scholar
Xue, Ok. et al. Tundra soil carbon is weak to speedy microbial decomposition below local weather warming. Nat. Clim. Change 6, 595–600 (2016).
Article
CAS
Google Scholar
Pecl, G. T. et al. Biodiversity redistribution below local weather change: impacts on ecosystems and human well-being. Science 355, eaai9214 (2017).
Article
Google Scholar
Cardinale, B. J. et al. Biodiversity loss and its affect on humanity. Nature 486, 59–67 (2012).
Article
CAS
Google Scholar
Li, D., Miller, J. E. D. & Harrison, S. Local weather drives lack of phylogenetic variety in a grassland neighborhood. Proc. Natl Acad. Sci. USA 116, 19989–19994 (2019).
Article
CAS
Google Scholar
Fei, S. et al. Divergence of species responses to local weather change. Sci. Adv. 3, e1603055 (2017).
Article
Google Scholar
Bascompte, J., García, M. B., Ortega, R., Rezende, E. L. & Pironon, S. Mutualistic interactions reshuffle the consequences of local weather change on crops throughout the tree of life. Sci. Adv. 5, eaav2539 (2019).
Article
Google Scholar
Kerou, M. et al. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and diversifications of archaeal ammonia oxidizers. Proc. Natl Acad. Sci. USA 113, E7937–E7946 (2016).
Article
CAS
Google Scholar
Taylor, A. E., Giguere, A. T., Zoebelein, C. M., Myrold, D. D. & Bottomley, P. J. Modeling of soil nitrification responses to temperature reveals thermodynamic variations between ammonia-oxidizing exercise of archaea and micro organism. ISME J. 11, 896–908 (2017).
Article
CAS
Google Scholar
Shi, Z. et al. Useful gene array-based ultrasensitive and quantitative detection of microbial populations in advanced communities. mSystems 4, e00296-19 (2019).
Article
Google Scholar
Ning, D. L. et al. A quantitative framework reveals ecological drivers of grassland microbial neighborhood meeting in response to warming. Nat. Commun. 11, 4717 (2020).
Article
CAS
Google Scholar
Liu, L. et al. Modifications in meeting processes of soil microbial communities throughout secondary succession in two subtropical forests. Soil Biol. Biochem. 154, 108144 (2021).
Article
CAS
Google Scholar
Verhamme, D. T., Prosser, J. I. & Nicol, G. W. Ammonia focus determines differential progress of ammonia-oxidising archaea and micro organism in soil microcosms. ISME J. 5, 1067–1071 (2011).
Article
CAS
Google Scholar
Guo, X. et al. Gene-informed decomposition mannequin predicts decrease soil carbon loss because of persistent microbial adaptation to warming. Nat. Commun. 11, 4897 (2020).
Article
CAS
Google Scholar
Frank, D. A. & McNaughton, S. J. Aboveground biomass estimation with the cover intercept methodology: a plant progress type caveat. Oikos 57, 57–60 (1990).
Sherry, R. A. et al. Lagged results of experimental warming and doubled precipitation on annual and seasonal aboveground biomass manufacturing in a tallgrass prairie. Glob. Change Biol. 14, 2923–2936 (2008).
Article
Google Scholar
Zhou, J. Z. et al. Microbial mediation of carbon-cycle feedbacks to local weather warming. Nat. Clim. Change 2, 106–110 (2012).
Article
CAS
Google Scholar
Li, D., Zhou, X., Wu, L., Zhou, J. & Luo, Y. Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie. Glob. Change Biol. 19, 3553–3564 (2013).
Google Scholar
Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA restoration from soils of various composition. Appl. Environ. Microbiol. 62, 316–322 (1996).
Article
CAS
Google Scholar
Wu, L. et al. Phasing amplicon sequencing on Illumina Miseq for sturdy environmental microbial neighborhood evaluation. BMC Microbiol. 15, 125 (2015).
Article
Google Scholar
Caporaso, J. G. et al. Extremely-high-throughput microbial neighborhood evaluation on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).
Article
CAS
Google Scholar
Suzuki, M. T. & Giovannoni, S. J. Bias attributable to template annealing within the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62, 625–630 (1996).
Article
CAS
Google Scholar
Takai, Ok. & Horikoshi, Ok. Speedy detection and quantification of members of the archaeal neighborhood by quantitative PCR utilizing fluorogenic probes. Appl. Environ. Microbiol. 66, 5066–5072 (2000).
Article
Google Scholar
Porat, I. et al. Characterization of archaeal neighborhood in contaminated and uncontaminated floor stream sediments. Microb. Ecol. 60, 784–795 (2010).
Article
Google Scholar
Francis, C. A., Roberts, Ok. J., Beman, J. M., Santoro, A. E. & Oakley, B. B. Ubiquity and variety of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl Acad. Sci. USA 102, 14683–14688 (2005).
Article
CAS
Google Scholar
Peiffer, J. A. et al. Range and heritability of the maize rhizosphere microbiome below discipline circumstances. Proc. Natl Acad. Sci. USA 110, 6548–6553 (2013).
Article
CAS
Google Scholar
Giardine, B. et al. Galaxy: a platform for interactive large-scale genome evaluation. Genome Res. 15, 1451–1455 (2005).
Article
CAS
Google Scholar
Kong, Y. Btrim: a quick, light-weight adapter and high quality trimming program for next-generation sequencing applied sciences. Genomics 98, 152–153 (2011).
Article
CAS
Google Scholar
Magoc, T. & Salzberg, S. L. FLASH: quick size adjustment of brief reads to enhance genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Article
CAS
Google Scholar
Edgar, R. C. UPARSE: extremely correct OTU sequences from microbial amplicon reads. Nat. Strategies 10, 996–998 (2013).
Article
CAS
Google Scholar
Caporaso, J. G. et al. QIIME permits evaluation of high-throughput neighborhood sequencing knowledge. Nat. Strategies 7, 335–336 (2010).
Article
CAS
Google Scholar
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench suitable with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).
Article
CAS
Google Scholar
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for speedy project of rRNA sequences into the brand new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Article
CAS
Google Scholar
Edgar, R. C. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. Preprint obtainable at bioRxiv https://doi.org/10.1101/081257 (2016).
Callahan, B. J. et al. DADA2: high-resolution pattern inference from Illumina amplicon knowledge. Nat. Strategies 13, 581–583 (2016).
Article
CAS
Google Scholar
Amir, A. et al. Deblur quickly resolves single-nucleotide neighborhood sequence patterns. mSystems 2, e00191-16 (2017).
Article
Google Scholar
Kembel, S. W. et al. Picante: R instruments for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).
Article
CAS
Google Scholar
Sievers, F. et al. Quick, scalable technology of high-quality protein a number of sequence alignments utilizing Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
Article
Google Scholar
Value, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–roughly maximum-likelihood bushes for big alignments. PLoS ONE 5, e9490 (2010).
Article
Google Scholar
Munoz, R. et al. Launch LTPs104 of the All-Species Dwelling Tree. Syst. Appl. Microbiol. 34, 169–170 (2011).
Article
Google Scholar
Oksanen, J. et al. Bundle ‘vegan’. Group Ecology Bundle, Model 2.9, 1–295 (The R Undertaking for Statistical Computing, 2013).
Chen, L. X. et al. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME J. 9, 1579–1592 (2015).
Article
Google Scholar
Nakagawa, S. & Schielzeth, H. A basic and easy methodology for acquiring R2 from generalized linear mixed-effects fashions. Strategies Ecol. Evol. 4, 133–142 (2013).
Article
Google Scholar
Martiny, J. B., Eisen, J. A., Penn, Ok., Allison, S. D. & Horner-Devine, M. C. Drivers of bacterial beta-diversity depend upon spatial scale. Proc. Natl Acad. Sci. USA 108, 7850–7854 (2011).
Article
CAS
Google Scholar
Andrews, S. FastQC: A High quality Management Device for Excessive Throughput Sequence Knowledge (Babraham Bioinformatics, 2010).
Li, W. & Godzik, A. Cd-hit: a quick program for clustering and evaluating massive units of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Article
CAS
Google Scholar
Patel, R. Ok. & Jain, M. NGS QC Toolkit: a toolkit for high quality management of subsequent technology sequencing knowledge. PLoS ONE 7, e30619 (2012).
Article
CAS
Google Scholar
Zhou, J. Z. & Ning, D. L. Stochastic neighborhood meeting: does it matter in microbial ecology? Microbiol. Mol. Biol. Rev. 81, e00002-17 (2017).
Article
Google Scholar
Jaumot, J., Bedia, C. & Tauler, R. Knowledge Evaluation for Omic Sciences: Strategies and Functions (Elsevier, 2018).
Thevenot, E. A., Roux, A., Xu, Y., Ezan, E. & Junot, C. Evaluation of the human grownup urinary metabolome variations with age, physique mass index, and gender by implementing a complete workflow for univariate and OPLS statistical analyses. J. Proteome Res. 14, 3322–3335 (2015).
Article
CAS
Google Scholar