Cited by 541Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesMethane Hydrates and Related Phenomena

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Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

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Castelle, Cindy J., Wrighton, Kelly C., Thomas, Brian C., Hug, Laura A., Brown, Christopher T., Wilkins, Michael J., Frischkorn, Kyle R., Tringe, Susannah G., Singh, Andrea, Markillie, Lye Meng, Taylor, Ronald C., Williams, Kenneth H., Banfield, Jillian F.·2015·Current Biology

DOI 10.1016/j.cub.2015.01.014

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Abstract

Background Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown. Results We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles. Conclusions The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.

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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,923
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 11,200
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 9,119
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128

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Spang, A., & Offre, P. (2018) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12701 · Cited by 4
Metagenomics a modern approach to reveal the secrets of unculturable microbes
Shamim, K., Mujawar, S. Y., & Mutnale, M. C. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-817497-5.00012-4 · Cited by 7
Halocins, Bacteriocin-Like Antimicrobials Produced by the Archaeal Domain: Occurrence and Phylogenetic Diversity in Halobacteriales
Najjari, A., Mejri, H., Jabbari, M., Sghaier, H., Cherif, A., & Ouzari, H. (2021) · IntechOpen eBooks · doi:10.5772/intechopen.94765 · Cited by 6
Human Archaea and Associated Metabolites in Health and Disease
Cai, M., & Tang, X. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00232 · Cited by 5
First evidence of the presence and activity of archaeal C3 group members in an Atlantic intertidal mudflat
Lavergne, C., Hugoni, M., Dupuy, C., & Agogué, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-30222-1 · Cited by 6
Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone–aquifer sediments
Zhong, S., Chen, Q., Hu, J., Liu, S., Qiao, S., Ni, J., & Sun, W. (2020) · Journal of Applied Microbiology · doi:10.1111/jam.14742 · Cited by 6
Transitions in microbial communities along two sediment cores collected from the landward walls of the New Britain trench
Wang, L., Liu, R., Wei, X. L., Wang, Z., Shen, Z., Cao, J., Wei, Y., Xie, Z., Chen, L., & Fang, J. (2020) · Marine Biology · doi:10.1007/s00227-020-03788-6 · Cited by 6
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR
Belmok, A., Rodrigues-Oliveira, T., Lopes, F. Á. C., Krüger, R. H., & Kyaw, C. M. (2021) · Brazilian Journal of Biology · doi:10.1590/1519-6984.247529 · Cited by 6
The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects
Takamiya, H., Kouduka, M., & Suzuki, Y. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.785743 · Cited by 5
Methane Cycle in a Littoral Site of a Temperate Freshwater Lake
Kallistova, A. Y., Koval’, D. D., Kadnikov, V. V., Toshchakov, S. V., Yusupov, S. K., Izotova, A. O., Vinogradova, E. N., Zekker, I., & Пименов, Н. В. (2023) · Microbiology · doi:10.1134/s0026261722602901 · Cited by 6
Variations in microbial community compositions and processes imposed under contrast geochemical contexts in Sicilian mud volcanoes, Italy
Chen, J., Chiu, Y.-P., Tu, T., Italiano, F., Wang, P., & Lin, L. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1461252 · Cited by 5
Archaeal blooms and busts in an estuarine time series
Guider, J. T., Yoshimura, K. M., Block, K. R., Biddle, J. F., & Walter, S. R. S. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16584 · Cited by 5
Femtoplankton: What’s New?
Colombet, J., Fuster, M., Billard, H., & Sime‐Ngando, T. (2020) · Viruses · doi:10.3390/v12080881 · Cited by 9
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Bruto, M., Oger, P., Got, P., Bernard, C., Melayah, D., Cloarec, L. A., Duval, C., Escalas, A., Duperron, S., Guigard, L., et al. (2023) · Molecular Ecology · doi:10.1111/mec.17179 · Cited by 5
Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs
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Kozlowski, J. A., Johnson, M. E., Ledesma-Vázquez, J., Birgel, D., Peckmann, J., & Schleper, C. (2018) · Ciencias Marinas · doi:10.7773/cm.v44i2.2825 · Cited by 5
Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean
Vipindas, P. V., Jabir, T., Venkatachalam, S., Yang, E. J., Jain, A., & Krishnan, K. P. (2023) · Extremophiles · doi:10.1007/s00792-023-01310-6 · Cited by 5
Evaluating groundwater ecosystem dynamics in response to post in-situ remediation of mixed chlorinated volatile organic compounds (CVOCs): An insight into microbial community resilience, adaptability, and metabolic functionality for sustainable remediation and ecosystem restoration
Huang, S.-W., Hussain, B., Chen, J., Asif, A., & Hsu, B. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.170874 · Cited by 5
Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth’s crustPreprint
Rahlff, J., Turzynski, V., Esser, S. P., Monsees, I., Bornemann, T. L. V., Figueroa-Gonzalez, P. A., Schulz, F., Woyke, T., Klingl, A., Moraru, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.22.215848 · Cited by 5
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Krause, S., Gfrerer, S., Reuse, C., Dombrowski, N., Villanueva, L., Bunk, B., Spröer, C., Neu, T. R., Kuhlicke, U., Schmidt‐Hohagen, K., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.28.441856 · Cited by 5
A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biospherePreprint
Momper, L., Casar, C., & Osburn, M. (2021) · bioRxiv · doi:10.1101/2021.05.06.442964 · Cited by 6
Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea
Takamiya, H., Kouduka, M., Kato, S., Suga, H., Oura, M., Yokoyama, T., Suzuki, M., Mori, M., Kanai, A., & Suzuki, Y. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae207 · Cited by 5
Control of Microbiome Composition and Agrichemical Remediation in Woodchip Bioreactors by Hydraulic Retention Time
Abdi, D. E., Tabares, M., Redekar, N. R., Parke, J. L., Reguera, G., & Fernandez, R. T. (2025) · ACS ES&T Water · doi:10.1021/acsestwater.4c01114 · Cited by 5
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Horizontal gene transfer and gene loss drove the divergent evolution of host dependency in Micrarchaeota
Rao, Y.-Z., Li, Y.-X., Li, Z.-W., Qu, Y.-N., Hedlund, B. P., Williams, T. A., Qi, Y.-L., Xie, Q.-J., Yang, H.-L., Zhang, Y.-Q., et al. (2025) · National Science Review · doi:10.1093/nsr/nwaf542 · Cited by 4
Aerobic Archaea in iron-rich springs
Teske, A. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0168-9 · Cited by 4

Authors: Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., Taylor, R. C., Williams, K. H., & Banfield, J. F.
Affiliations: University of California, Berkeley (US)
The Ohio State University (US)
Lamont-Doherty Earth Observatory (US)
Joint Genome Institute (US)
Pacific Northwest National Laboratory (US)
Lawrence Berkeley National Laboratory (US)
Corresponding author: Banfield, Jillian F.
ORCID: Castelle, Cindy J.
Wrighton, Kelly C.
Thomas, Brian C.
Hug, Laura A.
Brown, Christopher T.
Wilkins, Michael J.
Frischkorn, Kyle R.
Tringe, Susannah G.
Markillie, Lye Meng
Taylor, Ronald C.
Williams, Kenneth H.
Banfield, Jillian F.
Venue: Current Biology
Publisher: Elsevier BV
Published: 2015-03
Volume: 25
Issue: 6
Pages: 690-701
ISSN: 0960-9822 (ISSN-L)
DOI: 10.1016/j.cub.2015.01.014
OpenAlex: W2117349822
Cited by: 536
References: 72
Citations by year: 2026: 19 · 2025: 22 · 2024: 29 · 2023: 38 · 2022: 52 · 2021: 59 · 2020: 64 · 2019: 54 · 2018: 65 · 2017: 60 · 2016: 57 · 2015: 14
FWCI: 59.19
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 381 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Current Biology (publishedVersion)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders: US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (DE-AC02-05CH11231, DE-SC0004918)
US DOE Joint Genome Institute, a DOE Office of Science User Facility (DE-AC02-05CH11231)
DOE Office of Biological and Environmental Research
US DOE (DE-AC06-76RLO 1830)
Natural Sciences and Engineering Research Council of Canada postdoctoral fellowship
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Environmental Chemistry › Methane Hydrates and Related Phenomena
Keywords: genome-resolved metagenomics, fermentation, aquifer sediments, archaeal diversity
MeSH terms: Anaerobiosis, Archaea, Models, Biological, Models, Genetic, Phylogeny, Genome, Archaeal, Biodiversity, Metagenomics, Carbon Cycle

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Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

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