CoChat
Sign Up
PreprintCited by 7Bacteriophages and microbial interactionsCRISPR and Genetic EngineeringPlant and Fungal Interactions Research

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

Open access
Duan, Changhai, Liu, Yang, Liu, Ying, Liu, Lirui, Cai, Mingwei, Zhang, Rui, Zeng, Qinglu, Koonin, Eugene V., Krupovic, Mart, Li, Meng·2023·ISME Communications
DOI 10.1101/2023.08.24.554615PMC PMC10848311

Preprint — published as 10.1093/ismeco/ycad011 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome of Bathyarchaeia so far has not been characterized. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria , and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family ‘ Fuxiviridae ’ harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family ‘ Chiyouviridae ’ encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibition of host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.08.24.554615

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 103

  1. 10.1073/pnas.0511033103 · DOI
  2. 10.1038/ismej.2012.37 · DOI
  3. 10.1038/nature12033 · DOI
  4. 2015, Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous C renarchaeotal group lineage naturally enriched in anoxic sediments of the W hite O ak R iver estuary (N orth C arolina, USA). Environ. Microbiol, 17, 2228, 10.1111/1462-2920.12659 · DOI
  5. 10.1093/femsre/fuy023 · DOI
  6. 2016, Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments, Nat. Microbiol, 1, 16035, 10.1038/nmicrobiol.2016.35 · DOI
  7. 10.1126/science.aac7745 · DOI
  8. 10.1186/s40168-020-00820-1 · DOI
  9. 2021, Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “Candidatus Bathyarchaeia”, mSystems, 6, e00252
  10. 10.1073/pnas.1718854115 · DOI
  11. 10.1038/s41396-018-0321-8 · DOI
  12. 2022, Interactions between bacterial and phage communities in natural environments, Nat. Rev. Microbiol, 20, 49, 10.1038/s41579-021-00602-y · DOI
  13. López-García P , et al. Metagenome-derived virus-microbe ratios across ecosystems. ISME J., (2023). · DOI
  14. 10.1038/nrmicro2386 · DOI · Paper page
  15. 10.1038/ismej.2008.31 · DOI
  16. 10.1111/1462-2920.14513 · DOI
  17. Xiao X , et al. Viral Lysis Alters the Optical Properties and Biological Availability of Dissolved Organic Matter Derived from Prochlorococcus Picocyanobacteria. Appl. Environ. Microbiol. 87, (2021). · DOI
  18. 10.1038/424741a · DOI
  19. 10.1073/pnas.0401478101 · DOI
  20. 10.1126/science.1252229 · DOI
  21. 2009, CRISPR-Cas: an adaptive immunity system in prokaryotes, F1000 Biol Rep, 1, 95
  22. 10.1126/science.1138140 · DOI · Paper page
  23. 10.1093/nar/gkab133 · DOI
  24. 10.1038/nrmicro.2017.120 · DOI
  25. 10.1038/s41586-019-1786-y · DOI
  26. 2020, A jumbo phage that forms a nucleus-like structure evades CRISPR– Cas DNA targeting but is vulnerable to type III RNA-based immunity, Nat. Microbiol, 5, 48
  27. 2017, The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs, Annu Rev Virol, 4, 37, 10.1146/annurev-virology-101416-041616 · DOI
  28. 2020, Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies, Nat. Methods, 17, 471, 10.1038/s41592-020-0771-6 · DOI
  29. 10.1016/j.virusres.2017.11.025 · DOI
  30. 2022, Three families of Asgard archaeal viruses identified in metagenome-assembled genomes, Nat. Microbiol, 7, 962, 10.1038/s41564-022-01144-6 · DOI
  31. 2022, Genomes of six viruses that infect Asgard archaea from deep-sea sediments, Nat. Microbiol, 7, 953, 10.1038/s41564-022-01150-8 · DOI
  32. 2022, A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses, Nat. Microbiol, 7, 948, 10.1038/s41564-022-01122-y · DOI
  33. 2023, Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome, Nat Microbiol, 8, 231, 10.1038/s41564-022-01297-4 · DOI · Paper page
  34. 2023, Diverse viruses of marine archaea discovered using metagenomics, Environ. Microbiol, 25, 367, 10.1111/1462-2920.16287 · DOI
  35. 2019, Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes, Environ. Microbiol, 21, 1980, 10.1111/1462-2920.14462 · DOI
  36. 10.1073/pnas.1905682116 · DOI
  37. 2019, Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes, ISME J, 13, 618, 10.1038/s41396-018-0289-4 · DOI
  38. 2017, Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota, Curr. Biol, 27, 1362, 10.1016/j.cub.2017.03.052 · DOI
  39. 2021, Subgroup level differences of physiological activities in marine Lokiarchaeota, ISME J, 15, 848, 10.1038/s41396-020-00818-5 · DOI
  40. 2023, Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment, Sci. Adv, 9, eadf5069, 10.1126/sciadv.adf5069 · DOI
  41. 10.1093/nar/gkaa946 · DOI
  42. 2021, Viruses Defined by the Position of the Virosphere within the Replicator Space, Microbiol Mol Biol Rev, 85, e0019320, 10.1128/MMBR.00193-20 · DOI
  43. 2021, Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes, J. Virol, 95, e0067321, 10.1128/JVI.00673-21 · DOI
  44. 10.1371/journal.pbio.3001442 · DOI · Paper page
  45. 10.1007/s00792-017-0951-1 · DOI
  46. 10.1093/nar/gkw322 · DOI
  47. 1978, Primary structure of protein L19 from the large subunit of Escherichia coli ribosomes, Biochemistry, 17, 508, 10.1021/bi00596a021 · DOI
  48. 10.1038/s41467-019-08672-6 · DOI
  49. 10.1016/j.cell.2022.02.019 · DOI
  50. 10.1128/JVI.02270-15 · DOI
  51. 10.1128/JVI.01637-15 · DOI
  52. 10.1038/nrmicro2576 · DOI · Paper page
  53. Khomyakova MA , Merkel AY , Mamiy DD , Klyukina AA , Slobodkin AI . Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia. Front. Microbiol. 14, (2023). · DOI
  54. 2020, New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities, ISME J, 14, 1821, 10.1038/s41396-020-0653-z · DOI
  55. 10.1073/pnas.2011125117 · DOI
  56. 10.1128/JVI.02742-13 · DOI
  57. 10.1042/BST20120313 · DOI
  58. 2020, Structure and assembly of archaeal viruses, Adv Virus Res, 108, 127, 10.1016/bs.aivir.2020.09.004 · DOI
  59. 10.1093/nar/gkz1197 · DOI
  60. 2019, CRISPR–Cas in mobile genetic elements: counter-defence and beyond, Nat. Rev. Microbiol, 17, 513, 10.1038/s41579-019-0204-7 · DOI
  61. 2021, Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of Acidithiobacillia, Crispr J, 4, 656, 10.1089/crispr.2021.0051 · DOI
  62. 10.1016/j.cell.2022.10.020 · DOI
  63. 2021, Structure of a type IV CRISPR-Cas ribonucleoprotein complex, iScience, 24, 102201, 10.1016/j.isci.2021.102201 · DOI
  64. 10.1038/s41467-019-13205-2 · DOI
  65. 10.1016/j.molcel.2018.05.002 · DOI
  66. 10.1186/s12862-017-1081-1 · DOI
  67. Zhang Z , Pan S , Liu T , Li Y , Peng N . Cas4 Nucleases Can Effect Specific Integration of CRISPR Spacers. J. Bacteriol. 201, (2019). · DOI
  68. 10.1016/j.jmb.2015.03.013 · DOI
  69. 2022, Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases, Molecular cell, 82, 2714, 10.1016/j.molcel.2022.05.003 · DOI
  70. 2022, Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24, Nat. Commun, 13, 1931, 10.1038/s41467-022-29581-1 · DOI
  71. 2022, GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Res, 50, D785, 10.1093/nar/gkab776 · DOI · Paper page
  72. 2022, GTDB-Tk v2: memory friendly classification with the genome taxonomy database, Bioinform, 38, 5315, 10.1093/bioinformatics/btac672 · DOI
  73. 10.1093/nar/gky874 · DOI · Paper page
  74. 10.1093/bioinformatics/btp348 · DOI
  75. 10.1101/gr.186072.114 · DOI · Paper page
  76. 10.1038/nbt.4229 · DOI · Paper page
  77. 10.1038/s41467-022-30269-9 · DOI
  78. 2020, CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci, CRISPR J, 3, 462, 10.1089/crispr.2020.0059 · DOI
  79. 10.1186/1471-2105-8-209 · DOI
  80. 10.1038/nmeth.3176 · DOI · Paper page
  81. 10.1186/1471-2105-10-421 · DOI · Paper page
  82. Guo J , et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021). · DOI
  83. 10.1038/s41587-020-00774-7PMID-33349699 · DOI
  84. 10.1093/bioinformatics/btu153 · DOI
  85. 10.1093/nar/gkaa621 · DOI
  86. Steinegger M , Meier M , Mirdita M , Vöhringer H , Haunsberger SJ , Söding J . HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinform. 20, 473 (2019). · DOI · Paper page
  87. 2023, Proksee: in-depth characterization and visualization of bacterial genomes, Nucleic Acids Res., 51, W484, 10.1093/nar/gkad326 · DOI
  88. 2019, Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks, Nat. Biotechnol, 37, 632, 10.1038/s41587-019-0100-8 · DOI
  89. 10.1101/gr.1239303 · DOI · Paper page
  90. 10.1093/bioinformatics/btx157 · DOI
  91. 10.1093/bioinformatics/btx440 · DOI
  92. 2022, ColabFold: making protein folding accessible to all, Nat. Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  93. 10.1093/nar/gkh340 · DOI · Paper page
  94. 10.1038/s41579-019-0299-x · DOI · Paper page
  95. 10.1093/nar/gkw1065 · DOI
  96. 2023, Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees, Nucleic Acids Res, 51, W587, 10.1093/nar/gkad359 · DOI
  97. 2022, PLSDB: advancing a comprehensive database of bacterial plasmids, Nucleic Acids Res, 50, D273, 10.1093/nar/gkab1111 · DOI
  98. 10.1093/nar/gkz915 · DOI
  99. 2018, A Unified Resource for Tracking Anti-CRISPR Names, Crispr J, 1, 304, 10.1089/crispr.2018.0043 · DOI
  100. 10.1093/nar/gki524 · DOI · Paper page
  101. 2019, Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution, ISME J, 13, 2150, 10.1038/s41396-019-0418-8 · DOI
  102. 10.1093/nar/gkv451 · DOI
  103. 10.1007/s12275-021-1154-0 · DOI

Metadata

Authors
Duan, C., Liu, Y., Liu, Y., Liu, L., Cai, M., Zhang, R., Zeng, Q., Koonin, E. V., Krupovic, M., & Li, M.
Affiliations
  • Shenzhen University (CN)
  • Institut Pasteur (FR)
  • Hong Kong University of Science and Technology (HK)
  • National Institutes of Health (US)
Corresponding author
Li, Meng
ORCID
Venue
ISME Communications
Publisher
openRxiv
Published
2023-08-24
Volume
4
Issue
1
Pages
ycad011-ycad011
ISSN
2730-6151 (ISSN-L)
DOI
10.1101/2023.08.24.554615
PMC
PMC10848311
OpenAlex
W4390740627
Cited by
7
References
1
Citations by year
2026: 1 · 2025: 3 · 2024: 3
FWCI
1.91
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • ISME Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • National Natural Science Foundation of China (92251306, 32225003, 31970105)
  • Shenzhen University (2022B002)
  • National Key Research and Development Program of China (2022YFA0912200)
  • U.S. National Library of Medicine
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Immunology and Microbiology › Virology › Plant and Fungal Interactions Research
Keywords
archaea, metagenome-assembled genomes, virus families, CRISPR-Cas, host defense evasion, virome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review