Flemming, H. C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).
Google Scholar
Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).
Google Scholar
Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).
Google Scholar
Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).
Google Scholar
Castelle, C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015).
Google Scholar
Nunoura, T. et al. 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 (2011).
Google Scholar
Probst, A. J. et al. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat. Commun. 5, 5497 (2014).
Google Scholar
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).
Google Scholar
Weinbauer, M. G. & Rassoulzadegan, F. Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6, 1–11 (2004).
Google Scholar
Engelhardt, T., Kallmeyer, J., Cypionka, H. & Engelen, B. High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments. ISME J. 8, 1503–1509 (2014).
Google Scholar
Danovaro, R. et al. Virus-mediated archaeal hecatomb in the deep seafloor. Sci. Adv. 2, e1600492 (2016).
Google Scholar
Kyle, J. E., Eydal, H. S., Ferris, F. G. & Pedersen, K. Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden. ISME J. 2, 571–574 (2008).
Google Scholar
Labonté, J. M. et al. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front. Microbiol. 6, 349 (2015).
Google Scholar
Hylling, O. et al. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci. Rep. 10, 11879 (2020).
Google Scholar
Daly, R. A. et al. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat. Microbiol. 4, 352–361 (2019).
Google Scholar
Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167–170 (2010).
Google Scholar
Pauly, M. D., Bautista, M. A., Black, J. A. & Whitaker, R. J. Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 374, 20180093 (2019).
Google Scholar
Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3, 328–336 (2018).
Google Scholar
Henneberger, R., Moissl, C., Amann, T., Rudolph, C. & Huber, R. New insights into the lifestyle of the cold-loving SM1 euryarchaeon: natural growth as a monospecies biofilm in the subsurface. Appl. Environ. Microbiol. 72, 192–199 (2006).
Google Scholar
Probst, A. J. et al. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. ISME J. 7, 635–651 (2013).
Google Scholar
Bird, J. T., Baker, B. J., Probst, A. J., Podar, M. & Lloyd, K. G. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Front. Microbiol. 7, 1221 (2016).
Google Scholar
Hernsdorf, A. W. et al. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J. 11, 1915–1929 (2017).
Google Scholar
Moissl, C., Rachel, R., Briegel, A., Engelhardt, H. & Huber, R. The unique structure of archaeal ‘hami’, highly complex cell appendages with nano-grappling hooks. Mol. Microbiol. 56, 361–370 (2005).
Google Scholar
Rudolph, C., Wanner, G. & Huber, R. Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology. Appl. Environ. Microbiol. 67, 2336–2344 (2001).
Google Scholar
Rudolph, C., Moissl, C., Henneberger, R. & Huber, R. Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springs. FEMS Microbiol. Ecol. 50, 1–11 (2004).
Google Scholar
Schwank, K. et al. An archaeal symbiont-host association from the deep terrestrial subsurface. ISME J. 13, 2135–2139 (2019).
Google Scholar
Probst, A. J. & Moissl-Eichinger, C. “Altiarchaeales”: uncultivated archaea from the subsurface. Life 5, 1381–1395 (2015).
Google Scholar
Makarova, K. S. et al. Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles 18, 877–893 (2014).
Google Scholar
Vik, D. R. et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ 5, e3428 (2017).
Google Scholar
Anderson, R. E., Brazelton, W. J. & Baross, J. A. The deep viriosphere: assessing the viral impact on microbial community dynamics in the deep subsurface. Carbon Earth 75, 649–675 (2013).
Google Scholar
Rodrigues, R. A. L. et al. An anthropocentric view of the virosphere-host relationship. Front. Microbiol. 8, 1673 (2017).
Google Scholar
Munson-McGee, J. H., Snyder, J. C. & Young, M. J. Archaeal viruses from high-temperature environments. Genes 9, 128 (2018).
Google Scholar
Paez-Espino, D. et al. Uncovering Earth’s virome. Nature 536, 425–430 (2016).
Google Scholar
Philosof, A. et al. Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota. Curr. Biol. 27, 1362–1368 (2017).
Google Scholar
Ahlgren, N. A., Fuchsman, C. A., Rocap, G. & Fuhrman, J. A. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J. 13, 618–631 (2019).
Google Scholar
Gudbergsdottir, S. R., Menzel, P., Krogh, A., Young, M. & Peng, X. Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. Environ. Microbiol. 18, 863–874 (2016).
Google Scholar
Munson-McGee, J. H., Rooney, C. & Young, M. J. An uncultivated virus infecting a nanoarchaeal parasite in the hot springs of Yellowstone National Park. J. Virol. 94, e01213-19 (2020).
Zablocki, O., van Zyl, L. J., Kirby, B. & Trindade, M. Diversity of dsDNA viruses in a South African hot spring assessed by metagenomics and microscopy. Viruses 9, 348 (2017).
Google Scholar
Emerson, J. B. et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat. Microbiol. 3, 870–880 (2018).
Google Scholar
Trubl, G. et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems 3, 338103 (2018).
Google Scholar
Hochstein, R. A., Amenabar, M. J., Munson-McGee, J. H., Boyd, E. S. & Young, M. J. Acidianus tailed spindle virus: a new archaeal large tailed spindle virus discovered by culture-independent methods. J. Virol. 90, 3458–3468 (2016).
Google Scholar
Jahn, M. T. et al. Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. ISME J. 15, 1–11 (2021).
Anderson, R. E., Brazelton, W. J. & Baross, J. A. Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front. Microbiol. 2, 219 (2011).
Google Scholar
Chen, I. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).
Google Scholar
Bornemann, T. L. V. et al. Geological degassing enhances microbial metabolism in the continental subsurface. https://doi.org/10.1101/2020.03.07.980714 (2020).
Sharrar, A. M. et al. Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron Basin. Front. Microbiol. 8, 791 (2017).
Google Scholar
Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M. B. VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985 (2015).
Google Scholar
Kieft, K. et al. Virus-associated organosulfur metabolism in human and environmental systems. Cell Reports, in press (2021).
Allers, E. et al. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environ. Microbiol. 15, 2306–2318 (2013).
Google Scholar
Roux, S. et al. Minimum information about an uncultivated virus genome (MIUViG). Nat. Biotechnol. 37, 29–37 (2019).
Google Scholar
Breitbart, M. & Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284 (2005).
Google Scholar
Short, C. M. & Suttle, C. A. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl. Environ. Microbiol. 71, 480–486 (2005).
Google Scholar
Bautista, M. A., Black, J. A., Youngblut, N. D. & Whitaker, R. J. Differentiation and structure in Sulfolobus islandicus rod-shaped virus populations. Viruses 9, 120 (2017).
Google Scholar
Held, N. L. & Whitaker, R. J. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ. Microbiol. 11, 457–466 (2009).
Google Scholar
Baquero, D. P. et al. New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities. ISME J. 14, 1821–1833 (2020).
Google Scholar
Molnár, J. et al. Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLoS ONE 15, e0231864 (2020).
Google Scholar
Prangishvili, D., Garrett, R. A. & Koonin, E. V. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 117, 52–67 (2006).
Google Scholar
Deng, L., Garrett, R. A., Shah, S. A., Peng, X. & She, Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088–1099 (2013).
Google Scholar
Silas, S. et al. Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. Elife 6, e27601 (2017).
Google Scholar
Guo, T., Han, W. & She, Q. Tolerance of Sulfolobus SMV1 virus to the immunity of IA and III-B CRISPR-Cas systems in Sulfolobus islandicus. RNA Biol. 16, 549–556 (2019).
Google Scholar
Athukoralage, J. S. et al. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 577, 572–575 (2020).
Google Scholar
Bhoobalan-Chitty, Y., Johansen, T. B., Di Cianni, N. & Peng, X. Inhibition of type III CRISPR-Cas immunity by an archaeal virus-encoded anti-CRISPR protein. Cell 179, 448–458 e411 (2019).
Google Scholar
Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microbiol. Ecol. 13, 19–27 (1997).
Google Scholar
Wilhelm, S. W. & Suttle, C. A. Viruses and nutrient cycles in the sea—viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49, 781–788 (1999).
Google Scholar
Probst, A. J. et al. Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME J. 14, 1547–1560 (2020).
Google Scholar
Dong, X. et al. Fermentative spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME J. 12, 2039–2050 (2018).
Google Scholar
Vidakovic, L., Singh, P. K., Hartmann, R., Nadell, C. D. & Drescher, K. Dynamic biofilm architecture confers individual and collective mechanisms of viral protection. Nat. Microbiol. 3, 26–31 (2018).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Google Scholar
Probst, A. J. et al. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species. PLoS ONE 9, e99801 (2014).
John, S. G. et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ. Microbiol. Rep. 3, 195–202 (2011).
Google Scholar
Joshi, N. & Fass, J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle (2011).
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).
Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).
Google Scholar
Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282–1288 (2007).
Google Scholar
Bornemann, T. L. V., Esser, S. P., Stach, T. L., Burg, T. & Probst, A.J. uBin—a manual refining tool for metagenomic bins designed for educational purposes. https://doi.org/10.1101/2020.07.15.204776 (2020).
Couvin, D. et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 46, W246–W251 (2018).
Google Scholar
Medvedeva, S. et al. Virus-borne mini-CRISPR arrays are involved in interviral conflicts. Nat. Commun. 10, 5204 (2019).
Google Scholar
Iranzo, J., Faure, G., Wolf, Y. I. & Koonin, E. V. Game-theoretical modeling of interviral conflicts mediated by mini-CRISPR arrays. Front. Microbiol. 11, 381 (2020).
Google Scholar
Denman, R. B. Using Rnafold to predict the activity of small catalytic RNAs. Biotechniques 15, 1090-& (1993).
Lange, S. J., Alkhnbashi, O. S., Rose, D., Will, S. & Backofen, R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 41, 8034–8044 (2013).
Google Scholar
Moller, A. G. & Liang, C. MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ 5, e3788 (2017).
Google Scholar
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Google Scholar
Bischoff, V. et al. Cobaviruses—a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J. 13, 1404–1421 (2019).
Google Scholar
Boratyn, G. M. et al. Domain enhanced lookup time accelerated BLAST. Biol. Direct 7, 12 (2012).
Google Scholar
Grazziotin, A. L., Koonin, E. V. & Kristensen, D. M. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45, D491–D498 (2017).
Google Scholar
Remmert, M., Biegert, A., Hauser, A. & Söding, J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173–175 (2011).
Google Scholar
Marz, M. et al. Challenges in RNA virus bioinformatics. Bioinformatics 30, 1793–1799 (2014).
Google Scholar
Finn, R. D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 45, D190–D199 (2017).
Google Scholar
Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).
Google Scholar
Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).
Google Scholar
Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).
Google Scholar
Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, W200–W204 (2018).
Google Scholar
Meier-Kolthoff, J. P. & Göker, M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 33, 3396–3404 (2017).
Google Scholar
Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 14, 60 (2013).
Google Scholar
Göker, M., Garcia-Blazquez, G., Voglmayr, H., Telleria, M. T. & Martin, M. P. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS ONE 4, e6319 (2009).
Google Scholar
Bin Jang, H. et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632–639 (2019).
Google Scholar
Bolduc, B. et al. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect archaea and bacteria. PeerJ 5, e3243 (2017).
Google Scholar
Brister, J. R., Ako-Adjei, D., Bao, Y. & Blinkova, O. NCBI viral genomes resource. Nucleic Acids Res. 43, D571–D577 (2015).
Google Scholar
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Google Scholar
Moraru, C., Varsani, A. & Kropinski, A. M. VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12, 1268 (2020).
Guy, L., Kultima, J. R. & Andersson, S. G. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334–2335 (2010).
Google Scholar
Team RC. R: a language and environment for statistical computing. (R Foundation for Statistical Computing, 2019). https://www.R-project.org/.
Papadopoulos, J. S. & Agarwala, R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23, 1073–1079 (2007).
Google Scholar
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113 (2004).
Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Google Scholar
Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).
Google Scholar
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Google Scholar
Rambaut, A. FigTree, a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. http://tree.bio.ed.ac.uk/software/figtree/ (2006).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Barrero-Canosa, J. & Moraru, C. Linking microbes to their genes at single cell level with direct-geneFISH. In: An Overview of FISH Concepts and Protocols for Microbial Cells (eds Almeida, C. & Azevedo, N.). (Springer Nature, 2020).
Barrero-Canosa, J., Moraru, C., Zeugner, L., Fuchs, B. M. & Amann, R. Direct-geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms. Environ. Microbiol. 19, 70–82 (2017).
Google Scholar
Perras, A. K. et al. S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Front. Microbiol. 6, 543 (2015).
Google Scholar
Wallner, G., Amann, R. & Beisker, W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14, 136–143 (1993).
Google Scholar
Moissl, C., Rudolph, C., Rachel, R., Koch, M. & Huber, R. In situ growth of the novel SM1 euryarchaeon from a string-of-pearls-like microbial community in its cold biotope, its physical separation and insights into its structure and physiology. Arch. Microbiol. 180, 211–217 (2003).
Google Scholar
Flechsler, J. et al. 2D and 3D immunogold localization on (epoxy) ultrathin sections with and without osmium tetroxide. Microsc. Res. Tech. 83, 691–705 (2020).
Schlitzer, R. Data Analysis and Visualization with Ocean Data View, CMOS Bulletin SCMO. 43, 9–13 (2015).
Source: Ecology - nature.com
