Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.

Department of Aquatic Microbial Ecology Institute of Hydrobiology Biology Centre CAS Na Sádkách 702 7 370 05 České Budějovice Czech Republic

Faculty of Science University of South Bohemia Branišovská 31 370 05 České Budějovice Czech Republic

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Neuenschwander SM, Ghai R, Pernthaler J, Salcher MM. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. ISME J. 2018;12:185–98. doi: 10.1038/ismej.2017.156. PubMed DOI PMC

Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, Kohzu A, et al. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. Microbiome. 2021;9:24. doi: 10.1186/s40168-020-00974-y. PubMed DOI PMC

Giovannoni S, Temperton B, Zhao Y. Giovannoni et al. reply. Nature. 2013;499:E4–5. doi: 10.1038/nature12388. PubMed DOI

Ghai R, Mehrshad M, Mizuno CM, Rodriguez-Valera F. Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria. ISME J. 2017;11:304–8. doi: 10.1038/ismej.2016.110. PubMed DOI PMC

Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome. 2019;7:135. doi: 10.1186/s40168-019-0752-0. PubMed DOI PMC

Kang I, Kim S, Islam MDR, Cho JC. The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures. Sci Rep. 2017;7:42252. doi: 10.1038/srep42252. PubMed DOI PMC

Kim S, Kang I, Lee JW, Jeon CO, Giovannoni SJ, Cho JC. Heme auxotrophy in abundant aquatic microbial lineages. Proc Natl Acad Sci USA. 2021;118:e2102750118. doi: 10.1073/pnas.2102750118. PubMed DOI PMC

Buchholz HH, Michelsen ML, Bolaños LM, Browne E, Allen MJ, Temperton B. Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria. ISME J. 2021;15:1585–98. doi: 10.1038/s41396-020-00872-z. PubMed DOI PMC

Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics. 2017;33:3396–404. doi: 10.1093/bioinformatics/btx440. PubMed DOI PMC

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus genome (MIUViG) Nat Biotechnol. 2019;37:29–37. doi: 10.1038/nbt.4306. PubMed DOI PMC

Mavrich TN, Hatfull GF. Bacteriophage evolution differs by host, lifestyle and genome. Nat Microbiol. 2017;2:17112. doi: 10.1038/nmicrobiol.2017.112. PubMed DOI PMC

McMahon SA, Roberts GA, Johnson KA, Cooper LP, Liu H, White JH, et al. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. Nucleic Acids Res. 2009;37:4887–97. doi: 10.1093/nar/gkp478. PubMed DOI PMC

Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, et al. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev. 2007;71:495–548. doi: 10.1128/MMBR.00005-07. PubMed DOI PMC

Rybniker J, Nowag A, Van Gumpel E, Nissen N, Robinson N, Plum G, et al. Insights into the function of the WhiB-like protein of mycobacteriophage TM4 – a transcriptional inhibitor of WhiB2. Mol Microbiol. 2010;77:642–57. doi: 10.1111/j.1365-2958.2010.07235.x. PubMed DOI

Markine-Goriaynoff N, Gillet L, Etten JLV, Korres H, Verma N, Vanderplasschen A. Glycosyltransferases encoded by viruses. J Gen Virol. 2004;85:2741–54. doi: 10.1099/vir.0.80320-0. PubMed DOI

Mizuno C, Ghai R, Rodriguez-Valera F. Evidence for metaviromic islands in marine phages. Front Microbiol. 2014;5:27. doi: 10.3389/fmicb.2014.00027. PubMed DOI PMC

Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R. Expanding the marine virosphere using metagenomics. PLOS Genet. 2013;9:e1003987. doi: 10.1371/journal.pgen.1003987. PubMed DOI PMC

Bellas CM, Schroeder DC, Edwards A, Barker G, Anesio AM. Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems. Nat Commun. 2020;11:4403. doi: 10.1038/s41467-020-18236-8. PubMed DOI PMC