Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

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Abstract

Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans1,2,3,4. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature5, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 107 Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42–71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.

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Figure 1: Population genome landscape plot showing the genetic relationship of cultivated and viral-tagged T4-like phages of Synechococcus WH7803 from a single seawater sample and all available marine cyanophage genomes.
Figure 2: The 15 dominant T4-like Candidatus genomes assembled from the viral-tagged metagenome.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

Data for viral genomes have been deposited in GenBank under accession numbers JN371768 and KF156338-40; metagenomic data have been deposited in CAMERA under accession numbers CAM_P_0001068 and CAM_P_0000915; raw data including gp23 sequences and informatic pipelines, assemblies and data for figures are available at http://datadryad.org/resource/doi:10.5061/dryad.gr3ks.

Change history

  • 10 September 2014

    Minor changes were made to Extended Data Fig. 2.

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Acknowledgements

Funding was provided by the US Department of Energy (DOE) Joint Genome Institute (JGI) Community Sequencing Program, Biosphere 2, BIO5, US National Science Foundation (NSF) OCE0940390, and Gordon and Betty Moore Foundation grants to M.B.S., as well as NSF OCE1233760 and Burroughs Wellcome Fund grants to J.S.W. We thank J. Fuhrman for suggesting stable-isotope-labelled host DNA; A. Z. Worden and the CANON Initiative for the cruise opportunity; Worden laboratory members; the captain and crew of the R/V Western Flyer for operational/sampling support; J. B. Waterbury, S. W. Chisholm and A. Wichels for strains; the Tucson Marine Phage laboratory; Institute of Groundwater Ecology of Helmholtz Munich; and N. Pace, M. Young, S. W. Chisholm and S. Yilmaz for technical/analytical support and manuscript comments. We acknowledge the University of Arizona Genetics Core for viral-tagging metagenomic sequencing; iCyt and the Arizona Cancer Center and Arizona Research Laboratories (ARL) Division of Biotechnology Cytometry Core Facility for cytometry support; the University Information Technology Services Research Computing Group and the ARL Biotechnology Computing for high-performance computing clusters (HPCC) access and support. Community metagenomic sequencing was provided by the DOE JGI Community Sequencing Program under the Office of Science of the US DOE contract no. DE-AC02-05CH11231.

Author information

Affiliations

Authors

Contributions

L.D., P.H. and M.B.S. designed the experiments. L.D. collected samples. L.D., A.C.G. and B.T.P. performed the experiments. L.D., J.C.I.-E., J.S.W., P.H. and M.B.S. analysed data, interpreted results and wrote the paper.

Corresponding author

Correspondence to Matthew B. Sullivan.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Agarose gel of PCR products used for screening the 97 cyanophage isolates derived from this study.

Primers used have a well-understood and strong history in the literature and amplify a 400 bp region of the portal protein encoded gene (gp20) of T4-like phages. ΦC refers to phages S-MbC.

Extended Data Figure 2 The viral-tagging metagenome is less complex than the whole viral community metagenome.

a, Diversity of the viral-tagging (VT) metagenome shows a five-to-tenfold reduction when compared to the community metagenome by different metrics applied to protein clusters with only 17.5% (1,360 of 7,762) of the viral-tagging protein clusters occurring in the community metagenome (Venn diagram). b, The viral taxonomic profiles from each metagenome assigned by BLASTx search (e-value <0.001) against all phage genomes present in NCBI (1,218 genomes, December, 2013), and compared against the designations from cultured isolates (n indicates number of reads on top of metagenome bars and number of phage isolates on top of isolates bars; percentage of metagenome bars represent the percentage of reads used).

Extended Data Figure 3 Candidatus genomes assembled from the dominant viral-tagging metagenome populations that were not T4-like myoviruses.

a, Black boxes represent the predicted ORFs, blue box-plots reflect the intrapopulation locus-to-locus variation as described in Fig. 2. A cumulative distribution plot of the genome-wide locus-by-locus percentage nucleotide identity is represented to the right of each genome. Colours denote the taxonomic assignment for each gene, based on blastp best hits to nr, for detailed annotation refer to Supplementary Data 1. CGs, Candidatus genomes. b, Normalized (corrected for contig length) coverage of all Candidatus genomes including the rare non-T4-like ones (in dark grey). c, Quantification of the relative abundances of the non-T4-like Candidatus genomes.

Extended Data Figure 4 Genome sizing and location in silico experiments.

a, Variation along the genome was investigated by in silico breaking the genome into 30 kb fragments using a 5 kb sliding window to compare the similarity profile (ANI of the genome or fragment versus the reference genomes) of the fragment to that derived from the whole genome, just a subset shown. Where Pearson’s r is high (>0.95, the right side of the genomes in blue) the fragment profile parallels that of a genome-wide profile. b, These similarity profiles were converted to a correlation distance (1 − Pearson’s r) and then clustered using hierarchical clustering (linkage = ‘complete’ or furthest distance). Comparison of the clustering patterns showed that 30 kb fragments from within the ‘blue’ region of the genome are more closely related to those derived from their own genomes than other genomes, except for the co-isolated phages P-HM1 and P-HM2, which were the most similar genomes in the data set.

Extended Data Figure 5 Sensitivity analyses for recruitment parameters.

Recruitment, as described in the main text, required 95% nucleotide identity over 95% of the length of the reads, whereas here we examine lower stringency recruitment including 90% nucleotide identity over 90% of the length of the read, and 80% nucleotide identity over 90% of the length of the read. These results were consistent with those described in the main text (Fig. 2)—that is, most of the recruited reads are in the top 2% (see histogram on the right). Only four representative Candidatus genomes (CGs) are shown here.

Extended Data Figure 6 Comparison of neighbour-joining trees derived from viral-tagging and phylogenomic analyses.

The left panel represents Euclidean distances of the three-dimensional space reconstructed with the first three principal components in Fig. 1. The right panel represents the currently accepted cyano-T4 phage core phylogeny derived from analysis of 57 concatenated proteins totalling 20,638 amino acids.

Extended Data Figure 7 Exploring viral-tagging metagenomic population sequence space.

a, Whole genome comparisons of isolates S-MbCM25 and S-MbCM6 show that they are part of the same population as CG-05, while isolate S-MbCM7 appears to be part of the CG-11 population (lines connecting reciprocal blast hits >95% identity). Note in Fig. 1 how the variation (‘cloud’) associated with CG-05 and CG-11 overlap with their representative isolates. b, Alignment, based on homologues sequences within each contig, of all assembled T4-like viral-tagging contigs (>1.5 kb) against CG-01 as a reference genome. At the deepest point (around the 205 kb mark, orange bar) there are a total of 14 to 17 overlapping contigs. c, Rank abundance curve for the 26 most abundant Candidatus genomes (CGs) in the viral-tagging source waters. Values are derived from mean contig coverage values. The blue line quantifies the cumulative use of reads as more genomes are added.

Extended Data Figure 8 Flow diagram describing the bioinformatics processing steps.

a, We recruited reads to each Candidatus genome requiring at least 95% identity and a coverage of 95% of the entire length of the read. Each read was non-redundantly assigned and aligned to a Candidatus genome using default parameters in MUSCLE. b, For each Candidatus genome population, we generated 100 random Candidatus genome sequences by probabilistically resampling (using the observed occurrences) the metagenomic data that went into generating their consensus sequences.

Extended Data Table 1 Phage isolates used in the study of phage infectivity indication by viral tagging and plaques assay
Extended Data Table 2 Pairwise nucleotide and amino acid identity calculated between all shared genes for each pair of Candidatus genomes

Supplementary information

Supplementary Table 1

Morphological taxonomic assignation of published viral isolates on Synechococcus WH7803. (PDF 106 kb)

Supplementary Data 1

Annotation of open reading frames (ORFs) on 26 CGs (worksheet1) and all small contigs larger than 1.5 Kb (worksheet2). (XLS 566 kb)

Supplementary Data 2

This file contains source data for Table 1 (in the main paper), Extended Data Figure 3 and Extended Data Figure 7. (XLSX 37 kb)

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Deng, L., Ignacio-Espinoza, J., Gregory, A. et al. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513, 242–245 (2014). https://doi.org/10.1038/nature13459

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