Research ArticleMICROBIAL ECOLOGY

Biodiversity and distribution of polar freshwater DNA viruses

See allHide authors and affiliations

Science Advances  19 Jun 2015:
Vol. 1, no. 5, e1400127
DOI: 10.1126/sciadv.1400127
  • Fig. 1 Diagram depicting the global location of the freshwater environments studied.

    A detailed position of the Arctic lakes in Spitsbergen and photographs of the lakes at the time of sampling are shown. Coordinates (latitude/longitude) of the Arctic lakes: Lv1 (Lake Linnevatnet) (78°03.864′N; 13°46.308′E); Lv1Pond (Borgdammane) (78°04.254′N; 13°47.652′E); IR1 (Lake Tunsjøen) (78°03.375′N; 13°40.313′E); IR2 (78°02.935′N; 13°41973′E); SvL1 (Lake Nordammen) (78°38.279′N; 16°44.025′E); SvL2 (Lake Tenndammen) (78°06.118′N; 15°02.024′E). [Svalbard map was obtained from http://es.wikipedia.org/wiki/Svalbard#mediaviewer/Archivo:Topographic_map_of_Svalbard.svg and published under terms of the GNU Free Documentation License (http://commons.wikimedia.org/wiki/Commons:GNU_Free_Documentation_License_1.2).]

  • Fig. 2 Taxonomic distribution of assigned metagenomic reads from Arctic viromes.

    Results represent blastx hits against a viral genome database summarized by MEGAN (Meta Genome Analyzer). Only the 10 most abundant categories are shown.

  • Fig. 3 Ordination of individual freshwater viromes according to their taxonomic profiles.

    The figure represents the first two axes of a principal components analysis based on the taxonomic affiliation of assigned reads. (A) Projection of the individual viromes on the model. Viromes from the same environment are represented by equal forms. (B) Projection of the viral groups with a higher contribution to the model. The position of each group represents its association with each virome. The analysis indicates a strong partitioning of the viromes between polar and nonpolar viromes, driven mainly by the relative abundance of small circular ssDNA viruses and phages. U., unclassified; d, distance.

  • Fig. 4 Reference-independent cross-assembly (crAss) comparison of individual freshwater viromes.

    The dendrogram represents a hierarchical clustering (average-linkage method) of Wootters distance values derived from the cross-assembly of freshwater viromes. Viromes from the same environment are represented by equal forms. The analysis evidences very low fine-grain genetic overlap between viromes from different environments.

  • Fig. 5 Coarse-grain genetic overlap between environments.

    The heatplot represents the results of cross-tblastx searches between per-environment pooled viral metagenomes. Values (% of total reads with hits with E value <0.001) are registered within the boxes and color-coded. Horizontal labels represent viromes acting as query, and vertical labels represent viromes acting as reference.

  • Table 1 Summary of polar metagenomic assemblies.

    Lengths in bp.

    No. of
    contigs
    Sum
    (bp)
    Maximum
    size
    Average
    size
    N50No. of
    contigs
    ≥1000
    SvL122,47523,071,73245,1091,0261,3836,926
    IR113,18014,262,84443,7041,0821,4334,661
    IR225,49628,649,72110,0581,1231,5799,111
    SvL214,63714,096,6956,1029631,3005,259
    Lv112,62412,193,40830,8699651,1173,801
    Antarctic4,8345,452,144114,6031,1271,5281,294
  • Table 2 Ecological indices predicted for subsampled viromes.

    Results derived from PHACCS and GAAS (Genome relative Abundance and Average Size) analyses. SW, Shannon-Wiener index; Scenario, most likely rank-abundance scenario for the community (Log, logarithmic; Pow, power law).

    Average genome
    size (bp)
    RichnessEvennessSWScenario
    Bourget9,1653,0000.957.6Log
    Pavin21,2313150.854.9Pow
    Lv1Pond2,3872890.975.5Pow
    Lv12,8931070.954.4Pow
    SvL13,0411,0000.865.9Pow
    IR13,785810.924.0Pow
    IR23,3683,8060.816.68Pow
    SvL21,5705200.895.5Pow
    Effluent23,7479160.926.3Pow
    Nursery5,3146,0990.917.9Pow
    Park2,9397,2000.938.3Pow
    Potal34,069300.913.12Pow
    ArcticOcean70,3114800.976.0Log
    AntarcticSpr3,9112040.945.0Pow
    AntarcticSum33,4665620.764.8Pow
    ElBerbera93,6661,2970.745.3Log
    Hamdoum69,9767690.604.0Pow
    Ilij78,7525790.895.6Log
    Molamhar88,1803090.935.3Pow
    Tilapia60852,1617390.956.3Pow
    Tilapia50411,0113,8040.967.9Log
    Tilapia43930,7063,2840.937.6Log

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/1/5/e1400127/DC1

    Fig. S1. Significant circular ssDNA-related contigs.

    Fig. S2. Fine-grain genetic overlap between polar freshwater viromes.

    Fig. S3. Coarse-grain genetic overlap between viromes.

    Fig. S4. NJ trees depicting the relationships between phylogenetic marker genes.

    Table S1. Cross-contig analysis of Arctic viromes.

    Table S2. Taxonomic distribution (%) of assigned metagenomic reads from subsampled freshwater viromes.

    Table S3. Cross-contig analysis of pooled freshwater environments.

  • Supplementary Materials

    This PDF file includes:

    • Fig. S1. Significant circular ssDNA-related contigs.
    • Fig. S2. Fine-grain genetic overlap between polar freshwater viromes.
    • Fig. S3. Coarse-grain genetic overlap between viromes.
    • Fig. S4. NJ trees depicting the relationships between phylogenetic marker genes.
    • Table S1. Cross-contig analysis of Arctic viromes.
    • Table S2. Taxonomic distribution (%) of assigned metagenomic reads from subsampled freshwater viromes.
    • Table S3. Cross-contig analysis of pooled freshwater environments.

    Download PDF

    Files in this Data Supplement:

Navigate This Article