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Hidden diversity of soil giant viruses.
Nat Commun. 2018 11 19; 9(1):4881.NC

Abstract

Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants.

Authors+Show Affiliations

U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA. fschulz@lbl.gov.Department of Biology, University of Massachusetts, Amherst, MA, USA.U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.Department of Bioengineering, Stanford University, Stanford, CA, USA.U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.Department of Biology, University of Massachusetts, Amherst, MA, USA. jeffb@bio.umass.edu.U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA. twoyke@lbl.gov.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

30451857

Citation

Schulz, Frederik, et al. "Hidden Diversity of Soil Giant Viruses." Nature Communications, vol. 9, no. 1, 2018, p. 4881.
Schulz F, Alteio L, Goudeau D, et al. Hidden diversity of soil giant viruses. Nat Commun. 2018;9(1):4881.
Schulz, F., Alteio, L., Goudeau, D., Ryan, E. M., Yu, F. B., Malmstrom, R. R., Blanchard, J., & Woyke, T. (2018). Hidden diversity of soil giant viruses. Nature Communications, 9(1), 4881. https://doi.org/10.1038/s41467-018-07335-2
Schulz F, et al. Hidden Diversity of Soil Giant Viruses. Nat Commun. 2018 11 19;9(1):4881. PubMed PMID: 30451857.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Hidden diversity of soil giant viruses. AU - Schulz,Frederik, AU - Alteio,Lauren, AU - Goudeau,Danielle, AU - Ryan,Elizabeth M, AU - Yu,Feiqiao B, AU - Malmstrom,Rex R, AU - Blanchard,Jeffrey, AU - Woyke,Tanja, Y1 - 2018/11/19/ PY - 2018/04/12/received PY - 2018/10/30/accepted PY - 2018/11/20/entrez PY - 2018/11/20/pubmed PY - 2018/12/19/medline SP - 4881 EP - 4881 JF - Nature communications JO - Nat Commun VL - 9 IS - 1 N2 - Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants. SN - 2041-1723 UR - https://www.unboundmedicine.com/medline/citation/30451857/Hidden_diversity_of_soil_giant_viruses_ L2 - https://doi.org/10.1038/s41467-018-07335-2 DB - PRIME DP - Unbound Medicine ER -