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Applied and Environmental Microbiology, April 2009, p. 2259-2265, Vol. 75, No. 8
0099-2240/09/$08.00+0     doi:10.1128/AEM.02551-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Seasonal Dynamics and Metagenomic Characterization of Estuarine Viriobenthos Assemblages by Randomly Amplified Polymorphic DNA PCR{triangledown} ,{dagger}

Rebekah R. Helton1 and K. Eric Wommack1,2*

Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711,1 College of Marine Studies, University of Delaware, Lewes, Delaware 199582

Received 7 November 2008/ Accepted 5 February 2009

Direct enumeration and genetic analyses indicate that aquatic sediments harbor abundant and diverse viral communities. Thus far, synecological analysis of estuarine sediment viral diversity over an annual cycle has not been reported. This oversight is due in large part to a lack of molecular genetic approaches for assessing viral diversity within a large collection of environmental samples. Here, randomly amplified polymorphic DNA PCR (RAPD-PCR) was used to examine viral genotypic diversity within Chesapeake Bay sediments. Using a single 10-mer oligonucleotide primer for all samples, RAPD-PCR analysis of sediment viral assemblages yielded unique banding patterns across spatial and temporal scales, with the occurrence of specific bands varying among the sample set. Cluster analysis of RAPD-PCR amplicon banding patterns indicated that sediment viral assemblages changed with season and to a lesser extent with geographic location. Sequence analysis of RAPD-PCR amplicons revealed that 76% of sediment viral sequences were not homologous to any sequence in the GenBank nonredundant protein database. Of the GenBank sequence homologs, the majority belonged to viruses within the Podoviridae (24%) and Myoviridae (22%) viral families, which agrees with the previously observed frequencies of these morphological families in Chesapeake Bay sediments. Furthermore, the majority of the sediment viral sequences homologous to GenBank nonredundant protein sequences were phages or prophages (57%). Hence, RAPD-PCR proved to be a reliable and useful approach for characterization of viral assemblages and the genetic diversity of viruses within aquatic sediments.

* Corresponding author. Mailing address: Delaware Biotechnology Institute, 15 Innovation Way, Room 148, Newark, DE 19711. Phone: (302) 831-4362. Fax: (302) 831-3447. E-mail: wommack{at}dbi.udel.edu

{triangledown} Published ahead of print on 13 February 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, April 2009, p. 2259-2265, Vol. 75, No. 8
0099-2240/09/$08.00+0     doi:10.1128/AEM.02551-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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