Randomly amplified polymorphic DNA reveals tight links between viruses and microbes in the bathypelagic zone of the Northwestern Mediterranean Sea

Abstract

The study site located in the Mediterranean Sea was visited eight times in 2005 and 2006 to collect samples from the epipelagic (5 m), mesopelagic (200 m, 600 m), and bathypelagic (1,000 m, 2,000 m) zones. Randomly amplified polymorphic DNA PCR (RAPD-PCR) analysis was used to obtain fingerprints from microbial and viral size fractions using two different primers each. Depending on the primer used, the number of bands in the water column varied between 12 to 24 and 6 to 19 for the microbial size fraction and between 16 to 26 and 8 to 22 for the viral size fraction. The majority of sequences from the microbial fraction was related to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria, Firmicutes, and Eukaryota. Only 9% of sequences obtained from the viral fraction were of identifiable viral origin; however, 76% of sequences had no close relatives in the nr database of GenBank. Only 20.1% of complete phage genomes tested in silico resulted in potential RAPD-PCR products, and only 12% of these were targeted by both primers. Also, in silico analysis indicated that RAPD-PCR profiles obtained by the two different primers are largely representative of two different subsets of the viral community. Also, correlation analyses and Mantel tests indicate that the links between changes in the microbial and viral community were strongest in the bathypelagic. Thus, these results suggest a strong codevelopment of virus and host communities in deep waters. The data also indicate that virus communities in the bathypelagic zone can exhibit substantial temporal dynamics.

FIG. 1.

Percentage of significant hits in GenBank. The figure shows the percentage of significant hits in the nr and env_nt databases of GenBank for the microbial (A) and viral (B) sequences obtained from RAPD-PCR bands. Also, the percentage of sequences for which no close relatives could be found in either database is shown.

FIG. 2.

Taxonomic breakdown of significant hits to nucleic acid sequences obtained from microbial concentrates. The pie chart shows the number of significant hits in each of the phylogenetic groups (as a percentage of the total) based on comparing the nucleic acid sequences obtained from MICRO (A), MCRA (B), and MOPA (C) to the nr database of GenBank using tblastx.

FIG. 3.

Taxonomic breakdown of significant hits to nucleic acid sequences obtained from viral concentrates. The pie chart shows the number of significant hits to phage- and prophage-related sequences, as well as other phage-unrelated sequences (as a percentage of the total) based on comparing the nucleic acid sequences obtained from VIR (A), VCRA (B), and VOPA (C) to the nr database of GenBank using tblastx. The category “other” corresponds to significant hits in the groups Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Cyanobacteria, Euryarchaeota, and Eukaryota.