Impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures

Abstract

During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

FIG. 1.

Map of the sampling stations in the tropical Atlantic Ocean (A) and the North Sea (B). AF1, 28 January; AF2, 3 February; AF3, 6 February; NS1, 13 December.

FIG. 2.

Time courses of prokaryotic abundance in the treatments in experiments AF1, AF2, AF3, and NS1. The error bars represent the standard error of the mean obtained from 30 fields or 300 prokaryotic cells counted per filter. If no error bars are shown, they are smaller than the width of the symbol. Missing data points are due to problems in preserving these samples. N, number.

FIG. 3.

Development of viral abundance in the 0%Vir, 100%Vir-inactive, 100%Vir, and 200%Vir treatments in experiment AF1. The error bars represent the standard error of the mean obtained from 30 fields or 300 viral particles counted per filter. If no error bars are shown, they are smaller than the width of the symbol. N, number.

FIG. 4.

Effects of confinement and virus amendment on the numbers of peaks in the treatments in experiments AF1, AF2, AF3, and NS1, as determined by T-RFLP analysis. The numbers of peaks in the patterns obtained with the forward and reverse primers were combined for the Bacteria and the Archaea. Missing T-RFLP patterns due to problems with PCR amplification are marked by an X. The low bacterial richness in the 65%Vir treatment in experiment AF3 after 24 h is regarded as an outlier.

FIG. 5.

Example of T-RFLP patterns obtained with the archaeal reverse primer (958R) for Archaea with the 0%Vir, 100%Vir-inactive, 100%Vir, and 200%Vir treatments in experiment AF1 after 96 h of incubation. The T-RFLP patterns are centered on the region of interest, and the sizes of the OTUs in base pairs are noted next to the arrows.

FIG. 6.

Phylogenetic tree of the archaeal 16S rRNA gene sequences obtained in this study (in bold type) and sequences retrieved from GenBank, as inferred by maximum likelihood based on homologous nucleotide sequences from 49 to 926 bp (Escherichia coli numbering). The accession numbers of the reference sequences retrieved from GenBank are shown in parentheses. Numbers at the nodes represent percentages of bootstrap replicates supporting the branching order. The scale bar represents 0.10 substitution per nucleotide position.