Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

Abstract

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0-10 cm) could be discriminated from those of the intermediate (11-27 cm) and deep (28-40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.

Figure 1

(a) Picture of the 40 cm sediment core collected in Lake Pavin, the depths corresponding to the three clusters defined from RAPD-PCR analyses (Figure 1f) are indicated by a blue (upper layer), a red (intermediate layer) and a green (deep layer) rectangle. (b) Vertical distribution of viral densities ( × 10⁹ VLPs per gram of dry sediment), (c) Vertical distribution of prokaryotic densities ( × 10⁹ cells per gram of dry sediment), (d) virus-to-prokaryotes ratio, (e) frequency (i.e., percentage) of visibly infected cells (%), (f–h) cluster analyses from RAPD-PCR and temporal temperature gel gradient electrophoresis data performed for viruses and 16S rDNA archaeal and bacterial gene fragments, respectively. Hierarchical cluster analyses were performed as indicated in the experimental procedures section.

Figure 2

Transmission electron micrographs of typical freshwater viruses observed along the 40 cm sediment core from Lake Pavin. Magnification for each micrograph is indicated as follows: Myoviridae (a ( × 120 000), b ( × 50 000), c ( × 150 000)), Siphoviridae (d ( × 100 000), e ( × 40 000), f ( × 15 000), g ( × 60 000)), Podoviridae (h ( × 120 000)), tailless viruses (i ( × 150 000), j and k ( × 80 000), l ( × 120 000)). Scale bar=100 nm.

Figure 3

Transmission electron micrographs of unexpected and novel putative viruses observed along the 40 cm sediment core from Lake Pavin. Magnification for each micrograph is indicated as follows: a, c, j, appendix in n ( × 150 000); d, k ( × 120 000); h, i, l ( × 100 000); f ( × 80 000); b, e ( × 60 000); g, m, n ( × 40 000). Scale bar=100 nm.