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.

Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA

“…Offering greater sensitivity to virioplankton community changes than pulsed-field gel electrophoresis methods (36), RAPD-PCR has demonstrated shifts in viral communities across depth zones in the pelagic ocean (1), over seasonal scales in estuarine ecosystems (36), and most re- cently, in permanently anoxic freshwater sediments (35). This community fingerprinting approach was also important in demonstrating that lysogenic viral populations in deep-sea hydrothermal vent environments are a less diverse subset of the virioplankton communities found at the vents (4).…”

Combined effects of drought and the fungicide tebuconazole on aquatic leaf litter decomposition

“…Bacterial biomass was estimated from bacterial densities using a FACS Calibur flow cytometry system (Becton Dickinson Biosciences) and following the protocol of Borrel et al (2012). For each treatment and sampling date, one leaf disc (1 cm diameter) was conserved in 1 mL of TE buffer (10 mM Tris, 1 mM EDTA) and 1 mL of paraformaldehyde (2%, final concentration) and stored at −20 °C.…”

Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids

“…Functional studies proved to be highly challenging due to the lack of similarity between the protein sequences and structures of archaeal viruses and those from other viruses and cellular organisms (6)(7)(8)(9)(10). Among the morphotypes that are exclusively associated with archaea, spindle-shaped viruses are particularly widespread (11) and have been isolated from highly different environments, including deep-sea hydrothermal vents (12)(13)(14), hypersaline environments (15)(16)(17)(18), anoxic freshwaters (19), cold Antarctic lakes (20), terrestrial hot springs (21)(22)(23), and acidic mines (24).…”