The discovery of the numerical importance of viruses in a variety of (aquatic) ecosystems has changed our perception of their importance in microbial processes. Bacteria and Archaea undoubtedly represent the most abundant cellular life forms on Earth and past estimates of viral numbers (represented mainly by viruses infecting prokaryotes) have indicated abundances at least one order of magnitude higher than that of their cellular hosts. Such dominance has been reflected most often by the virus-to-prokaryote ratio (VPR), proposed as a proxy for the relationship between viral and prokaryotic communities. VPR values have been discussed in the literature to express viral numerical dominance (or absence of it) over their cellular hosts, but the ecological meaning and interpretation of this ratio has remained somewhat nebulous or contradictory. We gathered data from 210 publications (and additional unpublished data) on viral ecology with the aim of exploring VPR. The results are presented in three parts: the first consists of an overview of the minimal, maximal and calculated average VPR values in an extensive variety of different environments. Results indicate that VPR values fluctuate over six orders of magnitude, with variations observed within each ecosystem. The second part investigates the relationship between VPR and other indices, in order to assess whether VPR can provide insights into virus-host relationships. A positive relationship was found between VPR and viral abundance (VA), frequency of visibly infected cells (FVIC), burst size (BS), frequency of lysogenic cells (FLC) and chlorophyll a (Chl a) concentration. An inverse relationship was detected between VPR and prokaryotic abundance (PA) (in sediments), prokaryotic production (PP) and virus-host contact rates (VCR) as well as salinity and temperature. No significant relationship was found between VPR and viral production (VP), fraction of mortality from viral lysis (FMVL), viral decay rate (VDR), viral turnover (VT) or depth. Finally, we summarize our results by proposing two scenarios in two contrasting environments, based on current theories on viral ecology as well as the present results. We conclude that since VPR fluctuates in every habitat for different reasons, as it is linked to a multitude of factors related to virus-host dynamics, extreme caution should be used when inferring relationships between viruses and their hosts. Furthermore, we posit that the VPR is only useful in specific, controlled conditions, e.g. for the monitoring of fluctuations in viral and host abundance over time.

We have performed a systematic search for recombination in the region encoding coat protein and the 3' non-translated region in natural isolates of potyviruses, the largest group of plant RNA viruses. The presence of recombination, and the localization ofthe cross-over points, were confirmed statistically, by three different methods. Recombination was detected or suspected in 18 out of 109 potyvirus isolates tested, belonging to four out of eight virus species, and was most prevalent in potato virus Y, clear in bean common mosaic virus, and possible in bean yellow mosaic and zucchini yellow mosaic viruses. Recombination was not detected in the four other potyvirus species tested, including plum pox virus, despite the availability of numerous sequences for this last species. Though it was not specifically researched, no evidence for inter-specific recombination was found. For several reasons, including the fact that only a minor portion of the genome was analysed, the above figures certainly represent an underestimate of the extent of recombination among isolates of potyviruses, which might thus be a common phenomenon.

We describe the first virus-like particle of a hyperthermophilic euryarchaeote which was discovered in a strain of "Pyrococcus abyssi" previously characterized in our laboratory. This particle, named PAV1, is lemonshaped (120 nm ؋ 80 nm), with a short tail terminated by fibers, and resembles the virus SSV1, the type member of the Fuselloviridae, isolated from Sulfolobus shibatae. Sensitivity of the virus-like particle to organic solvents and detergents suggested that the envelope of PAV1 may contain lipids in addition to proteins. It contains a double-stranded circular DNA of 18 kb which is also present in high copy number in a free form in the host cytoplasm. No integrated form of the PAV1 genome could be detected in the host chromosome. Under standard growth conditions, the host cells continuously release PAV1 particles into the culture supernatant without spontaneous lysis, with a maximum reached in the late stationary phase. UV, gamma irradiation, treatment with mitomycin C, and various physiological stresses had no effect on PAV1 production. Screening of a large number of Thermococcales isolates did not permit to find a sensitive host. These results suggest that PAV1 persists in the host strain in a stable carrier state rather than a prophage.The Archaea domain comprises two major phyla, namely, the Crenarchaeota, including the extremely thermophilic sulfur-metabolizing Archaea of the orders Sulfolobales and Thermoproteales, and the Euryarchaeota, containing mainly the methanogens, the extreme halophiles, and the hyperthermophilic order Thermococcales (29). Our knowledge about archaeal viruses is still rather limited, and among known archaeal viruses that have been reported, only few have been studied in detail at the molecular level.All known crenarchaeotal viruses display unusual morphotypes and compose three novel families which were created to account for their unique features, namely, the filamentous Lipothrixviridae (2, 13, 32), the lemon-shaped Fuselloviridae (18,25), and the rod-shaped Rudiviridae (20). The dropletshaped Guttaviridae (3) have not yet been established as an acknowledged virus family. The best studied virus is the lemonshaped SSV1, whose original host is the hyperthermophile Sulfolobus shibatae. SSV1 is temperate and forms stable lysogens by site specifically inserting its 15.5-kb circular genome into the host chromosome (31). Its complete nucleotide sequence has been determined (19). In contrast, all but two of the as-yet-described viruses of extreme halophiles and methanogens have the classical head-and-tail morphology typical of many bacterial phages and have therefore been assigned to the virus families Myoviridae or Siphoviridae (1). There are two known exceptions, both showing a lemon-shaped morphology resembling SSV1, the type member of the Fuselloviridae. The first one was described as a virus-like particle (VLP) isolated from M. voltae strain A3 containing a circular double-stranded DNA of 23 kb, of which an integrated copy was found in the host chromosome (30). The second ex...