In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and establishment of lysogeny in aquatic ecosystems, which are prone to constant environmental fluctuations.

The usefulness of the polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) and partial sequencing of the cytochrome oxidase I (COI) gene was tested regarding the utility of these techniques in unraveling philometrid life cycles and, in particular, to determine putative paratenic host species. Our focus was to study three species of philometrids commonly found in the estuaries of South Carolina: Philometroides paralichthydis and Philometra overstreeti from the southern flounder, Paralichthys lethostigma and Philometra carolinensis from the spotted seatrout, Cynoscion nebulosus. A total of 473 fish in 19 species known to be potential prey of the spotted seatrout and the southern flounder were dissected. Of all nematode larvae found in the mesenteries of 53 fish of 10 species, 21 specimens were determined to be philometrids using PCR. The use of PCR-RFLP allowed the identification of larvae of P. carolinensis and P. overstreeti in the freshwater goby, Ctenogobius shufeldti, and P. overstreeti in mummichog, Fundulus heteroclitus. However, 12 RFLP profiles could not be matched to control species, thus demonstrating the limitation of this technique in areas where diversity of philometrids is not well known and higher than anticipated. Similarly, COI procedures provided unknown sequences that did not match those of nine philometrid species used as controls. We concluded that although both techniques showed some usefulness and promise, at this point, however, they demonstrate the need of increasing our knowledge of marine and estuarine philometrid biodiversity.

1. We explored the factors that potentially affect viral abundance, viral life strategies (lytic versus lysogenic cycle) and the relative importance of viral lysis and heterotrophic nanoflagellate grazing for prokaryote mortality in the euphotic zone of 19 freshwater lakes in a single geographical region (the French Massif Central). 2. Flow cytometry indicated that viral abundance ranged from 0.5 to 26.3 9 10 7 viruses mL À1 , exceeding prokaryote abundance by c. 16-fold on average. Multiple regressions revealed that prokaryotic abundance was the best predictor of viral abundance (r 2 = 0.74), suggesting that the prokaryotes were the major hosts for viral proliferation in these lakes.3. Viral life strategies varied with month of sampling (June, July, August 2010). Lytic infection was the prominent mode of viral infection in June and August, whereas lysogenic infection was more evident in July in the majority of sampled lakes. This temporal shift in viral strategy was controlled by the availability of phosphate and chlorophyll concentration via host cell growth, with high concentrations favouring lytic infection and low concentrations favouring lysogenic infection. Such antagonistic interactions between viral life strategies support the hypothesis that lysogeny may represent a survival strategy for viruses in harsh nutrient/host conditions. 4. The dominance of viruses over flagellates, or vice versa, as prokaryotic mortality factors differed between the lakes. By taking into account both forms of mortality, our study indicates that viruses and flagellates are likely to act additively in their effects on prokaryotes by regulating the proportion of the most active members of the prokaryotic community. Such a combined effect of viruses and flagellates may strongly influence the planktonic food web and whole-ecosystem functioning.